Solution Manual For Biology Exploring the Diversity of Life, 1st Edition

Table of Contents How to use this manual................................................................................i Teaching Strategies.....................................................................................iii 1 Light and Life................................................................................................1 2 Origins of Life.............................................................................................10 3 Selection, Biodiversity, and Biosphere......................................................17 4 Energy and Enzymes..................................................................................23 5 Membranes and Transport........................................................................30 6 Cellular Respiration....................................................................................37 7 Photosynthesis...........................................................................................47 8 Cell Communication ..................................................................................54 9 Cell Cycles ..................................................................................................59 10 Genetic Recombination.............................................................................65 11 Mendel, Genes, and Inheritance...............................................................71 12 Genes, Chromosomes, and Human Genetics ...........................................80 13 DNA Structure, Replication, and Organization .........................................89 14 Gene Structure and Expression ................................................................97 15 Control of Gene Expression ....................................................................105 16 DNA Technologies and Genomics............................................................114 17 Microevolution: Genetic Changes within Populations ...........................122 18 Species ....................................................................................................133 19 Evolution and Classification ....................................................................140 20 Darwin, Fossils, and Developmental Biology ..........................................147 Section I: Biodiversity..............................................................................157 21 Prokaryotes .............................................................................................160 22 Viruses, Viroids, and Prions: Infectious Biological Particles ...................166 23 Protists ....................................................................................................169 24 Fungi ........................................................................................................174 Section II: Plants......................................................................................178 25 Plants .......................................................................................................180 28 The Plant Body.........................................................................................186 29 Transport in Plants...................................................................................191 30 Reproduction and Development in Flowering Plants..............................197 31 Control of Plant Growth and Development.............................................203 Section III: Animals..................................................................................208 DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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26 Protostomes ............................................................................................210 27 Deuterostomes: Vertebrates and Their Closest Relatives ......................216 32 Introduction to Animal Organization and Physiology .............................222 33 Information Flow: Nerves, Ganglia, and Brains ......................................226 34 Sensory Systems......................................................................................232 35 The Endocrine System .............................................................................237 36 Muscles, Skeletons, and Body Movements.............................................243 37 The Circulatory System............................................................................247 38 Animal Reproduction...............................................................................252 39 Animal Development...............................................................................257 40 Animal Behaviour ....................................................................................263 41 Plant and Animal Nutrition .....................................................................267 42 Gas Exchange: The Respiratory System..................................................274 ........................................................................................................................

43 Regulation the Internal Environment......................................................279 44 Defences Against Disease .......................................................................288 45 Population Ecology..................................................................................294 46 Populations Interactions and Community Ecology..................................305 47 Ecosystems...............................................................................................316 48 Conservation of Biodiversity....................................................................322 49 Domestication..........................................................................................330

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Light drives and/or affects many biological processes, directly or indirectly.

2.

Light serves as an important source of energy, but can also be used by organisms to gather information about their surroundings.

LEARNING OBJECTIVES

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Students should be able to:



Define key terms (nature of light): light, photon, wavelength, electromagnetic spectrum, photosynthesis, chloroplast, pigment, chlorophyll, action spectrum, prokaryote, proton pump. [Knowledge]



Describe, in general terms, how the products of photosynthesis sustain most organisms on earth. [Comprehension]



Define key terms (light as information source): photoreceptor (rhodopsin, phytochromes as examples), opsin, retina, photoreceptor, eye, eyespot, compound eye, ommatidia, camera eye. [Knowledge]



Describe how organisms can sense light without image forming eyes. [Comprehension]



Describe, in general terms, the evolution of image forming eyes from early simple regions of photoreceptor cells. [Comprehension]



Define key terms (light damage): photosystem, ultraviolet radiation, thymine dimer, absorption spectrum, melanin, vitamin D. [Knowledge]



Provide an example of how light can damage biological molecules. [Comprehension]



Define key terms (light in ecology/behaviour): circadian rhythms, biological clock, melatonin, camouflage, pollination, phytoerythrin, light pollution, natural selection.

[Knowledge]

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

Provide an example of how daylight (or length of day) can affect physiology or behaviour of plants/animals. [Comprehension]



Describe circadian rhythms and their uses, contrasting the systems in plants and humans. [Comprehension/Analysis]



Describe the usefulness of colour in nature (e.g., sex selection, mimicry, warning…)

[Comprehension]



Describe different ways that colour influences animal behaviour, providing examples.

[Comprehension]



Explain the effect of water on light, and how this can influence marine life.

[Comprehension]



Define key terms (bioluminescence): bioluminescence/bioluminescent, ATP. [Knowledge]



In basic terms, explain how some organisms use bioluminescence. [Comprehension]



Explain why artificial light is problematic for many organisms and can be considered a form of pollution. [Comprehension]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

As light is so integral to photosynthesis, and involved in many biological phenomena (as described in this chapter), an understanding of the nature, properties and impact of light is vital to many areas of biological research.



Much of evolution has been shaped by selective forces relating to light (as energy source, information source, etc.).



Researchers are looking into ways of harnessing the energy of light, using biological (or biologicallyderived) molecules in biotechnology, nanotechnology and cancer treatment.

WHY SHOULD STUDENTS CARE? 

Understanding the role of light in various biological phenomena will be helpful throughout the course. It provides a way to link many topics in biology that students might otherwise view as isolated, tying biochemical/biophysical properties and processes to organismal, physiological and behavioural aspects.

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

Understanding how sensing light, even in the most basic way, can be useful to an organism can help students to appreciate and understand the gradual nature of evolution of the eye.



Understanding how light can damage biological molecules can provide useful information in understanding how skin cancer arises.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/ STUMBLING BLOCKS? 1.

The nature of light (wave and particle) can be confusing to students. Depending on the background preparation of your students, you may want to spend some time discussing this.

2.

It is often counterintuitive to students that colour is the result of those wavelengths of light that are NOT absorbed by a pigment. This is important in terms of the nature of pigments, and related to absorption spectra (which will be discussed in Chapter 7, Photosynthesis).

3.

There can be some confusion relating to the fact that light is key to photosynthesis and other vital biological processes, yet can damage biological molecules (even leading to development of cancers, in some cases). While this may initially be counterintuitive to students, this does provide an opportunity to discuss the properties of light that allow it to be so beneficial in many ways, yet cause damage to proteins and DNA.

4.

The information in this chapter includes a lot of details and terminology that students will not be familiar with, particularly if this is the first topic in an introductory course. Instructors are encouraged to use layman explanations for those terms they want students to understand, and to provide clear expectations regarding what students need to know vs. what is for interest at this stage.

5.

Many people have heard that the evolution of the camera eye is not possible, as an argument for intelligent design. This misconception may affect some student attitudes and we recommend that it be addressed (debunked) early, showing known examples of “intermediate” eyes. It can be used as an example of how science is done by looking at evidence, outside the commonly presented “scientific method”.

6.

Many students refer to the ‘use it or lose it’ issue and ask how long a structure can go unused before it gets ‘lost’.

7.

We have found that students are often confused by the levels of melanin and vitamin D production from photoconversion reactions in the body. Some students believe that vitamin D increases melanin production. A full understanding of how photons can be absorbed, transmitted or reflected may help prevent this confusion.

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WHAT CAN I DO IN CLASS? Depending on the time you have allotted to this chapter, and the objectives chosen for student learning, the various aspects of this chapter can be introduced very briefly, or explored more deeply. There is an opportunity to introduce themes that will extend across an introductory survey course, and you may want to draw student attention to this explicitly.

Many elements of the chapter could be drawn together using an example organism, such as a bird.

Energy is required for metabolism from food, which originates from plants, as result of photosynthesis. Bird eyes/vision are worth mentioning (especially considering pollinators – see below; raptors may also be useful examples).

Circadian rhythms and migration (melatonin believed to be involved in determining migratory direction, especially for first migration (Schneider et al 1994a; Schneider et al. 1994b) and reproduction (Sherwood et al 2002).

Light pollution effects on birds may be of interest. (One visible effect is when birds crash into windows – see Longcore and Rich, 2004). Some researchers believe that lights attracting insects may cause population declines and thus declining food source for insectivorous birds (or birds whose young are insectivorous); as insects that buzz about lights all night, then fall exhausted to ground, no longer have the energy to feed themselves or to procreate.

Light serves as information, typically as/through colour. Considering intersexual selection in birds, female choice is often on the basis of colour. Colour in birds has been shown to be indicative of health. Dietary changes that made blue-footed boobies more blue, also resulted in more robust immune system. Females often select males by virtue of the colour of a structure, in this case the feet.

It is an honest sign as to the strength of the immune system. (See Velando et al., 2006).

The “Why it Matters” introduction discusses Monet, and the changes in his painting relating to onset of cataracts. This could be explored, looking at the components of the human eye, and the mechanisms of (or, in the case of cataracts, the problems) perceiving light in the process of sight. There are web sites that can simulate vision affected by cataracts (see other resources), and you may want to show these in class. It may be useful to get students discussing how the physical development of a cataract results in blurry vision, considering the nature of light and how we use light as an information source in sight.

Prior to discussing vision, you can include a black slide (and turn off the lecture hall lights) to put the room in (temporary) darkness. (Alternatively, ask students to close their eyes.) Ask students: What has changed? What is the impact of this change? This leads into the idea of light as a source of information, and the biological mechanisms for sensing and using this information.

In discussing the eye, Figures 1.14, 1.15, 1.16 and 1.17 provide a good representation of eyes of varying complexity, and the evolution of the camera eye. These figures are especially useful in helping students to understand how the evolution of such a complex structure (the eye) could evolve gradually. Clicker question #2 may be used early in this discussion, and we recommend asking students to view the PBS video clip on evolution of the eye (see other resources).

Instructors may want to consider discussing a reinterpretation of the “use it or lose it” phrase – this is likely a gradual process; if the loss of a structure (or part of a structure) doesn’t disturb any other features, or doesn’t interfere with survival and/or reproduction then it may be maintained. Loss of the structure may provide a fitness advantage or the gene for that structure (and the ‘loss’ allele) may be linked to the allele of another gene that confers increased fitness to the individual). Again, this may be a bit complex early in an introductory biology course, but an instructor could return to this concept later if appropriate.

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Importance of colour – can show additional images of flowers (as well as Fig. 1.30) where petal colours attract particular pollinators. (Ask: How do animal pollinators vary? How would a night-flowering plant differ from one that blooms during the day?) An instructor could introduce idea of coevolution, using examples of certain flowering plants and their animal pollinators who have exerted selective forces upon one another, shaping evolution of both organisms. There is considerable concern regarding a decline in bee pollinators, which could have a significant impact on plants, including crop plants – relates to conservation biology efforts.

Ask students about mimicry with bright colours. This is only useful if deterring predators that can distinguish colours. This relates to bright colours for sexual selection in species that can see colours, and could lead into an introduction to sexual selection.

Students will probably be interested in seeing pictures of animals that lack eyes, and this can lead into a discussion about vision and fitness (at a very simple level!).

Introduction of photosynthesis – at this point, the major concept is the transformation of light energy into stored chemical energy. If this is an early chapter in the course, you may want to describe the conditions of life on earth prior to the appearance of photosynthetic microbes. Discussion question: How did early photosynthesis affect the conditions of Earth, and the life we see today? (This leads into concepts covered further in Chapter 2.) Not all photosynthesizers are green (e.g., red and brown algae). This observation can be used to explore different photosynthetic pigments, and adaptations to life under water.

Students are likely to find the effects of circadian rhythms in humans highly relevant. You may want to refer students to http://www.hhmi.org/biointeractive/clocks/fall/teenagers.html which is an easy article for students to read relating to the work of Mary Carskadon (see references below). This could lead to a debate about high school start times.

Ask/discuss: Why do animals have cycles relating to light? Why do plants have circadian rhythms? What similarities/differences exist?

Can introduce model organisms, as they will likely be mentioned throughout the course. Why do scientists use a fungus (Neurospora) to study circadian rhythms? How can we use information about fungal biology to help understand biology in other organisms? This could be an opportunity to have students consult the Purple Pages.

Damage by light – this is an opportunity to discuss cancer, which is a complex set of diseases, that will appear in many other chapters (e.g., cell signalling, cell cycle, genetics, gene regulation). Can ask students to consider the characteristics of light that are beneficial to life (which forms?) and aspects that can be detrimental.

Discuss pigments in role of photosynthesis (e.g., chlorophylls), vs. protection (e.g., melanin). We have found that our students are often very interested in melanin (skin colour). The role of melanin as a photoprotectant, as well as its biosynthesis can be an engaging topic. In most introductory courses, the pathways would be too advanced for students to know in detail, but the tyrosine precursor can be shown as an example of an important amino acid (it is a precursor for several important biological molecules), tyrosinase as an example of a biosynthetic enzyme, melanocytes as specialized skin cells (highlight the “cyt”, which appears in cell-related terms), and melanosomes as organelles within these cells. In discussing later topics, an instructor can revisit melanogenesis as a multi-layered example. Differences in pigmentation and ability to synthesize vitamin D via photoconversion can be discussed, asking about what occurs populations in regions where less exposure to sunlight occurs than in regions closer to the equator, and how diet can supply Vitamin D in such countries.

[Stumbling block 7] See lightpollution.org.uk website below for links to news stories and arguments that can be used in discussions/debates. (Major question posed: “Is light pollution killing our birds?”) See Navara and Nelson (2007) for a good discussion of the “dark side of light”.

Images of bioluminescent organisms (in addition to Fig. 1.35) can be shown to illustrate this phenomenon, which occurs in all sorts of organisms from tiny bacteria to octopi.

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We have found that students visibly enjoyed the camouflage pictures we showed when we were going through the "Light and Life" chapter. We have been starting each class with a new picture showing camouflage/mimicry. (For ideas, see the National Geographic photo gallery “The Art of Deception”: http://ngm.nationalgeographic.com/2009/08/mimicry/ziegler-photography) Clicker questions: 1.

A photosynthesizing organism could be A. B. C. D. E. F.

Green Red Brown Purple Any of the above colours. * Only two of the colours in A through D.

This question can be used in discussion of photosynthesis in different types of organisms (e.g., bacteria, algae, plants) and the different types of pigments that are present in the different photosynthesizers. There are brown and red algae, and purple photosynthetic bacteria. [Stumbling block 2] 2.

The vertebrate eye A. is very similar in structure and function to the eye of certain molluscs (squids and octopi).* B. could not have evolved from an ancestral patch of photosensitive cells (similar to eyespots possessed by certain single-celled protists and flatworms).

C. could not be made more effective or efficient.

D. is an example of an image forming eye, which is the only type of “eye” that could provide a selective advantage to an organism.

E. none of the above is true

This question relates to the common misconceptions about the so-called “irreducible complexity” of the vertebrate eye. [Stumbling block 5] There is considerable evidence of intermediate eye steps in evolution, and that even small improvements in a photoreceptive sensory structure (and corresponding neural developments) could provide significant selective advantages to the possessors of such structures. The vertebrate eye also exhibits some characteristics that probably would have been avoided if it had been designed as a perfect structure (e.g., placement of optical nerve, blood vessels).

WHAT OTHER RESOURCES ARE AVAILABLE? 

About.com Vision (Cataract vision simulated image) http://vision.about.com/od/eyediseases/ig/Eye-Disease-Simulations/ Cataract.htm



Low Vision simulation (requires plugin): http://www.webaim.org/simulations/lowvision-sim.htm



A useful article discussing some of the stumbling blocks regarding evolution of complex structures, such as the image-forming eye: Petto, A.J. and Mead, L.S. 2008.

Misconceptions About the Evolution of Complexity. Evolution: Education and Outreach. 1(4): 505-508.

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

PBS Evolution of the Eye – has an excellent short video that demonstrates incremental developments towards the camera eye: http://www.pbs.org/wgbh/evolution/library/01/1/l_011_01.html



HHMI – Seasonal Rhythms http://www.hhmi.org/biointeractive/clocks/seasons.html

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

Seasonal Rhythms – Sleepy Teens http://www.hhmi.org/biointeractive/clocks/fall/teenagers.html



Carskadon, M.A., Vieira, C., and Acebo, C. Association between puberty and delayed phase preference. Sleep 16(3):258-262, 1993.



Carskadon, M.A., Wolfson, A.R., Acebo, C., Tzischinsky, O., and Seifer, R. Adolescent sleep patterns, circadian timing, and sleepiness at a transition to early school days. Sleep 21(8):871-881, 1998.



We recommend obtaining permission to show portions of the David Attenborough BBC Private Life of Plants video – there are many beautiful clips of pollinators and flowers, adaptations that illustrate co-evolution.



Rodríguez-Gironés MA, Santamaría L. 2004. Why Are So Many Bird Flowers Red? PLoS Biology Vol. 2, No. 10, e350 doi:10.1371/journal.pbio.0020350.



Heiling, AM and Herberstein, M E. 2004. Predator-prey coevolution: Australian native bees avoid their spider predators. Proc Biol Sci. 271(Suppl 4): S196–S198.



Schneider T, Thalau H-P, Semm P, Wiltschko W. 1994a. Melatonin is crucial for the migratory orientation of pied flycatchers (Ficedula hypoleuca pallas). J Exp Biol.

194:255-262.



Schneider T, Thalau HP, Semm P. 1994b. Effects of light or different earth-strength magnetic fields on the nocturnal melatonin concentration in a migratory bird.

Neurosci Lett. Feb 28;168(1-2):73–75.



Sherwood,B., Cutler, D., Burton, J. Eds. 2002.Wildlife and Roads: the ecological impact. Imperial College Press, London.



Tarlow, Hau, Anderson, and Wikelski 2003. Diel changes in plasma melatonin and corticosterone concentrations in tropical Nazca boobies (Sula granti) in relation to moon phase and age. General and Comparative Endocrinology 133(3): 297 -304.



Navara and Nelson. 2007. The dark side of light at night: physiological, epidemiological, and ecological consequences. Journal of Pineal Research 43(3): 215224.



Longcore and Rich, 2004 – Ecological light pollution. Frontiers in Ecology and the Environment. 2(4):191-198.



LightPollution.org.uk http://www.lightpollution.org.uk/index.php?pageId=0



Ecology of the Night (Muskoka Heritage Foundation) http://www.muskokaheritage.org/ecology-night/

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

Velando et al., 2006 Pigment-based skin colour in the blue-footed booby: an honest signal of current condition used by females to adjust reproductive investment.

Oecologia 149(3): 535-542.



National Geographic photo gallery “The Art http://ngm.nationalgeographic.com/2009/08/mimicry/ziegler-photography)



Not all organisms depend on light! http://saturn.astrobio.net/exclusive/207/living-in-the-dark

of

Deception”:

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

All organisms are made up of cells.

2.

All cells share some common structures/characteristics, but there are some differences between cells within and between different organisms.

LEARNING OBJECTIVES Students should be able to:



Describe the cell theory. [Comprehension]



Identify how cell theory underlies topics in Biology, including remaining chapters in this textbook. [Synthesis]



Explain the steps that must have occurred to result in life (as defined here).

[Comprehension]



Compare different hypotheses (e.g., primordial earth and extraterrestrial) on the origin of life [Analysis/Evaluation]



Explain the steps that must have occurred to result in life (as defined here).

[Comprehension]

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

Compare different hypotheses (e.g., primordial earth and extraterrestrial) on the origin of life [Analysis/Evaluation]



Describe the "information system" of the cell, including the roles of DNA and RNA in this system. [Comprehension]



Describe the scenario of evolution of proteins and DNA, based on the development of life in an “RNA world”. [Comprehension]



Describe the impact of oxygenic photosynthesis on evolution of life. [Comprehension]



List the components and characteristics common to all cells. [Knowledge, Comprehension]



Explain, at a general level, the role of ATP in metabolism. [Comprehension]



Compare and contrast cells of bacteria and those of eukaryotes, identifying similarities and key differences between prokaryotic and eukaryotic cells.

[Analysis/Evaluation]



Define “life” in a scientifically meaningful way. [Knowledge]



Define ‘theory’ in a scientifically meaningful way. [Knowledge]



Describe the structure and functions of organelles (including the nucleus and other elements of the endomembrane system; lysosomes; mitochondria; chloroplasts) found in eukaryotic cells. [Comprehension]



Explain the relationship (and connections) between the plasma membrane, endoplasmic reticulum and Golgi complex in eukaryotic cells. [Comprehension]



Define endosymbiosis, describing the endosymbiotic theory of the origin and evolution of mitochondria and chloroplasts. [Comprehension]



Describe the major eukaryotic cytoskeletal elements, and their roles in the cell.

[Comprehension]



Compare and contrast the bacterial flagellum and the eukaryotic flagellum.

[Comprehension, Analysis]



Describe the steps that likely led to development of complex multicellular organisms from single-celled ancestral organisms. [Comprehension] DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Cell theory is one of the major themes underlying Biology. As the cell is the fundamental unit of life, what occurs in and around the cell is important in all aspects of Biology.



Similarities in different cell types allow the identification of fundamental cellular processes despite gross morphological differences. For example, use of E. coli, yeast, fruit flies, and Arabidopsis as model organisms allows observations into many processes that cannot easily be studied in other organisms.



The origin of life is of interest to many biologists for a number of scientific reasons. Public perception of the origin of life can have an impact on education, biological research funding and other aspects of science.



Exobiology and astrobiology are disciplines where scientists are involved in seeking evidence of extraterrestrial life.



The tenets of life that apply to populations (e.g., reproduction and evolution) are also of interest to biologists because they have implications for conservation biology.



Understanding the structures and functions of cells (and cellular components) is vital not only in understanding various aspects of biology, but in many aspects of health and disease.

WHY SHOULD STUDENTS CARE? 

Understanding the nature of life, and cell theory, is of value throughout the entire course, since this is one of the major themes in biology.



Research in cell biology has clear implications in human health/disease, as well as in many other applied aspects of biological research.



Bacterial cells are different from archaeal cells (although both are prokaryotic), and prokaryotes differ from eukaryotes. As students learn more about organisms, systems, etc., they will need to be aware of the key differences as well as the similarities of the different types of cells.



Understanding how bacteria differ from human cells has practical value when considering treatment of infections (most antibiotics exhibit selective toxicity – kill/inhibit bacteria, while leaving the host unharmed).

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 8.

Students typically view the term theory through its vernacular use (i.e., conjecture, speculation – perhaps unfounded). As theories, cell theory and the theory of evolution by natural selection have been supported with observation, withstood countless years of testing, and explain a wide variety of observations.

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9.

Although most textbooks assert that viruses are not alive, virology is considered a sub-discipline of biology, and viruses are often described in language that indicate that they are indeed considered living organisms.

10. Some students are a bit chemistry-phobic, and can be overwhelmed when discussing the types of reactions that might have created prebiotic materials/conditions. Instructors may wish to focus on the necessary processes of living organisms and how they relate to biochemical molecules to tie the biology of life to the chemicals of life.

11. Cells likely didn’t originate just once, but probably developed several to thousands of times, but only a few were able to reproduce (daughter cells that went on to reproduce themselves).

12. Students may have trouble with the concept that some cells are autonomous organisms (e.g., bacteria, archaea, protists), while others must be organized in tissues (in animals and plants) to comprise an organism. a.

Students may be uncomfortable at first with the questions of ‘Why are there cells?’ and ‘Why unicellular? Why multicellular?’ These are examples of questions where we don’t know what the “correct” answer is, and students can be encouraged to share their thoughts without risking being wrong.

13. It can be difficult for students to picture life without oxygen. Oxygen production via photosynthesis transformed Earth, and allowed for evolution of oxygen-requiring organisms. Students may not be aware that there are different types of photosynthesis, and that anaerobic bacteria (not plants) were responsible for oxygen production prior to evolution of plants and animals. a.

When we say an organism uses oxygen, it means that it brings oxygen into its cell(s) to be used in various processes including the maximal production of energy molecules. (E.g., when running and breathing hard, a person is bringing oxygen into cells, where it can be used in energy production.) Organisms that don’t use oxygen can use other chemicals to produce energy molecules.

14. Many students will not have encountered the three domains of life (Bacteria, Archaea and Eukarya), and will be under the impression that bacteria and archea are basically the same (or are very closely related). In discussion of prokaryotes and eukaryotes, we recommend mentioning that the bacteria and archaea are evolutionarily distinct, and that although archaea are microscopic and lack a true nucleus, they share many characteristics with eukaryotes.

15. The different cell components (bacterial cell structures, eukaryotic organelles, cytoskeletal elements) may prove overwhelming in terms of new vocabulary, and students may focus on memorization rather than comprehending the concepts (particularly structure and function). However, some understanding of the structure of the cell is helpful in understanding the various processes that occur in cells (and are discussed at greater length in Chapters 4-15).

WHAT CAN I DO IN CLASS? In addition to the theory of evolution by natural selection, cell theory is a major underlying concept for Biology (and this course). Highlight key similarities among different cells and organisms. This is the main chapter discussing cell biology, and will help orient students when discussing later topics (e.g., cellular respiration in mitochondria, photosynthesis in chloroplasts, etc.)

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At the beginning of class, students can be introduced to a news story about recent research developments involving cell biology – the story could be medical [if teaching pre-meds, majors, non-majors], agricultural [majors, agriculture] or biotechnological [majors, non-majors, engineers].

Johnson et al. (2008) reported an analysis of the original extracts of this experiment in Miller's material. The volcanic apparatus produced a wider variety of amino acids in 2008 than the classic experiments. Question: Ask students to speculate why the later analysis would have given different results than the original experiments. [Stumbling Block 3] Astrobiology can be introduced, using the “Why it Matters” material in the text. Students can be asked to consider individually, in pairs or in larger groups the questions: Would extraterrestrial life resemble aliens on Star Trek / Star Wars / etc? Why are most scientists who study in this area trained in disciplines such as chemistry (cosmochemistry), microbiology, and geology? (This may help students to understand why evidence of early life is harder to find.) What would scientists look for if seeking evidence of life on another planetary body, and why?

Brainstorm: If cells have been around for so long, there must some benefit to this form, so why have cells?

[Stumbling Block 5] Discussions can be set up to address issues relating to evidence of evolution: e.g., why fossil evidence has not been observed for all organisms; what evidence beyond fossils is considered (i.e., chemical evidence).

If time is available, and you have obtained rights to show the video in class, you may want to show Episode 1 “The Hidden Kingdom” from the BBC three-part series, “The Cell”. Host Adam Rutherford highlights the key historical experiments that identified cells, and development of cell theory, in an engaging and informative manner.

Ask students: How is the endomembrane system distinct from other membranes in a eukaryotic cell?

Students can be asked to create a table showing the components/organelles of cells, considering bacteria vs. eukaryotes (and plants vs. animals). Ideally, they should highlight common elements to all cells, and identify where different cell types vary. [Stumbling Block 8] Endosymbiosis is not something limited to the distant past! There are examples of organisms that scavenge chloroplasts (see the “solar-powered sea slug”, Elysia chlorotica, discussed in Chapter 3). Another current example: the amoeba Paulinella ovalis eats cyanobacteria, usually of the genus Synechococcus. Paulinella chromatophora does not obtain food in the same way, but obtains photosynthetic products from its two endosymbionts that divide when the amoeba divides. As the endosymbionts cannot survive outside the host, some biologists might argue that these are actually organelles (chloroplasts). (See Keeling 2004 for more information.)

In many processes, motor proteins must be associated with cytoskeletal elements. Figure 2.23 shows the motor protein kinesin associating with microtubules to move a vesicle or other cell structure. Additional examples that instructors can mention to students (and that may come up in later topics) include movement of chromosomes (microtubules and kinesins), muscle contraction (actin microfilaments and myosin) and movement of flagella/cilia (microtubules and dynein). The Kinesin home page (http://www.cellbio.duke.edu/kinesin/index.html) has some interesting information and visuals.

In considering the bacterial flagellum and eukaryotic flagellum, you may wish to introduce students to the idea of convergent evolution (see Chapter 19). In both cases, the “flagellum” is long and thin, and is used in liquid for propulsion (of the cell, or of liquid moving across the cell). The structures themselves are constructed very differently. The bacterial flagellum is a hollow tube composed of flagellin, with a rotary motor at the base, embedded in the cell wall/membrane; the eukaryotic flagellum is a much larger structure. The eukaryotic flagellum (and cilium) is an extension of the cell, within the plasma membrane, primarily made up of microtubules and associated motor and structural proteins, exhibiting sinuous movement by the action of dynein motor proteins and microtubule sliding. We recommend avoiding the term “prokaryotic flagellum”

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because the flagellum in archaea is actually more similar to the bacterial pilus than the bacterial flagellum.

[Stumbling Block 7, 8] Think-pair-share/discussion activity: How do cells of autonomous organisms (e.g., a yeast cell, bacterium or protozoan) vary from the cells found in multicellular organisms? Why? [Stumbling Block 3] Clicker question: Which of the following is considered a single-celled organism?

A. B. C. D. E.

Sperm Bacterium * Virus Plant None of the above

This question can be used in discussing characteristics of life. An instructor may want to describe a virus, gametes, etc., and then pose the question to their students. (Be aware that a brief discussion regarding why “sperm” cannot be considered an organism may be required!) Student responses can be used to lead into a debate: Should we consider viruses to be “organisms”? Divide students into groups to argue for and against the statement: “Viruses are not organisms”. Depending on class size, can divide into two or more groups to allow smaller discussions before bringing the debate to the larger group. [Stumbling Block 2] This discussion can be used to bring the topic of ‘What is life?’ full circle, encompasses much of the material addressed in this chapter, and highlights that debates still exist regarding the definition of ‘alive’.

WHAT OTHER RESOURCES ARE AVAILABLE? 

NASA Astrobiology: http://astrobiology.nasa.gov/about-astrobiology/



PBS – A Science Odyssey – People and Discoveries [Amino acids are created in laboratory]: http://www.pbs.org/wgbh/aso/databank/entries/do53am.html



Astrobiology Magazine - The Spark of Life: http://www.astrobio.net/news/index.php?name=News&file=article&sid=2985



Johnson AP, Cleaves HJ, Dworkin JP, Glavin DP, Lazcano A, Bada JL. 2008. The Miller Volcanic Spark Discharge Experiment. Science 321:404. | DOI: 10.1126/science.1161527



BBC The Cell Ep.1 The Hidden Kingdom http://www.bbc.co.uk/programmes/b00m5w92



Keeling, PJ. 2004. Diversity and evolutionary history of plastids and their hosts. Am. J. Bot. 91: 1481-1493.

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

Kinesin home page (created by Liz Greene and Steve Henikoff): http://www.cellbio.duke.edu/kinesin/index.html

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Evolution is a unifying theme in biology; understanding of evolution is necessary in order to fully comprehend findings in all fields of biology.

2.

Evolution is a change over time in the characteristics of a population. It is responsible for the unity (similarities) and diversity (differences) of life that we observe. Evolution of, and within, species is dependent on the immediate environmental conditions (both abiotic and biotic) and is limited by evolutionary history.

LEARNING OBJECTIVES Students should be able to:



Define key terms (general): biosphere, population, evolution, abiotic, biotic, biodiversity, autotroph, heterotroph, selection. [Knowledge]



Explain how organisms can be classified according to factors other than physical features. [Comprehension]



Explain why measuring biodiversity is important in conservation biology.

[Comprehension]



Explain how evolution of resistance in an organism (e.g., bacterial resistance to antibiotics) is shaped through mutation and selective processes [Comprehension]



Describe how selection is a major force responsible for evolution and biodiversity.

[Comprehension]



Describe how evolution explains (or is responsible for) the unity and diversity of life.

[Comprehension] DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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

Relate trends in biodiversity to latitude (abiotic/biotic factors). [Analysis]

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

Describe the different modes of nutrition employed by different organisms.



Describe abiotic and biotic factors that affect species distribution. [Comprehension]



Define selection and provide a biological example of this process.



Describe how abiotic factors might affect the global pattern of diversity.

[Comprehension]



Describe how biotic interactions might affect the global pattern of diversity.

[Comprehension]



Describe a local effect (e.g., topography) that can moderate temperature.

[Comprehension]



Define microclimate, comparing it to climate. [Knowledge]



Explain in general terms how the earth’s shape affects solar radiation intensity across latitudes. [Comprehension]



List advantages to life on land compared with life in water. [Knowledge]



List three challenges of living on land, compared with life in water. [Knowledge]



Describe the concept of adaptive radiation, using an example. [Comprehension]



Describe the conditions that may lead to adaptive radiation. [Comprehension]



Explain how evolution and adaptive radiation are not a choice. [Comprehension]



Explain why islands are great models for studying evolutionary processes.

[Comprehension]



Describe how abiotic and biotic factors might interact to limit where a species lives.

[Comprehension]



Describe how photosynthesis is not limited to plants. [Comprehension]



Describe how animals might use other organisms to photosynthesize and digest foods. [Comprehension]



Describe how the bodies and activities of a species may provide opportunities for other species. [Comprehension]

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

Describe, in general terms, Darwin’s contribution to the field of evolutionary biology. [Comprehension]



Summarize the main points of the theory of evolution by natural selection.

[Comprehension]



Define climate and weather. [Knowledge]



Describe the cause of variation in solar radiation intensity and seasonality on Earth.

[Comprehension]



Describe how wind patterns and solar radiation can create variations in rainfall across latitudes. [Comprehension]



Define producers, consumers, decomposers, primary consumers, mesopredators, omnivores, parasitism, mutualism. [Knowledge]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Biodiversity, the number of species, is key to the functioning of our planet. However, how to classify different species becomes difficult when we move away from classification of larger plants and animals. There is considerable debate among biologists about classification of bacteria.



Understanding of evolutionary relationships is useful in uncovering useful treatments for human diseases.



Conservation ecologists are trying to study biodiversity, protecting endangered species and preventing further ecological damage.

WHY SHOULD STUDENTS CARE? 

Evolution and selection are fundamental concepts in Biology (and most introductory Biology courses).



Selection can have significant consequences on human health (e.g., bacterial resistance to antibiotics).



Biodiversity of plants, fungi, and bacteria has allowed development of many therapeutic drugs, and potential exists for finding additional medicinally-important compounds, assuming we do not lose the organisms that produce these molecules.

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WHAT ARE COMMON STUDENT MISCONCEPTIONS/ STUMBLING BLOCKS? 16. Students often unknowingly misuse the terms population, evolution, and selection. This makes it difficult for them to understand the material presented as they are interpreting it according to a different definition than the intended one. (E.g., students often think of a population as a group of individuals from different species and evolution as a change in an individual, not a population, over time. Both misconceptions can impair a student’s ability to understand the major concepts underlying much of this field.) We recommend that instructors remind students frequently to use the biological definitions.

17. Evolution doesn’t occur in an individual. Students need to understand that selection affects an individual and the result of this is observed as evolution at the level of the population.

18. Students often believe that organisms choose their range and niche and fail to grasp the importance of chance in these roles.

19. Sometimes students believe that within the scientific community there still exists controversy regarding evolution (and thus think it is unnecessary to grapple with its abstract ideas). They confuse the vernacular use of theory (just a guess, etc.) and apply it in their biology classes. They fail to grasp that there is substantial evidence for evolution (as there must be in order for it to be a theory).

WHAT CAN I DO IN CLASS? This chapter discusses biodiversity and limited aspects of the evolutionary mechanism, natural selection (including adaptive radiation) emphasizing the close link between ecology and evolution. The similarities tying organisms together is a result of common ancestry, while the fantastic diversity of life can be explained by the action of evolutionary processes, such as selection.

The “Why it Matters” material can prompt discussion regarding the potential benefits of knowing an organism’s evolutionary history.

The link between biodiversity and evolution can be explored through the pictures of mimicry in the text. Many more of these can be found at National Geographic (The Art of Deception, August, 2009) http://ngm.nationalgeographic.com/2009/08/mimicry/ziegler-photography. These beautiful photographs capture the students’ imaginations and show wonderful examples of adaptation. This also links to concepts in Chapter 1, relating to light as an information source.

Discussions can be initiated by getting students to find news stories relating to biodiversity – either new species that have recently been found, or an issue in conservation biology. Before showing/telling students answers ask them why biodiversity might be important. Students are often interested in invasive species, particularly those in their geographic area. In Southern Ontario, the fast-growing vine, kudzu, was recently observed. Students can be asked to name some invasive species, and discuss the problems relating to such organisms when introduced into a new habitat.

Many students don’t understand (or have never really thought of) why, beyond aesthetic value, biodiversity is so valued. Challenge them to come up with two other reasons why biodiversity is necessary.

Rainforests are prime examples of biodiversity. The rainforest can be introduced as an example of biodiversity, and threats to rainforests can be discussed.

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Ask students to listen to a CBC report, or read a mass media article on evolution. In small groups or with the entire class, identify and examine the biases present within these presentations. Ask students to identify any parts of the report where the authors/reporters are incorrectly using evolutionary terminology.

Discussions can be initiated about the different types of diversity (i.e., species diversity, genetic diversity, and ecological diversity). Species diversity is what most students think of with the word biodiversity. Exploring species diversity allows you to touch on a number of topics – why do we not know how many species exist on Earth. Why do we know more about the number of species of larger organisms, e.g., birds, mammals, fungus compared to bacteria, archaea and one-celled eukaryotes? This leads directly into the difficulty in defining what exactly constitutes a species, as many of the definitions (e.g., the Biological Species Concept) only apply to a limited group of organisms. (Indeed, bacterial and archaeal species are far broader, on a genetic level, than those of plants and animals.)

Considering different types of symbioses, students can be encouraged to list different example partner organisms. An instructor can assign different relationship types to different groups (or pairs) of students, who can report back to the larger group after a few minutes to brainstorm and think about examples. Ask students to consider how a symbiotic relationship can change (e.g., from commensalistic to parasitic).

Ask: How would the chloroplast-stealing sea slug be classified in terms of trophic levels?

Clicker questions: 1.

Which of the following is an example of evolution (as defined in Biology)?

A. Joe’s extensive sun tanning resulted in genetic mutations that led to formation of melanomas (skin cancer).

B. A region in Southern Ontario experiencing gradually increasing temperatures has 10-fold larger numbers of cicadas than it did 17 years ago.

C. A culture of bacteria containing equal numbers of bacteria able to break down toluene as a carbon source and those that cannot are placed in a toxic waste area. In a month, 99% of sampled bacteria can break down toluene.* D. None of the above.

This question relates to the biological definition of evolution [Stumbling Blocks 1, 2].

2.

The relationship between bacteria causing pneumonia in a human host (e.g., Streptococcus pneumoniae) and the human would best be described as A. B. C. D.

mutualistic commensalistic parasitic * competition

This question could be altered to describe a different type of relationship, such as a commensal situation (e.g., Staphylococcus aureus living on human skin without causing disease).

WHAT OTHER RESOURCES ARE AVAILABLE? 

National Geographic has a considerable amount of material on diversity and selection (e.g., http://ngm.nationalgeographic.com/2008/11/borneo/white-text/4 and http://ngm.nationalgeographic.com/2009/08/mimicry/ziegler-photography)

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

National Geographic also has a short video (“A New Perspective on Biodiversity”_ that you may want to encourage students to view.



PBS Evolution of Camouflage is another short clip, focusing on camouflage/mimicry: http://www.pbs.org/wgbh/evolution/library/01/1/quicktime/l_011_03_56.html



Encourage students to look at (if you haven’t already done so for Ch. 1) the PBS clip on eye evolution.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1. Enzymes are vital for metabolic reactions to occur in the cell.

2.

Enzyme activity can be affected by physical conditions and the activity of some enzymes is subject to regulation.

LEARNING OBJECTIVES Students should be able to:



Define key terms (energy): kinetic energy, potential energy, thermodynamics, entropy, spontaneous reaction, enthalpy, endothermic, exothermic, reactants, free energy, concentration gradient, equilibrium, exergonic reaction, endergonic reaction, catabolic pathway, anabolic pathway, adenosine triphosphate (ATP), energy coupling, coupled reaction, ATP cycle. [Knowledge]



Define key terms (enzymes): activation energy, transition state, catalyst, enzyme, conformation, enzyme-substrate complex, cofactor, coenzyme, saturation, enzyme inhibitors (competitive, noncompetitive), allosteric regulation (including allosteric site, activator, inhibitor), futile cycle, feedback inhibition, enzyme activity, pH optimum, temperature optimum. [Knowledge]



Describe different forms of energy important in biology (e.g., heat, chemical, electromagnetic radiation). [Comprehension]

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

Compare and contrast the states of kinetic energy and potential energy, using an example for each. [Comprehension, Analysis]



Describe the laws of thermodynamics, providing examples of each. [Comprehension]



Compare and contrast energy exchange in isolated, closed and open systems.

[Analysis]



List and describe the factors that determine whether a reaction will be spontaneous.

[Knowledge, Comprehension]

DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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

List the free energy equation, describing the factors and explaining how they determine free energy. [Comprehension]



Distinguish between exergonic and endergonic reactions. [Analysis]



Determine if a particular reaction would occur spontaneously, provided adequate information (e.g., ∆G). [Application]



Compare and contrast catabolic pathway reactions and reactions of anabolic pathways. [Analysis]



Describe how cells use ATP to couple reactions. [Comprehension]



Describe the ATP cycle. [Comprehension]



Explain how enzymes serve as catalysts for biological reactions, listing mechanisms that can contribute to catalysis. [Comprehension]



Compare the “lock-and-key hypothesis” with the “induced-fit hypothesis”, and explain why the former has been superseded by the latter. [Analysis]



Compare and contrast competitive inhibition of enzymatic activity to noncompetitive inhibition. [Analysis]



Describe the role of a cofactor in many enzymes. [Comprehension]



Describe how temperature and pH affect enzyme activity. [Comprehension]



Determine the effect on enzyme activity, given information about a particular enzyme and reaction conditions. [Application]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

These concepts underlie biochemistry and physiology.



Problems with enzymes can result in medical/physiological problems, and researchers are seeking to understand and find treatments for such disorders.



Biotechnology often uses enzymes that carry out reactions we find economically/practically valuable.



Inhibition of certain enzymes can be valuable therapeutically (e.g., some antibiotics work as inhibitors of bacterial enzymes; some anti-cancer drugs target enzymes in cancerous cells).

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WHY SHOULD STUDENTS CARE?



These concepts underlie biochemistry and physiology (and are necessary to understand much of the material in introductory biology).



Reactions (catalyzed by enzymes) are vital for cellular function (e.g., DNA replication, cellular respiration, photosynthesis, etc.).



Problems with enzymes can result in medical/physiological problems.



Inhibition of certain enzymes can be valuable therapeutically (e.g., some antibiotics work as inhibitors of bacterial enzymes; some anti-cancer drugs target enzymes in cancerous cells).

WHAT ARE COMMON STUDENT MISCONCEPTIONS/ STUMBLING BLOCKS? 1.

Some students may be “chemistry-phobic”, and demonstrate some resistance to (or fear of) chemically-oriented material. Highlighting the importance of chemistry in biological structures and processes may help these students gain comfort with the material. (Remind students that the Purple Pages include useful chemistry reference material.)

2.

The idea that living systems demonstrate low entropy in surroundings of higher disorder may be confusing to some students, but this provides an opportunity to discuss the nature of living systems, and the need for cellular “work”.

3.

Students have problems remembering that a negative ∆G indicates energy available for use (exergonic), and a positive ∆G as a situation requiring energy (endergonic). We recommend frequent reminders that a negative ∆G indicates that the products contain less free energy than the reactants, and the opposite is true when ∆G is positive.

4.

The relation of ∆G to ∆H is confusing to many students. Explicitly working through the ∆H equation, and showying that ∆G is just a component of ∆H is helpful in addressing this stumbling block.

5.

It can be difficult to picture all of the different types of biochemical reactions that are simultaneously occurring in a given cell. In courses, we often can only show a single reaction or process, but we can remind students that in any living cell, many reactions are taking place (including both anabolic and catabolic reactions).

6.

Students also have some problems comprehending the contribution of enzyme and substrate concentration to rate of reaction. Also a problem is the importance of concentration to competitive and non-competitive inhibition controls of enzyme activity. As mentioned in #5 above, students tend to think of one enzyme molecule at a time rather than an entire system where concentration of all components becomes an important factor. Because of this, some students jump to the conclusion that if an inhibitory molecule is present then none of the enzyme molecules will be functional, when in actual fact, the number of enzymes affected is determined by the number of inhibitory molecules present relative to the substrate concentration (is determined by the ratio of enzymes and inhibitory molecules that are present). Students may not realize (or remember) that binding of an inhibitory molecule to the enzyme is a temporary event - it is not permanently bound to the enzyme. Instead, interactions between enzyme and substrate or enzyme and regulatory molecules are very quick and all DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

26

of these reactions are occurring in a dynamic system. This concept of rapid interaction between the two molecules may also come up during discussions of ligand receptor interactions (Chapter 8).

7.

Students have some difficulties understanding why phosphorylation leads to a conformational change, and why such a change in structure is important to activation or inactivation of a molecule (and thus to its function). For the change in structure, refer to a protein structure, and illustrate how the chemical components determine the bonds created, and thus the structure itself. This is also another example showing that structure and function are directly associated.

8.

In relation to the above, students are often surprised that molecules are not in a constant active state.

They have some problems comprehending why active and inactive enzyme forms are important to many systems, and why it could be potentially detrimental to have a molecule constantly in an active state. Students may not have yet considered why it is more efficient from an energy perspective to have an active and inactive state in these molecules. A pantry analogy could be brought up: you generally have the materials you need on hand to make a meal, but they aren’t always in their cooked and ready to eat state.

9.

Students may find enzyme inhibition and allosteric regulation confusing. Working through different examples in the larger context of metabolic pathways may be helpful in reinforcing these concepts.

WHAT CAN I DO IN CLASS? The “Why it Matters” talks about phosphatases, and a model of alkaline phosphatase (ALP) is included. This section shows why enzymes are important in living systems. Reversible phosphorylation is important in many biological processes, and future topics can link back to this information. Students may be interested to know that ALP (usually bacterial) is used in research, as a marker for pasteurization in milk by dairies (ALP should be denatured by pasteurization), and human ALP levels may be measured in diagnosis of certain conditions (e.g., bile duct blockage).

Depending on the background preparation of your students, you may want to provide an overview/review of chemical reactions. If your students have already encountered much of this material (check via knowledge-level clicker questions), you may want to spend less time on some of the more basic concepts, using class time to explore the major stumbling blocks, and/or connections to previous and future topics in the course.

In discussing free energy (∆G), showing graphs (such as Figure 4.10) to students can be helpful to demonstrate why exergonic reactions are associated with a negative value and endergonic reactions with a positive ∆G value.

(In most introductory courses, it is a good idea to walk students through the graph, explaining what each axis represents, to ensure that students understand what the graph is communicating.) A good exercise to assess understanding is to provide the ∆G associated with multiple chemical reactions that are coupled, and ask students to determine if there is enough energy for the anabolic reaction to occur. See clicker question below for an example.

It is likely that ATP has been mentioned previously (if Chapter 2 has been read/discussed), and links to Chapter 2 can reinforce the importance of this molecule, which is present in all living organisms. ATP is commonly called cellular energy “currency”, but you may want to ask students to brainstorm/suggest alternative analogies (e.g., rechargeable batteries).

There are many human enzymes that could be used in discussing the nature and characteristics of these biological catalysts. For example, Beta galactosidase is shown in Fig. 4.19. In humans, this is usually referred to as lactase. Lactose intolerance is a topic that often captures student interest, and in discussing the reaction and enzyme, the disorder can be used as an example of how this enzyme impacts human life. Depending on how much time you want to devote, you can bring in genetic and environmental factors into a discussion about lactose intolerance. (See review by Montgomery et al 2007 for more information.)

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The enzymes involved in alcohol breakdown can be used to illustrate a simple pathway. Alcohol dehydrogenase (ADH) is one enzyme in this pathway; ADH activity varies among individuals, with some general differences based on sex and geographic origins (this could lead into a discussion of alleles and phenotypes). ADH converts ethanol to acetaldehyde, which is subsequently converted to acetic acid by acetaldehyde dehydrogenase and glutathione. Consuming large amounts of alcohol can deplete glutathione reserves, leading to accumulation of acetaldehyde, which is considerably more toxic than alcohol. High levels of acetaldehyde can contribute to the unpleasant physical symptoms of a hangover.

The textbook highlights penicillin as a “Molecule behind Biology”. This is an example of a competitive inhibitor of enzyme action (here, transpeptidase [often called penicillin-binding protein or PBP], is required for cross-linking the peptidoglycan polymer in bacterial cell walls). We have found that students are often interested in antibiotics, and this example could be used in class when discussing enzyme inhibition. Other antibiotics also act as competitive inhibitors of enzymes in bacteria (e.g. sulfa drugs).

Heavy metal poisoning can be used as an example of (irreversible) non-competitive enzyme inhibitors. Many metals (e.g., silver, lead) have a strong affinity for sulfhydryl groups, and can bind to enzymes, inactivating them.

Discussion of heavy metal poisoning could provide a lead-in for discussing some of the controversial “chelation therapies” advertised by some alternative medicine practitioners, and students can be encouraged to investigate the claims, and evaluate the scientific evidence available.

Bring chewing gum with xylitol to class (or ask if any students are carrying such gum). Xylitol is a sugar alcohol (CHOH)3(CH2OH)2 that is used as a sugar substitute, and is added to some chewing gums. Xylitol does not appear to contribute to development of dental caries (cavities), and may actually provide additional dental benefits, inducing a “futile cycle” in Streptococcus mutans (a species associated with tooth decay). The bacteria take up xylitol (using energy for import) but cannot break down the molecule in metabolic reactions.

Enzyme activity is affected by several factors detailed in this chapter. You may want to discuss extremophiles, using examples of organisms that can survive high temperatures, low temperatures, acidic environments, basic environments, etc. There are practical/economic applications of some enzymes produced by some bacteria and archaea that live in these conditions (e.g., alkaline proteases and cellulases used in laundry detergents; Taq polymerase used in PCR).

Phosphofructokinase catalyzes the reaction Fructose-6-phosphate + ATP → Fructose-1,6-bisphosphate + ADP in the glycolytic pathway is often used as an example of an allosteric enzyme. ADP stimulates PFK activity; more unusually, ATP acts as a reactant and as an allosteric inhibitor. (This could be brought up or revisited when looking at Chapter 6, in discussing regulation of cellular respiration.)

An additional (alternate) example of enzyme allostery is bacterial aspartokinase. In bacteria and plants, the pathway that produces lysine is subject to feedback inhibition by lysine allosterically binding to aspartokinase.

(Animals lack this pathway, and must obtain this essential amino acid from their diets.) Lysine is produced industrially (for supplements, animal feeds) using a mutant strain of Brevibacterium flavum in which aspartokinase has an altered allosteric site, and is thus resistant to feedback inhibition.

“Unanswered questions” in this chapter highlights protein structure/function of enzymes, and the nature of ribozymes. If you discussed ribozymes in Chapter 2, you may want to continue to explore this topic; the possible therapeutic agents are likely to be of particular interest to many students.

Clicker questions: 1.

Reaction 1 has a ∆G = -3.5 kcal/mol, Reaction 2 has a ∆G = -7 kcal/mol, and Reaction 3 has a ∆G = +10 kcal/mol. Assuming that these reactions are directly coupled, determine whether or not there is sufficient energy for the anabolic reaction(s).

A. Yes, there is sufficient energy for the anabolic reaction(s).* B. No, there is insufficient energy for the anabolic reaction(s).

C. It is not possible to determine.

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This question could be modified/followed up to ask students to determine the actual free energy value after the completion of the reaction(s). [Stumbling block 3]

DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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2.

Enzymes are A. consumed by the time that a chemical reaction has completed.

B. able to recognize and alter specific substrates (reactants). * C. able to increase the energy yielded from a particular reaction (compared to the reaction without enzyme).

D. important in endergonic reactions, but not exergonic reactions.

This question is a knowledge-level question, and may help elicit misconceptions students have regarding the nature/role of enzymes.

3.

Mono Lake is a hypersaline and alkaline lake. It contains some bacteria, archaea, and insects, such as the ‘alkali fly’. Which of the following would be expected in organisms living in this lake?

A. B. C. D.

Enzymes have optimal activity at pH values > 7.* Enzymes have optimal activity at pH 7.

Enzymes have optimal activity at pH values < 7.

Enzymes are denatured.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Students may appreciate some of the enzyme animations from John L. Giannini (St.Olaf College, Northfield, MN): http://www.stolaf.edu/people/giannini/biological%20anamations.html



Montgomery RK, Krasinski SD, Hirschhorn JN, Grand RJ. 2007. Lactose and lactase--who is lactose intolerant and why? J Pediatr Gastroenterol Nutr. 45 Suppl 2:S131-7.



The Science Education Resource Center at Carleton College has an excellent website with information about life in extreme environments: http://serc.carleton.edu/microbelife/extreme/index.html



Tanzer, JM (1995). Xylitol chewing gum and dental caries. International dental journal 45 (1 Suppl 1):65-76.



Söderling EM, Ekman TC, Taipale TJ. 2008. Growth inhibition of Streptococcus mutans with low xylitol concentrations. Curr Microbiol. 56(4):382-5.



Lu, J. H., J. L. Chen, and C. C. Liao. 1994. Molecular breeding of a Brevibacterium flavum L-lysine producer using a cloned aspartokinase gene. Biotechnol. Lett. 16:449-454.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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1. The plasma membrane provides an important boundary between a cell and its surroundings.

2. Components in the plasma membrane are required for many cellular functions, with proteins playing many key roles.

LEARNING OBJECTIVES Students should be able to:



Define key terms (membrane structure): phospholipid, amphipathic, hydrophobic, hydrophilic, bilayer, micelle, fatty acid, unsaturated hydrocarbon, saturated hydrocarbon, desaturase, sterol, cholesterol, integral membrane protein, diffusion, transmembrane protein, peripheral membrane protein, cytoskeleton. [Knowledge]



Define key terms (membrane transport): selective permeability, passive transport, concentration gradient, simple diffusion, channel proteins, gated channel, carrier proteins, uniport, osmosis, aquaporin, hypotonic, hypertonic, isotonic, active transport pump, active transport, primary active transport, secondary active transport, proton/H+ pump, calcium/Ca2+ pump, membrane potential, electrochemical gradient, symport, cotransport, exchange diffusion, vesicle traffic, endocytosis, bulk-phase endocytosis, pinocytosis, receptor-mediated endocytosis, coated pits, clathrin, phagocytosis, exocytosis,. [Knowledge]



Describe the structure, and common components, of eukaryotic membranes.

[Comprehension]



Describe how the “fluid mosaic model” fits what is known about the plasma membrane, with respect to membrane structure/characteristics. [Comprehension]



Describe the factors affecting membrane fluidity. [Comprehension]



Describe the major functions of the eukaryotic plasma membrane. [Comprehension]

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

List and describe the key functions of membrane proteins. [Knowledge, Comprehension]



Compare and contrast simple diffusion and facilitated diffusion. [Comprehension, Analysis]



Determine if a particular substance (including gases, ions, small organic molecules, large organic molecules, water) could cross a simple phospholipid bilayer by diffusion. [Application]



Compare and contrast the different mechanisms by which water can cross a biological membrane. [Analysis]



Compare and contrast passive and active transport across eukaryotic membranes, providing examples of how transport mechanisms differ. [Analysis]



Compare and contrast uniport, symport and cotransport. [Analysis]



Correctly predict the flow of a particular substance (including gases, ions, small organic molecules, large organic molecules, water) along its gradient (concentration and/or electrochemical), provided information about relative concentrations on either side of a selectively permeable membrane. [Application]



Describe exocytosis and endocytosis, and provide examples of the types of cells in which these processes would be expected to occur. [Comprehension]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

As all cells contain a plasma membrane, understanding the structure and function of this component is vital for understanding many aspects of cellular biology.



Some disorders (channelopathies) are a result of defects in membrane proteins.



Resistance to some cancer therapies involves transport of chemotherapeutics across the plasma membrane.

WHY SHOULD STUDENTS CARE?



As the plasma membrane is common to all living cells, understanding the structure and function of these membranes is valuable in understanding cell biology and many physiological features relating to adaptation.



There are medical implications relating to membrane transport (see above).

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

Osmosis is important in physiological processes, including kidney function in animals.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/ STUMBLING BLOCKS? 20. Students often think of membranes as static, unchanging structures. The dynamic nature of membranes can be difficult to illustrate clearly. We recommend being explicit about this, and relating bulk transfer processes to the endomembrane system discussed in Chapter 2. Students can be reminded that membrane proteins are in flux, cholesterol levels may vary, and there can be other changes relating to environmental factors.

21. Membrane fluidity can be challenging for students to visualize. Factors that affect membrane fluidity (e.g., temperature, saturation of fatty acids, etc.) may also be problematic, particularly if the student doesn’t have an appreciation of what membrane fluidity is and the importance of fluidity in membrane function.

22. In most cases, cells are not functioning in isolation, although we present the cell as an individual entity when describing structure/function. It is a good idea to point out that in tissues, cells are not operating independently, but are constantly communicating with other cells, and reacting to signals received.

23. The effect of sterols (such as cholesterol) in membranes may be counter-intuitive to students who may be accustomed to thinking of cholesterol simply as “bad”. A discussion of low-density lipoprotein (LDL) vs. high-density lipoprotein (HDL) may be useful. (LDL is considered the “bad” cholesterol, leading to deposits in blood vessels; HDL is “good” cholesterol, associated with prevention of plaque deposits.)

24. Diffusion seems to be a simple concept, and this may lead students to underestimate its biological importance at a cellular and physiological level.

25. There are often issues relating to understanding and correct use of hypo/hyper/iso-tonicity. These are specific but relative terms, and cannot be used without context (e.g., the cytoplasm of a cell isn’t described simply as hypertonic, but could be hypertonic with respect to the surrounding liquid environment.

26. The concept of an electrochemical gradient can be confusing to some students. Introducing the chemical gradient prior to the voltage gradient, then combining the two may help students develop a better understanding. Sodium (Na +) transport is a good example that can be used to illustrate this.

(You may also want to refer students to some of the chemical information in the Purple Pages.)

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WHAT CAN I DO IN CLASS? The “Why it Matters” introduction introduces cystic fibrosis (CF), and the cystic fibrosis transmembrane regulator protein (CFTR). This is a good example of the importance of functional membranes in living things – even one defective protein can have devastating effects on the health, longevity and quality of life of an organism. (NB: Lap-Chee Tsui is profiled in this chapter, discussing the identification of the gene involved in CF.) Cystic fibrosis is a condition that can be used to illustrate many topics in introductory biology, including Mendelian genetics (as it is a loss-of-function mutation, autosomally inherited), human genetics (pleiotropic effects of the mutation), molecular genetics (the identification of the CF gene), genetic counselling and human physiology.

A debate could be held regarding the question: Should all Caucasians who plan to have children undergo screening for CFTR gene mutations? What differences might we expect regarding opinions on this in Canada vs. the U.S.A.?

Depending on the background preparation of your students, you may want to provide an overview/review of lipids (structure, characteristics, examples). If your students have already encountered much of this material (check via knowledge-level clicker questions), you may want to spend less time on some of the more basic concepts, using class time to explore the major stumbling blocks, and/or connections to previous and future topics in the course.

Physical models of membranes could be constructed (by you or your students) to help visualize the 3dimensional structure. Brainstorm: There are limitations to how certain characteristics can be shown via figures/models. How could the dynamic nature of a membrane be demonstrated? [Stumbling Block 1] Depending on the demographics of your class, you may want to briefly highlight some of the techniques and technology used to study membranes (e.g., patch clamping). This would likely be of interest to biology/biochemistry majors and those interested in biotechnology.

Ask students why boundaries are important in the world around us. Why are they important to a cell? Students can be encouraged to find everyday analogies to membrane components (e.g., gate and gatekeeper for certain types of membrane transporters).

Bring in, or ask students to think of different types of lipids that have varying levels of fluidity (e.g., wax, butter, oil). What external factors affect the fluidity of something like wax or butter? (You may want to discuss trans fats, profiled in the “Molecule Behind Biology” section, here.) Ask students to consider different factors that affect membrane fluidity (both external and relating to composition of the membrane). [Stumbling Block 2] Although nearly all membranes are composed of a lipid bilayer, there are some differences in membranes between members of the Archaea and other domains. Archaeal membranes have different lipids (phytanyls) linked to glycerol via an ester (rather than ether) linkage. Certain hyperthermophilic and/or acidophilic archaea have plasma membranes that superficially resemble a lipid bilayer, but are actually composed of a lipid monolayer (phospholipids on both surfaces of the membrane are linked by lipids spanning the membrane).

Ask students to predict the features this type of membrane would have and how this would be useful to this type of organism (living at high temperatures or in acidic conditions). (The monolayer provides additional membrane stability to these archaea.)

Diffusion can be demonstrated easily in class, using water and food colouring (or pigment powder) in a clear vessel. Adding a small quantity of dye to water, diffusion throughout the liquid is likely to occur completely by the end of class.

Discuss why aquaporins exist, when we know that water can pass through a lipid bilayer by simple diffusion.

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Osmosis can be demonstrated using eggs. Eggs are soaked in vinegar so that the shell can be removed, leaving the membrane intact. De-shelled eggs can be put into different solutions (water, an isotonic sucrose solution [approximately 0.3 M] and a concentrated sucrose solution) and left overnight before making observations and comparisons. Students can be asked to predict the outcome of this procedure, and explain the observed results. Encourage students to use the proper terminology relating to tonicity of the solution relative to interior of the egg in each case. [Stumbling Block 6] To introduce the concept of osmosis, you can ask students why we put salt on slugs, and what happens to the slug when subjected to this treatment.

The importance of osmosis can be demonstrated by discussing some of the tragic cases of “water intoxication” (hyponatremia) that have occurred in recent years. The story of the death of Jennifer Strange after participating in a radio station contest (“Hold your Wee for a Wii”) may be familiar to some students, but hyponatremia has affected marathon runners, a toddler under the care of a babysitter later charged with murder, and a student who died after an American hazing incident, among others. (In discussing these incidents, ask students to consider what happens at a cellular level when too much water is present. Why are sodium levels important?) Students could be encouraged to find news articles discussing these cases (or others), and evaluating the scientific accuracy of the reports. Students could be put into small groups to brainstorm guidelines to prevent water intoxication for at-risk individuals.

The CFTR protein is an example of an ABC (ATP binding cassette) transporter that can be used to explore the mechanisms involved in active transport. There are other human disorders that affect transporters, and you may want to provide additional examples.

Proton pumps are involved in many processes. There are many of these pumps in the stomach epithelium. Ask students why this is the case. You can follow up with: How might proton pump inhibitors (prescribed for some stomach disorders) work? This may provide a good example for discussing an electrochemical gradient.

[Stumbling Block 7] Release of neurotransmitters via exocytosis in nerve cells could be used to illustrate this type of bulk transport.

The tetanus toxin (produced by Clostridium tetani) is a powerful neurotoxin, and prevents release of synaptic vesicles at the presynaptic junctions of inhibitory motor neurons. The toxin blocks inhibitory impulses to muscles, interfering with the release of glycine or gamma-aminobutyric acid neurotransmitters. Muscles will contract continuously, leading to “spastic paralysis”, a painful condition that can involve seizures and trismus (“lock jaw”, as tetanus is sometimes called). Untreated, tetanus can be fatal.

“Unanswered questions” in this chapter include further analyses of aquaporins and entry of nanotubules via endocytosis. These might provide launching points to discuss where we might see advances in the near future, and other areas of future research in membranes and membrane transport.

Clicker questions: 1.

[Include image of transmembrane protein, such as the CFTR protein or other transporter, showing the transmembrane helices.] The membrane protein depicted here is A. Integral * B. Peripheral C. We can’t determine.

Transmembrane domains (with hydrophobic and hydrophilic regions) are necessarily integral.

2.

Which of the following processes (across the plasma membrane) are necessary for a living cell to function?

A. Diffusion of gases and water B. Facilitated transport of substrates down their concentration gradient DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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C. Active transport of ions D. Only 2 of the above processes in A through C are necessary.

E. All of the above processes in A through C are necessary.* This question reinforces the importance of all types of membrane transport in living cells. [Stumbling Block 5] 3.

If you have an animal cell and put it into a solution hypertonic to the cell cytoplasm, what will happen?

A. No change.

B. Net flow of water out of cell; cell shrinks.* C. Net flow of water into cell; cell swells (or bursts).

This question provides a chance to consider tonicity. It can easily changed to use a different cell type (e.g., plant, bacterial) or different solution (isotonic, hypotonic). [Stumbling Block 6]

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4.

You are a researcher trying to determine how a new drug is being taken up in cells. You have grown cells in tissue culture to study this. Treatment of cells with a clathrin inhibitor blocks uptake of the drug. This tells you that the transport is by A. B. C. D. E. F.

simple diffusion facilitated diffusion aquaporins ion gated channels endocytosis * exocytosis

Endocytosis relies on clathrin-coating for uptake, while other types of transport do not.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Canadian College of Physicians and Surgeons site for patients - cholesterol: http://www.cfpc.ca/english/cfpc/programs/patient%20education/cholesterol/ default.asp?s=1



Macalady JL, Vestling MM, Baumler D, Boekelheide N, Kaspar CW, Banfield JF. 2004. Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid. Extremophiles. 8(5):411-9.



Almond CS, Shin AY, Fortescue EB, Mannix RC, Wypij D, Binstadt BA, Duncan CN, Olson DP, Salerno AE, Newburger JW, Greenes DS. 2005. Hyponatremia among runners in the Boston Marathon. N Engl J Med. 352(15):1550-6.



Coverage of Jennifer Strange trial: http://www.injuryboard.com/national-news/thestrange-case-of-jennifer-strange-.aspx



Kerem B, Rommens JM, Buchanan JA, Markiewicz D, Cox TK, Chakravarti A, Buchwald M, Tsui LC. 1989. Identification of the cystic fibrosis gene: genetic analysis. Science 245(4922):1073-80.



Gadsby DC, Vergani P, Csanády L. 2006. The ABC protein turned chloride channel whose failure causes cystic fibrosis. Nature 440(7083): 477-83.



Ashcroft FM. 2006. From molecule to malady. Nature 440(7083):440-7. (A review of ion channel disorders involved in human diseases.)



Goldman, D. 2002. Membrane Transport of Chemotherapeutics and Drug Resistance: Beyond the ABC Family of Exporters to the Role of Carrier-mediated Processes. Clinical Cancer Research 8: 4.

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

The reactions and pathways in cellular respiration are used by most types of organisms to obtain energy (ATP) from the breakdown of organic compounds.

LEARNING OBJECTIVES Students should be able to: 10. Define key terms (chemical basis): redox (oxidation-reduction) reaction (including oxidation, oxidized, reduction, reduced), electronegativity, combustion, electron carrier, NAD+, NADH. [Knowledge] 11. Define key terms (mitochondria, process): intermembrane space, matrix, glycolysis, substrate-level phosphorylation, citric acid cycle, coenzme A, FAD, FADH 2, electron transport, cytochrome complex, prosthetic groups, ubiquinone, ATP synthase, oxidative phosphorylation, chemiosmosis, fermentation (including lactate fermentation, alcohol fermentation), anaerobic respiration, strict anaerobe, facultative anaerobe, reactive oxygen species (ROS), antioxidant. [Knowledge] 12. List and describe the [Knowledge/Comprehension]

three

parts/stages

of

cellular

respiration.

13. Describe the structure of the mitochondrion. [Comprehension] 14. Compare and contrast the location of cellular respiration in bacteria and archaea compared to (nearly all) eukaryotes. [Comprehension] 15. Explain how the membranes/compartments of mitochondria (structure) relate to the processes of cellular respiration (function). [Comprehension, Analysis] 16. Describe, in general terms, what occurs in glycolysis (including energy investments, energy yields and carbon inputs/outputs). [Comprehension]

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17. Explain what is meant by “glycolysis is an ancient pathway”. [Comprehension] 18. Describe the connection between glycolysis, pyruvate oxidation, citric acid cycle and the electron transport chain.[Comprehension] 19. Describe, in general terms, what occurs in the citric acid cycle (including energy investments, energy yields and carbon inputs/outputs). [Comprehension] 20. Describe, in general terms, what occurs in the respiratory electron transport chain and chemiosmosis (including energy investments, energy yields and carbon inputs/outputs). [Comprehension] 21. Describe the structure of ATP synthase, relating the different parts to the function of this enzyme. [Comprehension, Analysis] 22. Explain what is meant when it is said that electron transport and oxidative phosphorylation are coupled processes. [Comprehension, Analysis] 23. Describe the efficiency of cellular respiration compared to other types of fuel combustion (considering the estimated energy yield from a molecule of glucose.

[Comprehension] 24. Describe mechanisms involved in regulation of cellular respiration. [Comprehension] 25. Correctly determine the activity of phosphofructokinase, given presence/levels of ATP, citrate, and AMP. [Application] 26. Describe how anabolic reactions pathways/intermediates. [Comprehension]

relate

to

cellular

respiration

27. Explain how metabolism is possible in the absence of oxygen. [Comprehension] 28. Compare and contrast catabolism of carbohydrates, fats, and proteins. [Analysis] 29. Compare and contrast the characteristics of strict anaerobes and facultative anaerobes. [Analysis] 30. Explain how oxygen can be considered toxic. [Comprehension]

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31. Describe mechanisms in aerobic organisms involved in protection from toxic effects of oxygen. [Comprehension] 32. Integrate the cellular respiration pathways with other biochemical pathways that occur in living organisms. [Synthesis] 33. Correctly predict the outcome in cellular respiration if a particular key molecule (e.g.,

enzymes, mitochondrial structures) is damaged. [Analysis, Application]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? E. Cellular respiration reactions are key in many areas of biochemistry and physiology.

F. Energy, and this energy generation, is vital to almost every bodily function and process.

G. Problems with mitochondria/cellular respiration can result in serious medical/physiological problems (e.g., myoclonic epilepsy with ragged-red fibers MERFF; Kearns-Sayre syndrome, KSS), and researchers are seeking to understand and find treatments for such disorders.

WHY SHOULD STUDENTS CARE? 

Cellular respiration reactions are key in many areas of biochemistry and physiology (and are necessary to understand much of the material in introductory biology).



Many of the concepts introduced in this chapter (e.g., redox reactions, electron transport, chemiosmosis) are also important in photosynthesis.



Problems with mitochondria/cellular respiration can result in medical/physiological problems.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 

An understanding of energy levels of an atom, enzymes, membrane transport and ATP is needed to comprehend much of what occurs in cellular respiration. A review (in class, online, in tutorial) may be helpful, depending on the level of the students in the course, and the extent of coverage of those topics earlier in the course.

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

Students tend to mix up what occurs during reduction and oxidation, as they expect something to be lost during reduction and not gained. The textbook suggests the phrase “OIL RIG” to help students remember that “oxidation is loss”, “reduction is gain”, and another mnemonic phrase can be provided to students: LEO the lion says GER (Lose electrons oxidation, gain electrons reduction) is helpful. Explaining REDOX in terms of charge can also be helpful. For example gaining an electron actually reduces the charge as an electron is negative, and thus is associated with reduction. Loss of an electron (oxidation) results in a more positive condition. This will help the students understand why NAD+ to NADH is actually a reduction and not an oxidation. Oxidation is often associated with an oxygen, but remind students this is not always the case and should not be absolutely relied on as an indicator.



We have found that many students are focussed on simply memorizing steps/enzymes for the reactions, without considering the “bigger picture” of what is going on during these processes. Clear expectations from the instructor regarding what students are expected to know may help alleviate some of the anxiety associated with massive memorization (if, indeed, the instructor does not want students to memorize all of this information). Demonstrating to students the change in molecules throughout glycolysis, pyruvate oxidation and the citric acid cycle can be helpful. Whenever a kinase is involved something has been phosphorylated.



Students also tend to forget that electron transfer/movement between compounds is not always a complete process. A brief review of the impact of electronegativity and reference back to the types of covalent bonds (page F-8 of the purple pages) can be helpful.



Students often do not comprehend why so many steps are required to convert glucose into ATP. Demonstrating the difference in energy retained in the two scenarios (glucose straight to ATP, and glucose to ATP through many steps can help. Showing Figure 6.5 would aid during this explanation.



Students may have difficulty realizing that “cellular respiration” refers to many individual reactions, occurring in sets (glycolysis, pyruvate oxidation, citric acid cycle, electron transport and chemiosmosis). It is recommended that instructors explicitly mention that the term “cellular respiration” is generally used as shorthand to encompass the sum of all the reactions occurring in different stages (and locations in the mitochondrion).



Many students also fail to see the direct connection among the main components of cellular respiration namely glycolysis, pyruvate oxidation, Citric Acid Cycle, electron transport chain (ETC) and chemiosmosis. Demonstrating the ultimate products of each set of reactions and the stage at which each is used can be helpful. For example, NADH and pyruvate are products of glycolysis. NADH is then used in the ETC and pyruvate in pyruvate oxidation. Students may ask how these molecules cross the membrane. Use this teachable moment to refer back to different types of transmembrane proteins (chapter 5). This demonstration also emphasizes the importance of the ETC in ATP production as every respiratory component reduces DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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NAD+ and/or FAD, the products of which are only used by the ETC. The ETC is the only component that receives a product from every other set of respiratory reactions. 

Students know that aerobic respiration refers to the involvement of oxygen, but when asked where in the process oxygen is used, few can tell you. Demonstration of the necessity of oxygen in the creation of CO 2 is helpful as is pointing out that the terminal electron acceptor in the electron transport chain is O 2 (reference back to the importance of electronegativity in electron attraction will help students recognize why O2 is an ideal final acceptor). These explanations also help students understand why glycolysis can occur under anoxic conditions but not any cellular respiration component beyond that.



Chemiosmosis can be a challenging concept. We have found that many students do not fully understand the idea of membrane potential, which is problematic when looking at what occurs in chemiosmosis. Also, we’ve seen the following terms used interchangeably (without explanation): ion gradient, H + gradient, proton motive force. We recommend discussing what these refer to, and how they can overlap.



Students recognize that the electron transport chain is involved in pumping protons from one side of a membrane to another, but they tend to miss the importance of this process to the generation of an energy source (concentration/proton gradient).

They fail to think about why protons must be transferred from one side of the membrane to another. Referring back to concentration gradients, voltage gradients and driving force (called proton-motive force in this chapter) would be helpful.



How electrons from NADH and FADH 2 power the proton pumps is often not understood by students. A review of electron energy levels and the ground state can help. This review will also help students understand the contribution of electrons to photosynthesis (chapter 7).



Students often consider cellular respiration and photosynthesis to be “opposite reactions”, although they are not sets of reversible reactions, and the biochemistry is more complex than is often indicated (e.g., when presented as summary reactions).

While photosynthesis is not discussed in detail in this chapter, we recommend addressing this misconception early, perhaps comparing the major steps in each process side by side.



Related to the above, we have found that a common misconception is “animals carry out cellular respiration and plants carry out photosynthesis”, and that students may believe that plants do not perform cellular respiration. Highlighting the ubiquity of cellular respiration, in plants as well as animals, fungi, and many prokaryotes is recommended, though we also suggest reminding students that plants perform cellular respiration when addressing Chapter 7 (Photosynthesis).



As mentioned in previous chapters, it can be difficult to picture all of the different types of biochemical reactions that are simultaneously occurring in a given cell.

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While cellular respiration is occurring, the cell is carrying out other metabolic reactions. 

Students may find it non-intuitive that energy is actually expended in the first five steps of glycolysis (ATP is used to phosphorylate molecules). In later steps, energy is gained – ATP is generated. The net production of ATP and NADH outweighs the energy input. You may want to revisit Figure 4.11 (illustrating different types of metabolic pathways). We usually remind students that often an investment is necessary before one sees gain.



People often associate cellular respiration with mitochondria. However, glycolysis does not occur in mitochondria, and the cytosolic nature of this process should be emphasized. (Indeed, many scientists do not consider glycolysis as part of cellular respiration.) In discussing the ancient nature of glycolysis, students can be encouraged to think about the conditions for early life, when this pathway originated.

There may also be confusion regarding the correct regions of the mitochondrion where the Citric acid cycle, electron transport chain and ATP generation occur.



A minor issue is that the citric acid cycle is also known as the Krebs cycle or tricarboxylic acid cycle (TCA cycle). This should be mentioned, as some students have been taught the alternate term, and may not immediately recognize it refers to the same set of reactions.



Anaerobic respiration and fermentation may be counter-intuitive to students who are accustomed to thinking of oxygen as a requirement for all life (and reactions supporting life).



If a student is aware of the relatively large number of ATP molecules produced in the ETC/chemiosmosis, he/she may find the lower yields in fermentation to be perplexing when there are the higher-yield pathways in existence. It may be worthwhile to discuss the energy needs of smaller organisms vs. larger ones, and the need to “recycle” NAD+ and FAD.



Similarly, the idea of oxygen toxicity can be difficult for many students to grapple with. We suggest using the hydrogen peroxide demonstration discussed below in conjunction with an activity (e.g., clicker question) to explicitly address this misconception.

WHAT CAN I DO IN CLASS? The “Why it Matters” profiles Luft syndrome, a mitochondrial disorder. There are several types of mitochondrial disorders, and you may want to discuss others (or ask that students work in small groups to gather and share information about particular disorders). MERRF syndrome (or Myoclonic Epilepsy with Ragged Red Fibers) is one of the more commonly known mitochondrial disorders.

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This chapter links to several other earlier chapters, and it may be helpful to make these connections explicit to students, or encourage them to make these connections (e.g., in class, working in small groups, or as an assignment; concept mapping could be done to make this more visual). Energy is discussed in Chapters 1 and 4. (Chapter 4 also includes information about enzymes, feedback inhibition.) Chapter 2 discusses the endosymbiotic origin of mitochondria (and basic structure of the bacterial cell). Chapter 3 introduces the nutritional needs/methods of various types of organisms. Chapter 5 discussed membrane potential. Looking forward, many aspects of cellular respiration will relate to concepts in photosynthesis (Chapter 7).

As is the case with most chapters, there is considerable information in this chapter. In order to provide clear expectations to students, instructors should determine what they expect students to know, including the level of detail. Figures 6.7, 6.9, and 6.13 are particularly useful in discussing broad aspects of the processes without focussing on individual intermediate structures, enzymes, etc. [Stumbling block 2 ] When looking at the different phases/steps of the reactions in glucose oxidation, we recommend asking students to follow the carbons and phosphates in these reactions. This will force them to think about the reactions instead of just memorizing compounds and enzymes [Stumbling block 2, ]. Students can be asked, “When a phosphate is lost where did it go?” In cellular respiration, an ATP is often produced. Now the student can recognize the point where a molecule is produced instead of just memorizing that it occurs between those particular molecules. This can also be used for the production of CO 2. Upon comparison of two molecules it may be noticed that a carbon is lost, but where did it go? This also aids in the explanation of why O2 is so important to the Citric Acid Cycle.

With regards to Stumbling Block 3, students often do not understand what exactly is occurring when NAD+ becomes NADH. This misunderstanding partly stems from the addition of a proton during the reduction process. Figure 6.6 is a helpful visual. Have students compare the structure of the two molecules and determine the differences (i.e.

NAD+ has N+ and is lacking one H; NADH is neutral and has gained an H). Ask students to surmise what occurred to create the change; a common answer is addition of an electron and a proton. Demonstrate this scenario; 1 electron and 1H + would result in NADH+. Ask students, “What are we missing?”. At this point many recognize the need for another electron to create the neutral NADH molecule. This demonstrates to them why 2 electrons are always associated with the reduction of NAD +. At this point it is good to remind students that the electrons often travel with protons. This leads to the question, what happened to the proton that would have been associated with the 2 nd electron? In this case it is released, but this reminder will aid in understanding the events associated with the reduction of FAD. Instructors may want to have students read the Adams (2002) article in The Scientist, and follow up with in-class discussion. Example questions to ask: What type of human cell is particularly sensitive to damage from low ATP levels? Why? (The first question could be delivered as a clicker question.)

Figure 6.17 shows the detailed structure of ATP synthase. The figure legend mentions parts of the molecule. Ask students to try to label the diagram with the parts: basal unit, headpiece, stalk and stator. (This can be done in pairs, or small groups, or with the instructor at the DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

44

front labelling from student suggestions.) Discuss the different parts (structure) and how this enzyme synthesizes ATP (function).

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In discussing ATP synthase, instructors may want to direct students to the “People Behind Biology” profile of Peter Mitchell. The fact that the chemiosmotic theory was initially considered to be a radical hypothesis can be mentioned, as an example of how scientific progress occurs, with questioning and evaluating evidence expected as we continue to gather new evidence, test new hypotheses and analyze results.

In addressing Stumbling Block 9, providing the relative number of ATP produced via the ATP synthase under different concentration gradient strengths (and thus proton-motive forces) often helps students understand how the proton gradient serves as an energy source for ATP production. If there is a low proton-motive force (decreased concentration gradient), fewer ATP will be generated, while a stronger proton-motive force (increased concentration gradient) allows more ATP to be produced.

When discussing efficiency of cellular respiration, students can be asked to work through an everyday example involving a sugary food (as a written activity or clicker question).

E.g., Rocket candies are commonly seen at Halloween in Canada. This candy is produced by Ce De Candy's plant in Newmarket, ON. Nutritional info is available: Serving size: 7g Calories (kcal): 25 Carbohydrates: 6.1 g So, if you consume 4 rolls …

ATP: ~7.3 kcal How many molecules if we converted at 100% efficiency? 40% efficiency?

(Answers: 13.7 ATP molecules if 100% efficiency. At 40% efficiency, 5.5 ATP molecules.)

You may want to have students find information on the energy expenditure that is needed for certain types of activities (e.g., running a 5K race, walking 100 m, etc.) How many Rocket candies would be needed to carry out some example activities?

Phosphofructokinase catalyzes the reaction Fructose-6-phosphate + ATP → Fructose-1,6bisphosphate + ADP in the glycolytic pathway, and is often used as an example of an allosteric enzyme. ADP stimulates PFK activity; more unusually, ATP acts as a reactant and as an allosteric inhibitor. This is one of the most commonly discussed control points in cellular respiration, and can be used to highlight the use of allostery in enzymatic control.

In discussing fermentation, students may be interested in learning more about the industrial processes involved in making, wine, beer, sake, and fermented foods (e.g., kimchee). Lactic acid fermentation by bacteria is seen in production of certain dairy products (e.g., yogourt).

Students interested in human physiology will likely be interested in the lactic acid fermentation that occurs in muscles, leading to muscle cramps. (See paper by Allen, D. and Westernblad below.)

Most aerobic organisms have mechanisms to limit/repair damage from toxic oxygen species.

This can be demonstrated if you have access to agar plate cultures of E. coli and Lactobacillus or Leuconostoc. The catalase enzyme catalyses the conversion of hydrogen peroxide (H 2O2) to water and molecular oxygen. We can detect the presence of catalase in bacteria by adding a drop of hydrogen peroxide to a colony; vigorous bubbling shows the release of oxygen if catalase is present. If you have plates of such bacteria available, you can demonstrate this in the lab, or via a document camera. It is recommended that instructors ask students to predict DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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the outcome of the experiment prior to carrying it out, encouraging students to think more deeply about it.

Cyanide is profiled in the “Molecule behind Biology” box in this chapter. This well-known poison is likely to interest students, and could help reinforce understanding of electron transport.

“Unanswered questions” in this chapter will be of interest to most students, as they deal with human disease (mitochondrial proteins in Alzheimer disease, molecular genetics of oxidative phosphorylation complex assembly). Students could be asked to search for some of the relevant scientific literature published by the investigators mentioned in this section. The role of mitochondria in programmed cell death (PCD) may also be of interest to students (and lead into cellular signaling, in Chapter 8).

Clicker questions: 

What would be the potential consequence if 1 pyruvate molecule was produced per glucose molecule entering cellular respiration reactions?

A. No change to number of ATP produced.

B. Fewer ATP would be produced.

C. More ATP would be produced.

This question encourages students to think about the impact of upstream events/inputs on ATP yields. [Stumbling Block 7]. 

You isolate mitochondria, and put them in pH 8 solution (allowing some time to adjust). You then transfer the mitochondria into a solution of pH 4 (acidic) with ADP and Pi. In acidic solution, there is an excess of protons outside of the inner membrane. Will those protons pass through ATPases and generate ATP? 1. Yes * 2. No 3. I don’t know.

This question addresses Stumbling block 8. (These experiments were done as researchers tried to understand the mechanisms behind ATP generation in mitochondria.)

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WHAT OTHER RESOURCES ARE AVAILABLE? 2. GeneReviews: Mitochondrial Disorders Overview: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=mt-overview 3. Adams, A. 2002. Mitochondria: Cellular Energy Co. The Scientist. Volume 16 (13): 30.

4. Schweitzer, A.N. 2004. Pegging pathology on mitochondrial dysfunction. The Scientist. Vol 18 (10): 28-29.

5. Allen, D. and Westernblad, H. 2004. Lactic acid the latest performance-enhancing drug. Science 305: 1112-1113 6. A useful animation on the mechanics of ATP synthase can be found at http://www.grahamj.com/fivth2.html . This is a part of “Molecular Movies.org” http://www.molecularmovies.com/showcase/index.html which has many other useful videos.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Photosynthesis is arguably the most important biochemical process on Earth.

2.

Photosynthesis is a set of reactions that capture light energy into organic molecules that can be broken down for energy (by the plants themselves, as well as heterotrophs).

LEARNING OBJECTIVES Students should be able to:



Define key terms: mesophyll, stomata, primary acceptor, accessory pigments, absorption spectrum, action spectrum, photosystem I (PSI), photosystem II (PSII), antenna complex, reaction centre, P 700, P680, water-splitting complex, Ribulose-1,5bisphosphate carboxylase oxygenase (RuBisCO), carbon-concentrating mechanism, photorespiration, phosphoenolpyruvate (PEP), bundle sheath cells. [Knowledge]



List and describe the two parts/stages of oxygenic photosynthesis in general terms.

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

Describe the major plant structures involved in photosynthesis in a green plant (i.e., organ, tissue, organelle). [Comprehension]



Describe the structure of the chloroplast. [Knowledge]



Explain how the membranes/compartments of chloroplast (structure) relate to the processes of photosynthesis (function). [Comprehension]



List and briefly describe the pigments involved in photosynthesis. [Comprehension]



Explain why there are different pigments in an antenna complex. [Comprehension]



Describe the possible fates of an excited-state electron in a pigment molecule.

[Comprehension]



Relate the absorption spectrum of photosynthetic pigments in a given plant with the action spectrum of photosynthesis in that plant. [Comprehension]

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

Correctly interpret a figure showing absorption spectra of photosynthetic pigments and/or action spectrum of photosynthesis in a given plant. [Application, Analysis]



Describe, in general terms, what occurs in light-dependent reactions of photosynthesis (including energy investments, energy yields, oxygen, water and carbon inputs/outputs). [Comprehension]



Compare and contrast photosystem I and photosystem II. [Comprehension, Analysis]



Describe how ATP is produced in the light-dependent reactions. [Comprehension]



Explain the role of light for electron transfer in photosystems. [Comprehension]



Compare and contrast linear electron transport and cyclic electron transport.

[Analysis]



List and briefly describe the phases of the Calvin cycle. [Comprehension]



Describe, in general terms, what occurs in the light-independent reactions/Calvin cycle (including energy investments, yields and carbon inputs/outputs).

[Comprehension]



Describe ribulose 1,5-bisphosphate (RuBP), 3-phosphoglycerate, and glyceraldehyde3-phosphate (G3P) in terms of carbons/phosphates and role in the Calvin cycle.

[Comprehension]



Describe the importance of rubisco to life on Earth. [Comprehension]



Describe photorespiration, including the conditions that lead to it. [Comprehension]



Describe the challenges faced by, and strategies employed by aquatic photosynthesizers in terms of obtaining enough CO 2. [Comprehension]



Compare and contrast the carboxylase and oxygenase activities of rubisco. [Analysis]



Compare and contrast the C 3, C4 and CAM pathways of carbon fixation, indicating the advantages and disadvantages of each. [Analysis]



Identify various cellular processes, including biochemistry, energetics, necessary proteins and membranes that are similar in cellular respiration and photosynthesis.

[Synthesis]

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WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Photosynthesis is an ancient, important set of biochemical reactions.



Herbicide development is often directed at interfering with photosynthesis in target weeds.



Climate change has been linked to substantial increases in greenhouse gases (e.g., CO 2) as a result of human activity. Photosynthesis is a natural carbon sink (i.e., stores carbon compounds) that removes CO2 from the environment and can be used as a carbon offset. Researchers are studying ways of countering the effects of climate change with photosynthesizing plants.



The nature of some of the components of photosynthesis may have applications in other areas (e.g., photochemical switches, improved sunscreens, cancer therapies).

WHY SHOULD STUDENTS CARE? 

Nearly all life on Earth depends (directly or indirectly) on the products of photosynthesis.



Climate change has been linked to substantial increases in greenhouse gases (e.g., CO 2) as a result of human activity. Understanding the role of photosynthesis in capturing carbon can help students understand the importance of photosynthesizers in the environment.



Elements of photosynthesis are examples of biochemical reactions that appear in other reactions; an understanding of photosynthesis will help students with other concepts.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 27. Students may have difficulty realizing that “photosynthesis” refers to many individual reactions, occurring in sets. It is recommended that instructors explicitly mention that the term “photosynthesis” is generally used as shorthand to encompass the sum of all the reactions occurring in different stages (and locations in the chloroplast).

28. We have found that many students are focused on simply memorizing steps/enzymes for the reactions, without considering the “bigger picture” of what is going on during these processes. Clear expectations from the instructor regarding what students are expected to know may help alleviate some of the anxiety associated with massive memorization (if, indeed, the instructor does not want students to memorize all of this information).

29. The light-independent reactions (Calvin cycle) are sometimes referred to as the Calvin-Benson Cycle, or the dark reactions. The latter is most problematic, as the reactions are not restricted to the dark (while light reactions are, indeed, only possible when light is available).

30. Stroma (the chloroplast “cytoplasm” containing enzymes of the Calvin cycle) and stoma (singular; plural = stomata; pores in plant leaves allowing gas exchange) are words that students often mix up.

These terms should be explicitly defined, and used often if you expect students to know them both.

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31. The idea that three CO 2 molecules enter the Calvin cycle is often confusing to students, as is the idea that several steps are required just to regenerate the “starting molecule” (RuBP). Following carbon molecules through the cycle can help students better visualize this.

32. The dual carboxylase and oxygenase activity of rubisco can be extremely counter-intuitive. Context regarding the origin (in anoxic conditions before appearance of oxygen-generating cyanobacteria) and long history of this enzyme may help with understanding this concept.

33. Students may have preconceived notions that they will not be interested in plants (and that photosynthesis is not relevant to them), which may mean that there are challenges in engaging them with the material. Highlighting the importance of photosynthesis (in supporting nearly all life forms) may help, along with some of the environmental and applied aspects of photosynthesis research.

34. Students may be unaware that photosynthesis occurs in many other types of organisms beyond plants (e.g., some bacteria, archaea, algae). Instructors may want to remind students of Chapter 2, where the activity of ancient cyanobacteria led to an oxygenated atmosphere.

WHAT CAN I DO IN CLASS? The “Why it Matters” introduction highlights the scale of the CO2 fixation that is accomplished by photoautotrophs on Earth. This could be used to lead into discussion about the importance of CO2 fixation, and issues that we are facing with regards to global biodiversity and climate change issues. The nature and importance of phytoplankton can be highlighted.

Ask students to consider the term “photosynthesis” in terms of “photo-“ and “-synthesis”, relating these parts of the word to the different stages of reactions that occur.

Revisit Chapter 1 (Light and Life), reviewing the nature of photosynthetic pigments, and how the structure of these molecules is important in capturing energy from light.

Instructors may want to bring in actual plants to class to demonstrate the regions where photosynthesis occurs, and adaptations that allow plants to obtain the water, oxygen, and minerals they require. Using dissecting microscopes, aspects of leaf anatomy can be examined (in a small class, or lab; using a microscope camera for larger demonstrations). Prepared slides may be useful to show the cells and tissues within leaves.

Electron micrographs can be shown when discussing chloroplast structure.

If cellular respiration (Ch. 6) has already been covered, ask students to highlight where there are similarities and differences between photosynthesis and cellular respiration. You may want to provide students with a summary table to help guide them with this task:

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Photosynthesis

Respiration

Overall reaction Reactants Product(s) Cellular location Energetics (Energy required? Released?)

Chemical pathways/phases Summary (one sentence description)

Students can be encouraged to draw figures representing mitochondria and chloroplasts, and indicate where major phases of the reactions occur, including the electron transport chain, and chemiosmosis. E.g., Where do we see a high concentration of H+?

The animations of aspects of photosynthesis will be valuable to illustrate the important steps that occur. The Calvin cycle animation may help students with Stumbling Block 5.

Rubisco can be explored in terms of the structure and function of the enzyme, and the fact that the enzyme has both carboxylase and oxygenase activity. Ask students when in Earth’s history rubisco would have appeared, and what the conditions would have been like at that time. [Stumbling block 6] You may want to refer back to Chapter 2, and discuss the appearance of oxygenic photosynthesizers and importance of this to the life that evolved after significant amounts of O2 accumulated in the atmosphere.

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An activity can be done in class, with students considering and comparing the benefits and costs of C3, C4 and CAM photosynthesis under different conditions of temperature and humidity. (In order to do this, students will need to know what the differences are between these pathways.) If class size permits, teams can be assigned a type of photosynthesis to analyze.

Example C4 and CAM plants can be brought into class to demonstrate the different types of plants that carry out the variations of photosynthesis. (E.g., C4 – tropical grasses, maize, sedges; CAM – succulent cacti, such as jade plants.) Explicitly describing and highlighting the differences in leaf anatomy between C 3 and C4 plants in class (with a diagram or microscope picture) can be valuable, especially if students are not very familiar with plant cell/tissue types.

In a discussion, or one-minute paper activity, ask students to consider challenges that are faced by aquatic photosynthesizers. (This can lead into carbon-concentrating mechanisms in algae.)

We think of sugar as the product of photosynthesis, but it should be highlighted that the final storage product of photosynthesis is typically starch in most plants. (Sugars are converted to starch.) Sugar cane and sugar beets are unusual in storing the sugar sucrose. Plant breeding efforts increased the sugar content in the beets from 26% to the approximately 20% seen today. (This is an example of artificial selection.)

Clicker questions: 1.

In green plants, which of the following occur(s) during the light-dependent reactions?

A. B. C. D. E.

water is split into oxygen and hydrogen ions.

NADP+ is reduced. transport of electrons along an electron transport chain. chemiosmotic production of ATP. all of the above.*

This is a fairly straight-forward question addressing the major activities of the light reactions. [Stumbling Block 2] 2.

The reactions of the Calvin cycle A. B. C. D. E.

can only occur in the light. can only occur in the dark. can only occur when there are adequate quantities of CO2, ATP and NADPH.* Both A and C. Both B and C.

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This question can identify if students have the misconception that the Calvin cycle only occurs in the dark (as could be inferred from the term “dark reactions”, as this cycle is occasionally called). [Stumbling Block 3] 3.

Photosynthesis occurs in A. B. C. D. E.

plants only. plants and algae only. members of all three domains of life (bacteria, archaea, eukaryotes).* plants and bacteria only. all bacteria, all archaea, and certain eukaryotes.

There are organisms that carry out photosynthesis in all domains (prokaryotic and eukaryotic). [Stumbling Block 8]

WHAT OTHER RESOURCES ARE AVAILABLE?    



ScienceDaily - Newly Identified Enzymes Help Plants Sense Elevated CO 2 and Could Lead to Water-Wise Crops: http://www.sciencedaily.com/releases/2009/12/091213164705.htm Gust, D.; Moore, T.A.; Moore, A.L. 1994. Photosynthesis mimics as molecular electronic devices. Engineering in Medicine and Biology Magazine, IEEE. 13(1): 58 – 66. DOI 10.1109/51.265775 Does harvesting in Canada’s Forests Contribute to Climate Change? http://cfs.nrcan.gc.ca/news/473/ AspenFACE (Free-Air Carbon Dioxide Enrichment) Experiment - a multidisciplinary study to assess the effects of increasing tropospheric ozone and carbon dioxide levels on the structure and function of northern forest ecosystems: http://aspenface.mtu.edu/index.html While not directly focused on photosynthesis, there are some interesting aspects of plants at this site: http://plantsinmotion.bio.indiana.edu/plantmotion/starthere.html

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… Communication between, and within, cells is essential to normal cellular function.

Malfunction of even one component of one pathway can lead to serious disorders.

Each signalling molecule binds to a specific receptor on, or in, the target cell; this binding activates a chain of communication events within the cell that ultimately lead to a response that is specific to the signalling molecule and cell in question.

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LEARNING OBJECTIVES After completing the chapter, students should be able to:



Define key terms used to describe cell communication: ligand, receptor, signalling cell, target cell, signal amplification, modulation, inhibition, cross-talk. [Knowledge]



Explain, in basic terms, how a ligand-receptor interaction results in the activation of a signalling pathway. [Comprehension]



Explain in basic terms, how a signal is amplified following ligand-receptor interaction. [Comprehension]



Demonstrate the points of an intracellular pathway where modulation could occur.

[Comprehension]



Explain the significance of “cross talk” in modulating cellular response.

[Comprehension]



Explain how the same signalling molecule can initiate different responses in different cell types. [Comprehension]



Explain the significance of phosphorylation and dephosphorylation during intracellular signalling. [Knowledge/Comprehension]



Outline the sequential events of a particular pathway (e.g. cyclic AMP) following the binding of an associated chemical messenger to the receptor.

(Knowledge/Comprehension)

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

Predict the potential outcomes upon the individual inhibition of the various biochemical components associated with a particular pathway. [Application/Analysis] [Application/Analysis]



Predict the potential outcomes upon the individual enhancement of the various biochemical components associated with a particular pathway. [Application/Analysis] [Application/Analysis]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Cell communication is important for normal body function; and the malfunction of even one pathway can result in serious disorders or diseases.



Problems with cell signalling underlies some human illnesses. Understanding the molecules and pathways involved can be useful in determining potential treatments.



Better understanding of the intracellular mediators of pharmaceuticals and recreational drugs can help us to lessen side effects.



With knowledge of cellular communication insecticides and herbicides can be created that target specific species, and are thus safer. Presently, many poisons are general in their action and can have detrimental affects on many non-target animals and/or plants. (e.g., DDT )

WHY SHOULD STUDENTS CARE? 

A basic knowledge of mechanisms underlying body functions helps one make informed decisions regarding health-related matters. Many pharmaceuticals and recreational drugs act through cellular communication pathways; a basic understanding of how these chemicals may work illustrates how many unknowns still exist.



Cell communication is involved is every animal and plant response, many of which are discussed in this text and in subsequent biology courses.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS?

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Students often have difficulties envisioning the actual complexity of cell communication, at both intra and extra-cellular levels. They often have trouble relating this to proper functioning of a multi-cellular organism.

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Students may fail to grasp the advantages and disadvantages associated with the sequential and multi-step nature of cell signalling. (e.g. Advantage: Signal amplification and many points of modulation. Disadvantage: Multiple places wheresomething can go wrong).

There may be confusion regarding how G-proteins are activated. G-proteins are activated when GDP is removed and GTP added, NOT when GDP is phosphorylated.

WHAT CAN I DO IN CLASS? The “Why it matters” section uses air traffic control system as an analogy for cell signalling. Students can be asked to suggest other analogies involving the key elements involved in this type of signalling. (The internet may be one such example.)

Use volunteers in class to simulate signal transduction. Examples could include sending a message to the back of the classroom, or amplifying a response (e.g., borrowing the professor’s microphone in a large lecture hall).

Although much of this chapter focuses on cellular signalling in animal cells, it is worthwhile to remind students that similar systems exist in other multicellular organisms (including plants), and that even bacteria communicate with one another via small molecules (and use signal transduction systems to respond to environmental stimuli). The “People Behind Biology” profile of Doug Storey at the University of Calgary mentions the quorum sensing systems used by bacteria; this may be worth exploring if the course includes a microbiology component. The ubiquity of cellular signal transduction, even though some details differ between organisms, highlights the unity of all living organisms.

Highlight where defects in cellular signalling can result in human diseases, such as cancers. (We return to events that are involved in development of cancer in Chapters 9 and 15.)

Present the pathway(s) in question and have students determine the potential outcome(s) upon the individual enhancement and inhibition of each biochemical component.

For example, with regards to the cyclic AMP pathway: If G-protein inactivation is prevented (i.e. Gprotein remains active) what will occur?

Answer:

Adenylyl cyclase will continue to be activated and as such will continue to catalyze the creation of cyclic AMP from ATP, maintaining an increased concentration of cyclic AMP in the cell.

Cyclic AMP activates protein kinase A, and the more cyclic AMP present in the cell the more protein kinase A molecules will be activated.

Protein kinase A phosphorylates a particular molecule (specific to the cell type) which leads to the eventual cellular response. The more phosphorlylation that occurs the more intense the response will be.

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The neurotransmitter acetylcholine is good signalling molecule example to use when examining the cyclic AMP pathway. This is because the cellular response is muscle contraction strength and duration. The contractile response is correlated with cyclic AMP concentration and as such degree protein kinase activation.

Demonstration of cross talk (Fig 8.15) and/or signalling molecules targeting the same pathway (e.g. NO or Nitrates and Viagra) can be used to help demonstrate the complexity of communicative interactions.

With regards to NO or Nitrates and Viagra, this is a combination that has been demonstrated in various Hollywood movies as being a potential deadly combination and is known by many students.

Nitrates and Viagra both work through a cyclic GMP pathway, but students do not need to understand the specifics of the pathway, only that the two signalling molecules are acting on the same pathway simultaneously and lead to the same cellular response (vasodilation).

Simultaneous activation leads to an enhanced cellular response which in the Nitrate/Viagra case could lead to a deadly case of hypotension.

Clicker questions: 1.

What would occur if the phosphodiesterase associated with the cyclic AMP pathway were inhibited?

2.

CREB is a protein activated by protein kinase A. In its active form, CREB crosses into the nucleus and initiates transcription. Using this information, which method could you use to experimentally activate transcription in a cell?

A. Add a chemical that activates adenylyl cyclase * B. Add a chemical that deactivates G-proteins C. Add a chemical that activates phosphodiesterase D. Add a chemical that degrades protein kinase A

A. Cyclic AMP levels would decrease, protein kinase activation would be reduced, and the final cellular response would be reduced B. Cyclic AMP levels, protein kinase activation, and the final cellular response would remain unchanged C. Cyclic AMP levels would increase, protein kinase activation would be increased, and the final cellular response would be enhanced and/or prolonged * D. Cyclic AMP levels would remain unchanged, protein kinase activation would be reduced, and the final cellular response would be reduced

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WHAT OTHER RESOURCES ARE AVAILABLE? 

University of Arizona Cell Signalling Problem Set:



http://www.biology.arizona.edu/Cell_Bio/problem_sets/signaling/Index.html



Nobel Laureate – Earl SutherlandKresge N, Simoni RD, Hill RL (2005). Earl W. Sutherland’s discovery of cyclic adenine monophosphate and the second messenger system. JBC. 42(39): e39-e40.



Rall TW and Sutherland EW (1958). Formation of a cyclic adenine ribonucleotide by tissue particles. 232: 1065-1076.



Sutherland EW. 1992. Studies on the mechanism of hormone action. Nobel lecture. http://nobelprize.org/nobel_prizes/medicine/laureates/1971/sutherlandlecture.html



Wnt-secreted proteins play a crucial role in cell signaling during animal development; disruption of this signalling can result in degenerative diseases and cancer in humans:



Nusse R. 2005. Wnt signaling in disease and development. Cell Research. 15: 28-32.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Cell division is important in continuing the lineage of particular cells, essential for growth/repair of cells in multicellular organisms, and bacterial reproduction.

2.

A parent cell yields essentially identical daughter cells in mitotic and prokaryotic cell division.

LEARNING OBJECTIVES Students should be able to:



Define key terms (general): cell cycle, mitosis, meiosis, chromosome, ploidy, chromatid (and sister chromatids), chromosome segregation, spindle, centromere, centrosome, kinetochore. [Knowledge]

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

Define and explain stages in the eukaryotic cell cycle/mitosis: interphase, G 1 phase, S phase, G2 phase, G0 phase, prophase, prometaphase, metaphase, anaphase, telophase, cytokinesis. [Knowledge/Comprehension]



Determine the number of chromatids vs. chromosomes in G 1 and G2 phases of the cell cycle. [Comprehension]



Explain ploidy, providing a description of the difference between haploid and diploid. [Comprehension]



Describe the role of cytoskeletal elements and associated proteins in chromosome segregation. [Comprehension]



Describe differences between mitosis in animal cells and mitosis in plant cells.

[Comprehension] Define key terms in cell cycle regulation: checkpoint, cyclin-dependent kinases (CDK), cyclin, contact inhibition, cellular senescence, telomerase, oncogenes, metastasis, apoptosis, caspases. [Knowledge]



Describe the process of prokaryotic cell division. [Comprehension]

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

Compare and contrast cell [Analysis/Evaluation]

division

in

bacteria

to eukaryotic

mitosis.



Relate aspects of bacteria and eukaryotic cell division to the structure/function differences in the cells. [Analysis/Evaluation]



Relate differences in mitosis between animal and plant cells to the structure/function aspects of the different cells. [Analysis/Evaluation]



Describe how mitosis and prokaryotic cell division support the cell theory.

[Comprehension]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Cell division is a fundamental biological process, which is considered (and exploited) in all sorts of biological research (including any research involving propagation of cells in tissue culture).



Understanding of cell cycle control mechanisms can be of value in many biological processes, including many relating to human health (e.g., cancer, progeria).



Research on cell division is important to understand aspects of reproduction, regeneration, tissue culture (in many different organisms!).

WHY SHOULD STUDENTS CARE? 

Reproduction is one of the key characteristics of life, and cell division is essential to the reproduction of cells in growth and generation of new individuals (e.g., bacterial reproduction ) and development.



Understanding of the cell cycle (and controls of the cell cycle) can be of value in many biological processes, including many relating to human health (e.g., cancer research).  practical value of understanding cell cycle and consequences to heredity (e.g., domestic animal and crop improvements.



Preventing bacterial cell division could control growth of pathogens (e.g. identification of or development of new/improved antibiotics and disinfections).



Cell theory (all cells arise from other cells) is a fundamental unifying theme of biology.

A.

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WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 35. In mitosis and binary fission, students often do not realize that a parent cell no longer exists after creation of daughter cells.

36. Students may not be aware that a given chromosome contains both “old” and “new” DNA after S phase. DNA replication as a semi-replicative process may not immediately be connected to what occurs in eukaryotic chromosomes.

37. Bacterial chromosomes usually differ from eukaryotic chromosomes in several ways; most bacteria contain a single, circular, double-stranded DNA molecule. Bacterial chromosomes do not typically have centromeres nor telomeres.

38. Students can be confused about centromeres, and are often under the impression that they are not actually DNA (but are, instead, some “special button”).

39. Chromatids vs. chromosomes. Students often have difficulty understanding the difference between these terms. Diagrams and models may be useful to help students differentiate between chromatids and chromosomes.

40. Students can have difficulty with the concept of “chromosome number”, particularly when thinking about diploid (or polyploidy) cells.

WHAT CAN I DO IN CLASS? The “Why it Matters” material can prompt discussion regarding the potential benefits of tissue/organ/limb regeneration, and the difficulties that exist trying to replicate these processes in humans (i.e., why can’t humans regenerate limbs when they are injured?). Students could brainstorm in this activity.

Model organisms are described in the “Why it Matters” section and in Section 9.4f. This could prompt a discussion of model organisms in general, and/or the roles of Danio rerio and Caenorhabditis elegans in particular, in research. This may focus specifically on cell cycle research, or you may wish to expand the discussion to include other areas of interest.

Remind students of cell theory. This is best accomplished by having students identify the connection to this theme, via directed discussion or in-class questions.

You may want to begin by asking students questions: When do cells divide? Why do cells divide? What is required for cell division? What must occur before cells can divide? (Could have think-pair-share discussion to answer questions.) Student discussion for the latter question is particularly good at getting students to conceptually understand cell division rather than focusing on memorizing minute details of cell division.

Students may be interested in the topic of reproduction and development. Encourage students to consider the cell divisions involved in the development of a baby from the fertilized egg. Students can be given problems (to be done individually, in one-minute-papers, or think-pair-share) making estimates of rates of cell division that must occur in different organisms in development. This could also be an opener to the discussion of cell division – ”How did you get to be ‘you’ when you started off as one-cell (a fertilized egg)?”

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In discussing reproduction, it may be of interest (particularly to agriculture or biotechnology students) to discuss asexual reproduction, e.g., clonal reproduction of plants (i.e., propagation by cuttings, runners, etc. – production of new, genetically identical plants). This type of reproduction differs from sexual reproduction, as meiosis (gamete production) is not involved. See Figure 30.14 for image of Kalanchoe plant with many plantlets on leaf edge; Figure 30.15 shows plant tissue culture steps.

Ask students about the pros and cons of asexual vs. sexual reproduction in a population. (E.g., faster population growth is often observed with asexual reproduction, but lack of genetic variation may cause issues in some circumstances; with sexual reproduction – genetic variation, but more steps in which mistakes can occur and typically much slower with respect to population growth.) Some instructors may prefer to bring up such questions when making the transition to the next Chapter, which discusses meiosis and recombination.

Many students will know how many chromosomes humans have, but you may want to ask them the differences between the different chromosomes. This could also lead into a discussion about the differences between prokaryotic and eukaryotic chromosomes [Stumbling Block 3].

Have students act as chromosomes, demonstrating events in mitotic cell division. (Given preparation time, students can be encouraged to find some props to represent key molecules involved in the process.)

Help students visualize the processes. Student-prepared time-series diagrams may be helpful. Many students will benefit from hands-on models, using pipecleaners as chromosomes and moving/arranging them in “mitosis”.

Clicker questions and/or online quizzes/assignments could be used to give students opportunities to view cells in different mitotic stages, and gain experience identifying the stage based on appearance of nucleus/chromosomes.

Instead of providing students with details of mitosis, walk through the process as a group asking what step has to happen next. Students may be able to ‘discover’ that in most eukaryotes, the nuclear envelope needs to break down in order that the chromosomes can move to opposite ends of the dividing cell, rather than simply memorizing this step.

Students can be introduced to a news story about recent research developments in cancer, prior to discussion of the loss of regulatory controls in the cell cycle.

A hands-on activity can be carried out in small groups (or with volunteers in a larger class). Provide a ball of different coloured yarn/embroidery floss, resembling chromosomes in a diffuse state. Have students separate and “condense” individual chromosomes by colour. This demonstrates the usefulness of chromosome condensation. (If you have spent time discussing condensation in biochemical reactions, it is a good idea to let students know that the term is used differently in this context.)

Discussions can be initiated regarding biological events leading to cancer (relating to loss of cell cycle control).

Students can be prompted to relate relevant concepts from Chapter 8 to this topic.

Clicker questions: 1.

If a single cell undergoes 4 rounds of mitotic cell division, how many cells will result?

A. B. C. D. E.

4.

8.

16.* 32.

33.

This question addresses confusion about the destiny of a parent vs. daughter cells [Stumbling Block 1].

Encourage students to draw a diagram in answering the question. Peer instruction may be useful.

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Afterwards, ask students if they can construct and explain a mathematical formula that would help them determine the answer more quickly.

2. You are in the lab, and add radioactively labelled Phosphorous to cells just before they undergo S phase. After the cells have finished S phase, you isolate individual chromosomes, and can visualize the radioactive portions. In a single chromosome, which of the following would be expected?

A. One chromatid would be composed fully of radioactive DNA, while the DNA of the other chromatid would not have any radioactivity.

B. Both chromatids would have mixtures of radioactive and non-radioactive DNA. * C. The upper arms of the chromatids would be composed fully of radioactive DNA, while the lower portions would not have any radioactivity.

This question reinforces the difference between chromosomes and chromatids, and links the DNA replication in cell cycle to the mechanism of DNA replication as a semi-replicative process. Rather than the written answers, diagrams could also be used to show “radioactive” regions. A link to Chapter 13 (13.3) may be useful in discussing this question. [Stumbling Block 2].

3.

An animal cell is in G1 phase. The diploid chromosome number: 2n = 12. How many chromatids are present in a single cell?

A. 3 B. 6 C. 12 * D. 24

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This question provides practise considering the difference between chromosomes and chromatids, as well as the different stages in the eukaryotic cell cycle. It can easily be simplified (provide more information in the question stem) and/or modified to provide additional questions (e.g., change phase to G 2, change ploidy, change chromosome number). [Stumbling Block 5].

4.

A snail has 12 pairs of chromosomes. How many chromosomes do the nuclei of snails have during G 2 phase?

A. B. C. D.

6 12 24* 48

This question, although simple to an instructor, can provide practise to students in thinking about what “chromosome number” means in a diploid organism. [Stumbling Block 6]

5. Which of the following is/are true regarding cell division in both bacteria and eukaryotes?

A. Separation of replicated chromosomes occurs. * B. Breakdown of the nuclear envelope is necessary.

C. Kinetochores and microtubules are involved.

D. None of the above statements in A through C are true of cell division in both bacteria and eukaryotes.

Although there are many differences between bacterial cell division and mitotic division in eukaryotes, the separation of the hereditary material to daughter cells is intrinsic to both processes.

WHAT OTHER RESOURCES ARE AVAILABLE? 



The Biology Project, Department of Biochemistry and Molecular Biophysics, University of Arizona - Cell cycle and Mitosis Tutorial: http://www.biology.arizona.edu/Cell_bio/tutorials/cell_cycle/cells3.html Molecular Expressions Cell Biology Mitosis Java Tutorial: http://www.microscopy.fsu.edu/cells/mitosisjava/mitosisjava.html

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN…

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1.

Mechanisms exist for the rearrangement of DNA in prokaryotes and eukaryotes, which leads to genetic variability.

2.

Recombination occurs when two molecules of DNA with similar sequences are aligned. It can result in the shuffling of allele combinations on a chromosome and/or the gain/loss of genes on a chromosome.

3.

After meiosis, parent cell yields daughter cells that have half the chromosomes of the original cell.

4.

There are several mechanisms relating to creation and fusion of gametes that can lead to genetic diversity in eukaryote offspring.

LEARNING OBJECTIVES Students should be able to:



Define key terms in recombination: genetic recombination, homologous sequences, recombinant DNA (students often know recombination, but stumble with recombinant DNA). [Knowledge]



Define key terms in bacterial recombination: prototroph, auxotroph, replica plating, conjugation, F/sex pilus, F+ and F- cells (F factor?), Hfr cells, transformation, transduction, bacteriophage, prophage, lytic cycle, lysogenic cycle, partial diploid?.

[Knowledge]



Explain the difference between vertical vs. horizontal inheritance. [Comprehension]



Describe the similarities and differences between the different mechanisms of horizontal gene transfer in bacteria. [Comprehension]



Explain why longer conjugation events result in a greater number of donor genes entering the recipient than shorter periods of conjugation. [Comprehension]

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

Define key terms in meiosis/sexual reproduction: gametes, meiosis, sexual reproduction, fertilization, zygote, haploid, diploid, sporophyte, gametophyte, spore, maternal vs. paternal chromosomes, homologues, nondisjunction, sex chromosomes, synaptonemal complex, crossing over, chiasmata. [Knowledge]



Describe the general events of the meiotic phases: prophase I, prometaphase I, metaphase I, anaphase I, telophase I, interkinesis, prophase II, prometaphase II, metaphase II, anaphase II, telophase II, [Knowledge]



Relate the events of meiosis to Mendelian inheritance and Mendel’s two principles.

[Comprehension]



Compare the variation present in a population of clones with a population of organisms that use/engage in some recombination activity.



In very simple terms, explain the key differences between the life cycles of most animals, plants and fungi, considering haploid and diploid phases, and identifying where meiosis and mitosis can occur. [Comprehension]



Describe, in simple terms, the events and outcomes of the two divisions of meiosis (meiosis I and meiosis II). [Comprehension]



Determine the number of chromosomes in each daughter cell after each meiotic division, given the original chromosome number in the parent cell. [Application]



Using appropriate terminology, describe what independent assortment means in the context of meiosis. [Comprehension]



Compare and contrast the processes of mitosis and meiosis with respect to the events and outcomes. [Analysis/Evaluation]



Describe how each of the following can contribute to genetic variability: independent assortment in meiosis (including random segregation of homologous chromosomes in meiosis I and random segregation of chromatids in meiosis II); crossing over; random combination/fusion of gametes in fertilization.



Calculate the number of possible chromosomal combinations that can result simply from the independent distribution of maternal and paternal chromosomes.

[Application]



Describe the nature and action of mobile genetic elements and how they can contribute to genetic diversity. [Comprehension] B.

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WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Manipulation of bacterial gene transfer processes is an integral aspect of molecular biology and biotechnology techniques.



Events in meiosis affect genetics. Meiotic events explain the transmission of inherited traits.

Understanding of meiotic events allows us to calculate probabilities of inherited disease given parental genotypes.

WHY SHOULD STUDENTS CARE? 

The spread of antibiotic resistance genes in a hospital setting (by conjugation or other horizontal gene transfer processes) is an example of how genetic exchange in bacteria can have a major impact on humans and their health.



Understanding the events in meiosis is vital in comprehending processes of genetics, as discussed in later chapters. The movement of chromosomes in meiosis relates directly to Mendel’s observations (his Principles) and the inheritance of genetic characteristics

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 41. Students may not be aware that bacteria (and archaea) possess mechanisms that yield genetic diversity.

At a molecular level, genetic recombination is highly similar between bacteria, archaea, and eukaryotes, although specific details will vary. There is considerable new terminology in the bacterial recombination section, which students may struggle with if microbiology concepts have not already been introduced.

42. Students often think that what is true for humans is true for most organisms. However, unlike vertebrates, many organisms, such as fungi and plants, have a substantial haploid stage to the life cycle; students may not realize that haploid cells can undergo mitosis in such organisms.

43. While students may be aware that chromosome complement is halved in meiosis, they may not be fully cognizant that this halving is a necessary step prior to fusion of haploid cells to create a diploid cell with the correct number/complement of chromosomes. (Ask students what would happen if gametes contained the same number of chromosomes as somatic cells. Over generations, what would the result be?)

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44. Confusion often exists about the idea of homologous chromosomes. It is recommended that when discussing homologues, explicitly refer to maternal and paternal chromosomes, and remind students that homologues carry the same genes (though the alleles for each gene may vary). (E.g., address the fact that within the class, everyone’s chromosome 1 carries the same genes, but not necessarily the same alleles.) Crossing over will not make sense if students do not comprehend the nature of homologous chromosomes – it will seem highly random.

45. While many students feel that they “know meiosis”, they have simply memorized the stages, and may not fully understand the events that occur and how they relate to inheritance.

46. It is difficult to picture the 3-dimensional aspect of homologous chromosome pairing in synapsis.

Animations or physical models may better display the alignment of homologues than 2-dimensional representations.

47. Nondisjunction can be a difficult concept if the events occurring in “normal” meiosis are not fully understood.

48. Students often confuse self-fertilization in plants with asexual reproduction. Point out that fertilization is a term ‘reserved’ for sexual reproduction and it’s presence indicates sexual organisms.

WHAT CAN I DO IN CLASS? The “Why it matters” material introduces different types of sexual reproduction in animals in a marine environment. Additional examples of behaviours (e.g., courtship rituals) and adaptations (e.g., selfincompatibility in plants, hermaphrodism in certain animals) may be brought up to highlight the variety of ways in which organisms ensure the passing on of hereditary material (leading to a level of continuity, yet, in many cases, also yielding genetic diversity).

In a class discussion, have students suggest how conjugation, transformation and transduction provide genetic diversity to bacteria. How does this genetic variability compare to what occurs in eukaryotes?

When reviewing events in meiosis, students can model the chromosomes and process using pipe-cleaners or coloured strips of paper. For crossing over, coloured strips of paper can be ripped and taped to demonstrate exchange of material from non-sister chromatids.

The concept of nondisjunction in meiosis can be illustrated with the example of Trisomy 21 (Down syndrome).

You may want to give the class a thinking question to ponder prior to Chapter 11 and 12, asking why aneuploidy is usually so detrimental to humans (most aneuploid zygotes are not viable). Most known cases of aneuploidy exist for Chr 21, 22 and the sex chromosomes; instructors can show representative karyotypes and ask students why these would be the ones that would survive.

Meiotic cell division results in reduction of chromosome number, and increased genetic variability. Ask students why each of these are important in the context of sexual reproduction. Instructors may want to link this material to concepts of fitness and natural selection. (Asexual reproduction occurs in many different organisms. When would increased genetic variability be favourable? Why?) In discussing retrotransposons, examples with retroviruses (e.g., those that can cause human cancers) may pique student interest.

Clicker questions: 1.

Puffer fish sperm contains 21 chromosomes. Which of the following are the haploid & diploid (haploid; diploid) numbers for puffer fish?

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A. B. C. D. E.

21; 21 21; 42 * 42; 42 42; 84 21; 84

This question involves key terms (haploid and diploid) and the concept of meiotic reduction of chromosome number. [Stumbling Block 1] 2. Just considering the distribution of maternal and paternal chromosomes, how many different gametes could 1 individual pea plant (2n = 14) create?

A. B. C. D. E.

28 49 64 128 * 256

We can calculate this as 2n, so in this case, 27 = 128. Remind students that this is far less than the total variability seen if we consider all of the processes (such as crossing over) that occur.

3.

Somatic cells of fruit flies contain 8 chromosomes. If one a gamete producing cell in a female fruit fly undergoes meiosis to form eggs, and chromosomal nondisjunction occurs in a single chromosome during meiosis I, what is the chromosome number in each of the resulting eggs?

A. B. C. D.

4; 4; 3; 5 5; 5; 3; 3 * 8; 8; 9; 7 9; 9; 7; 7

This question highlights that nondisjunction in meiosis I will yield 4 cells with abnormal chromosome complement. Contrast with the outcome if nondisjunction occurs in meiosis II (see following question).

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4.

Somatic cells of fruit flies contain 8 chromosomes. If one a gamete producing cell in a female fruit fly undergoes meiosis to form eggs, and chromosomal nondisjunction occurs in a single chromosome during meiosis II, what is the chromosome number in each of the resulting eggs?

A. B. C. D.

4; 4; 3; 5 * 5; 5; 3; 3 8; 8; 9; 7 9; 9; 7; 7

Nondisjunction in meiosis II will result in 2 gametes with normal chromosome complement, while the others will have an additional or missing chromosome.

WHAT OTHER RESOURCES ARE AVAILABLE? 

University of Arizona Meiosis tutorial: http://www.biology.arizona.edu/CELL_BIO/tutorials/meiosis/main.html



Meiosis animation: http://www.biostudio.com/d_%20Meiosis.htm

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

In eukaryotes, many aspects of heredity are the result of the inheritance of two copies of each gene, with phenotype of offspring related to the particular alleles inherited.

2.

One allele for each gene is provided in the maternal gamete, with the other allele is contributed by the father. Only half of the parent’s alleles are contributed in a gamete, and there is randomness in terms of which of the two alleles (i.e., from the maternal vs. paternal parent) for a given gene are contributed.

LEARNING OBJECTIVES Students should be able to:



Define key terms in genetic crosses (including Mendel’s pea breeding experiments): character, trait, self- pollination, cross-pollination, true-breeding, P (parental) generation, F1 (first filial) generation, F2 (second filial) generation, testcross, monohybrid, dihybrid. [Knowledge]



Compare and contrast the genotypes of P, F1 and F2 generations.

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

Define key terms in genetics: dominance, recessiveness, segregation (Mendel’s Principle of Segregation), homozygous, heterozygous, independent assortment (Mendel’s Principle of Independent Assortment), incomplete dominance, codominance, multiple alleles, epistasis, polygenic inheritance, pleiotropy. [Knowledge]



Use rules of probability (the Sum Rule and Product Rule) to calculate genotypic/phenotypic probabilities in simple Mendelian problems involving one or two genes. [Application]



Explain how the Punnett Square is related to probabilities, and describe what different regions of a Punnett Square represent. [Comprehension]



Explain how events in meiosis support Mendel’s Principles and the Chromosomal Theory of Inheritance. [Comprehension]

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

Compare and contrast different modes of inheritance with relation to expression of dominance/recessiveness. [Analysis/Evaluation]



Explain how a heterozygote is informative in terms of the type of inheritance occurring. [Comprehension]



Correctly identify Mendelian patterns of inheritance, given information about a particular genetic cross (e.g., P, F1 and F2 phenotypes, numbers of each phenotype in offspring). [Evaluation]



Correctly identify patterns that are considered extensions to Mendelian inheritance given information about a particular genetic cross/situation (e.g., P, F 1 and F2 phenotypes, numbers of each phenotype in offspring). [Evaluation]



Suggest how alleles of individuals contribute to the presence of the alleles (and phenotypes) in a larger population, and how selection may have an effect on these numbers. [Synthesis]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Mendel’s work provided the foundation of the study of genetics. It ultimately provided the link between the theory of evolution by natural selection and the modern evolutionary synthesis.



There are many (>1800) human disorders that are inherited as monogenic traits, and researchers are working to better understand, and hopefully treat, these disorders.

WHY SHOULD STUDENTS CARE? 

Genetics provides the underlying mechanism involved in passing genes from parent to offspring (cells to new cells). It helps to explain why you both resemble, yet show differences from, your parents and siblings.



Understanding the mechanisms of genetics will be useful in other topics, such as biotechnology and evolution of populations (e.g., understanding the Hardy Weinberg equation).



There are many (>1800) human disorders that are inherited as monogenic traits, and many students will be interested in these diseases, particularly if they hope to enter a medical field.

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WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 49. Students often think that dominance and recessiveness imply characteristics relating to more common uses of those terms. (Dominance and recessiveness are relative terms in genetics – a phenotype of an allele cannot be dominant without reference to the phenotype of another allele.) Dominance does not (a) imply that a particular allele overpowers the other allele directly, nor that (b) the dominant allele is superior/better in terms of contributing to the fitness of the organism. Dominant alleles are not necessarily more common in the population than recessive alleles.

50. Many “rules” or “laws” taught in genetics have exceptions (some brought forward in subsequent chapters, including Chapters 12, 15). This can be confusing to students, so it is a good idea to discuss certain mechanisms/observations in ways that reveal exceptions exist for logical reasons. E.g., when discussing Mendel’s Principle of Independent Assortment, it may be useful to indicate that this works well when looking at genes present on different chromosomes, and ask students to consider whether this principle will be relevant if the genes are present on the same chromosome.

51. There may be misconceptions relating to probabilities. Students may intuitively think that the outcome of a previous event influences another event that is, in fact, independent of the first (e.g., if parents have a baby girl, there is an increased chance of the next child being male). Students also may not understand how there can be different possibilities leading to the same outcome (e.g., in the dice example in Figure 11.6, there are six different possibilities that would yield a seven with 2 dice).

52. Students often have misconceptions concerning the presence of certain alleles and expression of the gene product. The focus on genes often leads students to be unaware of the fact that it is the gene product, or lack thereof, that leads to the observed phenotype.

53. Incomplete dominance and codominance can be very confusing. In some cases, what appears to be incomplete dominance at the organismal level can be observed as codominance when looking at a cellular or molecular level. We recommend explicitly discussing the subjective aspects of these terms, and looking at particular examples while defining the level of phenotype under review. Students are often unaware that phenotype can refer to anything above the gene level.

54. Multiple alleles can be confusing to students who are accustomed to seeing genetics as binary situations (dominant vs. recessive). The ABO blood type example is the most commonly used example for multiple alleles, but it also includes codominance (A and B antigen expression in IAIB genotype) and complete dominance (IA or IB allele in combination with the recessive allele, i).

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55. Students are often unaware that in genetics problems/cases, we are looking at a very small subset of genes (and alleles). It can be useful to remind students of the differences between individual situations and the larger population.

56. Topics such as polygenic inheritance and epistasis may require a significant time commitment for students to gain real comprehension. If you are teaching an introductory survey course with limited time for this chapter, focusing on the most important concepts in Mendelian genetics (e.g., to better understand population genetics in later course material, such as the Hardy-Weinberg equation) is recommended.

WHAT CAN I DO IN CLASS? Instructors will need to decide at which level they want students to understand/know the material in this chapter. In some courses (e.g., non-majors Biology), and/or if pressed for time, a focus on misconceptions surrounding dominance/recessiveness, incomplete dominance and codominance may be adequate.

The “Why it Matters” material can be used to introduce the human genetic disorder of sickle-cell anemia, which can be used to illustrate different genetic phenomena (e.g., different dominance relationships, pleiotropy, environmental effects). This can also be used to tie in concepts relating to evolution, discussing the benefits of heterozygosity for the sickle cell allele in certain environments.

Many additional examples exist for different concepts in genetics. As our Biology undergraduate office has an aquarium with cichlids, we have used convict cichlid (Amatitlania nigrofasciata) colour (pink vs. grey), and had students read and try to work through a simple scientific paper: Itzkovich, J., Rothbard, S., and Hulata, G. 1981. Inheritance of pink body colouration in Cichlasoma nigrofasciatum Günther (Pisces, Cichlidae). Genetica 55: 15-16. Students were asked to read the paper before class, and in lecture, time was devoted to looking at not only the results of the study, but how the experiment was communicated in the paper. If you wish, you can have students draw out the crosses performed by the authors. Some of the new vocabulary in the paper will need to be explored, and textbook examples can be used to demonstrate this.

There are many human disorders that are single gene traits and may be introduced as further examples. The NCBI Online Mendelian Inheritance in Man (OMIM) system (http://www.ncbi.nlm.nih.gov/omim/) can be used to illustrate how researchers are managing data regarding these disorders. You could design activities (homework, lab) where students use OMIM to seek information about particular disorders. Cystic fibrosis is a common example of a recessive disease. We have also used Trimethylaminura (fish odour syndrome) for example, caused by defect in the FMO3 gene; the normal protein encoded by that gene is required to produce the enzyme that breaks down trimethylamine. Affecteds excrete trimethylamines in their sweat, breath, etc., and smell like rotting fish, leading to social and psychological problems in many sufferers. There is no cure, although some individuals can reduce odour via diet (thus, this condition could also be used to address environmental effects).

Huntington’s Disease can be used as an example of a disorder involving a dominant disease allele, and could also lead into ethical discussions regarding testing, as age of onset may be after child-bearing years. Dominantly inherited disorders are good for pointing out misconceptions surrounding the common idea that a dominant allele is superior, and also to highlight that such alleles are not necessarily more common in a population.

When discussing probability, students can be involved in small trials of coin-tossing (e.g., coin tosses in small groups, combine data from several groups) or rolling dice. [Stumbling Block 3] We have found that it is worthwhile to have students work through the different possibilities of rolling a 7 with two dice, as shown in Figure 11.6, and repeat the exercise with different dice toss combinations/totals. This can be done in small groups, and an instructor can provide dice to groups of students (all in a small class, or demonstration groups in a larger class setting).

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In an activity or assignment, have students draw alleles on chromosomes going through meiosis, through gamete production and fertilization in example genetic crosses. (This may highlight the concept of independent assortment.) Coloured strips of paper or pipecleaners can be used to provide a 3-dimensional perspective on these events.

Be sure to provide example questions to help students develop skills in genetics problem-solving. During explanations, instructors are encouraged to make expert thinking transparent (we often skip steps or omit assumptions that students will not be aware of).

Clicker questions:

Which of the following is NOT true?

A. There can be several alleles for a given gene.

B. Genome sizes vary between different organisms.

C. A chromosome has many different genes.

D. A gene may contain multiple genomes. * E. An allele is present at the locus for the particular gene.

This question can be used to check student understanding of key terms in genetics, and the relative hierarchy that exists between them. If students are having difficulty with vocabulary, understanding key concepts will be problematic.

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In the case where a particular gene has one allele that is dominant while the other is recessive, which of the following is true?

A. The recessive allele is less common in the general population compared to the dominant allele.

B. It will not be possible to observe a phenotypic difference between the homozygote for the dominant allele and the heterozygote. * C. The dominant allele prevents the expression (at the transcriptional level) of the recessive allele in heterozygous individuals.

D. Individuals who are homozygous for the recessive allele will exhibit less fitness than heterozygotes or individuals homozygous for the dominant allele.

This question relates to Stumbling Block 1. It can highlight misconceptions commonly held by students about the idea of dominance/recessiveness.

3.

Convict cichlids may be grey or pink, and colour is determined by a single gene. You bring home a grey male and a grey female, who spawn to produce 15 grey fry, and 5 pink fry. If you look at a single grey convict cichlid from the batch of offspring, which of the following is true?

A. You know the genotype (relating to colour) of this individual fish.

B. You know the phenotype (relating to colour) of this individual fish. * C. Both A and B.

This question highlights the fact that in complete dominance, we cannot necessarily tell if an individual is homozygous or heterozygous for the dominant allele. [Stumbling Block 1] This can lead to a follow-up question: 4.

Convict cichlids may be grey or pink, and colour is determined by a single gene. You bring home a grey male and a grey female, who spawn to produce 15 grey fry, and 5 pink fry. If you look at the female grey convict cichlid parent, which of the following is true?

A. You know the genotype (relating to colour) of this individual fish.

B. You know the phenotype (relating to colour) of this individual fish.

C. Both A and B. *

While the phenotype alone is not informative, the fact that there are pink offspring indicate that both the parents must be carriers, and heterozygous for the colour alleles (so we can determine genotype).

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5.

You are flipping a coin. The first toss gives you heads. What is the probability that your second toss will be heads?

A. B. C. D.

0 (0%) 0.5 (50%) * 0.25 (25%) 1 (100%)

This can be used to illustrate probabilities and independent events (product rule). It could be modified to predict the results of actual coin tosses (which would need to be done several times to gather useful data).

[Stumbling Block 3] A follow-up question shows how this rule can be applied in a human genetics case: 6.

A couple has a child with cystic fibrosis (homozygous recessive for gene). If the couple has another child, what is the probability of this child having CF? A. 0 (0%) B. 2/3 (66.7%) C. 1/2 (50%) D. 1/4 (25%)* E. 1 (100%)

7.

Helen has a sibling with cystic fibrosis (homozygous recessive disease); she and her parents are unaffected. What is the probability that Helen is a carrier for this condition?

A. 0 B. 2/3 * C. 1/2 D. 1/4 E. 1/9 F. 1

This question involves some thinking, particularly if students are accustomed to just using the ratios for dominant:recessive conditions. Helen’s parents must both be carriers, and students may assume that there is a 50% chance that Helen is a carrier, as that would be the expected probability if we have no other information.

However, we know she is not affected (i.e., cannot be homozygous recessive for the cystic fibrosis allele), so this reduces the possibilities of her genotype to CC (1/3) or Cc (2/3). A follow up question can take this further.

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8.

Helen, from the previous question, marries Omar, who also had a sister with cystic fibrosis. If the couple has a child, what is the possibility of the child having cystic fibrosis?

A. 0 B. 2/3 C. 1/2 D. 1/4 E. 1/9 * F. 1

Using the previous logic, the probability of Helen being a carrier is 2/3, and the same is true for Omar. We multiply the probability of Helen being a carrier (2/3) by the probability of Omar being a carrier (2/3), and the probability of two carriers having an affected child (1/4).

9. Hurler syndrome is a rare recessive genetic disorder due to a deficiency of laronidase enzyme. The buildup causes many symptoms, and organ failure may lead to death. Aldurazyme® (laronidase) enzyme replacement therapy can reduce some of the symptoms. Which of the following best describes the basis of this treatment?

A. The treatment changes the patient’s genotype from homozygous to heterozygous.

B. The treatment provides functional laronidase protein which the patient is unable to express as a gene product. * C. The treatment allows the patient to produce functional laronidase protein.

D. The treatment changes the dominance of the patient’s alleles from complete recessive to a codominant relationship.

E. More than one of the above statements in A through D are correct.

This question may help students consider what is happening at the level of gene expression. Many metabolic disorders are treated via enzyme replacement therapy, but gene therapy is being investigated as a future treatment. [Stumbling Block 4] 10. Lee has blood type A. The following are all possible genotypes of his parents, EXCEPT: A. IAIA x IAIA B. IAIA x IAi C. IAi x ii D. IAi x IAIB E. All of the above combinations in A through D are possible genotypes for Lee’s parents. * This is an example of multiple alleles in the ABO blood type system. Lee could be genotype IAIA or IAi, so there are many possible parental genotypes that could result in those allele combinations. [Stumbling Block 6]

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WHAT OTHER RESOURCES ARE AVAILABLE? 

NCBI Online Mendelian Inheritance in Man (OMIM) http://www.ncbi.nlm.nih.gov/omim/



University of Utah Learn.Genetics: http://learn.genetics.utah.edu/content/begin/traits/

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Linked genes do not follow the principle of independent assortment, and give us clues as to locations of genes on chromosomes.

2.

Sex-linked genes show distinct patterns of inheritance.

LEARNING OBJECTIVES Students should be able to:



Define key terms in linkage/sex-linkage: genetic linkage, recombination, recombination frequency, linkage map, parental and recombinant progeny, sexlinked, SRY gene, reciprocal cross, genetic counselling, pedigree, carrier, X chromosome inactivation, Barr body. [Knowledge]



Define key terms in chromosomal defects: deletion, duplication, translocation, reciprocal translocation, inversion, aneuploid, euploid, polyploidy. [Knowledge]



Define key terms in nontraditional patterns of inheritance: cytoplasmic inheritance, genomic imprinting. [Knowledge]



Relate recombination and nondisjunction as discussed in this chapter to the concepts presented in Chapter 10. [Analysis/Evaluation]

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

Explain how a reciprocal cross is useful in terms of determining if sex-linkage is occurring. [Comprehension]



Correctly identify genetic linkage, given information about a particular genetic cross (e.g., P, F1 and F2 phenotypes, numbers of each phenotype in offspring). [Evaluation]



Calculate recombination frequencies in genetic problems where genes are linked.

[Application]



Construct a linkage map for three or more genes exhibiting linkage. [Application]

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

Correctly identify sex-linkage, given information about a particular genetic cross (e.g., P, F1 and F2 phenotypes, numbers of each phenotype in male vs. female offspring).

[Evaluation]



Use a simple pedigree (exhibiting patterns of inheritance that can be determined from the pedigree and associated information) to solve human genetics problems.

[Application]



Explain how chromosomal alterations can affect the genotype and phenotype, providing examples of particular chromosomal alterations. [Comprehension]



Describe X-inactivation, and how this can affect the phenotype in females for certain alleles present on the X chromosome. [Comprehension]



Relate patterns of inheritance and the rules of probability to genetic counselling.

[Analysis/Evaluation]



Explain why aneuploidy of sex chromosomes in humans is more common than aneuploidy of autosomes. [Comprehension]



Describe nontraditional patterns of inheritance and how they differ from the socalled “traditional” patterns of inheritance. [Analysis/Evaluation]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Genome mapping relates to the location of genes on chromosomes. The human genome project was one of the most famous studies involving sequencing/mapping of all human genes.



Considerable research is devoted to studying causes of, and seeking treatments for genetic disorders in humans. Knowledge of the locus of a gene helps in studying these disorders.



Linked genes have been used as markers for particular genetic disorders in humans.

WHY SHOULD STUDENTS CARE? 

This chapter explicitly ties events in meiosis to genetics. It also provides a reminder that organelles carrying their own genomes (mitochondria, chloroplasts) have an effect on the organism in nonMendelian inheritance (Chapter 6, 7). Some topics relate to gene expression (covered in Chapter 15), and can be used to link concepts from these two chapters.

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

Students may be interested in genetic counselling, which highlights the everyday considerations faced by many individuals at risk of certain genetic conditions (or passing along deleterious alleles to their children).



Chromosomal alterations are responsible for certain human disease conditions (e.g., Down syndrome, chronic myelogenous leukemia); unusual sex chromosome combinations can affect fertility, other physical or physiological characteristics.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 57. It can be confusing to students that the principle of Independent Assortment mentioned in Chapter 11 is effectively violated when genes are located close together on the same chromosome.

58. Students often assume that dominant alleles and recessive alleles will assort together (e.g., that pr+ vg+ alleles and pr vg alleles are more likely to assort together than pr+ vg, and pr vg+ alleles). Linked alleles that assort together are those found on the same homologue. This misconception can lead to difficulties in recognizing parental vs. recombinant allele combinations.

59. It can take some time to be able to work through the steps required in mapping linked genes, particularly if the most distant genes do not exhibit linkage. The idea that distant genes on the same chromosome may not exhibit linkage is problematic for many students. Reviewing what occurs in crossing over, and going through example cases where genes are more than 50 map units apart can help students visualize and understand why this occurs.

60. The gene notation for Drosophila genes can be very confusing to students. It is worthwhile to go over the concept of “wild type” vs. mutant alleles, and discuss how systems of gene nomenclature can vary between organisms.

61. Genetic counselling may appear far more simple than it actually is. In textbooks/classes, we usually present clear-cut examples, but this is not always the case in the everyday world. In particular, it should be highlighted that although there is a pedigree symbol for carriers, we do not always know which individuals are asymptomatic carriers for recessive disorders. The small numbers of offspring (compared to those of fruit flies, peas, or other model organisms) and the inability to conduct controlled genetic crosses necessarily limits the information available from human matings.

62. Sex-linkage problems can be confusing to students who are accustomed to thinking of all genes being present as two alleles. Highlighting why males need to be considered independently of females can help students remember to do this when working with problems involving X linked traits.

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63. The concept of X-inactivation usually prompts some confusion. Astute students will also recognize the impact of having a deleterious recessive allele on the active X chromosome, so instructors may wish to address this situation explicitly. In some cases, females exhibit mosaicism for certain traits; in other cases, enough of the functional/normal allele is left active and produce adequate levels of the enzyme/protein so that little or no phenotypic effect is observed. It also depends on whether the affected gene is active in a certain tissue.

64. Genomic imprinting is a complex and confusing topic, even for upper level students. Instructors may want to consider whether this is appropriate for their courses, and if so, the level of detail that they wish to explore.

65. “Sex-linked genes” typically refers to X linked genes, not Y linked genes. Students may (understandably) assume that it refers to both, as the X and Y are both sex chromosomes.

WHAT CAN I DO IN CLASS? Again, instructors will need to decide at which level they want students to understand/know the material in this chapter. In certain courses (e.g., non-majors), awareness of linkage and sex-linkage concepts may be appropriate, while instructors in other courses may wish to provide students with opportunities to more deeply explore topics that will be in upper-level genetics courses.

The “Why it Matters” section provides a glimpse into another human genetic disorder, progeria. This can also lead into other human genetic diseases, particularly sex-linked disorders (such as hemophilia, also discussed in this chapter) and others commonly seen by genetic counsellors.

Instructors may want to introduce Drosophila melanogaster (the fruit fly) as a model organism. This insect was vital in Thomas Morgan’s experiments that provided evidence of genes being inherited on chromosomes.

Drosophila is still an important model organism, in areas beyond genetics. (Refer to Purple Pages pg. F-36.)

Drosophila gene notation (a plus sign, “+”, indicates the wild type allele for that particular gene) should be discussed to help students understand the examples included in the text (Section 12.1; Figures 12.2, 12.3).

Example problems are valuable here, and you may want to provide some for students to work through before or during class. As in the previous chapter, instructors are encouraged to make expert thinking transparent during explanations (we often skip steps or omit assumptions that students will not be aware of). Remind students that much of what was learned from Chapter 11 is used in this chapter (e.g., 3:1 phenotypic ratio with heterozygote cross dominant/recessive condition).

Additional pedigrees can be used (e.g., in problem sets) to help students become accustomed to the symbols and recognizing patterns of inheritance. (Pedigrees can be found in some human genetics papers; these may provide more ambiguous evidence than ones typically shown in textbooks/class!) If you used the example of Trimethylaminura (fish odour syndrome) in Chapter 11, you can show the pedigree used in: Dolphin CT, Janmohamed A, Smith RL, Shephard EA, Phillips IR. 1997. Missense mutation in flavin-containing monooxygenase 3 gene, FMO3, underlies fish-odour syndrome. Nat Genet. 17(4): 491-494. (Depending on your class, you may wish to also show some of the molecular aspects relating to the genetics.)

For X-inactivation, the textbook presents examples of coat colour in cats, and a human condition involving sweat gland distribution. Activity: you can have students draw out different genetic crosses, working out the possible gametes, and phenotypes of males vs. females in each case.

In discussing chromosomal alterations, myelogenous leukemia (CML) can be used as another example. This disorder often results from what was originally a balanced translocation in an asymptomatic carrier, but offspring that inherit only one of the translocated chromosome exhibit the disease. This disease is also a good example of how alterations in the cell cycle lead to cancer, and how understanding of the molecular nature of the disorder (the hybrid bcr/abl gene formed by the translocation stimulates unregulated tyrosine kinase activity) has led to a very specific treatment. Until the 1990s, the only successful treatment of CML was to destroy the patient's bone marrow and then restore blood-cell production by transplanting stem cells from the bone marrow of a compatible donor. However, the drug Imatinib (sold as Gleevec©) was designed to specifically inhibit enzymatic activity of the tyrosine kinase encoded by bcr/abl, and has shown amazing effectiveness in clinical trials.

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Down syndrome may be caused by trisomy of chromosome 21, or a translocation where part of chromosome 21 fuses with another chromosome. This could be used to lead into a discussion about possible causes of Down syndrome, and genetic counselling for mothers over 30 years of age.

Illustrating non-disjunction visually (or using props, such as pipecleaners) may help students better understand events that lead to aneuploidy.

Students may be surprised to learn how many common crop plants are polyploid. This has had an impact on human society in domestication of many plants, including the most commonly used cereal grains (e.g., bread wheat is hexaploid, but ancestor plants had different levels of ploidy).

When looking at nontraditional patterns of inheritance, mitochondrial sequencing may be introduced. Analysis of mitochondrial DNA (mtDNA) has been used for tracking ancestry through females to track the ancestry of many species (including humans!) for hundreds of generations. In forensics, analysis of mtDNA may be performed on remains that are too old for reliable nuclear DNA analysis, although mtDNA sequences are not specific to one individual. (This is also possible for hair samples lacking a follicle. There are mitochondria, but not nuclei present.) The textbook includes a list of human diseases caused by mutations in genes of mitochondria (Table 12.3). Instructors may want to ask students to consider which parts of the body/tissues would be most adversely affected by mtDNA mutations. (This can be related to Chapter 6.)

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Clicker questions:

Fig. 1 – Chromosomes before Meiosis You are working with a 2n = 4 organism. Fig 1 shows chromosomes just before Meiosis I. If normal crossing over occurs, which of the following combinations would be possible going into metaphase I?

Option 1 

Option 2 

Option 3 

E. Only Option 1 * F. Only Option 2 G. Only Option 3 H. More than one of the options (1 through 3) above would be possible.

I. None of the above options (1 through 3) would be possible.

Students sometimes have problems understanding what occurs in crossing over. This can lead to problems with comprehension of how linked genes may be reassorted during crossing over. [Stumbling Block 2]

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You are working with fruit flies that are heterozygous for glass eye (gl+ gl) and ebony body e+ e). When you do a test cross with these flies, you obtain the following progeny: A. B. C. D.

93 glass eye, grey body 89 normal eye, ebony body 8 glass eye, ebony body 9 normal eye, grey body

Based on these results, which of the following is/are true?

A. B. C. D. E.

The hairless and ebony body genes assort independently.

The parental arrangement of these genes on the chromosomes was gl+ e+ and gl e .

The parental arrangement of these genes on the chromosomes was gl+ e and gl e+ . * It is not possible to determine the parental arrangement of these genes on the chromosome.

Both A and D are true.

Students must recognize not only that linkage is occurring, but that glass eye and grey body progeny and normal eye, ebony body are the parental types, with the other two classes being recombinant types. This also reveals the original allele combinations in the heterozygote parents. [Stumbling Block 2, 3] A follow up question:

Based on the above results, which of the following is true?

A. The hairless and ebony body genes are not genetically linked.

B. The hairless and ebony body genes are genetically linked, 9.3 map units apart.

C. The hairless and ebony body genes are linked, 8.5 map units apart.* To answer this question, the students must calculate the frequency of recombination (number of recombinant progeny divided by total number of progeny).

4.

Zoe is unaffected but her father has hemophilia (a recessive, sex-linked condition). Zoe marries Don, who does not have this condition. What is the probability that Zoe and Don will have a child with hemophilia?

A. 0 B. 1/2 (0.5) C. 1/4 (0.25) * D. 1/8 (0.125) E. 1

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Although the condition is sex-linked, we still expect to see a 3:1 ratio of unaffected:affected. The following question highlights the difference we see in terms of different sexes: 5. If Zoe and Don (from previous question) have a son, what is the probability he will have hemophilia?

A. 0 B. 1/2 (0.5) * C. 1/4 (0.25) D. 1/8 (0.125) E. 1 A son may be XHY (normal) or XhY (hemophiliac). [Stumbling Block 6] 6.

An orange male cat mates with a female black cat. Which of the following would be likely of their offspring? Reminder: tortoiseshell = patches of orange and black.

A. B. C. D. E.

A tortoiseshell female. * A tortoiseshell male.

A black female.

An orange female.

An orange male.

The male would be XOY; the female XBXB. Offspring could be: XBY - black male XBXO – tortoiseshell female [Stumbling Block 7] 7. A person whose cells have one (1) Barr body could be: A. a female, genotype XX.* B. a male, genotype XY. C. a female, genotype XXX. D. a male, genotype XXXY. E. C or D. XY individuals will not have Barr bodies. C and D individuals would have 2 Barr bodies. This question can be modified (e.g., change the number of Barr bodies mentioned in the question). You could alternatively show a karyotype of an individual who has an unusual number of sex chromosomes, and ask students how many Barr bodies they would see in cells from that person. [Stumbling Block 7]

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WHAT OTHER RESOURCES ARE AVAILABLE? 

NCBI Online Mendelian Inheritance in Man (OMIM) http://www.ncbi.nlm.nih.gov/omim/



University of Utah Learn.Genetics: http://learn.genetics.utah.edu/content/begin/traits/



MITOMAP – mitochondrial DNA database http://www.mitomap.org/



The Interactive Fly http://www.sdbonline.org/fly/aimain/1aahome.htm

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

The nature and characteristics of DNA allow it to serve as an efficient information storage (hereditary) molecule, and allows for copying in replication.

2.

Errors in DNA replication in DNA can result in mutations that may be deleterious but may lead to evolutionary change.

LEARNING OBJECTIVES Students should be able to:



Define key terms (DNA structure/historical research): deoxyribonucleic acid (DNA), biotechnology, transformation, bacteriophages/phages, virus, nucleotide, nitrogenous base, purine, (adenine, guanine), pyrimidine (thymine, cytosine), sugarphosphate backbone, phosphodiester bond, X-ray diffraction, double-helix model, complementary base pairing, antiparallel. [Knowledge]

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

Define key terms (DNA replication): semiconservative replication model, dispersive replication model, DNA polymerase, nucleotide triphosphates (dATP, dGTP, dCTP, dTTP), 5’ end, 3’ end, DNA helicase, replication fork, single-stranded binding proteins, topoisomerase, RNA primer, primase, leading strand, lagging strand, discontinuous replication, Okazaki fragments, leading strand template, lagging strand template, DNA ligase, telomere, telomerase, replication origin, base-pair mismatch, proofreading mechanism, mismatch repair, mutation. [Knowledge]



Define key terms (DNA organization): eukaryotic chromosomal proteins (histones, nonhistone proteins), chromatin, major eukaryotic histones [H1, H2A, H2B, H3, H4], nucleosome, nucleosome core particle, linker, 10 nm chromatin fibre, 30 nm chromatin fibre/solenoid, euchromatin, heterochromatin, nucleoid, plasmid, rolling circle replication. [Knowledge]



Explain why an understanding of the structure of the DNA as the hereditary molecule was important in later related work. [Comprehension]

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

Describe key points of the experiment carried out by Griffith that demonstrated a “transforming principle” that could change pneumococcal bacteria at the genetic level. [Comprehension]



Describe key points of the experiment carried out by Avery, McCarty, MacLeod identifying DNA as the “transforming principle”. [Comprehension]



Describe key points of the experiment carried out by Hershey and Chase that supported that DNA as the hereditary molecule. [Comprehension]



Identify the elements of the scientific method in each of the above experiments (i.e., hypothesis, positive control, negative control). [Comprehension]



Describe the relevance of Chargaff’s observations of base ratios in terms of what we know about DNA structure. [Comprehension]



Describe what is meant by “polarity” of the polynucleotide chain of DNA. [Comprehension]



Explain how the double-helix model explains the structure of DNA. [Comprehension]



List and describe the different bonds that are present in an intact, double-stranded DNA molecule. [Knowledge, Comprehension]



Explain why Rosalind Franklin can be considered as one of the discoverers of DNA structure, along with Watson and Crick. [Comprehension]



Explain how the nitrogenous bases of DNA can represent genetic information.

[Comprehension]



Compare and contrast the models of semiconservative replication and dispersive replication. [Comprehension, Analysis]



Explain how Meselson and Stahl’s experiment supported the semiconservative replication model. [Comprehension]



Describe the process of DNA replication, including the roles of major enzymes involved in particular steps. [Comprehension]



Correctly predict the effect on DNA replication if one or more of the key enzymes is missing/non-functional. [Application, Analysis]



Describe the structure of telomeres and the role of telomerase in linear chromosome replication. [Comprehension]

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

Explain why DNA repair mechanisms are necessary. [Comprehension]



Describe the process of mismatch repair. [Comprehension]



Explain why DNA must be organized (i.e., made more condensed/compact) in living cells. [Comprehension]



Describe chromatin, and the role of eukaryotic histones. [Comprehension]



Relate what is known about the Barr body to chromatin packing in eukaryotes.

[Comprehension, Evaluation]



Compare and contrast the organization of DNA (i.e., how DNA is made compact) in bacteria vs. eukaryotes. [Comprehension, Analysis]



Describe the process of rolling circle replication in bacteria. [Comprehension]



Describe the effects of serious errors in DNA replication on the eukaryotic cell cycle.

[Comprehension, Evaluation, Synthesis]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

DNA is the common hereditary molecule for all living organisms (and some viruses).



Understanding the structure of DNA allows insight into many areas of research, including human disease, biotechnology, evolution and many others.



The process of DNA replication is important, and errors can lead to mutations that can have significant impact (e.g., introducing evolutionary change, causing cancer).



DNA packaging in eukaryotes is involved in genetic regulation.

WHY SHOULD STUDENTS CARE? 

Understanding the nature of DNA, and DNA replication is important in understanding many cellular, biochemical and genetic phenomenon and processes. (Indeed, if progressing through the concepts in the textbook, understanding the composition and structure of DNA shines light on the nature of the chromosomes discussed in the cell cycle and genetics.)



DNA has become a common term in the news, crime shows, and science fiction movies.

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

Students may have heard of telomerase in the context of “anti-aging” initiatives.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 66. This chapter includes many landmark experiments. These are elegant and important experiments that established fundamental aspects of the DNA molecule, its role, and structure. However, first year students can get lost in the details and history, especially with so many experiments under consideration. Instructors who wish their students to be familiar with these studies are encouraged to explore them from a context of the scientific method, using problem-solving and logic in each case.

Also, experienced biologists tend to refer to the different experiments by the names of the investigators. Introductory biology students will have more difficulty with this, and may develop better understanding if the experiments are described in terms of what the experimenters did (e.g., Meselson and Stahl experiment – DNA replication, comparing the models of semiconservative model to conservative and dispersive models.)

67. Students can become bogged down in the details of DNA composition, structure (and history in research). Instructors are encouraged to make expectations explicit with respect to what students are expected to know. (Do you want students to know the distance between base pairs? Details of all the historical experiments?)

68. DNA polarity (i.e., 5’ and 3’ ends) is something that many students find confusing. Instructors may want to not only describe this (in terms of the different ends of DNA sugar-phosphate backbone of the complementary strands) but provide some questions (clicker questions, online quizzes, homework).

69. The idea of the lagging strand in DNA replication can be non-intuitive. Students must have an understanding of the polarity of the DNA molecule (see above), and the restricted directionality of DNA polymerase (5’  3’) for this to make sense. An animation, and/or step-by-step representation of the events that occur in discontinuous synthesis will also be helpful in illustrating this.

70. The nature of telomeres and role of telomerase can be difficult to understand. The nature of linear chromosomes, the requirement to use RNA primers at the onset of replication and the subsequent removal of those primers must be understood in order to comprehend how linear chromosomes become shortened with each round of replication. Visuals and animations may be of value here.

71. We have found that students do not understand why all our cells do not make telomerase (especially if they are familiar with research efforts relating to aging and telomeres). A discussion of the nature of cancer (uncontrolled cell division) as mentioned on page 287 may be helpful in this context.

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72. Students often think that DNA repair mechanisms fix all errors, and cannot understand how mutations can arise. The term mutation also has negative connotations, so it may be worthwhile mentioning that mutations may be beneficial, detrimental, or (most commonly) neutral to the organism.

73. Students are often not accustomed to thinking about chromosomes containing anything other than chromatin, although there are many proteins associated with DNA (histone and non-histone proteins in eukaryotes).

74. As bacteria lack a nucleus, students may be unaware of the need for bacterial DNA to be organized.

While the mechanisms by which DNA is made more compact vary (in bacteria, DNA gyrase is required for supercoiling; no histones are present but other proteins are associated with bacterial DNA), bacteria must also condense their chromosome(s).

75. While it’s not mentioned specifically in this chapter, archaeal DNA is also organized, and has histonelike proteins associated with it. (The histones are similar to eukaryotic ones, but assemble as tetramers rather than octomers.) Thus, it can be misleading to discuss “prokaryotic DNA organization” without clarifying which mechanisms are involved in bacteria, and which ones are used by archaea.

WHAT CAN I DO IN CLASS? The “Why it Matters” introduction describes the discovery of ancient bear ancestor DNA, and the promise and challenges of analyzing DNA samples from many thousands (or even millions!) of years ago. This can lead into a discussion about the possibility of finding DNA samples in space or extraterrestrial bodies, and some of the considerations of using DNA in forensic cases. A debate could be held between students (or teams of students) about the reliability of DNA analysis when samples may have been degraded/contaminated.

Many historical studies are presented in this chapter. Each landmark experiment can be assigned to a small group of students for group presentations to the larger group. Provide clear expectations of what each group should address in their presentation (e.g., the prevailing understanding prior to the experiment, how the scientific method was used, interpretation of the results, impact on biology). Instructors may want to have a discussion about why we care about these experiments carried out so long ago.

This chapter provides opportunities to link to other concepts that may have previously been covered, or will be covered in future. E.g., In the context of the cell cycle, DNA replication is what occurs in S phase (Chapter 9); the information encoded by the nitrogenous bases is what provides the genetic instructions on chromosomes (Chapter 10, 11, 12). Organization of DNA (euchromatin vs. heterochromatin) is related to regulation of gene expression (Chapter 15). Manipulation of DNA, and the DNA replication process has allowed us to develop key techniques in genetic engineering, biotechnology (Chapter 16).

Understanding the structure of DNA may be assisted using figures and animations with clear explanations. If you have access to a physical model, you may want to bring that to class. Students can be encouraged to make their own physical models exemplifying the major features of DNA. Animations and a step-by-step overview of the events that occur in DNA replication will be helpful for students to understand the process.

In-class, or as homework, provide scenarios where a key replication enzyme is missing, and have students (individually or in small groups) determine the extent of the DNA replication process that would occur.

Provide examples of different types of errors in DNA replication for students to consider potential consequences of. (E.g., What happens if there is an error that can be fixed? What if the a base-pair substitution is made, and not fixed? What if there is a chemical intercalated and replication cannot continue?) This activity

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can explore the results on the gene product, and (possibly) the cell cycle (if DNA damage is significant enough).

The “Molecule Behind Biology” section in this chapter talks about nucleoside analogues as antiviral therapy.

This will probably be of interest to students, particularly those planning to enter health-related professions.

Some nucleoside analogues are also used in cancer therapies. Ask: What are the benefits of such therapies?

What are the risks? How do strategies against viruses differ from those used in treating cancers? How can such therapies be used without drastically affecting all of the body’s cells?

A discussion about telomeres (i.e., why they are needed in eukaryotic chromosomes) and telomerase can be run in class. You may want to show some of the recent research information regarding telomerase, and encourage students to talk about the potential benefits and risks of using telomerase as anti-aging therapies.

A demonstration of the benefits of histone-packaging can be done. First, wool can be shown loose, vs. in a ball, and students can consider the differences between the different types of organization. Spools and twine can be used to demonstrate DNA (twine) associating with histones (spools). Long lengths of loose twine will be difficult to stuff into a flexible container (e.g., a cloth bag). Spooling the twine into a chromatin-like structure will allow a more compact organization.

Clicker questions:

In DNA replication J. the template strand is read in a 5’  3’ direction.

K. the template strand can be read in either direction (5’  3’ or 3’  5’) depending on the genetic information encoded on the strand.

L. DNA polymerase catalyzes new synthesis is in a 3’  5’ direction.

M. DNA polymerase catalyzes new synthesis is in a 5’  3’ direction. * N. More than one of the above is true.

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Practise using the terminology relating to the different ends of DNA will help students become familiar with it. This question can also lead into a discussion regarding the need for RNA primers in DNA replication. [Stumbling Block 3] Consider a cell with a mutation in the DNA ligase enzyme that renders the protein nonfunctional. Assuming that all of the other DNA replication enzymes are still fully functional, how much of the process of DNA replication would be expected to occur?

O. Leading strand synthesis would take place, but lagging strand synthesis would not be initiated.

P. None; no part of the DNA replication process could occur.

Q. Helicase would unwind the DNA helix, but synthesis would be blocked.

R. Both the leading and lagging strand would be synthesized, but Okazaki fragments would not be joined together. * This question requires that students consider the events that occur in DNA replication, and the enzymes required at each step. It is possible to generate a number of similar questions, using different enzymes; a very similar question is present in the test bank. [Stumbling Block 4]

Eukaryotic chromosomes are composed of S. DNA. T. histone proteins.

U. nonhistone proteins.

V. all of the above (A through C). * W. only two of the above (A through C).

[Stumbling Block 8]

WHAT OTHER RESOURCES ARE AVAILABLE? 

Howard Hughes Medical Institute (HHMI) has a number of beautiful animations, including DNA replication: http://www.hhmi.org/biointeractive/dna/animations.html



James Watson’s description of the work he carried out with Francis Crick: Watson, J.D. The Double Helix: A Personal Account of the Discovery of the Structure of DNA (1968), Atheneum.



Galmarini CM, Mackey JR, Dumontet C. 2002. Nucleoside analogues and nucleobases in cancer treatment. The Lancet Oncology 3(7): 415-424.

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

Bodnar AG, Ouellette M, Frolkis M, Holt SE, Chiu CP, Morin GB, Harley CB, Shay JW, Lichtsteiner S, Wright WE. 1998. Extension of life-span by introduction of telomerase into normal human cells. Science 279(5349): 349-352.



Kim NW, Piatyszek MA, Prowse KR, Harley CB, West MD, Ho PL, Coviello GM, Wright WE, Weinrich SL, Shay JW. 1994. Specific association of human telomerase activity with immortal cells and cancer. Science. 266(5193): 2011-2015.



Sandman K, Reeve JN. 2000. Structure and functional relationships of archaeal and eukaryal histones and nucleosomes. Arch Microbiol. 173(3): 165-169.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Transcription and translation are sequential processes that allow information encoded in a gene to be copied as RNA, and expressed (usually as proteins).

LEARNING OBJECTIVES Students should be able to:



Define key terms (historical research): alkaptonuria, Neurospora crassa, auxotroph, one-gene-one-protein hypothesis, polypeptide, one-gene-one-polypeptide hypothesis.

[Knowledge]



Define key terms (transcription): transcription, translation, template strand, messenger RNA (mRNA), ribosome, genetic code, codon, transfer RNA (tRNA), sense codons, start/initiator codons, stop (nonsense/termination) codons, RNA polymerase, promoter, transcription unit, TATA box, transcription factor, terminators, untranslated region, precursor-mRNA (pre-mRNA), 5’ cap, poly(A) tail, intron, exon, mRNA splicing, spliceosome, small ribonucleoprotein particles (snRNPs), small nuclear RNA (snRNA), ribozyme, alternative splicing, exon shuffling. [Knowledge]



Define key terms (translation): initiation, elongation, termination, anticodon, wobble hypothesis, aminoacylation/charging, aminoacyl-tRNA, aminoacyl-tRNA synthetase, ribosome (including large and small subunits), ribonucleoprotein, ribosomal RNA (rRNA), ribosome sites: A (aminoacyl) site, P (peptidyl) site, E (exit) site, initiator DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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tRNA, ribosome binding site, peptidyl-tRNA, peptidyl transferase, release factor (termination factor), polysome, pepsinogen, signal peptide (signal sequence), signal recognition particle (SRP), SRP receptor, mutation, base-pair substitution, missense mutation, nonsense mutation, silent mutation, frameshift mutation, gene expression.

[Knowledge] 

Describe the key points of the experiment carried out by Beadle and Tatum.

[Comprehension]



Explain what is meant by the “one-gene-one-polypeptide hypothesis”, and why this has replaced the “one-gene-one-protein hypothesis”. [Comprehension]

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

Explain how the processes of transcription and translation differ between prokaryotes and eukaryotes. [Comprehension]



Explain how each base in DNA/mRNA can be considered as a letter of an alphabet, and how these are used to make “words” in the genetic code. [Comprehension]



Describe the key points of the experiment carried out by Nirenberg and Leder, establishing the identity of most of the codons. [Comprehension]



Describe the different types of codons. [Comprehension]



Provided a genetic code table, determine the amino acid, initiator codon, or terminator codon encoded by a given mRNA sequence. [Application]



Provided a genetic code table, determine the amino acid, initiator codon, or terminator codon encoded by a given gene (DNA) sequence. [Application]



Correctly determine the sequence of a particular anticodon if provided a codon sequence (and vice versa). [Application]



Explain what is meant by the degeneracy (or redundancy) of the genetic code.

[Comprehension]



Relate the degeneracy (or redundancy) of the genetic code to the wobble hypothesis.

[Comprehension]



Explain what is meant by the “reading frame” of mRNA. [Comprehension]



Explain what is meant by the universality of the genetic code. [Comprehension]



Relate the universality of the genetic code to the unity of life. [Comprehension, Analysis]



Describe the basic structure of a gene. [Comprehension]



Describe the process of transcription, including the steps and key proteins involved.

[Comprehension]



Compare and contrast the processes of DNA replication and transcription. [Analysis]



Describe the different eukaryotic RNA polymerases in terms of their functions.

[Comprehension]



Correctly determine the sequence of mRNA transcribed from a given DNA template or coding strand sequence. [Application]

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

Describe the post-transcriptional modifications that occur in production of eukaryotic mRNAs. [Comprehension]



Describe a spliceosome in terms of composition and function. [Comprehension]



Explain how introns contribute to variability of proteins encoded by the same gene.

[Comprehension]



Describe the roles of different forms of RNA in converting the information in a gene to a protein. [Comprehension]



Describe the structure of a ribosome. [Comprehension]



Describe the process of translation, including the key proteins and nucleic acids involved [Comprehension].



Explain the steps newly synthesized polypeptides go through before they are considered to be complete. [Comprehension]



Describe how proteins can be trafficked to different cellular locations. [Comprehension]



Describe the different types of point mutations. [Comprehension]



Determine the potential impact of each type of mutation on the final protein product (phenotype). [Application]



Explain how phenotype is related to genotype at a molecular level [Comprehension, Analysis].



Explain why most mutations in a multicellular organism do not result in phenotypic change. [Analysis]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Transcription and translation are fundamental processes of life.



Understanding details of transcription and translation at the molecular level can shed light on processes where genetic regulation occurs at various levels, and may reveal ways to manipulate such processes in genetic engineering, treatment of diseases, etc.



Mutations underlie many disease conditions in humans, including genetic disorders and cancer.



Introduction of a mutation in a gene can allow scientists to study the effect of knocking out the gene, which can reveal the gene’s function.

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WHY SHOULD STUDENTS CARE? 

Understanding the processes involved to convert genetic information into proteins is important in understanding many cellular, biochemical and genetic phenomenon and processes.



The next chapter (15) discusses regulation of gene expression, which cannot really be followed if one does not know what is involved in transcription and translation.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 76. It can take some time for students to understand transcription and translation well, and use the terms appropriately. Many students feel that they have an understand these processes, having been introduced to the terms in high school. Some may even think that replication and transcription are interchangeable.

77. Students may have trouble with the idea that some genes directly code for RNA, and are not translated into proteins. When talking about the different types of RNA (tRNA, rRNA, snRNA), it is a good idea to reinforce that these molecules are encoded by specific genes.

78. As with Chapter 14, polarity (i.e., 5’ and 3’ ends of DNA and mRNA) is something that many students find confusing.

79. The relationship between DNA (with template and coding strands), mRNA transcript and final polypeptide may be challenging for some students to grasp, particularly if they are struggling with the polarity of these molecules. The fact that the template strand can also be referred to as the "minus strand" or "antisense strand" while the coding strand is sometimes called the "non-template strand”, "plus strand", or "sense strand" can add to student confusion, especially if various terms are used interchangeably without explanation.

80. Students may not be aware that in a DNA molecule, a strand that serves as the template for one particular gene can also be the coding strand for a different gene.

81. The terms “upstream” and “downstream” with respect to nucleic acid sequences can be confusing.

When discussing gene structure, using a figure (e.g., Figure 14.7) demonstrating upstream and downstream of the transcription unit visually is recommended.

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82. The terms “initiation”, “elongation” and “termination” are used to describe stages in both transcription and translation, which can be particularly confusing for students still struggling to distinguish between transcription and translation.

83. There are many different enzymes involved in transcription and translation. The name of the enzyme is typically informative, and we suggest highlighting this when discussing the enzymes and steps they catalyze.

84. We have found that students often do not realize the impact of blocking translation (or transcription) in cells. These are fundamental processes that must occur in nearly all living cells.

85. The idea of non-coding DNA can be non-intuitive to many students.

86. Students can have difficulty remembering, and understanding the different types of point mutations.

Frameshift mutations can be particularly challenging for students to understand in terms of the impact on the final product encoded by the gene.

87. Protein sorting requires students to think holistically about the cell. This is not always easy to do, particularly when we spend a lot of time on minute details of individual molecules.

WHAT CAN I DO IN CLASS? The “Why it Matters” introduction provides a reminder to students of the importance of particular proteins, highlighting the mussel product, byssus. Students can be asked what other proteins are important consumer products? What proteins are made through biotechnology?

Students may need an orientation to the genetic code table to understand how to use it to determine what a particular codon encodes. (If you are not sure of the background knowledge of your students, a pre-test can be helpful.)

A reminder of the polarity of DNA and RNA is recommended, showing examples of a DNA template strand, the complementary coding strand and the mRNA transcript with 5’ and 3’ ends indicated for each. The 5’ → 3’ direction of RNA synthesis (while DNA is read 3' → 5' in transcription) is similar to what occurs when synthesizing a complementary DNA strand in DNA replication (Chapter 13). [Stumbling Block 3, 4] An in-class activity or homework assignment can be given to students where example DNA sequences are provided, and students are asked to determine sequences of:   

the mRNA transcript. codons/anticodons. the amino acid sequence of the final polypeptide.

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You may want to visit the NCBI PubMed site to search for your favourite gene sequences. Students can also be encouraged to do this!

Students (individually or in pairs) can be asked to compare the different types of RNA molecules:

Table: Comparison of different ribonucleic acid molecules Type of RNA mRNA rRNA tRNA snRNA

Structure

Role/Function

Transcription and translation tie the molecular structure of DNA to the phenotype that is observed. If genetics (Chapters 11, 12) has been discussed already, then instructors may want to encourage students to consider the impact of particular genetic mutations on what is observed at a phenotypic level.

Animations and step-by-step overviews of the events that occur in transcription and translation will be helpful for students to understand these processes.

Have students brainstorm to list the various processes/steps that require complementary base pairing. (E.g., addition of new bases in new strand of DNA replication to existing strand, template DNA to mRNA in transcription, mRNA codon to tRNA anticodon). How are these processes similar? Different?

The 2009 Nobel Prize in Chemistry was awarded to Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for their studies of the ribosome. Hold a discussion, asking students why these studies can be considered important enough to award such a major prize.

The “Molecule Behind Biology” section in this chapter talks about amanitin toxin. This could be used to introduce other toxins that can affect translation (e.g., diphtheria toxin blocks translation in eukaryotes; many antibiotics, such as tetracycline and streptomycin block translation in bacteria).

Discuss use of signal peptides in genetic engineering (e.g., targeting certain proteins to particular organelles.)

Students may be interested to know that a variety of diseases are the result of altered signal peptides (Laurila and Vihinen 2009).

Problem: Have students work through the effects of various types of point mutations (missense, nonsense, frameshift) on a given sequence in terms of the final polypeptide product.

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E.g., Original sequence (coding strand) AGTTCCTACAAAATGGAGCTGTCTTGGCATGTAGTCTTT Variant 1 AGTTCATACAAAATGGAGCTGTCTTGGCATGTAGTCTTT Variant 2 AGTTCCTACAAAATGGACCTGTCTTGGCATGTAGTCTTT Variant 3 AGTTCCTAGAAAATGGAGCTGTCTTGGCATGTAGTCTTT Variant 1 = silent mutation; Variant 2 = missense mutation; Variant 3 = nonsense mutation Clicker questions:

Which of the following statements is true of both bacteria and eukaryotes?

X. Transcription is carried out in the nucleus and mRNA transcripts are exported to the cytoplasm where translation can occur.

Y. Pre-mRNA molecules have 5’ cap and a 3’ poly(A) tail, exons and possibly introns.

Z. Translation of a particular mRNA molecule can begin before transcription of that mRNA is complete.

AA. Instead of thymine (found in DNA), uracil is present in RNA.* BB.None of the above statements is true of both bacteria and eukaryotes.

This question focuses on the fact that while aspects of transcription and translation are similar across the Domains, there are some differences in the processes between bacteria and eukaryotes.

The promoter sequence is CC.upstream of the transcription unit of the gene. * DD. downstream of the transcription unit of the gene.

EE. within the transcription unit of the gene.

Stumbling Block 6.

If a cell lost functional peptidyl transferase, what would you expect to see?

FF. mRNA copies of the gene will not be generated.

GG. tRNA molecules cannot be charged with the appropriate amino acids.

HH. amino acids cannot be added to the initial amino acid of the protein being translated. * II. the completely translated polypeptide chain cannot be released from the ribosome.

JJ. mRNA splicing cannot occur.

Variants of this question can be constructed substituting other enzymes for peptidyl transferase. [Stumbling Block 8].

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Diphtheria toxin (produced by the bacterium Corynebacterium diphtheriae) arrests protein synthesis in human cells. What is the effect on cells containing diphtheria toxin?

KK. The cells will be killed. * LL. The cells will live, but will not be able to divide.

MM. The cells will live, but will not be able to secrete proteins.

Students may be interested to know that one diphtheria toxin molecule – even one particular fragment of the toxin! – can kill a human cell. [Stumbling Block 9]

WHAT OTHER RESOURCES ARE AVAILABLE? 

Howard Hughes Medical Institute (HHMI) has a number of beautiful animations, including transcription and translation: http://www.hhmi.org/biointeractive/dna/animations.html



NCBI Pub Med – Nucleotide: http://www.ncbi.nlm.nih.gov/sites/entrez? db=nuccore&itool=toolbar



The 2009 Nobel Prize in Chemistry - Studies on the structure and function of the ribosome: http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/press.html



Laurila, K. and Vihinen, M. 2009. Prediction of disease-related mutations affecting protein localization. BMC Genomics 10:122 doi:10.1186/1471-2164-10-122.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Not all genes are expressed at all times by all cells - differential expression of genes occurs through regulatory mechanisms.

LEARNING OBJECTIVES Students should be able to:



Define key terms in bacterial gene expression regulation: promoter, operon, repressor and (bacterial) activator. [Knowledge] DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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

Define key terms in eukaryotic gene expression regulation: TATA box, chromatin remodelling, general transcription factor, (eukaryotic) activator, coactivator, DNA methylation, genomic imprinting. [Knowledge]



Describe the phenomenon of “differential gene expression”. [Comprehension]



Explain roles of differential gene expression in bacteria and in eukaryotes.

[Comprehension]



Correctly identify the outcome of specific situations discussed in this chapter, given particular conditions (e.g., expression of lac operon in E. coli grown in media containing glucose and lactose). [Application]



Define key terms in eukaryotic posttranscriptional, translational and posttranslational regulation: alternative splicing, micro-RNAs (miRNAs), RNA interference (RNAi), small interfering RNA (siRNA), ubiquitin, proteasome. [Knowledge]



Compare and contrast bacterial regulation of gene expression and eukaryotic regulation of gene expression. [Analysis/Evaluation]



Compare (one or more of) transcriptional, posttranscriptional, translational and posttranslational mechanisms of regulation of gene expression. [Analysis/Evaluation]



Explain combinatorial gene regulation. [Comprehension]

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

Describe the steps involved in RNA interference. [Comprehension]



Explain how proteins are degraded via a proteasome. [Comprehension]



Describe the steps that occur in development of cancer. [Comprehension]



Describe how regulation of gene expression relates to cell cycle control.

[Analysis/Evaluation]



Discuss the complexity of cancer biology and the difficulty in finding effective treatments. [Synthesis]



Discuss the “central dogma”, in light of what is known about the various mechanisms of gene expression regulation in eukaryotes. [Synthesis]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Gene expression (and control thereof) explains many bacterial adaptations in different environments/conditions, and aspects of differentiation seen in multicellular organisms.



Understanding of gene expression control mechanisms can be of value in many biological processes, including many relating to human health (e.g., cancer research).



Manipulation/exploitation of regulatory mechanisms is of value in molecular biology laboratories (studying biology), and possibly in development of therapeutics.

WHY SHOULD STUDENTS CARE? 

Regulation of gene expression is responsible for many observations in biology, particularly in multicellular organismal development (e.g., the changes from embryo to differentiated animal/plant).



Understanding of control mechanisms can be of value in many biological processes, including many relating to human health (e.g., antibiotic resistance in bacteria that cause dangerous infections, cancer research in humans).



Practical applications exist in exploiting gene expression mechanisms in molecular biology and biotechnology (currently microbial manipulation, but we are likely to see more eukaryotic applications in future).



Differences between regulatory mechanisms in bacteria vs. those of eukaryotes reveals some of the diversity between these domains, and potentially the evolutionary history and relationship between the organisms within these groups.

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WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 88. Students often mix up transcription and translation. Students may need a review of these terms/processes. If students mix up these terms, they will have difficulty comprehending the various levels of control. If these processes have not been thoroughly explored previously, it will be worthwhile to explain them here, and refer to them without jargon initially, and later add the appropriate terminology.

89. Sometimes, students think that all genes are transcribed and translated in the cell. (Others do not fully understand that all somatic cells of an organism contain the same genes.) In an organism, all genes are not all expressed at the same time. Gene regulation is a dynamic process, depending on many different factors (e.g., how rapid the response needs to be, investment in macromolecules). The spatial, temporal and situational aspects of gene expression are all dimensions of which to be aware.

90. There can be confusion about cell differentiation in multicellular eukaryotes. Certain metazoan cells are totipotent (can differentiate into specific tissues), while differentiated cells are generally restricted to perform particular functions (with some differences in gene expression relating to differentiation).

91. Differences between regulation in bacteria vs. eukaryotes can be confusing, particularly since we see some overlap in terminology (though these often are not referring to identical proteins/processes).

Different arrangement of transcriptional units exist in bacteria (operons) compared to eukaryotes, as well as the regulatory proteins involved. The differences in bacterial structure compared to eukaryotes (with regards to nuclear membrane, decoupling of transcription and translation) can help students understand why differences in regulation of gene expression exist.

92. The idea of “prokaryotic gene expression regulation” is problematic. While studied members of the Archaea show some similarities to organisms in domain Bacteria (e.g., operons, polycistronic transcripts), they also show a number of similarities to eukaryotes (e.g., TATA box in promoter regions, RNA polymerase II similarities, multiple transcription factors required).

93. Many people consider cancer to be a single disease. Cancer encompasses many, many diseases resulting from aberrations in a wide variety of cells/genes (usually with more than one factor leading to carcinogenesis). Cancer also is usually the result of a series of events/mutations (i.e., a multi-step progression), not just a single incident. Even a person with a genetic predisposition (e.g., carrying the BRCA2 gene) will not necessarily develop cancer if other steps do not occur. The diversity of cancers is part of the reason why it is so difficult to find a “cancer cure”.

94. This chapter goes into considerable detail on some complex processes. In an introductory survey course with limited time for this chapter, focusing on the most general aspects of bacterial and eukaryotic gene expression will avoid introducing confusion.

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WHAT CAN I DO IN CLASS? If limited time is available, focus on the idea that while all cells of an organism share the same genes, the genes are not all expressed at once, and gene expression is regulated. Questions: Why would regulation of gene expression be beneficial to: a bacterium? A human? (You may need to prompt students to consider energy expenditure.) An analogy can be introduced: in everyday life, we can carry out a lot of different activities. Do you carry out every activity every day?

Students can be introduced to a news story about recent research developments in cancer, prior to discussion of the loss of regulatory controls in cancer. What is a tumour? How does a tumour arise, and grow?

The “Why it Matters” material can be used to introduce gene expression in embryonic development. It can also lead to a discussion about stem cells, and research that uses them. This could provide opportunity to debate some of the issues relating to using stem cells (in research, and therapeutically), including the potential benefits [Stumbling Block 3] and ethical considerations. Clicker questions could be used for opinion polling to provide peer anonymity.

It can be worthwhile to highlight the importance of gene expression in the relationship between genotype and phenotype. A gene without the necessary regulatory regions (and regulatory proteins) is inert. Variations in regulation can have a major impact on the phenotype.

Students can be provided with the following questions to consider when looking at the various types of gene regulation mechanisms (bacterial and eukaryotic): What is happening in terms of gene expression under different conditions? (Why?) How is the regulation occurring? (What molecules and regulatory regions are involved?)

Students often do not see the relevance of bacterial gene regulation with the classic examples of lactose catabolism and tryptophan biosynthesis. There are many other examples of regulation of gene expression in bacteria that can be shown. For example, in methicillin resistant Staphylococcus aureus (MRSA), the mec gene complex includes the resistance gene mecA (which encodes an alternative penicillin binding protein – can be described as providing an alternative way of building/repairing major cell wall component, bypassing the antibiotic targetted pathway, as well as mecI (encodes repressor of mecA transcription unless methicillin present) and mecR1 (encodes a sensor that recognizes methicillin [inducer], and induces cleavage of repressor in presence of antibiotic). (There are several papers that provide information – e.g., Hanssen, A.M., and Ericson Sollid, J.U. 2005. SCCmec in staphylococci: genes on the move. FEMS Immunology & Medical Microbiology 46: 8-20.) This could be introduced by having students discuss what they know about antibiotic resistance, MRSA, and problems facing physicians/researchers in treatment of infectious diseases. After introduction of the mec gene complex, give students time to compare this example to the negative regulation of transcription mechanism in the E. coli lac operon. (An example of positive regulation of gene expression via an activator protein would be the VanR/S system in Vancomycin resistant Enterococci – see Courvalin P. 2006.

Vancomycin resistance in gram-positive cocci. Clin Infect Dis. 42 Suppl 1:S25-34.)

NOTE: It is recommended that the term “prokaryotic gene regulation” be avoided in discussing many of the bacterial gene expression mechanisms. In many ways, archaeal gene expression can resemble bacterial gene expression, but in other ways (including types of regulatory proteins), there are more similarities to what occurs in eukaryotes. Instructors may wish to briefly mention this, to reinforce that the domain Archaea is as distinct from the domain Bacteria as to the domain Eukarya. Also, while introductory Biology textbooks do not discuss post-transcriptional/post-translational mechanisms of regulation in bacteria, these do occur (although many eukaryotic mechanisms differ from those in bacteria).

Instructors will need to determine (and share expectations of) how much detail they wish students to understand/remember of the eukaryotic gene expression regulation mechanisms, as the textbook provides a comprehensive, detailed description. In courses focused on molecular biology/genetics, time and examples can DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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be provided to help students understand the details of these processes. In more general survey courses, instructors may want students to focus on the diversity of mechanisms employed in eukaryotes to regulate gene expression, and major aspects that differ between them.

Figure 15.6 is a summary figure showing the levels where regulation can occur in eukaryotic cells. Instructors can return to this figure frequently, to help students visualize the hierarchy of regulation mechanisms in relation to transcription/translation processes and location in the cell.

Think-pair-share/discussion activity: How are transcriptional regulation mechanisms of gene expression similar between bacteria and eukaryotes? How do they differ? [Stumbling Block 4] In smaller classes, small groups can be assigned to do short presentations of different gene expression regulation mechanisms to the larger group. (Students will need clear expectations and some lead time to prepare.)

Recent research papers on many of the eukaryotic gene expression regulatory mechanisms can be shown, to give students an appreciation for the interest in understanding (and potentially exploiting) these systems. For example, some examples from the RNA interference literature could be introduced (at very basic level) as this is a “hot” topic. Think-pair-share/discussion activity: What other practical applications could RNAi yield?

(These could include medical, biotechnological, agricultural applications.)

In real life, multiple levels of regulation can exist in relation to particular genes. Insulin production and secretion is a good example of this. (See Ren et al 2007 for details and figures.) Students can be introduced to the complexity of the regulation of gene expression (although it is not recommended that students be expected to comprehend or recall all of the details involved in insulin gene expression in an introductory course).

The importance of gene expression regulation in cancers has been the focus of much research, and this is likely to capture interest of many students (particularly those in health-care related studies, or those hoping to enter professional programs in fields such as medicine, nursing, pharmacy, etc.) Instructors can simply show examples of some of the research being conducted, or introduce some of the key findings at a simplified level appropriate for students in an introductory course.

Discussions can be initiated regarding the difficulties of treating cancer (relating to underlying cause(s)). The role of viruses in some cancers could be discussed in the context of HPV vaccines, and some of the debates surrounding vaccination of young girls against HPV. [Stumbling Block 6] Clicker questions: 1.

The antibiotic erythromycin acts against bacterial ribosomes, preventing polypeptide (protein) elongation. So, in bacteria …

F. G. H. I.

Erythromycin blocks DNA replication.

Erythromycin blocks transcription only.

Erythromycin blocks translation only.* Erythromycin blocks both transcription and translation.

This question can be used to check for student comprehension of transcription and translation. Peer instruction may be adequate to help students who have some confusion between the different processes, or you may wish to conduct a short review, referring to Chapter 14. [Stumbling Block 1] 2. You have two cultures of E. coli cells. Flask 1 contains growth media with both glucose and lactose; Flask 2 does contains lactose only. Which of the following would be expected regarding transcription of genes in the lac operon?

A. B. C. D.

Flask 1 -> no expression; Flask 2 -> expression * Flask 1 -> no expression; Flask 2 -> no expression Flask 1 -> expression; Flask 2 -> no expression Flask 1 -> expression; Flask 2 -> expression DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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This question can check for understanding of how environmental conditions affect gene expression of cataoblic pathway genes in bacteria (or, at least, if students have read the textbook). Peer instruction can be used if 50% or fewer of class answer correctly when question introduced. Instructors could use this question to determine how much time to devote to discussing the lac operon in class. This question can be easily modified (change sugars present). [Stumbling Block 2]

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3.

You have two cultures of E. coli cells. Flask 1 contains growth media where the amino acid tryptophan is plentiful (and available for use by the bacteria); Flask 2 does NOT contain tryptophan. Which of the following would be expected regarding genes in the trp operon?

A. Flask 1 cells have higher levels of expression than those in Flask 2.

B. Flask 2 cells have higher levels of expression than those in Flask 1. * C. Cells in both flasks will have equivalent levels of expression.

This question can check for understanding of how environmental conditions affect gene expression of anabolic pathway genes in bacteria (using textbook example of tryptophan operon). Peer instruction can be used if 50% or fewer of class answer correctly when question introduced. [Stumbling Block 2] 4.

You have two cultures of E. coli cells. Flask 1 contains growth media where the amino acid arginine is plentiful (and available for use by the bacteria); Flask 2 does NOT contain arginine. Which of the following would be expected regarding genes in the arg operon?

A. Flask 1 cells have higher levels of expression than those in Flask 2.

B. Flask 2 cells have higher levels of expression than those in Flask 1. * C. Cells in both flasks will have equivalent levels of expression.

This question can check for understanding of how environmental conditions affect gene expression of anabolic pathway genes in bacteria. Ideally, students can make the connection between this situation and that of the tryptophan example in Q3, and you can provide the opportunity to discuss benefits of this type of regulation in terms of energy/macromolecule expenditure. Peer instruction can be used if 50% or fewer of class answer correctly when question introduced. [Stumbling Block 2] 5.

Some plants can be grown from single cells grown as an undifferentiated mass of cells (“callus”) in the laboratory. With appropriate treatment, the callus cells will form plant roots and/or shoots. The callus cells have the most similarity to human: A. B. C. D.

Stem cells.* Sperm and oocytes.

Smooth muscle cells.

Fingernail and hair cells.

This can be used to prompt a discussion about differentiation of cells in eukaryotes (and the mechanisms by which gene expression can be regulated in this process). [Stumbling Block 3]

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6.

Mechanisms regulating expression by modification or processing of a translated protein: A. will usually be among the more rapid ways to allow a cell to adapt to changes (in environment, physiologically).

B. will usually be among the slowest ways to allow a cell to adapt to changes (in environment, physiologically).

C. are more energetically costly than transcriptional and post-transcriptional mechanisms.

D. are less energetically costly than transcriptional and post-transcriptional mechanisms.

E. Both A and C. * F. Both B and D.

This question can highlight the costs/benefits of different types of mechanisms involved in regulation of gene expression. [Stumbling Block 2] 7.

Which of the following types of cells would have promoter proximal elements recognized by activators in most cells?

A. B. C. D.

Hemoglobin Housekeeping * Myosin Hormone-producing

This question reinforces the idea of differential gene expression, with recognition that some genes (housekeeping genes) more likely to be expressed in an organism’s cells compared to highly specialized products. [Stumbling Block 2] 8. RNA interference shows promise as a technology for all of the following EXCEPT: A. B. C. D. E. F.

Improvement of plant nutrition (genetic engineering of crop plants).

Screening for certain human cancers.

Treatment of certain human cancers.

Treatment of HIV infection (AIDS) by interfering with viral gene expression.

Treatment of methicillin-resistant Staphylococcus aureus infection by interfering with bacterial gene expression. * RNAi shows promise for all of the above.

This is an example of a question that can be used to check to see that students are aware that RNAi occurs in eukaryotes (with considerable interest in the biology and potential applications relating to this type of regulation), but does not occur in bacteria. Depending on the background of your students, you could simplify this question. [Stumbling Block 4]

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9.

Which of the following is/are true regarding cancer?

A. While cancer can occur in different regions of the body, it is considered a similar disease in terms of pathology and treatment.

B. Most cancers are the result of a single mutation.

C. Viral DNA integration into human genes can result in cancer.* D. More than one of the above is true.

This question addresses some of the key points relating to cancer. [Stumbling Block 6]

C.

10. All of the following statements are true regarding identical twins EXCEPT: A. The twins originated from fusion of a single egg and single sperm.

B. The sequence of nucleotides in DNA of the somatic cells is expected to be the same in each twin.

C. Patterns of DNA methylation and chromatin modeling are expected to be the same in each twin. * D. Both twins are of the same sex.

E. The blood type of the twins is expected to be the same.

This question may be used to introduce the idea of epigenetic inheritance.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Stem Cell Network (a Canadian site): http://www.stemcellnetwork.ca/



Nova ScienceNow – The RNAi Cure?: http://www.pbs.org/wgbh/nova/sciencenow/3210/02-cure.html



Ren J, Jin P, Wang E, Liu E, Harlan DM, Li X, and Stroncek DF. 2007. Pancreatic islet cell therapy for type I diabetes: understanding the effects of glucose stimulation on islets in order to produce better islets for transplantation. Journal of Translational Medicine 5:1.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Our understanding of how DNA works allows biologists to exploit biological processes in genetic engineering and biotechnology.

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2.

Much basic and applied research is made possible via DNA technologies.

3.

The genomes of many organisms have been sequenced, and because of evolutionary relatedness may provide considerable biological information about humans and other organisms.

LEARNING OBJECTIVES Students should be able to:



Define key terms (DNA technologies): biotechnology, basic research, applied research, DNA cloning, recombinant DNA, restriction endonuclease (restriction enzyme), restriction fragments, sticky ends, DNA ligase, restriction site, genomic DNA, cloning vector, plasmid, blue-white screening, DNA hybridization, nucleic acid probe, genomic library, reverse transcriptase, complementary DNA (cDNA), cDNA library, intron, polymerase chain reaction (PCR), DNA amplification, agarose gel electrophoresis. [Knowledge]



Define key terms (applications): restriction fragment length polymorphisms (RFLPs), Southern blot analysis, DNA fingerprinting, short tandem repeat (STR), genetic engineering, transgene, transgenic, expression vector, germ-line cells, stem cells, blastocyst, knockout mouse, gene therapy (germ-line gene therapy, somatic gene therapy), pharming, animal clone, callus, Rhizobium radiobacter (Agrobacterium tumefaciens), Ti (tumour inducing) plasmid, T DNA, Bt toxin, genetically modified organisms (GMOs). [Knowledge]



Define key terms (genome analysis): genome, Sanger sequencing method, dideoxynucleotide, dideoxy sequencing, structural genomics, functional genomics, whole-genome shotgun sequencing, bioinformatics, sequence similarity search, data mining, comparative genomics, DNA microarrays (DNA chips), proteome, proteomics, protein microarrays (protein chips). [Knowledge]

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

Explain how genetic engineering is considered an area of biotechnology, while biotechnology is not restricted to genetic engineering. [Comprehension, Analysis]



Compare and contrast basic and applied research. Suggest examples of each.

[Comprehension, Analysis]



Describe the purpose of DNA cloning. [Comprehension]



Describe, in general terms, how a fragment of genomic DNA can be cloned and expressed in E. coli. [Comprehension]



Describe the natural role of restriction endonucleases(enzymes) in bacteria, and how we can exploit these enzymes in the laboratory. [Comprehension]



Given a (short) DNA sequence, and knowing the restriction site of a particular restriction endonuclease, determine the number of cuts that would be made, and whether ends would be sticky or blunt. [Application]



Explain why it is useful to include a gene for antibiotic resistance in the plasmid vector when cloning. [Comprehension]



Describe the process (including the key steps and reagents) of blue-white screening.

[Comprehension]



Explain how DNA hybridization techniques can be used to identify a particular nucleic acid sequence. [Comprehension]



Compare and contrast the different types of genomic libraries. [Comprehension]



Describe how complementary DNA (cDNA) is produced. [Comprehension]



Describe the key steps of the polymerase chain reaction (PCR), including the enzymes and other materials involved. [Comprehension]



Explain why a heat-stable DNA polymerase is useful in PCR. [Comprehension]



Describe the process and purpose of agarose gel-electrophoresis. [Comprehension]



Describe, using an example, how DNA technologies can be used in human disease diagnosis. [Comprehension]



Describe the processes involved in DNA fingerprinting. [Comprehension]



Given a simple example of DNA fingerprinting data, determine if alleles are shared between the tested individuals. [Application] DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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

Describe two different example situations where DNA fingerprinting could be (or has been) used. [Comprehension]



Explain how and why some bacteria have been genetically engineered .

[Comprehension]



Compare and contrast germ-line and stem-cell techniques of animal genetic engineering. [Comprehension, Analysis]



Describe the steps involved in the production of a knockout mouse using stem cell genetic engineering. [Comprehension]



Compare and contrast germ-line and somatic cell gene therapy. [Comprehension, Analysis]



Describe the challenges that exist for human gene therapy. [Comprehension]



Describe the process of animal cloning used to clone “Dolly” the sheep.

[Comprehension]



Explain what is meant by “pharming”, comparing animal pharming to plant pharming. [Comprehension, Analysis]



Describe how the agent of crown gall disease has led to a method of introducing transgenes into certain plants. [Comprehension]



Describe why plants are considered to be well suited to genetic engineering.

[Comprehension]



Describe three different examples of established transgenic plant characteristics.

[Comprehension]



Describe public concerns about genetically modified organisms (GMOs) and what regulations/agreements exist relating to GMOs. [Comprehension]



Describe the principles behind, and major steps involved in, the Sanger method of DNA sequencing. [Comprehension]



Explain the difference between structural genomics and functional genomics.

[Comprehension]



Describe why bioinformatics is used in analyzing genomic data. [Comprehension]



Describe key structural features of the human genome. [Comprehension]

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

Describe DNA microarray technology, and its potential uses. [Comprehension]



Given a DNA microarray result for an experiment, identify which genes show differential expression. [Application]



Explain why proteomics may be considered a more challenging field than genomics.

[Comprehension]



Describe protein microarray technology, and its potential uses. [Comprehension]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

DNA technologies are an important part of the toolkit used by many biological researchers to study various organisms.



Many researchers are involved in genetic engineering projects to improve crop plants, fight disease, produce economically important biological molecules and many other potentially beneficial applications.



Genomic and proteomic studies are providing a wealth of data that may help scientists understand the biology of organisms in a variety of ways (e.g., gene expression in cancer, evolutionary relationships between different organisms, changes in antibiotic resistance genes in bacterial isolates, etc.).



Public concerns about genetic engineering and GMOs can have effects on the work carried out by some scientists (e.g., if funding is not available).

WHY SHOULD STUDENTS CARE? 

DNA technologies are important in studying biology at a molecular level. A student may use several of these techniques during his or her academic career.



DNA technologies are key in forensic analysis, biotechnology, medical diagnoses, and could provide more economic and socially valuable applications in future.



Public opinion regarding genetic engineering and GMOs is often negative. Awareness of the science behind the technologies, and the potential risks and benefits will allow students to develop informed opinions on this topic.

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WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 95. A good background in molecular biology (structure of DNA, transcription, translation) and genetics is important to be able to understand the techniques described in this chapter. Students can be encouraged to review aspects of Chapters 11-15, if necessary. Depending on the background of the students, instructors may choose to focus only on a few of the actual techniques in detail.

96. Widespread mentioning of DNA technology in popular TV shows, books, and movies may lead to students thinking that they understand these technologies, although they do not know the processes nor underlying principles. It can also cause students to believe that these techniques are inexpensive, simple to perform, and can be carried out in a matter of minutes.

97. There is a lot of terminology in this chapter that may overwhelm students. This is compounded by the fact that many of the biotechnological and genomic terms can be referred to by abbreviations (e.g., PCR, STRs, RFLPs, GMOs).

98. Many people have trouble understanding the nature and value of basic research (although applied research seems to be more easily comprehended).

99. It can be challenging to understand the events that take place in cloning (and other techniques).

Students may be easily lost in the details, rather than focusing on the logic and concepts behind the processes. (It should also be noted that “cloning” has different meanings, both used in this chapter!)

100. The topic of animal cloning may be influenced by emotional responses/opinions held by students.

This is also likely to be true regarding GMOs. It is recommended that instructors provide opportunities to discuss the ethical aspects as well as the scientific details.

101. Conversely, many students are not aware that there are limits to what current technologies are able to achieve, such as in the area of gene therapy. Highlighting the problems faced in gene therapy trials, especially after considerable optimism may allow students to be more aware of the obstacles faced by biological researchers … and the tragic consequences that have, on occasion, resulted.

102. Although genomes of many organisms have now been sequenced, people often do not realize that the sequence data alone do not provide much information (nor miracle cures). These data must be analyzed and mined in order to gain insight into biological function, possible disease predictors/causes, etc. The data obtained from genomic (and proteomic) studies is usually massive, and analysis usually requires computer assistance and specialized software. Many proteomic and genomic technologies are also very new, and may require optimization/refinement before we can obtain useful information.

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WHAT CAN I DO IN CLASS? The “Why it Matters” introduction describes recent work undertaken by J. Craig Venter to sample seawater bacteria for genomic analyses. Students may be interested in hearing more about Venter’s work, including his involvement (at Celera) in the race to sequence the human genome. (See “other resources” for more information.) Ask: What is the value of sequencing genomes of sea microbes?

A pre-test of DNA terminology and aspects of molecular biology may help students (and you) determine where review is necessary prior to discussing the techniques illustrated in this chapter. [Stumbling Blocks 1, 3] Presentation of DNA technologies (any techniques from this chapter) with clear, step-by-step figures will help students understand the processes, and reinforce the specialized vocabulary of these techniques. The video animations (available via CNow) are highly recommended (to be shown in class, and recommended to students to view/review on their own). [Stumbling Blocks 3, 5] In a discussion about basic and applied research, choose one or two of the “applied” techniques described in this chapter, and ask students to determine where basic research was necessary to develop these techniques.

(Many of the landmark molecular biology experiments are described in earlier chapters of the textbook.)

[Stumbling Block 4] If possible, provide a laboratory exercise or demonstration of some of the techniques discussed in the chapter, such as agarose gel electrophoresis of DNA digested by restriction endonucleases. [Stumbling Block 5] The Virtual Biology Laboratory Molecular Biology exercises provide simulation exercises for students to work through (on their own time, or in a laboratory with computer stations) relating to examples of the types of techniques explored in this chapter. Other online activities (see the University of Utah site listed under “other resources”) may also be useful. [Stumbling Block 5] Set up a group activity, assigning each group a different type of country: self-sufficient industrialized country; impoverished developing country; industrialized country reliant on food imports; economically growing developing country. Ask the groups to consider the risks/benefits of GMO crop plants, and draft a position statement from the perspective of their assigned country. (You may want to choose a specific plant – e.g., golden rice [mentioned in text], or golden yams [see other resources below.) Representatives of each group can share the position statement with the larger group, and answer questions from other students. [Stumbling Block 6] Students (individually or in groups/teams) can be given the task of finding information about the case of Saskatchewan farmer Percy Schmeiser, sued by the large agricultural biotech company Monsanto for patent infringement for growing genetically modified Roundup-resistant canola. (Monsanto sells both the Roundup herbicide and the canola seeds.) A debate or mock trial could be staged to have students argue each side of the issue.

Students can be asked to determine (individually or in small groups) which organisms were chosen for sequencing first. Discuss: Why were these organisms chosen (what characteristics were considered)?

Individual students, or groups of students can be assigned a sequenced organism, with the task of finding out more about that particular species’ genome (e.g., size, estimated number of genes) using the online NCBI PubMed tools. (Instructors should provide an overview of these tools, perhaps walking through the exercise with an example.) Students can share their findings in class or online so that the larger group can see the diversity of what has been found. Discuss the uses that can be made from knowing about the genome of the organism. (Choosing organisms from all domains, and from a variety of types within the domains will likely provide a wider range of genome characteristics.)

Clicker questions:

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Could you carry out the polymerase chain reaction (PCR) if you did NOT have a heatstable DNA polymerase, but had a DNA polymerase that worked between 25 C and 42C? NN. No. OO. Yes, but the extension stage would need to be carried out at a lower temperature than normally used in PCR. PP. Yes, but many replication errors would be expected in the amplified DNA. QQ. Yes, but the enzyme would need to be added after the annealing stage for each cycle.* PCR is a rapid and convenient technique, thanks to the availability of thermostable DNA polymerases (such as Taq polymerase). When PCR was first developed, enzyme had to be added to the reaction mixture in each cycle. [Stumbling Blocks 1,2]

Inclusion of an antibiotic resistance gene in a cloning vector (plasmid) when introducing recombinant plasmid into bacteria by transformation RR.means that only bacteria that did not acquire the plasmid will grow on media containing that antibiotic.

SS. means that only bacteria carrying the plasmid will grow on media containing that antibiotic. * TT.increases the efficiency of transformation of the bacteria.

UU. allows the researcher to screen colonies by colour after incubation on media containing that antibiotic.

Stumbling Block 5.

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Human gene therapy VV. is well-established, and routinely used in treating certain genetic diseases.

WW. has never been successful in practise.

XX. appears to involve risks when using current virus vectors.* YY. is illegal and prohibited world-wide.

While there have been successes in human gene therapy trials (for treatment of adenosine deaminase deficiency, sickle cell disease), there have also been many difficulties, including severe immune responses and development of leukemias. [Stumbling Block 7]

WHAT OTHER RESOURCES ARE AVAILABLE? 

Howard Hughes Medical Institute (HHMI) has a number of animations, including Somatic Cell Nuclear Transfer Animation, Gene Chip Manufacturing, Genetic engineering, and Human genome sequencing: http://www.hhmi.org/biointeractive/dna/animations.html



J. Craig Venter biography on J. Craig Venter Institute website: http://www.jcvi.org/cms/about/bios/jcventer/



Curiosity creates cures (National Institute of General Medical Sciences, NIH) – discusses value, impact of basic research: http://publications.nigms.nih.gov/curiosity/



Human Genome Project Information - DNA forensics http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml



University of Utah - Genetic technology information, virtual labs http://learn.genetics.utah.edu/



BioCassava Plus project: http://biocassavaplus.org/



Monsanto vs. Schmeiser lawsuit: http://www.percyschmeiser.com/

Fox JL. 2001. Canadian farmer found guilty of Monsanto canola patent infringement.

Nat Biotechnol. 19(5): 396-397.

Sechley KA, Schroeder H. 2002. Intellectual property protection of plant biotechnology inventions. Trends Biotechnol. 20(11): 456-461.

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Evolution is a theory that has substantial evidence to it. There are mechanisms or processes of evolution, of which natural selection is only one, that drive evolutionary change.

2.

Microevolution is a change over time in the allele frequencies (and thus, characteristics) of a population and there are several mechanisms responsible for evolutionary change. However, only natural selection leads to a population becoming a better fit to the environment that it inhabits, i.e., natural selection is the only evolutionary mechanism that leads to adaptation.

3.

Much of the terminology used in evolutionary biology has quite specialized meanings. Many of these words may be used in everyday language, but do not mean the same thing - vernacular definitions cannot be applied to the science.

LEARNING OBJECTIVES Students should be able to:



Define key terms (general): population, microevolution, phenotypic variation, qualitative and quantitative variation, polymorphism, mean value of characteristic.

[Knowledge]



Explain why variation in populations is important to evolution. [Comprehension]



Classify a phenotypic character as exhibiting quantitative or qualitative variation.

[Comprehension]



Explain how two individuals of the same species can have different genotypes, but the same phenotype or how two individuals could have the same genotype, but different phenotypes. [Comprehension]



Interpret, from a graph of a quantitative character, the degree of variability (variation) of that character in that population. [Application, Analysis]

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

Explain how the degree to which an organism’s phenotype is determined by its genotype affects the evolutionary change of a population. [Comprehension]



Explain how twin studies and artificial selection experiments are useful in determining the heritability (genetic basis) of a character. [Comprehension]



Define key terms (genetic aspects): gene pool, genotypic frequency, allele frequency, relative abundance, genetic equilibrium. [Knowledge]



Differentiate between genotype frequency and allele frequency. [Knowledge, Comprehension]



Calculate frequencies of alleles or genotypes given information on the number of individuals with specific genotypes. [Application]



Explain how the Hardy-Weinberg principle acts as a null model/hypothesis for evolution. [Comprehension]



List the 5 conditions of the Hardy-Weinberg (HW) principle under which a population of diploid organisms can reach genetic equilibrium. [Knowledge]



Explain why microevolution will not occur under the conditions of HW. [Comprehension]



Explain why given allelic frequencies for a certain gene in a population, one could not determine the alleles’ dominance relationship. [Comprehension]



Relate the HW equation to probabilities of gametes and offspring in a Punnett square. [Application, Analysis]



Define the agents of microevolutionary change: mutation, gene flow, drift, and natural selection, as well as non-random mating. [Knowledge]



Describe the different effects of microevolutionary processes on genetic variation of a population. [Comprehension]



Describe, in simple terms, several ways in which variation is generated.

[Comprehension]



Explain how although infrequent mutations can alter the evolution of a population.

[Comprehension]



Describe the random nature of mutations. [Comprehension]

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

Explain, briefly, how mutations would be passed from one generation to the next.

[Comprehension]



Describe how gene flow between two populations results in the populations becoming more similar. [Comprehension]



Describe how population bottlenecks and founder events can lead to genetic drift.

[Comprehension]



Explain why the effects of genetic drift increase as the population size decreases.

[Comprehension]



Describe the implications that genetic drift has for conservation biology. [Application]



Define adaptation, fitness, and relative fitness. [Knowledge]



Explain how natural selection acts on phenotypic variation to alter the genetic structure of a population. [Comprehension]



Explain why natural selection is the only mechanism of evolution to result in adaptation. [Comprehension]



Explain why a character that is strongly influenced by the environment would not respond to (either artificial or natural) selection. [Comprehension/Analysis]



Explain why natural selection exerts little effect on a genetically determined phenotype that appears in postreproductive life (e.g., Huntington’s Disease, late-onset cancer). [Comprehension/Analysis]



Differentiate between directional, stabilizing, and disruptive selection and their effects on the variability and mean value of a character within a population.

[Comprehension]



Identify, given a scenario, which forms of natural selection is/are at work. [Analysis]



Explain , using an example, how sexual selection has resulted in showy structures in males. [Comprehension]



Differentiate between intersexual and intrasexual selection. [Comprehension]



Relate the 5 conditions of the Hardy-Weinberg principle to the various mechanisms of evolution (microevolutionary processes). [Analysis]



Describe how inbreeding can result in an increase in recessive phenotypes and a decrease in heterozygotes. [Comprehension] DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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

Describe how diploidy can hide harmful recessive alleles from natural (or artificial) selection. [Comprehension]



Explain why alleles coding for dominant traits don’t, through natural selection, always replace recessive or rare alleles. [Comprehension]



Describe heterozygote advantage and frequency-dependent selection. [Comprehension]



Define the neutral variation hypothesis and its impact on a population’s genetic variability. [Knowledge]



Describe why there are limits to adaptive evolution (i.e., why organisms can never be perfectly adapted to their environment). [Comprehension]



Explain how both the unity and diversity of life can be explained by the theory of evolution by natural selection. [Comprehension, Synthesis]



Explain why individuals do not evolve and why evolution is considered a population process. [Comprehension]



Explain why evolution is not progressive. [Comprehension]



Explain using an example, how microevolutionary processes might act simultaneously. [Comprehension/Analysis]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Evolution is a central concept to all disciplines of biology. Understanding the processes that bring about evolutionary change is important for understanding evolution and its impact on all biological fields (e.g., cell biology, behaviour, ecology, medicine).



Understanding the processes that bring about evolutionary change is important to fields such as medicine where growing antibiotic resistance among bacteria puts human health at risk.



Many human diseases are caused by recessive alleles. By furthering our knowledge of the intersection of natural selection and medical genetics, it may be possible to find strategies to prevent/treat some genetic disorders

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WHY SHOULD STUDENTS CARE? 

Selection can have major consequences on human health (e.g., bacterial resistance to antibiotics) and economics (e.g., domesticated animals and crops).



Although we like to attribute all of our features to adaptation, it is important to understand that there are other forces that bring about evolutionary change.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 103. As mentioned in Ch. 3, students are familiar with the argument that “Evolution is just a ‘theory’”, where opponents to evolution use the term theory in its vernacular, not its scientific definition.

Because evolution explains a general pattern, has a mechanism(s), and has substantial evidence behind it, it is considered a theory. (It may be worthwhile to review the difference between a hypothesis and a theory in science). Sometimes students believe that within the scientific community there still exists controversy regarding evolution (and thus think it is unnecessary to grapple with its abstract ideas).

They fail to grasp that there is substantial evidence for evolution (as there must be in order for it to be a theory) 104. Some students will not have enough genetics background to understand changes in allele frequencies necessary for evolution. They may also forget that many hereditary traits still have some environmental component. When shown an example of selection for a trait, students often don’t realize that there will always be some variation and that through selection there is a shift in the mean average value of the population. When selection acts, although it may decrease genetic variation, it most often doesn’t completely eliminate it for the character of interest.

105. Students often view the processes of evolution as occurring independently of each other. However, you can have multiple forces of evolutionary change acting concomitantly. Mutations must constantly introduce variation in order to have evolutionary change.

106. Students don’t realize that what seem like minor changes in habitat can spell major changes in terms of who gets to survive and reproduce. They may believe that organisms choose their range and niche and fail to grasp the importance of chance in these roles.

107. Students often view selection as survival of the fittest, using the common definition of ‘fit’ and thus think that only the strongest survive. In some circumstances it pays to be the most cowardly or sneaky. Also, it is not enough to just survive. You must also reproduce and make a contribution to the next generation in order to be deemed ‘fit’. (Sometimes it is chance who survives, e.g., in a catastrophe, and has nothing to do with fitness.)

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108. Like many people, students can be essentialists viewing the nature around them as unchanging (except in the face of catastrophe). They may see a gopher as a gopher and gophers have always been this way and they’ll never change.

109. Students often have a difficult time with the random nature of mutation confusing this with the nonrandomness of selection. Mutation is a random process, in terms of where a mutation is going to occur within the genome and whether it is beneficial, deleterious or neutral. Natural selection, on the other hand, is anything but random. Students often think that if mutation is random then natural selection is random; or if natural selection is not random, then mutation is not random. Also, students may expect that if a character would be useful to survive in an environment, then an organism would acquire it. The fossil record is full of examples that counter this. (E.g., question posted on Talk Origins suggested that evolution could not be true because if it was, then why didn’t the Inuit, who live in a cold environment, have fur? This question illustrates that often adaptation is viewed as ‘you get what you need’, rather than ‘you get what you get, and if it’s good enough, great; if it’s not, goodbye.’ The environment doesn’t induce specific mutations such that a population can become adapted to the environment.

110. It should be emphasized that for gene flow to occur it is not enough for an individual(s) to migrate to a new population, but that they must also mix their individual alleles with those of their new population through reproduction.

111. Genetic drift and its roots in chance are also difficult for students to grasp. I.e., for catastrophes, they may want to attribute inferiority to an individual that has died because of the catastrophe. (E.g., stepping on ants kills them randomly.)

112. Selection acts on phenotypes, and this is ultimately seen as selection at the genetic level. Phenotypes that are largely due to environment have very little effect on the evolution of a population.

113. Change over a lifetime is not adaptation - it is development or senescence. Adaptation occurs to a population as a whole and is the result of natural selection acting on individuals within the population.

Again, this is a misconception driven by the common use of the word ‘adapt’, rather than its evolutionary meaning.

114. Evolution is not goal directed (although natural selection can be directed). Just as an organism doesn’t gain characteristics because they need them, they don’t lose characters because they don’t use them (rather, their loss may be have a beneficial or neutral effect on their fitness).

115. Not all traits are adaptive and not all change in a population is due to selection. All traits have evolved from previously existing structures and thus, are likely constrained in some way and not perfect. It is impossible to optimize all aspects of a trait (e.g., you cannot have the largest car AND the most fuel efficient car) without some compromise on the part of both characteristics in terms of how they perform in the environment. Also, in a natural setting there is likely more than one selective pressure/factor acting on a population. Natural selection is like an editor and can only work with what it’s presented with (‘mutation proposes, selection disposes’). Sometimes that compromise is not good enough to survive and reproduce in the environment and the population may go extinct.

WHAT CAN I DO IN CLASS? If you are covering material from Ch. 17 before genetics (Chapters 11, 12), you may want to provide a basic genetics background overview or refresher for students, looking at the definition of alleles and genes, and the general characteristics of the meiotic process, with respect to segregation of alleles, and generation and maintenance of variation through crossing over, independent assortment and fertilization. However, this is not necessary; most of this chapter can be addressed without delving into genetic details.

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The “Why it Matters” material can prompt discussion regarding the potential benefits of knowing an organism’s evolutionary history.

A clicker question that addresses the different uses of the word theory (educated guess, which is actually a hypothesis) can be used to deal with Stumbling Block 1. You may want to tell students that over the course of their first year, they’ll have the opportunity to devise many hypotheses, but it’s unlikely that they’ll have an established theory by the end of the year. Discussions can be initiated about what a theory is. You can bring up other theories: theory of gravity; atomic theory, etc. Ask students if they would refuse to believe these theories.

Get students to listen to a CBC report, or read a layman’s media article on evolution. Ask them if/how it furthered their knowledge and understanding of evolution. Post links to Quirks and Quarks (CBC) or make students listen to a segment as an assignment. Many segments deal with the evolutionary history of organisms in an interesting and accessible manner.

There are many great articles at an accessible level for first year students in Scientific American (e.g., Jablonski (2009). The Naked Truth: Why Humans Have No Fur. Scientific American Feb 2010). These might make up assigned readings that are later discussed in class.

Gene flow can be discussed as allele flow. New variants of genes enter or leave the population through migration.

Find examples for the evolutionary processes that are different than those presented in the books (see suggestions here and below). (e.g., rock pocket mice.)

Relate natural selection to the genetic changes in the population. E.g., changes in beak size have been correlated to changes in bmp4 (bone morphogenic protein 4) expression during development. Instructors may want to introduce (simple) figures from the literature to give students an opportunity to interpret the figures in the context of this material.

Chance and drift activity/demonstration: toss coin 20 times; toss coin 500 times; toss coin 5000 times – the ration of heads:tails becomes closer to 50:50 the more coin tosses. This can be used to demonstrate the disproportionate significance of genetic drift in small populations that can cause allele frequencies to randomly change.

Predict/observe/explain activity: Coin Toss experiment – use coin sides to represent alleles. Predictions can be made individually, or in small groups. Students can carry out the experiment in groups and then report frequency changes to the class or can elect a ‘mother’ and a ‘father’ who toss coins to determine which of their alleles they pass on in each mating. First determine the frequency of each allele in generation 1. Then perform coin toss to determine which alleles get passed on from each parent. Then calculate the allele frequencies in generation 2.

Mating 1 2 3 4 5

Mother R1 R2 R2 R3 R1 R1 R1 R2 R2 R3

Generation 1 Father R2 R3 R3 R3 R1 R3 R1 R1 R1 R3

Generation 2 First Child Second Child

Activity: Students are randomly given a piece of paper at the beginning of the class (white and red or blue and red). Bottleneck effect: clicker question – how many people in the classroom with blonde hair, red hair, brown hair, black hair. Next, students with a coloured slip of paper are told that they have been killed in a catastrophe. They can no longer respond to clicker questions. Ask the hair colour question again and see if there is a difference in the population. Discuss what would happen now as these are the only individuals that can contribute to the next generation of this population.

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Clicker questions: 1.

A population of skunks includes some individuals with stripes and others with spots. This would be categorized as what type of variation J. K. L. M.

Quantitative Qualitative Neither quantitative nor qualitative.

Both quantitative and qualitative. *

This question allows students to exercise their knowledge about categorizing variation. It can also bring up the complexity of science. What if there is variation in terms of the number of stripes for those individuals that exhibit stripes? What if a stripe is just made up of many spots? Also, variation may be more subtle than what we are looking for.

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2.

Two types of squirrels, grey and black live in approximately equal frequencies, in a forest. After a very bad windstorm there are more grey squirrels than black squirrels. What is the most likely cause of this change in genotypic frequency?

A. B. C. D.

Disruptive selection Founder effect Genetic drift * Gene flow

This question focuses on the random nature of genetic drift. It also addresses the idea that not all loss of individuals (and their alleles) is due to natural selection. [Stumbling Block 5, 12, and 13].

3.

Over the past century human height has increased and this has been attributed to improved nutrition and health care (and thus, less disease). What can be said about the trait of height in humans?

D. E. F. G.

It is evolving because it is clearly changing over time.

It is evolving because it is a population that is changing over time.

It is not evolving because the change is not genetic in nature (not hereditary). * It is not evolving because each individual is different in terms of their height.

Phenotypic changes in a population that can be attributed to environment are not considered evolutionary change; genetic change is necessary for evolution. [Stumbling Block 5, 12, and 13].

4.

Species A are the predators of Species B. Species A can chase after their prey at a speed of 40-50 km/hr. With respect to the speed of Species B, what do expect selection pressure to result in?

A. B. C. D. E.

A speed of 50-55 km/hr.

A speed of 52-58 km/hr.

A speed of 56-59 km/hr.

A speed of 57-60 km/hr.

A speed of 58-61 km/hr.

Natural selection doesn’t predict what will be helpful in the future, but rather what works now. There should be little difference in survival selection pressure on any individuals of Species B that can outrun their predators, regardless of how much faster than their predators they are (if they’re just fast enough to get away, that’s good enough). [Stumbling Block 7].

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5.

Ear length in rabbits is determined by one gene; longer ears help to detect prey better. If ear length gradually changes over time, what are the changes that have occurred?

A. The trait of each rabbit within the population gradually changes.

B. The proportion of rabbits with specific traits changes within the population.* C. The rabbits with longer ears learn more successful behaviours that are passed from parent to offspring.

D. As predators become more abundant mutations occur that allow ear length (and hence predator detection) to increase.

This reminds students that evolution is a population process that can result because of differences in reproduction (natural selection) in previous generations. Evolution is not due to changes in the individuals over their lifetime. [Stumbling Block 11].

6.

Which of the following birds is the most fit?

1) Harold

2) Martin*

3) Ronald

4) George

Body Length

20 cm

12 cm

10 cm

15 cm

# Offspring surviving to adulthood

19

28

22

26

Age at death

4 yrs

5 yrs

4 yrs

6 yrs

Comments

Very healthy & smart

Mated with many birds.

Very fast & smart

Has the largest territory.

This deals with a common misconception that the largest or strongest, or smartest are the most fit. However, Darwinian fitness solely deals with the reproductive output of an individual. It is the ability of an individual to produce offspring relative to the ability of other individuals within the population to produce offspring.

Adaptations increase the fitness of an individuals with a specific trait, relative to those individuals without that trait. [Stumbling Block 5 and 11].

WHAT OTHER RESOURCES ARE AVAILABLE? 

National Geographic has a considerable amount of material on diversity and selection (e.g., http://ngm.nationalgeographic.com/2008/11/borneo/white-text/4 and http://ngm.nationalgeographic.com/2009/08/mimicry/ziegler-photography)

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

Howard Hughes Medical Institute has a dvd Evolution: Constant Change and Common Threads



There are several lectures pertaining to Darwinism, selection, etc., on iTunesU (e.g., from the University of Cambridge, UK).



If students have had some exposure to genetics, the Nova series ‘What Darwin Never Knew’ may be of interest as it emphasizes evolution through mutations in genetic regulatory regions (‘switches’). There is also a large online library of movie clips relating to evolution (and some online games!).



Shubin, Neil (2008) Your Inner Fish: A Journey into the 3.5 billion year history of the human body.



Talk Origins (http//www.talkorigins.org) is a site devoted to providing expert answers to anti-evolution claims (e.g., creationist or intelligent design statements).



The Understanding Evolution website has a lot of great explanations, good analogies and highlights some of the research being done in evolutionary biology. http://evolution.berkeley.edu/evolibrary/home.php (good cartoon of walking and squishing bugs – chance event that bug gets killed)



Scott, Eugenie C. (2007) What’s wrong with the “Teach the controversy” slogan?

McGill Journal of Education 42(2): 307-315,



Gregory (2009) has a great diagram of Darwin’s Inferences and Observations (as compiled by Mayr) that shows the ecological and the genetic halves of natural selection.



Sexual selection – Birds of Paradise clip from Planet Earth is a great example of the plumage and work that a male engages in to get a mate.



Any of the work done by Rosemary and Peter Grant on the Galapagos finches. E.g., Abzhanov A, Protas M, Grant BR, Grant PR, and Tabin CJ. 2004. Bmp4 and morphological variation of beaks in Darwin’s finches. Science 305(5689): 1462-1465 and Grant BR and Grant PR. 1993. Evolution of Darwin’s finches caused by a rare climatic event. Proc. Biol. Sci. 251(1331): 111-117. As well, see The Beak of the Finch: A Story of Evolution in Our Time by Jonathan Weiner.)

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Defining ‘species’ (what a species is and what makes one species separate from another species) is tricky. There is no one definition that can be applied to all the different types of organisms ( e.g., bacteria, one-celled eukaryotes, colonial eukaryotes, plants, tetrapods, etc.) because of the diversity encompassed within these groups. However, scientists that study these specific groups have developed ‘rules’ that allow them to be fairly consistent within a phylum.

2.

There are multiple species concepts; some can only be used under certain conditions or for certain types of organisms.

3.

There are no set number of changes that occur before an organism becomes a new species. Similarly, there is no predetermined time for speciation to occur.

LEARNING OBJECTIVES Students should be able to:



Define key terms: speciation, macroevolution, hybrids, hybridization. [Knowledge]



Explain why differentiation of two similar looking organisms as different species might be useful. [Comprehension]



Describe the definition of a species according to the Biological Species Concept, the Phylogenetic Species Concept, the Ecological Species Concept, and the Morphological Species Concept. [Knowledge]



Compare and contrast the four species concepts (listed above), addressing their uses and limitations. [Comprehension]



Given a scenario, determine which species concept would be most appropriate to determine if two organisms were the same species. [Application]



Define terms applying to reproduction: hermaphrodite, androdioecious, gynogenetic, hybrid vigour. [Knowledge]

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

Explain why the Biological Species Concept is not useful for classifying asexual organisms, fossil organisms, hybrids, androdioecious/gynogenetic organisms, and those organisms that can reproduce both sexually and asexually (e.g., Daphnia pulex).

[Comprehension]



Describe how Biological Species Concept could explain why individuals of a species typically look alike. [Comprehension]



Identify the one evolutionary mechanism that could not occur if two groups of organisms are identified as separate species according to the Biological Species Concept. [Synthesis/Evaluation]



Define prezygotic and postzygotic isolating mechanisms. [Knowledge]



Define and recognize examples of prezygotic isolating mechanisms: ecological/habitat isolation, temporal isolation, behavioural isolation, mechanical isolation, and gametic isolation. [Knowledge/Application]



Identify which prezygotic isolating mechanisms inhibit mating attempts, and which limit fertilization, but not mating attempts. [Application/Analysis]



Define and recognize examples of postzygotic isolating mechanisms: hybrid inviability, hybrid sterility and hybrid breakdown. [Knowledge/Application]



Explain how hybrid breakdown can be a reproductive isolating mechanism if the F 1 (hybrid offspring of two species) is viable and fertile. [Comprehension, Analysis]



Define the three geographic modes of speciation: allopatric, parapatric and sympatric, as well as hybrid zone. [Knowledge]



Recognize an example of allopatric speciation. [Analysis]



Explain why geographic isolation does not necessarily lead to reproductive isolation.

[Comprehension/Synthesis]



Describe the evolution of a species cluster. [Comprehension]



Explain why islands provide such good examples of allopatric speciation.

[Comprehension]



Explain why natural selection cannot directly promote the evolution of reproductive isolating mechanisms between allopatric populations. [Comprehension]



Explain what secondary contact is and its importance in determining speciation according to the Biological Species concept. [Comprehension] DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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

Describe a ring species and its relation to gene flow and the concept of subspecies.

[Comprehension]



Describe how differences in mating habitat, time of mating, or food source could lead to sympatric speciation. [Comprehension]



Link the mechanisms of evolution with the development of new species when one population gets divided (allopatric speciation). [Synthesis]



Link the mechanisms of evolution with the development of new species when both species occupy the same area (sympatric speciation). [Synthesis]



Identify two factors that can influence gene flow between populations. [Analysis]



Explain how groups of individuals can become genetically isolated within a continuous population. [Comprehension]



Explain the significance of polyploidy or chromosomal alterations in speciation of organisms (e.g., plants). [Comprehension]



Differentiate between autopolyploidy and allopolyploidy and their role in speciation.

[Analysis]



Explain how an organism’s mobility could affect the genetic relatedness of dispersed populations. [Comprehension/Analysis]



Explain how a species could vary over its geographic range. [Comprehension]



Describe hybrid vigour with respect to domesticated organisms. [Comprehension]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

To understand speciation is to understand how evolution produced the diversity of life.



Currently, environmental changes are causing extinction and speciation. However, extinction rates are increasing such that speciation cannot keep up with the current extinction rate. This means there is a net loss of diversity.



There is a need to identify pathogenic species, and develop appropriate treatments (ideally selectively toxic, not harming the host while killing/inhibiting the pathogen).

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WHY SHOULD STUDENTS CARE? 

To understand speciation is to understand how evolution produced the diversity of life.



Currently, environmental changes are causing extinction and speciation. However, extinction rates are increasing such that speciation cannot keep up with the current extinction rate. This means there is a net loss of diversity.



Being able to classify species can be important in terms of medical applications (e.g., identifying certain pathogens).

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 116. Students may not understand that not all of the species concepts are applicable to all organisms, or they may try and apply one concept in all scenarios without examining the limitations of that concept (e.g., the Biological Species Concept cannot be applied to asexually reproducing organisms like bacteria).

117. Students may tend to compartmentalize their knowledge and feel uncomfortable applying their understanding of different evolutionary mechanisms (e.g., gene flow, natural selection, drift and mutation) to speciation.

118. The idea that geographic isolation does not automatically confer genetic (reproductive) isolation can be difficult for many students, especially those that still believe that if a trait is necessary to survive an environment then that organism will develop it. It is often hard for students to understand why some organisms when separated for a few generations, develop reproductive isolation, whereas other organisms (e.g., humans) may have existed in separate isolated populations for many many generations; however, when individuals of different human populations are brought together, there are no reproductive isolating mechanisms.

119. Students may not be familiar with basic geology. You may want to review continental drift, as well as some other geological processes, as these are the cause of many examples of allopatric speciation.

(E.g., Fig. 18.19 refers to geographic separation and speciation of wrasse populations due to uplift of the Isthmus of Panama.)

120. Based on their knowledge of the Biological Species Concept, students may have problems understanding ring species or clinal variation.

121. Students often confuse allopatric, sympatric and parapatric speciation. Mentioning the roots of these words may alleviate this issue.

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122. Students typically get confused with polyploidy, particularly the differences between autopolyploidy and allopolyploidy. They can often get caught up in the mechanics of the situation, losing sight of the fact that polyploidy can rapidly result in speciation. You may wish to limit material from this chapter based on the level and background of your students.

123. There are a variety of outcomes with secondary contact, but students may struggle to consider these as they want to attribute geographic isolation with the inability to no longer interbreed.

124. What presents a geographic barrier to gene flow for one type of organism may not be a barrier to another. E.g., the Grand Canyon is a large physical barrier to squirrels and mice, but not to larger mammals that can go down the trails, across and up the other side, or birds that can fly over it; the Canadian Rockies are another example.

WHAT CAN I DO IN CLASS? The “Why it Matters” introduction highlights the importance of being able to name an organism. This could be used to lead into a discussion about why it would be useful to be able to classify different organisms (link to Chapter 3 – Biodiversity). You could bring up an example where one of two closely related species is a disease vector. For example, only mosquitoes of the genus Anopheles are malarial vectors, whereas those of genus Aedes are vectors for yellow fever. Knowing which genus/species causes/carries a specific disease can lead to development of better, individualized control mechanisms for each vector.

Get half the students to write a minute paper on how changes in climate and environment might drive speciation, while the other half writes about how these same changes can promote increased extinction. Put students into groups of four, with two having written about speciation and two about extinction, to discuss what they think environmental change on the rapid scale with which is currently occurring, is affecting more: speciation or extinction. (You could proceed to a debate on this topic.)

Ask students to consider the unique opportunity that ring species allow in the study of speciation. (It is a situation whereby we can study two different species and their intermediate forms that connect them.)

Ask students to find examples of allopatric, parapatric and sympatric speciation from the literature. Citations of these examples can be collected online (e.g., in a course management system) and then discussed in class. (You may want to take this opportunity to discuss referencing in scientific communication, and introduce students to one or more of the formats used by major Biology journals, if this hasn’t already been done in class or lab.)

Students can be encouraged to draw diagrams illustrating the steps involved in allopatric, sympatric and parapatric speciation. This may help with Stumbling Block 6.

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Ask students to consider how they could manipulate a population to maximize the rate of divergence (i.e., speciation) and what characteristics the experimental organism would possess in order to facilitate this manipulation.

Clicker questions: 4.

During allopatric speciation, which of the following mechanisms of evolution could contribute to the reproductive isolation of the populations?

1. natural selection 2. mutation 3. genetic drift 4. gene flow F. G. H. I. J.

1, 2, 3, and 4.

1, 2 and 3 only.* 1, 3 and 4 only.

2, 3, and 4 only.

2 and 3 only.

This question addresses the concept that populations need to be genetically isolated from one another, which means that gene flow is prohibited in some way. Separation of the populations can lead to a founder effect that can be exacerbated by mutation and natural selection. [Stumbling Block 3] 5.

A population of goats becomes separated by a river and no gene flow between the two populations.

After many generations, the river dries up and the goat populations come back into contact. After this secondary contact, which of the following is/are possible?

F. The two populations do not attempt to interbreed.

G. The two populations attempt to interbreed where the populations overlap, but no offspring result.

H. The two populations attempt to interbreed where the populations overlap, but the hybrid offspring are sterile.

I. The two populations interbreed and produce fertile hybrid offspring.

J. All of the above (A-D) are possible.*

This question addresses Stumbling Block 8 and can lead into a discussion that may help with Stumbling Block 9.

6.

In some species (e.g., Drosophila), individuals can reject sperm of another species. This would best be classified as A. B. C. D.

behavioural isolation. mechanical isolation gametic isolation* habitat isolation.

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This question applies to material in the Learning Objectives relating to pre- and post-zygotic isolating mechanisms.

7.

Polyploidy can allow rapid speciation to occur. It would most likely be involved in what type of speciation?

A. B. C. D.

Allopatric speciation.

Sympatric speciation.* Genetic speciation.

Parapatric speciation.

This question addresses Stumbling Block 7.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Species, Speciation and the Environment. Eldredge, Niles. Highlights the role of environment in development of new species, as well as the continuation of previously existing species. http://www.actionbioscience.org/evolution/eldredge.html



Speciation and Biodiversity. Interview with Edward O. Wilson re: current extinction and speciation rates. http://www.actionbioscience.org/biodiversity/wilson.html



Eldredge, N. 1998. Life in the balance: our failure to recognize our connection with the global ecosystem lies behind the biodiversity crisis facing our planet today.

Natural History. June. (Can be found online at: http://findarticles.com/p/articles/mi_m1134/is_n5_v107/ai_20776794/? tag=content;col1)



http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/Speciation.html Online Biology Textbook by John Kimball.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Being able to differentiate species can often be extremely important (e.g., poisonous [false morels] vs. edible mushrooms [true morels]).

2.

Just because two organisms look alike does not mean that they are the same species or group of organisms. Often similarity in appearance is due to convergent evolution.

LEARNING OBJECTIVES DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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Students should be able to:



Define key terms: systematics, taxonomy, phylogeny, taxonomy, classification, taxonomic hierarchy, family, orders, classes, phyla, kingdoms, domains, convergent evolution. [Knowledge]



Describe, briefly, the Linnaean system of classification. [Comprehension]



List, from most inclusive to least inclusive, the terms: phyla, classes, order, kingdoms, family, genus, species, domains. [Knowledge]



Relate the above terms, and their degree of inclusion to the relative number of organisms found in each. [Application]



List one major goal of systematics. [Knowledge]



Describe what is represented by a phylogenetic tree. [Comprehension]



Define terms used in systematic character evaluation: genetically dependent/independent, homology (homologous), analogy (analogous), homoplasy (homoplasious). [Knowledge]



Compare and contrast homology, analogy, and homoplasy, with respect to the information they provide regarding shared ancestry. [Analysis]



Explain how homologies are useful in preparing phylogenies. [Comprehension]

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

Differentiate between homologous and analogous characters and their use in systematics. [Analysis]



Describe what information can be derived from the comparison of homologous characters. [Comprehension]



Given the relationship between several groups of organisms identify structures (e.g., forelimbs and wings of tetrapods) as homologous or homoplasious (analogous).

[Analysis]



Explain why systematists would look at characters that are genetically independent.

[Comprehension]



Relate homologous traits to developmental and genetic homologies. [Comprehension, Analysis]



Define mosaic evolution, ancestral characters and derived characters. [Knowledge]



Differentiate between ancestral characters and derived characters, and their use in determining evolutionary relationships. [Analysis]



Explain how mosaic evolution, ancestral characters and derived characters are related. [Comprehension]



Describe how outgroup analysis (or comparison) is used to identify ancestral or derived characters. [Comprehension]



Given the pervasiveness of a character within animals or plants, use outgroup analysis to determine whether the character is ancestral or derived. [Analysis]



Define terms relating to phylogenetic classification: principle of monophyly, monophyletic taxa, polyphyletic taxa, paraphyletic taxa, principle/assumption of parsimony, clade. [Knowledge]



Explain how systematists apply the assumption of parsimony to derivation of phylogenetic trees. [Comprehension]



Describe how a traditional evolutionary systematist determines evolutionary relationships. [Comprehension]



Explain, using the terms paraphyletic, monophyletic etc., how traditional evolutionary systematics results in the misclassification of birds and reptiles.

[Comprehension, Analysis] o OR Compare and contrast classification of birds and reptiles by a traditional evolutionary systematist and a cladist. [Analysis] DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

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

Explain how cladistics and traditional evolutionary systematics are used to classify organisms. [Comprehension, Analysis]



Describe how the principle of parsimony is used in the construction of cladograms.

[Comprehension]



Differentiate between convergent evolution and parallel evolution. [Analysis]



Describe how the principle (or assumption) of parsimony is used to construct phylogenetic hypotheses. [Comprehension, Analysis]



Differentiate traditional evolutionary systematics and cladistics in their use of species classification. [Analysis]



Given a table of derived characterstics, construct a simple cladogram. [Analysis]



Compare molecular phylogenetics with traditional systematics. [Analysis]



Explain how the concept of a molecular clock indicates the time of divergence for traits. [Comprehension]



List advantages and disadvantages to using molecular data as clues to evolutionary relationships. [Knowledge]



List the types of DNA used for dating evolutionary divergence and differences in when they are used. [Knowledge]



Describe two ways that researchers can synchronize molecular clocks. [Comprehension]



Describe why differences in non-coding regions of the genome more likely reflect the ‘actual ticking of the molecular clock’ than do coding sequences. [Comprehension]



Explain why molecular sequences must be aligned before they can be compared.

[Comprehension]



Describe the features (characters) systematists use when constructing phylogenetic trees. [Comprehension]



Identify the molecule Carl Woese used to classify organism into three domains.

[Knowledge]



Describe the characteristics of the molecule Woese used that made it a good molecular clock. [Comprehension]

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WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Communication requires clear and precise understanding of what organism is being discussed.



Identifying closely related plants may help to uncover sources of medically useful chemicals. E.g., If one species contains a medically active chemical, related species may also contain that same component.



Identification of species can be used to determine species at risk and help to protect them from extinction.



Medicine and plant pathology benefit from the identification of parasites/pathogens.



Agricultural productivity may benefit from plant systematics. E.g., If wild relatives of cultivated plants are located, these can be bred with current cultivars to provide resistance genes, etc. Also discovery of new plant species/crops can add variety to restricted diets of most of the world’s populations.

WHY SHOULD STUDENTS CARE? 

Communication requires clear and precise understanding of what organism is being discussed.



Being able to differentiate species can often be extremely important (e.g., poisonous [false morels] vs. edible mushrooms [true morels]).



A precise definition of the organismal group of interest aids in the discovery of medicinal compounds in closely related plants.



As well better identification can be used to determine species at risk and protect them from extinction.



Students will encounter phylogenetic trees/cladograms in future chapters/courses, as they are used to illustrate evolutionary relationships.



Phylogenetics (and diagrammatic representations of phylogeny) is used to follow the evolutionary history of organisms providing us with information as to the relatedness of different groups of organisms.

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WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 125. Students may think that they phylogenetic trees are permanent and inflexible. It is best to refer to phylogenetic trees as hypothetical evolutionary relationships, as they can change depending on new evidence. Phylogenetic trees represent a visual hypothesis of the evolutionary relationships in a phylogeny.

126. Related to Stumbling Block 1 students may think that a phylogenetic tree is static and not realize that rotation about a node (where one lineage diverges into two) can occur (i.e., the order of the branching does not matter).

127. Cladistics is often confusing for students, particularly as they may see cladograms as separate from phylogenetic trees. However, cladograms are just a more specific type of phylogenetic tree that are based on shared derived characteristics.

128. Students can have a difficult time distinguishing between homologous characters and homoplasious characters (perhaps because of similarities between the terms).

129. The principle of parsimony can be confusing. After all, if a trait can evolve in more than one lineage, why is it not as likely that it will evolve twice in the same lineage? For example, the text talks about the classification of birds in one lineage. This suggests that a shared feature among them – feathers – was found in their common ancestor. This is more parsimonious compared to a hypothesis that places feathered organisms in more than one lineage, which would suggest that feathers arose independently in two or more lineages.

130. The discrepancy between classification of birds and different reptiles by traditional systematists and cladists may not be apparent to students. You may want to get them to research the differences and similarities of the two.

WHAT CAN I DO IN CLASS? The “Why it Matters” introduction highlights that similar morphology on its own is not enough to classify the evolutionary relationship between organism. This could be used to lead into a discussion about convergent evolution and how one would distinguish between examples of convergent evolution and homology.

Examples of bird wings, butterfly wings, and bat wings could be used to examine these different terms. You could bring up an example where one of two closely related species is a disease vector. For example, mosquitos of the genus Anopheles are malarial vectors, whereas those of genus Aedes are vectors for yellow fever. Knowing which genus/species causes/carries a specific disease can lead to development of better, individualized control mechanisms for each vector. This is true also with bacterial pathogens.

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Ask students why systematics and classification is important. Get them to brainstorm practical applications of such knowledge.

Students could be divided into small groups and asked to figure out how to construct a cladogram using a table showing shared derived characters (e.g., Question for Discussion #3, p438). This may help with Stumbling Block 2 and 3 Ask students why phylogenetic hypotheses based on DNA sequences may be more accurate than those based on amino acid sequences. If students have already seen the material from Chapter 14, have them consider different types of point mutations (e.g., missense, nonsense silent) and their effects on protein sequence.

Given a phylogenetic tree, ask students to manipulate that tree by rotating about a node (e.g., see below). This may help with Stumbling Block 6.

You could show students examples of skulls. They could work in groups to examine all of these skulls and determine a list of shared characteristics and derived characteristics. (Students will likely need some direction, including information about dentition and other features to observe, to work on this problem.)

Ask students to look through Chapter 23 at the protists. In groups they could identify what sort of taxa they would consider protists to be. (E.g., is it a monophyletic, polyphletic and/or paraphyletic taxon?)

Clicker questions: 8.

When systematists use morphological or behavioural traits to reconstruct the evolutionary history of a group of animals, they assume that K. L. M. N. O.

phenotypic characters reflect underlying genetic similarities and differences.* the animals use exactly the same traits to identify appropriate mates. these traits were responsible for speciation events in the past. the adaptive value of these traits can be explained. variations are produced by environmental effects during development.

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This question helps students to see what assumptions are made when creating phylogenetic trees.

9.

Which of the following pairs of structures are homoplasious?

K. L. M. N. O.

The wing skeleton of a bird and the wing skeleton of a bat.

The wing of a bird and the wing of a fly.* The eye of a fish and the eye of a human.

The bones in the foot of a duck and the bones in the foot of a chicken.

The wing structures of apterosaur and those of a bird.

This question gets students to analyse different characters and determine whether they are homoplasious. You may want to use a variation of this question by asking students which of the above pairs of structures are homologous. Stumbling Block 4 10. A monophyletic taxon includes E. F. G. H. I.

an ancestor and all of its descendants.* an ancestor and some of its descendants. organisms from different evolutionary lineages. an ancestor and those descendants that still resemble it. organisms that resemble each other because they live in similar environments.

This question addresses Stumbling Block 7.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Evolution 101: Understanding Phylogenies. http://evolution.berkeley.edu/evosite/evo101/IIBPhylogenies.shtml



Evolution 101: Using the Tree for Classification. http://evolution.berkeley.edu/evosite/evo101/IIDClassification.shtml



The molecular clock and estimating species divergence. Nature Education 1(1). http://www.nature.com/scitable/topicpage/The-Molecular-Clock-and-EstimatingSpecies-Divergence-41971



Evolution 101: Molecular Clocks. http://evolution.berkeley.edu/evosite/evo101/IIE1cMolecularclocks.shtml

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… DARWIN, FOSSILS, AND DEVELOPMENTAL BIOLOGY

149

1.

Darwin was not the first to propose ideas about evolution. Much of Darwin’s theory of evolution by natural selection was greatly influenced by others.

2.

Darwin amassed much observational evidence, particularly during his voyage on the Beagle, that species change over time and that species come from other species. We have, and are still, accumulating a great deal of evidence that evolution occurred and is still occurring.

3.

Through changes in the genes that regulate development, dramatic changes in morphology, etc., can be observed. That is, extensive changes at the level of the DNA would not be necessary to yield the diversity of species that we see.

4.

Although the fossil record is incomplete, we have many fossil assemblages, including transitional forms that show us that species have changed over time.

LEARNING OBJECTIVES Students should be able to:



Define key terms (relating to influences on Darwin’s theory of evolution): biogeography, comparative morphology, vestigial traits, Scala Naturae, catastrophism, biological evolution, uniformitarianism, gradualism. [Knowledge]



Define key terms (relating to explanations of Darwin’s theory of evolution): artificial selection, natural selection, descent with modification. [Knowledge]



Explain why Lamarck’s hypotheses (principles) of use and disuse and inheritance of acquired characteristics leading to evolutionary change are not supported..

[Comprehension]

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150



Describe the influence of the disciplines of biogeography, comparative morphology and geology on Darwin’s development of natural selection as a mechanism of evolutionary change. [Comprehension, Analysis]



List Lamarck’s four major contributions to evolutionary thought. [Comprehension]



Identify, of Lamarck’s four major contributions to evolutionary thought, the three that were integral to Darwin’s hypothesis of how evolution occurred. [Knowledge]



Explain what is meant by ‘organisms change in response to their environments’.

[Comprehension]



Explain the influence of uniformitarianism and gradualism had on Darwin’s development of his theory of evolution by natural selection. [Comprehension]



Explain what is meant by the phrase ‘like begets like’. [Comprehension]



Describe Darwin’s observations regarding the appearance of organisms on islands compared to those on the closest mainland. [Comprehension]



Describe Darwin’s explanation of the above observation. [Comprehension]



Explain why Darwin’s evolution by natural selection is a scientific theory.

[Comprehension]



Explain the impact of Thomas Mathus’s Essay on the Principles of Population on Darwin’s development of evolution by natural selection. [Comprehension]



Differentiate between natural selection and artificial selection. [Analysis]



Summarize Darwin’s five observations and two inferences, assigning each observation to the category ecology or genetics. [Comprehension]



Explain how Darwin’s explanations of diversity and adaptive traits differ from those of his predecessors. [Comprehension]



Describe how the process of natural selection is non-random. [Comprehension]

151



Describe how variation, overreproduction, the struggle for existence, and differential reproduction each play a role in Darwin’s theory of evolution by natural selection.

[Comprehension]



Explain why the fossil record is incomplete. [Comprehension]



List two ways in which there is bias in the fossil record. [Knowledge]



Explain the difference between absolute and relative dates with respect to fossils.

[Comprehension]



Describe, in general terms, the principles behind radiometric dating. [Comprehension]



Explain how fossils found in sedimentary rock are dated. [Comprehension]



Define the follow terms (earth history and biogeography): plate tectonics, continental drift, continuous distribution, disjunct distribution, dispersal, vicariance, biotas, biogeographical regions, endemic species. [Knowledge]



Sketch a diagram illustrating the model of plate tectonics. [Comprehension]



Describe the conditions that create disjunct distribution and continuous distribution.

[Comprehension]



Describe the process(es) that lead to the formation of distinct regional biotas and/or biogeographical regions. [Comprehension]



Explain, using plate tectonics, the distribution of a given fossil organism.

[Comprehension]



Differentiate between convergent evolution and parallel evolution. [Comprehension]



Define the following terms (interpretation of evolutionary lineages): adaptive radiation, anagenesis, cladogenesis, gradualist hypothesis, punctuated equilibrium hypothesis. [Knowledge]



Using an example, explain how previous hypotheses about evolutionary lineages must be reinterpreted with the advent of new fossil information. [Comprehension]

152



Using a diagram/graph, illustrate the differences between anagenesis and cladogenesis, and between gradualism and punctuated equilibrium. [Comprehension]



Define the following terms (macroevolutionary trends): preadaptation, allometric growth, heterochrony, neoteny, pedomorphosis metamorphosis. [Comprehension]



Explain how allometry can create morphological differences in closely related species. [Comprehension]



Explain how heterochrony can lead to morphological differences in closely related species. [Comprehension]



Define evolutionary developmental biology (‘evo-devo’). [Knowledge]



Explain how the study of development macroevolutionary trends. [Comprehension]



Define homeotic genes and relate them to a genetic tool-kit. [Knowledge]



Explain how Hox family genes and the Pax-6 gene are examples of tool-kit genes.

[Comprehension]



Explain, using an example (e.g., Pitx1, Hox genes, Bmp2), how changes in developmental regulatory genes can be a genetic switch between different morphologies. [Comprehension]



Relate developmental [Comprehension, Analysis]

switches

to

helps

allometric

our

growth

understanding

and

of

heterochrony.

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Evolution is a fundamental concept (arguably the fundamental concept) of biology.



Darwin’s contributions to evolutionary thought are immeasurable. He fleshed out a mechanism by which evolutionary change could occur, providing a notable scientific breakthrough in our understanding of the world around us.



Darwin accumulated a great deal of evidence for the idea that species change over time and are related by a common ancestry. Since then, more evidence has amassed, making evolution by natural selection one of the best-supported theories in science.

153



Evolution by natural selection provides a well-supported explanation for how the diversity of organisms are adapted to a wide variety of environments on the planet.



Genetic switches, that is changes in developmental regulatory genes, allow for dramatic morphological changes with very few changes in DNA sequence.

WHY SHOULD STUDENTS CARE? 

Information presented in this chapter can help students to understand and appreciate the wealth of evidence (e.g., artificial selection, fossil record, biogeography, genetic homologies) supporting the idea that all species are related and change over time.



New fossil discoveries are constantly being reported. Basic knowledge of the fossilization process increases the appreciation for recent fossil discoveries, especially those in transitional assemblages.



Anti-evolutionists often promote the idea that a great number of genetic changes have to occur in order for diversity to arise and argue that statistically these would be impossible. However, a small number of changes in regulatory genes that affect the timing and expression level of developmental genes can dramatically affect morphology.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 131. Darwin was not the first to propose ideas about how evolution could occur. Much of Darwin’s theory of evolution by natural selection was heavily influenced by other naturalists or geologists.

Students may have a tendency to ‘want’ to memorize details of Darwin’s predecessors. We recommend that instructors help students focus on larger concepts, and avoid becoming mired in minute historical details.

132. Darwin amassed a great deal of evidence showing that species do change through time and that species are related. He made a huge number of observations and then came to this conclusion when he analyzed his collections and observations. As a scientist, he incorporated ideas and observations from other disciplines to inform his own work.

133. Students may not realize that a fossil is not necessarily only a skeleton of an organism. In fact, it is any trace of an organism that lived in the past and includes: bones (skeleton), teeth, scales, shells, tracks, imprints, petrified wood, and dung.

134. Although the fossil record is incomplete, we have many fossil assemblages, including many transitional forms for fundamental morphological innovations. Students may not understand how fossilization occurs and that it requires very specific conditions. Fossils then need to be found and this is itself poses a huge problem. Most fossils are found in sedimentary rock (igneous and metamorphic are exposed to heat and pressure and few fossils survive). Then only a small proportion of the rocks that contain fossils are exposed and in easily accessible locations.

135. Darwin didn’t have the tools to explain all of natural selection that we have today. For example, he had no definitive concept as to how variation arose in a population and how it was passed on. (The Great Modern Synthesis helped to fill in these gaps.)

154

136. Many anti-evolutionists argue that a great deal of coordinated random mutations would have to had occur in order for the diversity of life as we see it to have evolved. However, small changes in regulatory genes can have major impacts on morphology. This may help students to better understand how we can be 97% similar to chimpanzees and yet be quite different.

137. When we talk of rapid mass extinctions occurring in the past, we are referring to events that are rapid on a geologic time scale. Geologic or deep time is often very difficult for many people to conceptualize and they will resort to a simplistic perspective that interprets descriptions of time relative to their own scales of a lifetime. This is why rates of extinction today are so alarming, because they are dramatically increased. They are occurring within one human lifetime and offer no time period over which any large multicellular organism could adapt.

138. Students may have difficulty conceptualizing the environment changing so dramatically as it has over the past several hundred million years. Showing an animation (see ‘Other Resources’) of plate tectonics/continental drift can help students better visualize movement of the continental plates and shifts in latitude and relative positions for these continental masses. With movement to different latitudes comes a shift in climate. Similarly, changes in the relative position of a region of a continental plate (e.g., formerly a coastline, now in continental interior, where no moderating influence of a large body of water) can drastically alter the climate of that region.

139. Some students also have difficulty with continental plates shifting about as they cannot ‘feel’ this movement (neither do they feel the Earth’s rotation). Relating the speed of the movement to something tangible – e.g., continents are said to move at approximately the same speed that fingernails grow – may help some students with this abstraction.

140. Adaptive radiation is a rapid diversification of species due to new opportunities (e.g., new environments, new niches). In each of the new environments/niches there are different selective pressures; these select for different phenotypes and thus, diversification.

141. The appendix is often cited as a vestigial organ and many people may believe it serves no function.

However, although its function is reduced it does have a role in immunity. This is not as great a role relative to its function in closely related organisms (e.g., non-human primates).

142. Students may have minimal knowledge of geography, which is necessary for discussions of fossil locations, biogeography, etc.

WHAT CAN I DO IN CLASS? The “Unanswered Question” offers an exercise that can be done in small groups. Propose a situation where students are studying a mouse population of individuals that are either brown or black. The environment has brown soil. Which mice would be more easily seen by hawks? Ask students to design an experiment that would allow them to determine whether black or brown mice are better adapted. What if the type of predator changed (e.g., snakes rather than a bird)? What if the soil composition changed (e.g., with an increase in darker organic material)?

Students have been told that Lamarck was wrong and that inheritance of acquired characteristics doesn’t explain adaptation or evolution. Get students to think about why it is wrong: ask them how they would explain structural, developmental and molecular homologies if they were a result of inheritance of acquired characteristics.

Ask students to determine the relationship between the different levels of homologies (structural, developmental, and molecular). Can one type of homology be present without the others? [Stumbling Block 5]

155

The aardvark, giant anteater, and the pangolin are distantly related mammals, found in different parts of the world, but all are adapted to consume ants and termites. With their similar diets, what morphological similarities would they have? Would these be due to parallel evolution, convergent evolution or homology?

In a discussion, get students to explain differences in the fossil distribution of two different organisms using plate tectonic theory.

Ask students to split into small groups to work on explaining why it is that characters that we see in living organisms today are, in fact, adaptations to the environments in which their ancestors lived, rather than the environment in which they live today.

The end of this chapter discusses that with changes in just few genes that regulate development, large morphological changes can arise. If you have permission (public performance rights), you could have a class viewing of ‘What Darwin Never Knew’? This program clearly links changes in a few ‘genetic switches’ to morphological changes responsible for the diversity of life.

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Clicker questions:

The forelimbs of a sheep, the wings of a duck, and the flippers of a dolphin are examples of ZZ. AAA. BBB. CCC. DDD.

vestigial structures. homologous structures. * acquired characteristics. artificial selection. uniformitarianism.

Iguanodon fossils are found in the U.S., some parts of Canada, Europe, and the Gobi Desert, whereas Triceratops fossils are found only in North America. The most likely explanation for this distribution is EEE. All the Triceratops in Europe died off much earlier than Iguanodons.

FFF. The Iguanodon taxa outcompeted Triceratops when North America and Eurasia were still connected.

GGG. The Iguanodon taxa existed when North American and Eurasia were still connected; Triceratops arose only after North America separated from Europe.* HHH. Iguanodons were likely aquatic and terrestrial and swam the distance between North America and Europe.

You may want to show a map as some students may not know geography that well.

Continental drift helps us to understand the distribution of fossils and living organisms. Taxa that arose before a supercontinent broke apart are predicted to be widely distributed (across the continents). Conversely, taxa that arose after the split of a supercontinent are expected to have a much more restricted distribution. [Stumbling Blocks 8, 9, 12] Fossils are more likely to be found of organisms that III. were very abundant.

JJJ. were widely distributed.

KKK. had hard body parts.

LLL. existed for a very long time.

MMM. All of the above.

NNN. None of the above.

This deals with the bias inherent to the fossil record. That is, not all organisms have an equal possibility of becoming fossilized. Thus, information can often be skewed in favour of those organisms with the above characteristics. [Stumbling Block 2, 4]

157

The aardvark, giant anteater, and the pangolin are distantly related mammals, found in different parts of the world, but all are adapted to consume ants and termites.

Would their morphological similarities most likely be due to OOO. parallel evolution PPP. convergent evolution QQQ. homology RRR. Vestigial structuring WHAT OTHER RESOURCES ARE AVAILABLE? 

Charles Darwin & Evolution (Christ’s College, Cambridge). Information about Darwin’s personal and scientific life. Provides Darwin’s ideas regarding evolution of barnacles, pigeons, worms, and humans, as well as his work on botany and geology. http://www.christs.cam.ac.uk/darwin200/pages/



Examples of transitional fossils, mimicry, etc. http://www.christs.cam.ac.uk/darwin200/pages/index.php?page_id=g



The complete work of Charles Darwin online. http://darwin-online.org.uk/



What Darwin Never Knew. Documentary available from Nova that discusses genetic switches and their role in evolution. http://www.pbs.org/wgbh/nova/beta/evolution/darwin-never-knew.html.

Also interactive website at Nova: http://www.pbs.org/wgbh/nova/beta/evolution/gene-switches.html



What is Evo Devo? http://www.pbs.org/wgbh/nova/beta/evolution/darwin-never-knew.html



Neoteny in humans relative to the chimpanzee. Mitteroecker et al. (2004) Comparison of cranial ontogenetic trajectories among great apes and humans. J Hum Evol 46(6): 679-97. See also: Penin et al. (2002). Ontogenetic study of the skull in modern humans and the common chimpanzees: neotenic hypothesis reconsidered with a tridimensional Procrustes analysis. Am J Phys Anthropol 118(1):50-62.



Kathleen K. Smith. 2003. Time’s arrow: heterochrony and the evolution of development. Int J Dev Biol 47: 613-621.



Plate tectonics animations: http://www.ucmp.berkeley.edu/geology/tectonics.html



United States Geological Survey: This Dynamic Earth. http://pubs.usgs.gov/gip/dynamic/dynamic.html 158



Clip from National Geographic – The Early Earth and Plate Tectonics. http://www.youtube.com/watch?v=QDqskltCixA

BIODIVERSITY: SECTION I CHAPTER 21 PROKARYOTES CHAPTER 22 VIRUSES, VIROIDS, AND PRIONS CHAPTER 23 PROTISTS CHAPTER 24 FUNGI COVERAGE CONSIDERATIONS Instructors may wish to cover Chapters 21-27 in the order presented in the textbook, which is the traditional way that diversity is shown in survey courses. Alternatively, Chapter 22 may be introduced at the beginning of this chunk, reflecting the fact that viruses, viroids and prions are not actually cellular life forms, and do not exhibit the same type of evolutionary relationships shown in other chapters.

This section includes many different organisms, with associated details/terminology, so students may feel very overwhelmed. Students may be tempted to simply try to memorize everything without considering the unifying and differentiating features of the different types of organisms. Instructors can choose learning objectives to restrict coverage to what is necessary for the curriculum, and accordingly make expectations explicit to students to reduce anxiety, and forestall the tendency for students to engage in surface learning in an attempt to “cram” when studying this material.

In the textbook, plants (Ch. 25) and animals (Ch. 26, 27) are introduced as part of the Diversity unit.

Depending on the curriculum of your course, you may wish to augment the plant and animals chapters with additional material from Sections II and/or III (particularly if you do not plan to cover those chapters in great depth).

The material covered in these chapters may require explicit reminders regarding evolutionary relationships (e.g., what phylogenetic trees show, the difference between monophyletic and paraphyletic, that domains are considered monophyletic).

159

overview of Section 1 IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Life exhibits diversity, with great variation in size, morphology, physiology, metabolism and reproduction. (This variety is also reflected in differences in genetic sequences.)

2.

Biologists have attempted to classify organisms based on evolutionary relationships. We can make some hypotheses about relationships by comparing the similarities and differences between organisms.

3.

While there is diversity across different phyla, all life is based on cells, and many features are shared based on evolutionary history (i.e., are homologous). (All organisms descended from a common ancestor.)

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? Note: These Stumbling Blocks will be referred to in multiple chapters of this section.

I.

Students commonly believe that humans are the “top” of the evolutionary tree, with the implication that humans are somehow better than other organisms. Our species is a relatively new addition (branch) to the evolutionary tree, and arguments can be made that many other organisms (including the so-called “lower” organisms) are more exquisitely adapted for evolutionary success than we are. It may be worthwhile to remind students that evolution is not directed, and that more recently evolved organisms are not any better than ones that appeared earlier.

II.

Many people are under the impression that most/all microbes (bacteria, fungi) are bad or dangerous. While pathogens and pests tend to be given a lot of attention, in fact, most microorganisms (prokaryotic and eukaryotic) do not harm us, and we rely on the activities of many of them to live.

III.

Certain terms, such as “prokaryote”, “protist”, and “microbe”, can lead to some misconceptions. These terms are commonly used in biology, but are not evolutionarily meaningful (i.e., prokaryote refers to any organism in the domains Bacteria and Archaea; protists are a “grab-bag” of various eukaryotes including slime molds, algae, and animallike protozoa; microbes include various small organisms, both prokaryotic or eukaryotic).

We recommend using these terms sparingly, and being explicit about the phylogenetic limitations of these terms.

160

IV.

Nearly all descriptions of organisms in the three domains (i.e., Bacteria, Archaea, Eukarya) are generalizations; exceptions may exist for most characteristics/features! (E.g., the chromosomal material of bacteria is normally described as being a single, doublestranded, circular chromosome, but certain bacteria such as Streptomyces and Borrelia spp. may have numerous linear chromosomes; most plants carry out photosynthesis, but there are parasitic, achlorophyllous plants, as shown in Chapter 3, 3.5 Biotic factors.)

V.

While all introductory Biology textbooks devote considerable attention to the biology of plants and animals, there are many, many other types of organisms. (And although we devote much of our time discussing plants and animals, they are not “better” than other organisms.)

VI.

Fungi are not plants, nor are they prokaryotes. Students will likely need to be reminded that these organisms are eukaryotic, and evolutionary distinct from other eukaryotes (such as plants, animals, and protists).

VII. Students often think of plants as the only organisms that can photosynthesize. However, there are some photosynthetic bacteria, archaea, and protists.

161

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Prokaryotes include Bacteria and Archaea; while superficially similar, the domains are evolutionarily distinct.

2.

Bacteria are not merely pathogens; most bacteria do not harm humans, and, in order to survive, we rely on many of the activities carried out by bacteria.

LEARNING OBJECTIVES Students should be able to:



Describe the similarities and differences between the Bacteria and Archaea. [Comprehension]



Explain what is meant when we say that bacteria and archaea are ubiquitous on Earth.

[Comprehension]



Using examples, describe features of bacteria and/or archaea that allow them to survive in harsh environments that don’t have those elements we view as typical to life. [Comprehension]



Describe, using examples, roles of bacteria and archaea in geological/biogeochemical cycles.

[Comprehension]



Describe use of bacteria and archaea in industrial purposes (e.g., bioremediation, food production, waste water treatment). [Comprehension]



Describe a biofilm. Provide an example of a biofilm that is beneficial to humans & one that is harmful. [Comprehension]



Describe examples of bacteria living with/in/on other organisms in various symbiotic relationships. [Comprehension]



Draw a Venn diagram showing similar and different features across the 3 domains.

[Comprehension]



Describe the difference between an obligate anaerobe and a facultative anaerobe.

[Comprehension]

162

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

The term prokaryote can reinforce the misconception that bacteria and archaea are the same. It can be difficult to get past the morphological similarity to consider the differences between these tiny organisms. (Bats and birds both have wings, but we would not mistake them as the same organism.)

An explicit description of what “prokaryote” means (including the limitations of the word, in any kind of evolutionary sense) may help. Some microbiologists avoid using the term prokaryote when teaching, restricting themselves to speaking of bacteria and/or archaea specifically. [For more re: the term “prokaryote”, see Pace 2006.] Similarly, we recommend avoiding the term “Archaebacteria”, as this can give students the impression that archaea are just another form of bacteria.

2.

Bacteria and archaea are often regarded as “lower” organisms. However, these simple organisms are very efficient, are found all over the planet in a diversity of niches, and evolutionarily can be regarded as extremely successful.

3.

When students think of bacteria, they are likely to think of disease-causing strains. These tend to be mentioned most often, and are the best-studied bacteria. However, the vast majority of bacteria do not harm us (and some can be beneficial, directly or indirectly). To date, pathogenic archaea have not been discovered, although some archaeal species have been observed in the human mouth and gut.

4.

Bacteria and/or archaea can survive in environments that humans consider “extreme”. It can be difficult for students to comprehend that life can survive at extremes of temperature, pH, etc.

5.

Students may also think that harmful bacteria are closely related. However, pathogenic bacteria are not classified within a single group. Even within one species, you may have pathogenic strains and those that are not.

6.

Many microorganisms, including bacteria, live in biofilms, but this is not commonly known. In the lab we study organisms individually, grown in artificial conditions (i.e., in pure cultures on agar media, or in broth cultures), but in real life they form communities with other bacteria, other microorganisms. (E.g., dental plaque.)

7.

Some bacteria exhibit resistance to antimicrobial compounds. Students often are under the impression that resistance is developed “as needed”, not realizing that use of antibiotics selects against those bacteria who do not already have resistance to the drug.

WHAT CAN I DO IN CLASS? Ask students to brainstorm: Why study bacteria? Why study archaea?

It is recommended that instructors focus on major features found in all bacteria and all archaea, clearly highlighting some of the variations within these domains. [Stumbling Block IV] One of the learning objectives can be done in class: have students work together to draw a Venn diagram showing the similar features between all three domains (e.g., cell structure and composition: hereditary material (histones, introns, structure, and types of RNA pol), cell walls (when present) membranes, activities associated with membranes (structure of lipids in plasma membrane), , type of flagella (org’s within each group with flagella, but flagella are different); chromosomal structure (i.e., circular vs linear); meiosis & sexual reproduction. Some of this material, such as translation and transcription, can be linked to material from other chapters.

163

It can be tempting to introduce many microbiological topics when going through this chapter, but if this is just a small portion of an introductory course, there is considerable vocabulary for first year students to deal with, as well, as some difficult concepts.

E.g., Covering gram negative and gram positive bacteria is likely not very meaningful unless there are related lab activities to demonstrate this (e.g., students actually gram stain E. coli and Bacillus subtilis cells, compare appearance under oil-immersion lens light microscopy), or medical identification exercises that deal with how Gram staining would be used as an early differentiation step in a series of tests that gradually narrow down the organism based on physical and biochemical characteristics. As well, if an instructor wishes to explore the nature of the bacterial cell wall (which can be compared to the cell walls of plants, fungi, etc.), then differences between the cell walls of gram negative and positive bacteria can be introduced at a basic level. However, we would strongly recommend focussing on the functional similarities of cell walls across the different domains/kingdoms rather than spending too much time concentrating on small details of differences between cell walls of different types of bacteria.

The study of microorganisms, such as bacteria and archaea, in the lab has both advantages (e.g., short generation time, small space required) and challenges (e.g., difficult to see morphology, avoid contamination) compared to studying other organisms. If there are no associated microbiological lab exercises, instructors may want to briefly discuss some of the specialized equipment and techniques used to study bacteria in the laboratory. Ask students to brainstorm what potential advantages and disadvantages there are to using bacteria and archaea as model organisms (compared to other model organisms).

Debate the use of term “prokaryote”. Should this term be used in Biology classes/texts? This could be done as individual or small-group assignments, or as larger team-led debates in class. [Stumbling Block III, 1] Ask students to consider the conditions of life on Earth when the earliest organisms appeared. (This links to Chapter 2.) Which organisms that exist today could possibly have survived those conditions? How? Could a human being survive such conditions? [Stumbling Block I, 2, 3] Link photosynthesis, as discussed in this Chapter, to what is discussed in Chapters 7 and 2. Have students discuss the differences between the way photosynthesis is carried out by photosynthetic proteobacteria (e.g., green and purple sulfur bacteria), and by cyanobacteria. How does photosynthesis in these organisms differ from photosynthesis in plants? Why might this be? Asking such questions can lead into a discussion of endosymbiosis that builds upon what may have been explored in Chapter 2. (Stumbling Block VII) Some discussion of pathogens will likely be of interest to students, and clicker questions (see below) can be used to expose some misconceptions. (E. coli is a good example of a bacterial species that includes commensal, beneficial and parasitic strains - refer to Purple Pages pF-35). Case studies can be used to explore various types of bacterial diseases (Anderson 2006 includes several, which can be modified for the level/background of your students.) (Stumbling Block 3, 5) Iterate how definition of a species has limitations when it comes to classifying bacteria/archaea (see below).

Bacterial and archaeal species are considerably broader than those of most eukaryotes (i.e., individuals within a given bacterial species can have genetic variation unheard of in a plant or animal species). Instructors can link material from Chapters 3 and 18 to discuss the problems in defining a species and the associated issues when trying to classify specific organisms. Ask: Why is important to be able to classify bacteria into species? What impact does bacterial taxonomy/classification have on medicine? Biotechnology?

Small groups/teams can be assigned the task of discovering beneficial activities and applications of certain species/groups of bacteria and archaea, and presenting their findings to the larger group (orally, or via course webpages). [Stumbling Block 3, 9] If discussing the biofilm lifestyle of many bacteria and archaea, students may be interested in learning about cystic fibrosis patient lung infections caused by bacteria, such as Pseudomonas aeruginosa. Medically, the biofilm mode of growth is an important issue as it likely has an impact on the efficacy of antibiotic treatments against such infections. See Chapter 8, People Behind Biology. [Stumbling Block 6]

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ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 3 (see Chapter 17 below):



Selection. Use of antibiotics does not cause individual bacteria to become resistant; antibiotics provide selective force that can result in population change (resistant bacteria survive).

Chapter 3 (see Chapter 46 below):



Trophic levels. Ask: What’s the difference between a chemoheterotroph and a photoautotroph?

Chapter 8:



Quorum sensing – reinforces the common nature of signal transduction across the domains.



Chapter 8 “People Behind Biology” highlights Doug Storey’s research, which also relates to the biofilm lifestyle of bacteria in CF infections. Similar signalling systems may exist also in Archaea – for more information, see Paggi et al. (2003).

Chapter 9:



Cell division occurs in bacteria and archaea. How does binary fission differ from mitotic cell division in eukaryotes? (What are some possible reasons for these differences?)

Chapter 10:



Concerns about the ability to spread antibiotic resistance elements through horizontal gene transfer is one part of the larger issue of antibiotic resistance in bacteria.

Chapters 13, 14:



Transcriptional and translational machinery and processes are described in these chapters, including differences between bacteria and eukaryotes.

Chapter 17:



Within the section on natural selection, tie in antibiotic resistance in bacteria and how this develops. Although most people only think about the pathogenic bacteria developing resistance, it should be noted that other types of bacteria also develop resistance. This evolutionary adaptation could prove problematic as organisms we don’t currently regard as significant pathogens could develop virulence in future.

Chapter 46:



Trophic levels. Some bacteria can photosynthesize and thus form part of the large primary producer trophic level. This can be related to material in Chapter 3 regarding classification of organisms according to their modes of nutrition.



Biofilm lifestyle aspects can also be linked to this chapter.

Chapter 47:



Bacteria and archaea play central roles in biogeochemical cycles, including those required to make available nutrients required for the survival of life on Earth.

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Chapter 48:



Students often focus on conservation of larger organisms and may not fully realize the impact of loss of species of bacteria and archaea, as well as other microorganisms. These organisms have important roles in the sustaining life.

Clicker questions:

Which of the following is/are true of bacteria?

A. Most species are pathogenic (cause diseases).

B. As extremely simple organisms, they are considered to be less successful, evolutionarily, than Homo sapiens.

C. They are the same as archaea, biochemically and physiologically, but appeared slightly later in Earth’s history.

D. None of the above is true of bacteria. * E. Only 2 of the above (in A through C) are true of bacteria.

This question addresses issues in Stumbling Blocks I, II, V, 1, 2, and 4.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Pace, N.R. 2006. Time for a change. Nature 441 289.



Paggi RA, Martone CB, Fuqua C, De Castro RE. 2003. Detection of quorum sensing signals in the haloalkaliphilic archaeon Natronococcus occultus. FEMS Microbiol Lett. 221(1): 49-52.



Anderson, R. P. 2006. Outbreak: Cases in Real-World Microbiology. ASM Press. 336 pages.

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Viruses are obligate parasites, and require a host cell to display characteristics of life.

LEARNING OBJECTIVES Students should be able to:



Explain why viruses cannot be considered living organisms. [Comprehension]



List characteristics common to all viruses. [Knowledge]



Compare and contrast the following types of viruses: helical virus, polyhedral virus, enveloped virus, complex polyhedral virus. [Comprehension, Analysis]



Describe the impacts of viruses on humans, other animals, and plants. [Comprehension]



Describe the importance of bacteriophages on bacteria. [Comprehension]



Describe, using an example, a situation in which viruses could be considered beneficial to humans. [Comprehension]



List the basic steps of viral infection and replication in any host organism/cell. [Knowledge]



Highlight the importance of mutations and recombination in the success of viruses.

[Comprehension]



Describe how viroids and prions differ from each other and from other viruses.

[Comprehension]

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WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS?

1.

Although we do explain that viruses/viroids/prions are “biological entities”, rather than true life forms, it is common for viruses to be described in the same ways we use to discuss actual cellular organisms. This, along with the fact that we include chapters on these entities just as we do for living organisms - animals, plants, etc., can be confusing to students.

2.

Viruses are often viewed in a purely negative way, usually are associated with diseases. However, they do some things viewed as useful by humans, and potential exists for further exploitation of viruses in biotechnology.

WHAT CAN I DO IN CLASS? There are similarities in terms of how viruses infect host cells, regardless of the type of host cell (animal, plant, bacterial). It is recommended that you review the viral infection cycle (using the animation of bacteriophage replication) early on. Discuss similarities first, and only then should some of the variations seen with different viruses/hosts be explored.

Debate: Should viruses, viroids and prions be discussed in biology classes/textbooks in the same way we look at plants, animals, bacteria, fungi, etc.?

Highlight and discuss potential beneficial uses of bacteria: phage therapy (alternative to antibiotics), control of insect pests (e.g., spruce bud worm); molecular biology (e.g., cloning, reverse transcriptase, etc.).

Case studies describing specific viral infections could be of interest in this section. For example, the appearance, impact, and identification of the SARS virus could be discussed. Similarly, there could be a discussion of scrapie and other prion diseases in livestock; concerns regarding human prion diseases could be raised when discussing prions.

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 10:



Viral nucleic acids can often undergo recombination.



Processes in viral replication involve some viral-encoded proteins, but require host cell machinery (described in this chapter as used by the host).



Retrotransposons use reverse transcriptase to move about the eukaryotic genome. Because of their similarity to viruses it is thought that retrotransposons might be the remains of viral infections.

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Chapter 46:  Interspecific interactions: viruses are examples of obligate parasites. (They do not have all the required material to replicate themselves.)

Clicker question:

A virus can best be described as: F. A biological entity that lacks a true nucleus but contains DNA, proteins, ribosomes and ATP. G. A biological entity containing nucleic acid that cannot reproduce outside a host cell. * H. A self-replicating molecule of DNA or RNA. I. A misfolded protein that can cause disease.

J. A single-celled parasitic organism.

This question addresses Stumbling Block 1.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Negrete A and Kotin RM. 2008. Strategies for manufacturing recombinant adeno-associated virus vectors for gene therapy applications exploiting baculovirus technology. Briefings in Functional Genomics 7(4): 303-311.



Bauzon M and Hermiston TW. 2008. Exploiting diversity: genetic approaches to creating highly potent and efficacious oncolytic viruses. Curr Opin Mol Ther 10(4): 350-355.



Crew MD and Phanavanh B. 2003.

Exploiting virus stealth technology for xenotransplantation: reduced human T cell responses to porcine cells expressing herpes simplex virus ICP47. Xenotransplantation. 10(1): 50-59.



Bell JC, Garson KA, Lichty BD, and Stojdl FD. Oncolytic viruses: programmable tumour hunters. Current Gene Therapy 2(2): 243-254.

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… The term “protist” refers to a wide range of eukaryotes that demonstrate considerable diversity (in morphology, lifestyle, ecology), but the protists are not a monophyletic group.

LEARNING OBJECTIVES Students should be able to:



Describe, using examples, how some protists can impact human health, welfare & economy.

[Comprehension]



Discuss the ecological importance of organisms considered to be protists, providing examples. [Comprehension]



Explain what is meant when it is said that the protists are not a monophyletic group.

[Comprehension, Analysis]



Describe the steps involved in secondary and tertiary endosymbiosis. [Comprehension]



Describe how Euglena exhibits both plant and animal characteristics, but is considered to be neither a plant nor an animal. [Comprehension, Analysis]



Explain how some algae (and other protists) exhibit characteristics that likely show the transition from a unicellular organism to a truly multi-cellular organism. [Comprehension]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

From an evolutionary standpoint, “protist” is another messy term, and the grouping of these organisms is artificial. These are eukaryotes that are considered to be neither animals, plants, nor fungi, yet demonstrate features of at least one of these groups!

2.

Most people think of these organisms as microbes, because many of them are microscopic. However, there is considerable diversity in morphology and size demonstrated by the organisms discussed in this chapter, with some algae (e.g., kelp) being quite large.

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3.

Students may not think that these organisms impact their lives. However, many of these organisms have important ecological roles (e.g., primary producers, carbon sinks, etc.) that affect the environment. Some protists can negatively impact human health (e.g., malaria), or that of other plants/animals.

4.

Endosymbiosis events can be confusing for students to understand, particularly when looking at secondary and tertiary events.

5.

Although we usually discuss photosynthesis in plants, most photosynthetic activity on Earth is carried out by the phytoplankton (i.e., photosynthetic protists).

WHAT CAN I DO IN CLASS? Ask: What defines a “protist”? Ask students to consider the various types of organisms discussed in this chapter to attempt to identify the characteristic features of protists. This can lead into a discussion about the difficulty of considering these organisms as a single group, and the “grab-bag” nature of protists. Students may not be aware that this term is an artifact from a time when we didn’t have the techniques that we do today to examine organisms. [Stumbling Block III, 1] We recommend a strong focus on the ecological & environmental aspects of the organisms in this chapter.

(Instructors can work through all the different protist groups, or choose to introduce students to larger themes that link protists among themselves and with other groups). The ecological importance of this group includes not only the phyto- and zooplankton as the major component of the bottom trophic levels, but also the negative consequences of algal blooms and red tides (dinoflagellates). Some protists are essential in global carbon cycling (e.g., algae involved in photosynthesis and calcification). [Stumbling Block V, 3] Ask: What is a carbon sink? How do some protists contribute to the phenomenon of carbon sinks? Which protists are involved? What is the link between carbon sinks and global climate change?

Evolutionary biologists think that plants, animals and fungi are all derived from ancient protist-like organism.

Discuss in small groups or as a class: What characteristics would you predict this ancestor would have?

Examine the evolution of multicellularity (e.g., advantages of multicellular life, such as aspects relating to surface area-to-volume ratios, providing examples of simple multicellular protists – e.g., green algae) and compare multicelluar life to colonial and unicellular life, using Volvox, a colonial organism with a few specialized cells, as a potential link between unicellular and multicelluar lifestyles.

In small groups, or as a class activity, get students to classify the organisms in this chapter into those demonstrating similarity to: [1] animals (e.g., paramecium – moves, eats prey); [2] plants (e.g., algae); [3] fungi (e.g., slime molds). This can be done on flip chart sheets, online or by writing on an overhead projector/doc cam.

Follow-up discussion activity: Why aren’t these organisms considered to be actual animals/plants/fungi?

Some protists can be toxic/parasitic to humans. Case studies can be used to highlight some examples: e.g., malaria, red tides, trichomonas, and“beaver fever” (Giardiosis). [Stumbling Block 3] Many of the organisms have economic importance. Ask students to find examples of economically important protists. Some examples are:

  

Food (e.g., kelp, nori) Omega-3 fatty acids – we eat fish to get these, but they don’t actually synthesize these themselves; they obtain these oils from certain algae.

Carageenan – creamy texture used in ice cream, pudding, weight loss products, toothpaste, meat, lotion, and paints.

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  

Alginic acid – used in latex treatment, as charcoal briquette binding agent, and also to give creamy texture in some foods.

Diatomaceous earth – diatom remains (silica “shells”) stop slugs etc., in gardening; also used in filters (e.g., pools), and insulating material.

Agar, agarose – useful in the laboratory (e.g., growth media, agarose gels for electrophoresis).

[Stumbling Block 3] Endosymbiosis is brought up in Chapter 2, and expanded upon within this chapter (see Fig. 23.31). Differences seen among the various protist groups provide interesting observations in terms of events in endosymbiosis, if an instructor wishes to explore this process. Discussion about the origin of plastid membranes (using diagrams) in the chloroplasts resulting from primary, secondary or tertiary endosymbiosis is recommended. The Glaucophyta are interesting in this context – the chloroplast actually contains polymer peptidoglycan, normally present in bacterial cell walls (and not in other plastids). Biologists suspect that the glaucophyte chloroplast resembles the ancestral chloroplast that resulted in the chloroplasts present in plants. (See: http://hypnea.botany.uwc.ac.za/phylogeny/classif/glau1.htm) [Stumbling Block 4] Conversely, some protists have lost a plastid! This appears to have occurred in the trypanosomes (which include animal parasites, causing sleeping sickness, leishmaniases, and Chagas' disease). The genomes of these protists include a number of plastid- and plant-derived genes.

Many aquatic protists demonstrate considerable diversity in various physical characteristics, and in terms of biological processes. A link to Chapter 9 can be made, showing some variation from what we see in plant and animal mitosis. E.g., Euglena (and other protists) has a nuclear envelope that remains intact during mitosis. Ask students how mitosis can occur if the nuclear envelope is present during the process. [Stumbling Block IV] Activity – Divide the class up into small groups. Remind them that protists use three kinds of motility: flagella, cilia and amoeboid movement. In groups, have students identify cells in the human body that use one of these three forms (i.e., provide an example of cells that use each form).

Challenge students to a one minute paper – Why is it harder to treat human diseases caused by protists, such as Giardia, than diseases caused by bacteria? (Hint: selective toxicity – we are more similar to other eukaryotes than we are to bacteria, so drugs that affect protists are more likely to be toxic to our own cells.) This could also be modified as a in-class clicker question.

Discuss the use of several protists as model organisms (could introduce some recent research): Tetrahymena, Chlamydomonas reinhardtii, and Dictyostelium discoideum [slime molds – they live part of life individually (amoebalike); then under certain conditions individuals come together in a mass that acts in a coordinated effort].

Throughout this material, some examples of interesting organisms that could be highlighted are: Plasmodium – causes malaria; Chlamydomonas nivalis – cause of “watermelon snow”! Although the snow (and organism!) is red, this is an example of a green alga; this species has carotenoids to protect against UV exposure – link to Chapter 1); Dinoflagellates – exhibit bioluminescence (link to Chapter 1), and can be involved in coral bleaching (link to Chapter 47) and symbiosis (e.g., zooxanthellae) (link to Chapter 46). Oomycete phytopathogens – e.g., Phytophthora infestans, agent of the potato blight involved in Irish Famine. (This organism is commonly cited as a fungus, but the oomycetes are examples of fungi-like protists!)

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 1:



Many different pigments found in different protists.

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

Bioluminescence exhibited by some protists.

Chapter 7:



Photosynthesis – biochemical reactions, and mechanisms for algae to concentrate CO 2.

Chapter 46:



Symbiotic interactions. Zooxanthellae (protists) are required for healthy function of coral reefs. One reason for coral bleaching (this lack of colour is due to symbiont expulsion) is stress due to changes in water temperature.

Chapter 47/48:



Roles of certain protists in global cycles (e.g., food web, as primary producers; carbon cycling).

Clicker questions:

1. Which of the following is NOT considered to be a “protist”?

A. slime mold B. amoeba C. kelp D. a member of the phytoplankton E. moss * F. All of the above are considered to be protists.

Many students might not know what many of these organisms look like, so it might be interesting to show pictures of these organisms along with the question.

2. The most ancestral “chloroplast” likely exhibited:

K. a single bounding membrane.

L. at least 3 bounding membranes. * M. a mitochondrion that developed photosynthetic capability.

N. no DNA. [Stumbling Block 4]

3. The latest stage for evolving the double membrane seen in modern-day algal chloroplasts is thought to be the combining of O. Two ancestral nonphotosynthetic prokaryotes.

P. Two ancestral photosynthetic prokaryotes.

Q. A nonphotosynthetic eukaryote with a photosynthetic eukaryote.

R. A photosynthetic prokaryote with a nonphotosynthetic eukaryote. * S. Mitochondria with an already established plastid.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Bhattacharya et al. 2003. Photosynthetic eukaryotes unite: endosymbiosis connects the dots.

BioEssays 26.1: 50-60.

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 

Keeling, 2004. Diversity and evolutionary history of plastids and their hosts. Am. J. Bot. 91: 1481-1493.

Martin, W., and Borst, P. 2003. Secondary loss of chloroplasts in trypanosomes. PNAS 100: 765-767.

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Fungi play some key ecological roles, particularly in decomposition but also in mutualistic relationships with plant roots and photosynthesizing lichen partners.

LEARNING OBJECTIVES Students should be able to:



Define key terms: hyphae, mycelium, septum, spores, karyogamy, plasmogamy, endophyte, photobiont, and mycobiont. [Knowledge]



List three key characteristics that distinguish fungi from other eukaryotes (nature of cell wall, type of nutrition). [Knowledge]



Describe absorptive nutrition. [Comprehension]



Discuss fungi’s ecological importance as decomposers. [Comprehension]



Discuss how fungi are medically (pests/pathogens) and economically (producers of commercial compounds) important. [Comprehension]



Describe two symbiotic relationships of fungi, one of which is harmful, the other which is not. [Comprehension]



Describe differences in production of spores by asexual and sexual methods. [Comprehension]



Discuss the impact of parasitic fungi (chytrid Batrachochytrium dendrobatis) on conservation efforts in frogs. [Comprehension]



Compare the lifestyle of a saprotrophic fungus to one in a mutualistic symbiosis.

[Comprehension, Analysis]

175



Describe the structure of lichen, indicating the roles of the different partners. [Comprehension]



Discuss the importance of lichen in ecosystems. [Comprehension]



Discuss the roles of each partner in mycorrhizae. [Comprehension]



Describe the effect of mycorrhizal fungi on plant growth. [Comprehension]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

The life cycles of fungi are quite diverse and students may get lost in the details. Instructors may want to focus on the similarities among the cycles: typically both sexual and asexual reproduction occur in a given fungus.

2.

Details associated with differentiating the various groups are quite numerous. If you choose to cover the different fungal groups, you may want to focus on the reproductive structures that differ between them (and keep these descriptions very basic).

3.

When students think of fungi, they typically think of mushrooms, in particular the fruiting body.

Many mistake this reproductive structure as the complete body of the fungus and fail to realize that the majority of the fungus is underground, growing as filamentous mycelia.

4.

As with other microbes, often people think only of the potential negative impact associated with certain members of fungi. Yet, we rely heavily on the action of fungi as decomposers, and there are many beneficial uses/impacts of fungi.

5.

Students often think, mistakenly, that yeast (better known as Saccharomyces cerevisiae) is a type of bacteria (prokaryote). This valuable model organism is a fungus, and thus a eukaryote.

WHAT CAN I DO IN CLASS? Ask: How do fungi differ from bacteria, plants and animals?

Discuss the ecological roles of fungi. For example, ‘What would happen if we suddenly lost all fungi?’

Compare life cycles of different fungi, asking students (individually or in small groups) to identify the common elements that exist across the different phyla.

Discuss the economic relevance of fungi. For example, tempeh is a food produced from soybeans inoculated with a bread mold. Mycelium holds soybeans together, produces enzymes that increase the content of some B vitamins, and makes soybean protein easier to digest. Rhizopus species (R. arrhizus, R. nigricans) are used in the production of oral contraceptives, anaesthetics, while others (Rhizopus spp) are used in the production of industrial alcohol and meat tenderizer. Trichoderma spp are used in biological control of other fungi because they’re attracted to hyphae of other fungi, which they use as food. Commercial mixtures of multiple strains of dormant spores of beneficial mycorrhizal fungi are available. Innoculation of crops/gardens with these mycorrhizae can produce greater quantities of crops/plants.

Mushrooms are often what people first think of when the term “fungus” is used. Canada has a thriving mushroom industry! (See Mushrooms Canada FAQ – link provided in Resources - for more details.)

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Some fungi produce compounds that could be valuable medically. E.g., Polysaccharides from mushrooms have been shown to have antitumor, immunomodulating properties. Some products have been developed using these compounds (e.g., krestin, lentinan, schizophyllan). See Wasser (2002).

Relate material within this chapter to that of chapters dealing with evolution. Endomycorrhizae have been found in fossils of early plants and may have played a critical role in the transition of plants from water to land.

At this time, soils may have been poorly developed (low nutrient levels, etc.), and plant roots themselves not very complex. Mycorrhizal fungi would have provided additional surface area beyond that of the roots, allowing plants to more effectively absorb water from the environment. As obtaining adequate water is one of the biggest challenges of transitioning from an aquatic environment to a terrestrial one, mycorrhizal colonization would have provided a major advantage to early plants. Coevolution of mycorrhizal fungi and plants has shaped what we see in plants today (see Brundrett 2002).

Debate: As noted in the text, conifers and some other types of plants cannot grow properly if their roots do not form associations with fungi. These obligate associations provide the plant with minerals such as nitrogen and phosphate; in return fungi receive carbohydrates synthesized by the plant. In some instances, however, the plant receives proportionately more nutrients than the fungus does. Ask students if they would still classify such associations as mutualistic. What evidence would they look for to determine whether the association between a plant and an endophyte was mutualistic?

One minute paper: How could you determine if a symbiotic relationship between a fungus and another organism was mutualistic, commensal, or parasitic?

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ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 6:



Fermentation is carried out by yeast species and is important in production of alcohol and bread production.

Chapter 46



In addition to mycorrhizae, lichens are another example of mutualistic symbioses of fungi with a photosynthesizing organism (either cyanobacterium or alga). Lichens play important roles as facilitators in their communities and are among the first to colonize a new area.

Through their erosive activities they are involved in soil formation.

Clicker questions:

1. Which of the following best describes lichen? It is T. A fungus that breaks down rock to provide nutrient for an alga.

U. the last organism(s) to colonize bare rocks & convert them to soil.

V. an organism that spends part of the life cycle as a photosymbiont and part as a mycobiont.

W. an association between a basidiomycete and an ascomycete.

X. an association between a green alga and a fungus.

This question addresses Stumbling Block 4, as well as material from Chapter 46 (see Additional Links to Other Chapters). With modifications, this question could also be used to ask about mycorrhizae.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Brundrett, M.C. 2002. Coevolution of roots and mycorrhizas of land plants. New Phytologist 154: 275 - 304.



Mushrooms Canada FAQ: http://mushrooms.ca/fresh/production.aspx



Wasser, S.P. 2002. Medicinal mushrooms as a source of antitumor and immunomodulating polysaccharides. Appl. Microbiol. Biotechnol. 60: 258-274.

SECTION II: PLANTS CHAPTER 25 PLANTS CHAPTER 28 THE PLANT BODY CHAPTER 29 TRANSPORT IN PLANTS 178

CHAPTER 30 REPRODUCTION AND DEVELOPMENT IN FLOWERING PLANTS CHAPTER 31 CONTROL OF PLANT GROWTH AND DEVELOPMENT COVERAGE CONSIDERATIONS In the textbook, plants (Ch. 25) are introduced as part of the Diversity unit, with later chapters (28-31) devoted to specific aspects of plant anatomy, physiology, etc. The range of coverage of plant biology can vary widely between different introductory Biology courses. If the curriculum warrants, each of the chapters in this section may be covered to a greater or lesser extent. In some cases, we envision instructors including key aspects from each chapter, but not requiring students learn all material from every chapter. It is even possible that an instructor may want to consider aspects of plant biology alongside those of animals (Section III), allowing students to compare and contrast adaptations between the kingdoms.

Again, we highly recommend that instructors carefully consider which learning objectives they feel are necessary (rather than simply including all of them) to meet their own course’s curricular outcomes.

OV E RV I E W O F S E C T I O N I IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Although sessile, plants display a great deal of diversity and exhibit adaptations that allow them to be successful in a wide variety of environments.

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WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? Note: These Stumbling Blocks will be referred to in multiple chapters of this section.

VIII. Many students consider plants to be “boring”. This alone can prove to be a stumbling block in terms of engagement/motivation to learn. Depending on the students (e.g., pre-med vs. agricultural vs. biotechnology vs. non-science majors), student interest may be captured by highlighting recent applied research findings, the economic importance of plants, environmental relationships, and aspects of plant biology that directly and indirectly affect human health and well-being.

IX. Students often do not realize that plants share features with animals (and other organisms). While we often do focus more on the differences between kingdoms, the unity of life also is demonstrated by the many features shared by animals and plants.

X. Sometimes students think that all algae and fungi are also considered plants. (Note: Certain algae, the coleochaetes, are very close relatives of plants; some biologists do consider green algae to be in the same kingdom as plants. This is not the case for other algal lineages, though.)

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

There are similarities between plants and animals in terms of their survival on land (i.e., adaptations involved in the transition from water to land).

2.

Adaptations in plants colonizing land are reflected in the sequential changes between the different plant groups (bryophytes, seedless vascular plants, gymnosperms, angiosperms).

LEARNING OBJECTIVES Students should be able to:  Describe features that would help determine if an organism is a plant. [Comprehension] 

Define: gametophyte sporophyte, vascular tissue, mutualism, haploid phase/diploid phase. [Knowledge]



Describe the environmental challenges plants face on land. [Comprehension]



Describe why mutualistic associations with fungi were likely required for the evolution of land plants.

[Comprehension]



Compare and contrast green algae to land plants. [Comprehension]



Describe adaptations that enabled terrestrial plant life. [Comprehension]



Describe adaptations that specifically limit water loss. [Comprehension]



Describe, in general terms, the life cycle of land plants. [Comprehension]



Draw a diagram of a generalized life cycle of a land plant. [Comprehension]



Compare and contrast the dominance of haploid/diploid phases in bryophytes, seedless vascular plants, seed-producing plants. [Comprehension]

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

Describe the phylogenetic relationships among the major groups of land plants, highlighting the development of major adaptations. [Comprehension]



Describe adaptations found in all vascular plants (both seedless and seed-producing) differentiating them from non-vascular plants. [Comprehension]



List the characteristics of the seedless vascular plants. [Knowledge]



Describe why seedless vascular plants require a moist environment. [Comprehension]



Discuss the ecological importance of the seedless vascular plants. [Comprehension]



Discuss the economic importance of the seedless vascular plants. [Comprehension]



Describe a seed, contrasting it to the embryo structures of mosses and seedless vascular plants.

[Comprehension, Analysis]



Describe the evolution and importance of seeds. [Comprehension]



List four features unique to angiosperms. [Knowledge]



Discuss the characteristics that allowed angiosperms to become so successful. [Comprehension]



Describe the methods of pollination used by angiosperms. [Comprehension]



Describe some of the specialized flowers formed by some angiosperms. [Comprehension]



Describe the coevolution of angiosperms and their pollinators. [Comprehension]



Describe the various methods of seed dispersal of angiosperms. [Comprehension]



Describe the coevolution of angiosperms and animals with respect to seed dispersal. [Comprehension]



Compare and contrast the features of plants to those of algae, and of fungi. [Comprehension, Analysis]

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WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

While people know that plants do not move, students may not make the connection between the “anchored” lifestyle of plants and the various adaptations that have appeared over the evolutionary history of plants (resulting in the features we see in different groups).

2.

Students may not be aware that there are many types of plants, not all of which fit the “typical” idea of a plant (e.g., having roots, leaves, pollen, flowers, seeds). They may not know about the differences between mosses, ferns and other seedless vascular plants and the seed plants (gymnosperms, angiosperms).

3.

Alternation of generations is something that often confuses students. It may be useful to show real examples of sporophytes and gametophytes to help students make what seems like an abstract concept more concrete (in terms of structures, function).

4.

It can be easy to think of organisms evolving in isolation. However, the close relationship between certain plants and animals (e.g., pollinators, seed dispersal agents) means that plant evolution has helped shape that of animals, and vice versa.

WHAT CAN I DO IN CLASS? The Why it Matters section describes the achlorophyllous plant, Monotropa uniflora (ghost flower/Indian pipe).

This could be used to lead into a discussion of what defines a plant – that is, what features help to determine if an organism is a plant if not all of them contain chlorophyll and are capable of photosynthesis. This can also help students understand how plants are distinct from fungi and algae. [Stumbling Block III, 2] Assign students (in small groups) to identify economic and/or ecologically important species of mosses, seedless vascular plants, gymnosperms, and angiosperms. (More students could be assigned to the seed plants.)

Are most crops, etc., seed plants? Is evol’n of social human groups tied to angiosperms? (or at least seed plants?)

Brainstorm the challenges, for a non-motile organism, of living on land,. Once a list has been generated, have students (in pairs or teams, in larger classes) identify which adaptations are present in plants (and which types of plants, if not present in all groups). This allows students to consider the differentiating features of the different groups of plants, which is likely to allow deeper learning than if you simply tell them.

If possible, have students observe in the laboratory (or bring in to class for demonstration) living mosses, ferns, and seed plants to identify differences in leaves, roots, and reproductive structures (if visible), and relate these to the evolutionary trends that occurred in plants.

Ask students: What are some benefits for plants that have the ability to colonize land?

Show representative life cycle diagrams of different plant types, and the generalized one shown in Figure 25.1.

Ask students to compare the different life cycles, and identify the adaptations that may have led to changes between the different life cycles. (Also direct students to Figure 25.8, which nicely shows the evolutionary trends of sporophyte vs. gametophyte dominance.)

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If you wish to discuss homospory/heterospory, you may want to walk students through Fig. 25.9b in class and assist students with labelling various structures and identifying the differences in the spores, as it may not be clear to an unfamiliar eye.

If the laboratory component provides time to explore aspects of plant biology, C-fern (model plant) experiments can be a good way for students to actually work with and see the different parts of the plant life cycle (various experiments are available – see Additional Resources). Alternatively, demonstration C-ferns could be raised to show in class/lab. We’ve found that students enjoy seeing the release of sperm from the male gametophyte when water added. Not all plant cells are non-motile, at least in bryophytes and seedless vascular plants! It also highlights the necessity of a moist environment for sexual reproduction of some plants.)

Also in the lab, or as a demonstration, students can observe the structures in a large seed (e.g., bean). This can be helpful in discussing the features of seeds that are beneficial to gymnosperms/angiosperms.

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 1:  Photosynthesis is introduced, as well as light-activated phytochrome.

Chapter 7:  Photosynthesis is a major feature of nearly all plants.

Chapter 10:  A review of meiosis, and haploid/diploid stages of life cycles may be helpful when discussing differences between plant groups.

Chapter 28:  More information on plant structures/tissues.

Chapter 29:  Water availability (transport in plants with vascular systems) is important for life on land.

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Chapter 30:  Trends in reproduction have led to adaptations seen in the flowering plants.

Chapter 31:  Plants have developed ways of controlling growth, responding to the environment. Such adaptations have likely helped in success colonizing various terrestrial niches.

Clicker questions: 1.

Major evolutionary trends in plants include all of the following, EXCEPT:

A. a shift from production of one type of spore to two types of spores.

B. a shift from dominant sporophyte to dominant gametophyte generation. * C. the development of seeds.

D. the development of distinct root, shoot and vascular systems.

E. All of the above are evolutionary trends in plants.

A, C, and D are all evolutionary trends. However, we also see a shift from a dominant gametophyte generation to a dominant sporophyte generation. [Stumbling Block 3.] It might be helpful for students to review the terms gametophyte and sporophyte (with diagrams) after asking this question.

2.

Which plant(s) require water as a medium for sexual reproduction?

A. Flowering plants (e.g., sunflower, grass) B. Conifers (e.g., pine, spruce) C. Ferns* D. All of the above require water as a medium for sexual reproduction.

E. Two of the above (in A through C) require water as a medium for sexual reproduction.

Similar questions could be constructed, but including mosses as another type of plant requiring water for transport of sperm to the egg. [Stumbling Block 2.]

3.

The plant structures most similar (i.e., analogous) to the amniotic sac in animals, in terms of dealing with challenges of life on land would be:

A. Roots B. Leaves C. Spores D. Seeds * E. Pollen Seeds, like amniotic sacs in animals, help protect the embryo in an environment that can lead to desiccation.

[Stumbling Block II.]

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4.

Which of the following developments contributed to the ability of plants to grow large/tall?

A. Lignin synthesis. * B. Fertilization without water requirement.

C. Reduction of the gametophyte stage.

D. The shift to heterospory from homospory.

Lignin is a very strong, durable polymer. It reinforces xylem cells, and provides structural support to plants.

(See the “Molecule Behind Biology” in this chapter for more on lignin).

5.

All of the following types of flowers would be expected to be pollinated by animals EXCEPT: A. B. C. D. E.

nectar-containing brightly coloured fragrant patterns visible in UV spectrum leading to centre of flower.

All of the above are characteristics we’d expect of flowers pollinated by animals. *

WHAT OTHER RESOURCES ARE AVAILABLE? 

Vanishing Tall Grass – CBC Quirks & Quarks – Jan 23 rd. http://www.cbc.ca/quirks/archives/0910/qq-2010-01-23.html#3



C-fern: http://www.c-fern.org/ Information, teaching ideas, and image gallery.



David Attenborough BBC Private Life of Plants videos – Stunning footage of various aspects of plant biology. We highly recommend all episodes, but if time is limited, instructors may wish to focus on the pollinator-plant relationships, if you have permission to show in class.



D. J. Beerling. 2007. The Emerald Planet: how plants changed Earth's history. Oxford University Press, New York. 288 pages. While this book is written at a level that can be understood by nonbiologists, instructors may find ideas and interesting stories/research findings to bring to the classroom.

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Plants have different structures and systems, consisting of different types of tissues, specialized to carry out particular functions. These are analogous to many systems within animal (i.e., their own) bodies.

LEARNING OBJECTIVES Students should be able to:  Define: organ, tissue, root system, shoot system, primary cell wall, cellulose, plasmodesmata, middle lamella, secondary cell wall, lignin, totipotency, apical meristem, primary tissues, primary plant body, primary growth, secondary growth, lateral meristems, secondary tissues, cotyledons, monocot, eudicot, ground tissue system, vascular tissue system, dermal tissue system. [Knowledge] 

Describe the general features of plant cells. [Comprehension]



Compare and contrast the functions of root and shoot systems of angiosperms. [Comprehension]



Describe the general function of the plant vascular system. [Comprehension]



Compare and contrast the plant vascular system and those of animals. [Comprehension, Analysis]



List the three different tissue systems in plants. [Knowledge]



Compare and contrast the three types of ground tissue systems: parenchyma, collenchyma, and sclerenchyma. [Comprehension]



Provided a figure of a plant section, label the cell types and the types of tissues those cells represent.

[Comprehension, Application]



Explain why sclerenchyma cells die after lignification occurs. [Comprehension]

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

Compare and contrast the two types of sclerenchyma cells: sclereid and fibres. [Comprehension]



Describe the defining features, cellular components, and functions of the ground tissue system.

[Comprehension]



Compare and contrast the two vascular tissues: xylem and phloem in terms of structure and function.

[Comprehension]



Define, with respect to structure and function (components of vascular tissue): tracheids, vessel members/elements, vessels, protoplasts, sieve tube members, sieve tube, companion cells. [Knowledge]



Compare and contrast the two dermal tissues: epidermis and periderm. [Comprehension, Analysis]



Define, with respect to structure and function (components of the dermal tissue): epidermis, cuticle, guard cells, stoma, trichomes (including root hairs). [Knowledge]



Compare and contrast the functions of the three plant tissue systems. [Comprehension]



Describe the three different types of steles. [Comprehension]



Describe specific physical adaptations that limit water loss. [Comprehension]



Relate the functions to the structure and tissue systems of roots. [Comprehension]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

Students can find the many different cell types, tissues, systems and plant organs to be daunting. If there is not a significant focus on botany in the course, instructors are encouraged to determine which terms students must know and make expectations explicit to students.

2.

There are different tissue systems in plants (ground, vascular, dermal) and there are also different systems (root, shoot). Students can find the multiple use of the term ‘systems’ confusing, and mix them up.

3.

Growth in plants is different in many ways from what occurs in animals, which is what students will be most familiar with. Explicit discussion of derminate vs. indeterminate growth, and meristematic growth can help students understand what occurs in plants.

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4.

Secondary growth (i.e., woody growth) can be difficult to visualize. If this is to be included in your course, we recommend using visual resources to help students conceptualize the process.

WHAT CAN I DO IN CLASS? Understanding the different cell types, tissues, and various parts of a flowering plant is best done by observing them directly, if possible. We recommend that students be provided with the opportunity, in lab or in class demonstrations, to view whole intact plants and then examine the plants in more detail to gain a hands-on experience with as much of what is described in this chapter as possible. This would likely require use of both dissecting and light microscopes, as well as slides (pre-prepared/commercial, or made in lab by students) showing examples of different cell and tissue types from different parts of the plant body. This can be an opportunity for students to make both written and drawn observations, and compare these to what is in the textbook or other resources.

Plant tissue culture is an important technique in plant biotechnology. Discuss: How does understanding of different plant cell/tissue types help us with biotechnology? Why is totipotency an important characteristic of the cells used in tissue culture? (Students may need to refer to Chapter 16 for more information or review of biotechnology concepts.)

Ask students what is meant by the statement: Dead cells are extremely important to a living plant. Does this statement also apply to animals?

Brainstorm: What plant tissues/systems do we eat? (Fruits are easy … encourage students to think of other plant parts that humans eat.) This can be used to lead into a discussion of modified plant parts. There are various modified plant parts, not all of which are eaten – e.g., roots: prop roots, corms; leaves: tendrils, spines; and stems: rhizomes, stolons. Some of these structures are involved in vegetative propagation.

CengageNOW provides a number of useful animations that demonstrate different aspects of plant anatomy and growth. If discussing secondary growth, we highly recommend showing some of these animations to help students picture what occurs in this process. [Stumbling Block 4] Humans rely on plant secondary growth tissues (primarily wood). Brainstorm the various ways that we might use these tissues. Instructors may wish to discuss cork (replaces epidermis of shoots/roots of plants that undergo secondary growth). The cork oak tree (Quercus suber),is a tree indigenous to the Mediterranean, and a major export product of Portugal. Cork is harvested from living trees, but can only be harvested about once every decade. It takes around nine years to regenerate the cork layer. Ask students what features of cork cells make this a useful product to us. In recent years, other types of closures and synthetic corks have become more popular in wine packaging. Student teams can be assigned sides on a debate (synthetic vs. natural corks). They may wish to consider wine quality, cost, and environmental/ecological aspects.

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ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 2:  Features of cells.

Chapter 7:  Photosynthesis – mostly in leaves.

Chapter 16:  Biotechnology – tissue culture and totipotency.

Clicker questions: 1.

In plants, which of the following is NOT true of growth?

A. Cell division occurs only in meristematic regions.

B. Primary growth increases the length of roots and shoots.

C. Secondary growth increases the girth of roots and shoots.

D. As in animals, most plants demonstrate determinate growth.* E. All of the above are true of plant growth.

This question addresses Stumbling Blocks 3 and 4.

2. Which of the following is a cell type of vascular tissue?

A. parenchyma.

B. collenchyma.

C. sclerenchyma.

D. phloem * E. periderm Similar questions can easily be constructed to give students practise matching cell types with the appropriate tissue systems. (Practise may be beneficial, given all the different terms, many of which sound similar.) Stumbling Blocks 1 and 2.

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3. When we discuss the “plant tissue systems” and the “root and shoot systems”, these terms refer to

A. the same systems in both cases.

B. ground, meristematic and vascular tissue; the parts of the plant below and above the soil, respectively. * C. the different types of steles; those parts of the plant that grow below and above ground, respectively.

D. systems involved in primary growth; systems involved in secondary growth, respectively.

E. None of the above.

Stumbling Block 2.

WHAT OTHER RESOURCES ARE AVAILABLE?  Images of cork oat (including harvest of cork): http://www.forestryimages.org/browse/subthumb.cfm?sub=7071&start=1 

Wigel D, Jürgens G. 2002. Stem cells that make stems. Nature 415(6873): 751-754.

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Transport in plants occurs in two separate systems, one for transport of water and dissolved minerals taken up by roots and distributed to the rest of the plant; one for movement of sugars produced by photosynthesis in leaves, transported to the rest of the plant.

LEARNING OBJECTIVES Students should be able to:  Define/describe: passive transport, active transport, transport proteins, membrane potential, secondary active transport (symport/antiport) [Knowledge] 

Define key terms (membrane transport): selective permeability, concentration gradient, simple diffusion, channel proteins, gated channel, carrier proteins, uniport, osmosis, aquaporin, hypotonic, hypertonic, isotonic, active transport pump, primary active transport, secondary active transport, proton/H+ pump, electrochemical gradient, symport, cotransport, antiport. [Knowledge]



Define key terms (specific to plant membrane transport): bulk flow, xylem sap, osmosis, water potential, solute potential, turgor pressure, megapascals, central vacuole. [Knowledge]



Describe the role(s) of proton gradients in moving substances across a plant cell’s plasma membrane.

[Comprehension]



Describe the importance of water potential with respect to plant cells. [Comprehension]



Compare and contrast the three pathways along which water travels to the root xylem. [Comprehension, Analysis]



Describe the effect of the Casparian strip on water and solute transport into the stele. [Comprehension]



Describe how roots take up ions. [Comprehension]

192



Define key terms (water transport in plants): transpiration, cohesion, adhesion, surface tension, root pressure, guttation. [Knowledge]



Describe the key steps in the cohesion-tension mechanism of water transport model. [Comprehension]



Describe how leaf anatomy contribute to cohesion-tension forces. [Comprehension]



Describe the conditions that cause the opening and closing of stomata. [Comprehension]



Describe adaptations plants exhibit for conserving water in dry climates. [Comprehension]



Define key terms (transport of organic substances in plants): translocation, phloem sap, source, sink, transfer cells. [Knowledge]



Describe the nature of the organic substances transported by the phloem. [Comprehension]



Compare and contrast translocation and transpiration. [Comprehension]



Describe the steps involved in the pressure flow mechanism. [Comprehension]



Describe how sucrose moves from a source into the sieve tubes and is then unloaded at a sink.

[Comprehension]



Compare the vascular system in plants to the vascular system of animals. [Comprehension, Analysis]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

People are often accustomed to thinking of the “vascular system” as a system found only in animals (e.g., the human system of blood vessels). It can be counterintuitive to students that plants, in fact, have two separate systems (one for transport of water/minerals and one for transport of sugars) usually moving in different directions. Instructors may want to discuss how some terms are used for systems that have similar functions, but very different structures and mechanisms.

2.

If students do not have a good understanding of principles of water and solute movement across membranes in cells, many of the concepts in this chapter will be difficult to comprehend. Chapter 5 should be reviewed (in class, or by students on their own time).

193

3.

We’ve observed that students sometimes find the concept of water potential to be challenging, particularly when considering actual values of water potential, solute potential, pressure potential, etc.

Depending on the focus of your course (i.e., if plant physiology is not one of the major areas of coverage), you may choose to introduce this topic without using numeric equations (i.e., focusing on the broader concepts).

4.

Understanding the different pathways for water movement in roots (apoplastic, symplastic, transmembrane) can be difficult if students don’t know the organization of tissues in the root well enough to picture the cellular arrangement, and thus, possible routes for water to enter the root. If so, students may need to review Chapter 28.

5.

Properties of water (including surface tension and cohesion) are important in plant transport processes; understanding of these properties helps comprehension of how water can move upwards in a plant (i.e., against gravitational forces). If students are not familiar with the chemical characteristics of water, it may be worthwhile to discuss, referring to the relevant Purple Pages (F-11 – F-13).

6.

The direction of fluid flow in the phloem is changeable because regions of the plant that serve as source vs. sink may vary. This can be difficult for students to conceptualize.

WHAT CAN I DO IN CLASS? Pretest: Chapter 5 introduced the principles of water and solute movement across membranes.

Assigning/using review questions on this material (see end of chapter questions and IM suggestions) could be used (online, as clicker questions, etc.) to determine how well students grasp/remember the major ideas from this chapter. [Stumbling Block 2] Transport of substances required for life is important in any organism. Students can be encouraged to identify and compare the challenges faced by different types of organisms [e.g., bacteria, fungi, small (non-vascular) plants such as mosses, large (vascular) plants, small aquatic animals, large terrestrial animals] in ensuring that water and important solutes are distributed throughout the organism. (Consider how high water must rise in a tall tree!) [Stumbling Block 1] This chapter illustrates how biological structure and function are linked. Highlight: The root and shoot systems are linked via the vascular system. Roots anchor the plant and take up water and minerals that the xylem then distributes throughout the entire plant (i.e., upwards). The shoot system is responsible for the photosynthetic work of the plant. Sugars are made (mostly in leaves), and must also be shared with other parts of the plant, including the roots. [Stumbling Block 1] If an instructor wishes students to know about water potential, solute potential, etc., we recommend explaining Figure 29.4 in detail. [Stumbling Block 3] Figure 29.6 illustrates the different pathways for water movement into roots from the soil. If this is something you expect students to learn, they can be asked to draw/build additional figures/models showing the different pathways from different perspectives (e.g., longitudinal section, 3-dimensional model). Students should refer to Chapter 28 when considering plant anatomy/organization. This activity could be done as an out-of-class assignment, or during class/lab, time permitting. [Stumbling Block 4] A demonstration of water tension/cohesion can be performed in class, or in the laboratory. (See exercise: http://serc.carleton.edu/introgeo/demonstrations/examples/surfacetension.html). To maximize learning opportunities, we suggest using demonstrations after having students predict the outcome of the experiment, observe the demonstration, and then explain (after reflection/discussion) the results. [Stumbling Block 5]

194

Aspects of natural selection (Ch. 17) and coevolution (Ch. 46) can be introduced using questions at the end of the chapter. Questions #2 and #3 (pg. 714) could be used as discussion questions in class.

End of chapter self-test question #10 (pg. 714) could be used to introduce maple sap collection, which students may be interested in. (Depending on your region, some students may have visited a maple syrup farm.)

Follow up question to students: Why does maple sap have to be boiled before it is sold as maple syrup? (The sap contains approximately 1-5% sugar; evaporation of water can concentrate the sugars to about 85%.)

Students may be surprised by the high pressure in the phloem. The example of aphid consumption of phloem (pg. 709-710) resulting in excess being secreted as “honeydew” through the insect’s anus (possibly to be consumed by other insects) is likely to be remembered by students. (Alternatively, drops may fall onto surfaces below … such as parked cars. This can result in sticky windshields and other car surfaces.)

Discussion question: How can gardeners reduce transpiration (a) in greenhouses? and (b) in gardens/fields?

(Instructors may wish to pose these questions to students after asking them to consider self-test question #6 pg. 713.)

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 2:  Features of cells.

Chapter 7:  Photosynthesis (including C4 and CAM pathways).

Chapter 24:  Fungi – mycorrhizal fungi form mutualistic symbioses with many plants; associations with plant roots effectively increases surface area to better absorb water, minerals.

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Clicker questions:

1. All of the following processes contribute to the movement of liquids in the xylem, EXCEPT:

A. transpiration/evaporation B. tension C. cohesion D. sap translocation * E. All of the above processes contribute to movement of liquids in xylem.

Translocation occurs in movement of organic substances via phloem. The other processes relate to the water properties involved in xylem transport. [Stumbling Block 5]

2. Evolution of the xylem was important in plants because

A. the lignified cells of this tissue provided structural support.

B. it allowed efficient uptake and transport of water in plants.

C. it allowed efficient distribution of organic compounds (e.g., sugars) made by photosynthetic tissues.

D. All of the above (A-C).

E. Only two of the above in A-C.* This question links to Chapter 25. Development of the vascular system was important in helping plants obtain water, as well as providing the structural support via the lignified cells of the xylem.

3. Aphids feeding on plants sometimes secrete liquid from the anus during feeding.

This is because

A. phloem is being transported under too much pressure for the aphid to process.* B. the aphid tissues are hypertonic to the water being consumed by the aphid from the xylem.

C. aphid mouthparts create suction pressure that is much higher than the pressure within the vascular systems of the plant, and this suction removes more fluid than is actually required by the insect.

This links to the example on pg. 709-710.

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WHAT OTHER RESOURCES ARE AVAILABLE? 

E Steudle , and C Peterson. 1998. Review article. How does water get through roots? J. Exp. Bot. 49: 775-788.



Dorothy Merritts and Robert Walter, Franklin and Marshall College. Adhesion, Cohesion, and Surface Tension Demonstration (Teaching entry-level geoscience students): http://serc.carleton.edu/introgeo/demonstrations/examples/surfacetension.html



Maple syrup information: http://www.ontariomaple.com/maple-festivals/central-ontario.html http://www.siropderable.ca/home.aspx

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Flowering plants have sexual and asexual options for reproduction.

LEARNING OBJECTIVES Students should be able to:  Define key terms (life cycles): sporophyte, spores, gametophytes, gametes, alternation of generations.

[Knowledge] 

Describe the overall life cycle of a flowering plant. [Comprehension]



Describe how the two life phases differ in structure and function. [Comprehension]



Define key terms (structures of a flower): receptacle, sepals petals, stamens, filament, anther, pollen sacs, carpels, ovary, ovules, style, stigma, imperfect flowers, monoecious, dioecious. [Knowledge]



Given a diagram, identify the structures of a flower. [Knowledge]



Define key terms (pollen and egg production): microspores, pollen grain, pollen tube, ovule, micropyle, megaspores, polar nuclei, egg cell, embryo sac. [Knowledge]



Describe the function of the pollen grain. [Comprehension]



Describe the formation of a mature male gametophyte (pollen), beginning with microsporocytes in a flower’s anthers, and identifying structures as haploid or diploid. [Comprehension]



Describe the biological role of flowers. [Comprehension]



Describe the physiological changes that must occur before an angiosperm can produce a flower.

[Comprehension]

198



Describe the development of a female gametophyte, beginning with the megasporocyte in an ovule of a flower’s ovary, and identifying each structure as haploid or diploid. [Comprehension]



Define key terms (reproduction): pollination, fertilization and germination. [Knowledge]



Describe how pollen from different plants can be differentiated. [Comprehension]



Explain how self-incompatability can prevent self-fertilization (or closely related plants).

[Comprehension]



Explain why self-incompatability may have evolved. [Comprehension]



Describe the process of double fertilization. [Comprehension]



Explain how endosperm tissues are derived. [Comprehension]



Define key terms (fruit and seed production): fruit, pericarpsuspensor, cotyledon, seed coat, radicle, endosperm, hypocotyl, epicotyl, plumule, coleoptile, coleorhizae, dormancy, imbibition, differentiation. [Knowledge]



Describe the purpose of fruits (for the plant). [Comprehension]



Differentiate between simple fruits, aggregate fruits and multiple fruits. [Comprehension]



Describe the function of a seed. [Comprehension]



Describe a structure found in animals analogous to seeds. [Comprehension]



Compare and contrast the structure of eudicot and monocot seeds. [Comprehension]



Summarize the general changes a seed undergoes as it matures. [Comprehension]



Define key terms (asexual angiosperm reproduction): totipotent, vegetative reproduction, fragmentation, apomixes, somatic embryo, callus. [Knowledge]



Compare and contrast the three modes of asexual reproduction that occur in flowering plants.

[Comprehension, Analysis]



Describe how totipotency is exploited in plant tissue culture systems. [Comprehension]



Describe differentiation in the early plant embryo. [Comprehension]

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WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

Pollen and eggs are gametes, not gametophytes, as some students may think. (Remind students that the gametophyte produces gametes. The gametophyte can be large in some types of plants, such as mosses, or consist of only a few cells, as in angiosperms.) Making this distinction may be facilitated by explicitly going over Section 30.2b, which talks about pollen grains (the male gametophyte) and Section 30.2c, which talks about eggs (the female gamete).

2.

Students often confuse the seed with the egg, thinking that the seed is unfertilized. It can be helpful to point out that the strong, water-resistant seed coat would prohibit fertilization by a wimpy little sperm.

3.

Double fertilization can be confusing to students. They often think that this refers to two sperm fertilizing a single egg. (In fact, one sperm unites with one egg nucleus, forming the zygote; the other sperm nucleus fuses with the polar nuclei to form the endosperm.)

4.

Self-incompatibility is often a problematic concept. Use of many examples/questions will help students learn this phenomenon, as will concentrating on why self-incompatibility is useful.

5.

Students often confuse self-fertilization with asexual reproduction. Self-fertilization introduces variety into offspring, while asexual reproduction produces genetically identical offspring (clones).

Energetically, it may be a cheaper strategy as well in that the pollen grains do not have far to travel.

6.

Students often have the misconception that asexual reproduction is an inferior reproductive strategy.

However, this means of reproduction serves a multitude of organisms quite well.

WHAT CAN I DO IN CLASS? The “Why it Matters” section discusses the disturbing threat to pollinators required for reproduction of many important crop plants. Instructors may wish to introduce some of the research findings of Canadian scientist Dr. Laurence Packer (see: http://www.yorku.ca/gradbiol/faculty/profiles/laurencedp.html ) who studies various aspects of bees, including conservation genetics, biodiversity, etc.

Canadian author Douglas Coupland’s novel, Generation A, incorporates loss of pollinators as a central theme.

Depending on the nature of your course, and if time permits, a discussion of this idea (and treatment of it in the book) could be undertaken. (Recommended for non-science major introductory courses).

Chapter 25 discusses the diversity of plants, and the prevalence/success of the angiosperms (flowering plants).

Much of this success relates to the reproductive strategies of flowering plants. Ask: How do flowers display diversity? How do flowers and fruits contribute to the success of plants in different environments? (If you can show the Private Life of Plants, this would illustrate some of the coevolutionary adaptations seen in angiosperms.)

In discussing outcrossing vs. self-fertilization, students may need reminders of what occurs in production of gametes (i.e., meiosis – Chapter 10). Ploidy may also need review, especially when discussing haploid gametes/tissues, diploid zygote, and triploid endosperm. Discussion of alleles (e.g., in self-incompatibility) may also necessitate review of concepts from Chapters 11 and 12.

200

Depending on the background of your students, you may want to discuss some of the mechanisms involved in self-incompatibility (e.g., different signalling pathways leading to RNA /protein degradation, death of pollen).

See Takayama and Isogai (2005) for more details.

If the course includes a laboratory component, examining different types of flowers under the dissecting microscope can provide a glimpse of the diversity exhibited by members of the angiosperms.

We recommend going through the steps of sexual reproduction in flowering plants in some detail, using relevant figures from the text (e.g., Figures 30.3, 30. 4, 30.6) and online animations via CengageNOW. In particular, double fertilization should be reviewed, with clear explanations as to why it is considered “double”.

[Stumbling Block 3] For discussion: Grocery stores, restaurants, etc., categorize fruits and vegetables in terms of how these items are used as food. How does this relate to the biological definition of a fruit? Which vegetables would be considered “fruits” in a biological sense? (What are other types of vegetables composed of?)

It might help to relate seeds to eggs laid by birds and other reptiles that have hard shells. Ask: Are bird eggs fertilized? The hard shell on the egg that provides protection would only hinder sperm penetration if it was unfertilized. [Stumbling Block 2] Ask: How does a seed “know” when to germinate? (Hints: How could a seed tell what time of year it is? What will a new plant need in order to grow?) [Stumbling Block 2] To introduce vegetative (asexual) reproduction, examples of common ways of artificially propagating plants can be demonstrated in class or lab. (E.g., Spider plant “baby spiders”, Kalanchoe plantlets, cuttings, and potato “eyes”.)

Students may be interested in the biotechnological potential of plant tissue culture, made possible because of the totipotency of (some) plant cells. (Students may need to review/read Chapter 16 to understand aspects of this process.) Brainstorm possible applications of plant tissue culture.

Many types of fruits are only brightly coloured and sweet when fully ripe. Ask students what adaptive advantage this might provide to the plant producing such fruits. (This can be linked to end-of-chapter discussion question #3, pg. 733, for a more extensive activity/assignment.)

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 31:  Dormancy/germination involve plant hormones.

Chapter 46 & 17:  Coevolution of plants & animals Clicker questions: 1.

In flowering plants, the female gametophyte is the __________ and the female gamete is the ____________.

A. B. C. D. E.

pollen; seed. ovary; egg. * seed; ovary. egg; seed. embryo; egg.

[Stumbling Block 1 and 2] 201

2.

If a plant exhibits self-incompatibility through the S gene, what would you expect if a S1S3 plant encounters pollen from a S1S4 plant?

A. All pollen from the S1S4 plant can successfully pollinate the S1S3 plant.

B. Only S1 pollen can successfully pollinate the S1S3 plant.

C. Only S4 pollen can successfully pollinate the S1S3 plant. * D. No pollen from the S1S4 plant can successfully pollinate the S1S3 plant.

This is similar to the example illustrated in Figure 30.8. [Stumbling Block 4] 3.

If a plant exhibits self-incompatibility through the S gene, what would you expect if a S1S3 plant encounters pollen from a S1S1 plant?

A. All pollen from the S1S1 plant can successfully pollinate the S1S3 plant.

B. Only S1 pollen can successfully pollinate the S1S3 plant.

C. No pollen from the S1S1 plant can successfully pollinate the S1S3 plant. * This is a variant of the previous question. [Stumbling Block 4]

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4.

Consider the costs and benefits of asexual and sexual reproduction. Plants that grow in uniform/stable environments would likely exhibit ____________ reproduction, while those in more variable environments would be expected to exhibit ____________ reproduction.

A. sexual; asexual.

B. asexual; sexual. * C. asexual; asexual.

D. Plants can only reproduce sexually.

This question addresses the common misconception that asexual reproduction is an inferior means of reproduction compared to sexual reproduction. Both are good strategies, often in different environments.

Stumbling Block 6]

WHAT OTHER RESOURCES ARE AVAILABLE? 

Dr. Laurence Packer (York http://www.yorku.ca/gradbiol/faculty/profiles/laurencedp.html



NSERC-CANPOLIN The http://www.uoguelph.ca/canpolin/index.html



Douglas Coupland. 2009. Generation A. Random House Canada. 320 pages.



David Attenborough BBC Private Life of Plants videos – Stunning footage of various aspects of plant biology. We highly recommend all episodes, but if time is limited, instructors may wish to focus on the pollinator-plant relationships, if you have permission to show in class.



Takayama S, Isogai A. 2005. Self-incompatibility in plants. Annu Rev Plant Biol. 56:467-89.

Canadian

University) Pollination

webpage: Initiative:

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Plants produce hormones/signals that regulate aspects of growth, development and responses to the environment.

LEARNING OBJECTIVES Students should be able to:  Define key terms: hormone, signalling compound, phototropism, polar transport, acid-growth hypothesis, bolting, senescence, abscission, tropisms, nastic movement. [Knowledge] 

Compare and contrast the following compounds in terms of where they are synthesized, the tissues they affect, and their effects: auxins, gibberellins, cytokinins, ethylene, and abscisic acid.

[Comprehension]



Describe the ways that chemical signals to plant cells can alter cell functions. [Comprehension]



Describe the function of a second messenger in plant cell signalling. [Comprehension]



Describe the effects of two chemicals involved in plant defence. [Comprehension]



Describe the hypersensitive response as a form of plant defence. [Comprehension]



Compare and contrast phototropism, gravitropism and thigmotropism. [Comprehension]



Compare tropisms and nastic movements in terms of their causes and responses. [Comprehension]



Describe the different effects of photoperiodism. [Comprehension]



Describe how light:dark cycles can influence flowering. [Comprehension]

204



Describe the importance of light in plant growth and responses. [Comprehension]



Describe how dormancy is an adaptive response to a plant’s environment. [Comprehension]



Relate the incidence of dormancy in plants to geographic location. [Comprehension]



Compare and contrast the nature and role of hormones in animals to those of plants. [Comprehension, Analysis]



Define gene-for-gene recognition. [Knowledge]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

Students often think of plants as static, passive organisms. While plants do not display mobility as many animals do, they still sense and respond to environmental conditions and signals.

2.

While both plants and animals produce signal molecules called “hormones”, there are some key differences between these that students may not be aware of. Animal hormones are produced in endocrine tissues/organs and transported via the blood to parts of the body with the appropriate receptors that can then respond. Plant hormones (sometimes called “plant growth regulators” to differentiate them from animal hormones) are produced in a variety of plant cells, and effects may occur near the production site.

3.

Although “hormones” are different in plants and animals, most aspects of cellular signalling are similar. Students may not realize that the material discussed in Chapter 8 applies to plants, not just animals.

4.

There are a number of plant hormones/signalling chemicals discussed in this chapter. Some of these are involved in multiple effects, and overlap exists between some compounds. This can be confusing to students, and we recommend deciding and explicitly communicating which hormones/signalling compounds you expect students to know, and the extent of understanding expected for each.

5.

The term “secondary metabolite” can be confusing. Secondary does not refer specifically to anything regarding the actual chemical reactions, but reflects the idea that biologists do not consider production of these compounds as “essential” for basic survival of the cells. Secondary metabolites are produced by certain plant cells, but can benefit the entire plant (e.g., through defence).

6.

Gene-for-gene recognition can be challenging for students to understand. The roles of the R (Resistance) and Avr (Avirulence) genes can be confusing. Even the term “gene-for-gene recognition” is confusing to students who have been correctly told that genes themselves do not usually “act”, and knowing that the products of the genes are usually where we see biological effects.

7.

Effect of night length on flowering can be problematic to understand, particularly as we typically refer to plants as “short day” or “long day”, although day length is not the critical factor in flowering.

WHAT CAN I DO IN CLASS? Chapter 1 introduced aspects of light affecting life, including photomorphogenesis, and circadian rhythms.

These processes involve signalling, described in this chapter. Ask: Why is light so important in plant life?

[Stumbling Blocks 1 and 7]

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Brainstorm: If plants are sessile, what types of responses can they have to their environment? This list can then be used to explore the different types of responses in more detail and the signaling involved. [Stumbling Block 1] A review of some of the key points from Chapter 8 (cell communication) may be helpful in discussing signal transduction in plants. It may also serve to remind students that cell signalling is vital to multicellular life.

[Stumbling Block 3] Ask students to compare animal hormones to those of plants. Individually, or in small groups, they can compare the types of compounds, where they are produced, and the action of hormones in plants vs. those of animals. [Stumbling Block 3] Leaf cuttings are used to propagate some commercial plants, whereby a leaf is cut from the parent plant and placed in a growth medium. After some time, adventitious shoots and roots develop from this cut leaf, producing a new plant. Ask: Are all the cells in the original leaf tissue equally likely to give rise to the new structures? If not, which one(s) are most likely to have done so? (Instructors may wish to relate this to concepts discussed in Chapter 16.)

Discuss: Why is orientation so important in plant growth? What would happen if you slowly rotated a growing plant?

Brainstorm: What are some of the challenges faced by plants growing in Canada vs. a rainforest? (Hint: Consider photoperiodism, dormancy). What are some of the differences between the different regions of Canada (e.g., Think of the lower mainland of BC, badlands of AB, Northern Territories, Niagara region, PEI – how do these regions differ in climate, latitude?).

Bring Mimosa plant to class/lab for a demonstration of thigmotropism. Ask students what the benefits of such reactions would be? (E.g., deter herbivores, may dislocate herbivorous insects, etc.) Students may be interested in thigmotropisms that are used by carnivorous plants to capture prey. (See “BBC Life” Venus Flytrap example.)

Ask: What is “chemical defence” in plants? How is “gene-for-gene recognition” like an coevolutionary arms race? (This can be related to the predation section in Ch. 46.)

Students will likely be interested by the fact that many of the compounds used in drugs (both pharmaceutical and recreational) are secondary metabolites produced by plants (or molecules derived from plant molecules).

In plants these compounds likely deter pests/herbivores, but because of the action of some such chemicals, we can exploit them for our own purposes. Brainstorm examples of such drugs. (Link to Chapter 46 re: herbivorous predation.)

If you have explored extremophilic bacteria and archaea, you may want to discuss the similarities and differences of adaptations of prokaryotes to those of plants able to withstand what humans consider to be “extreme” environments. E.g., Some salt-tolerant plants cope with osmotic pressure by producing compatible solutes to counter the effects of a high solute environment, as do many halotolerant bacteria/archaea.

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 11:  Gene-for-gene recognition – students should understand what a dominant allele is.

Chapter 30:  Seed dormancy/germination involve plant hormones.

Chapter 46:  Defence mechanisms against predation (specifically herbivory).

Clicker questions:

206

1.

What do auxins, gibberellin and cytokinins all have in common?

A. B. C. D.

They stimulate cell division. * They stimulate stomata closure under water stress.

They promote seed germination.

They trigger defence responses.

[Stumbling Block 1] 2.

Tanya brings her bananas to work in a plastic case that has small holes throughout (a “Banana Guard”  http://www.bananaguard.com/ ). She’s noticed that the bananas are less likely to be bruised and squishy when she uses the case. The case helps the fruit avoid the effects of which hormone?

A. B. C. D.

auxin ethylene * cytokinin gibberellin

[Stumbling Block 4] 3.

A flowering plant growing near the equator would be expected to be A. day-neutral * B. short-day C. long-day

Plants growing at/near the equator will experience little change in length of day (night) throughout the year. It may be necessary to review how day length varies with latitude. [Stumbling Block 7] 4.

Plant resistance/defence pathways are expected to be stimulated if A. the plant has the dominant R allele and the pathogen has the corresponding dominant Avr allele. * B. the plant has the dominant R allele and the pathogen LACKS the corresponding dominant Avr allele.

C. the plant LACKS the dominant R allele and the pathogen has the corresponding dominant Avr allele.

D. the plant has the dominant R allele and the pathogen has the corresponding dominant Avr allele.

E. the plant LACKS the dominant R allele and the pathogen also LACKS the corresponding dominant Avr allele.

[Stumbling Block 6]

WHAT OTHER RESOURCES ARE AVAILABLE? 

David Attenborough BBC Life, Episode 9 – This episode shows how various plants deal with life’s challenges, and includes footage of the Venus Flytrap capturing prey.



Banana Guard by Aberrant Designs Inc. http://www.bananaguard.com/



Alan Crozier (Ed), Mike N. Clifford (Ed), Hiroshi Ashihara (Ed). 2006. Plant Secondary Metabolites: Occurrence, Structure and Role in the Human Diet. Wiley-Blackwell. 384 pages.

207

SECTION III: ANIMALS CHAPTER 26 PROTOSTOMES CHAPTER 27 DEUTEROSTOMES: VERTEBRATES AND THEIR CLOSEST RELATIVES CHAPTER 32 INTRODUCTION TO ANIMAL ORGANIZATION AND PHYSIOLOGY CHAPTER 33 INFORMATION FLOW: NERVES, GANGLIA, AND BRAINS CHAPTER 34 SENSORY SYSTEMS CHAPTER 35 THE ENDOCRINE SYSTEM CHAPTER 36 MUSCLES, SKELETONS, AND BODY MOVEMENTS CHAPTER 37 THE CIRCULATORY SYSTEM CHAPTER 38 ANIMAL REPRODUCTION CHAPTER 39 ANIMAL DEVELOPMENT CHAPTER 40 ANIMAL BEHAVIOUR COVERAGE CONSIDERATIONS Coverage of animal anatomy and physiology can vary widely between different introductory Biology courses. If the curriculum warrants, each of the chapters in this section may be covered to a greater or lesser extent. In some cases, we envision instructors including key aspects from each chapter, but not requiring students learn all material from every chapter.

Instructors may wish to look at the material from Chapters 41 through 44 (includes nutrition, gas exchange, regulation of the internal environment, immunity), as they may wish to integrate some of these processes into discussions of animal form, function, lifestyles and physiology.

It is possible (and even suggested) that for appropriate topics an instructor may want to consider aspects of animal physiology and anatomy alongside those of plants (Section II), in order to emphasize the commonality of many forms of life, while highlighting the differences that make these groups unique.

Again, we highly recommend that instructors carefully consider which learning objectives they feel are necessary (rather than simply including all of them) to meet their own course’s curricular outcomes.

OV E RV I E W O F S E C T I O N I I I IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1. Animals, characterized by the consumption of other organisms, multicellularity, and movement at some point during their development, display an amazing diversity of adaptations that allow them to be successful in a wide variety of environments.

208

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? Note: These Stumbling Blocks will be referred to in multiple chapters of this section.

XI. Many students consider humans and their traits to be “the best” or “superior “. This can prove to be a stumbling block because they may see all other organisms and their traits as inferior to those of humans. It is best to approach the various features of animals from an adaptive standpoint (you may even want to discuss pre-adaptation/exaptation) and draw comparisons to humans (e.g., what would allow this organism, but not humans, to survive in this type of environment). Instructors may want to start with examples and ask students to find out about these organisms in terms of where they live, what they eat, when they eat, where they reproduce, how often, etc., and then draw comparisons between examples.

XII.Students often do not realize that animals share features with plants (and other organisms).

While we often do focus more on the differences between kingdoms, the unity of life also is demonstrated by the many features shared by animals and plants. We recommend that instructors highlight these commonalities in the appropriate sections.

XIII. Systems do not operate in isolation, although we usually study/discuss them as though this were the case (in part, because of the complexity of such systems). Reminders of the interconnectedness of physiological systems discussed in these chapters, and processes that involve coordination of several systems (e.g., movement) are recommended.

209

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

All animals are heterotrophs (although a few have devised ways to be phototrophic) that are motile at some stage in their lives.

2.

Most animals, with the exception of sponges have defined tissues (exception: sponges), and exhibit either radial or bilateral symmetry. Bilateral animals can be divided into two major lineages based on their early embryonic development: the protostomes and deuterostomes. Protostomes include arthropods (insects, crustaceans), cnidarians (jellyfish and corals), and molluscs (gastropods, octopoda).

LEARNING OBJECTIVES Students should be able to:



Define key terms (general): animal, motile, sessile, tissues, germ layers, diploblastic, triploblastic, symmetry (radial, bilateral), asymmetry, aceolomate, pseudocoelomate (coelom, pseudocoelom, shizocoleom, enterocoelom) mesenteries, hydrostatic skeleton, cleavage (spiral, radial, determinate, indeterminate), archenteron, blastopore, segmentation, gastrovascular cavity, gastrodermis, metamorphosis, polymorphic development, peritoneum, mesenteries, monoecious, dioecious. [Knowledge]



Describe the three characteristics that distinguish animals from plants. [Comprehension]



Given an animal, describe the type of symmetry it possesses. [Comprehension, Analysis]



Describe the hypothesis that colonial protists gave rise to animals. [Comprehension]



Describe the three types of primary tissue/germ layers (endoderm, mesoderm ectoderm), and their functions. [Knowledge]



Define key terms (orientation): anterior, posterior, dorsal, ventral, cephalization. [Knowledge]

210



Compare and contrast protostomes and deuterostomes in terms of: the number of embryonic tissues, symmetry, presence/absence of body cavity, and early embryonic events (e.g., cleavage, origin of mouth/anus). [Comprehension]



Draw differences between protostomes and deuterostomes in tems of cleavage patterns, coelom formation, and origin of the mouth and anus, labelling the archenteron, blastopore, coelom, gut, mouth and anus. [Knowledge]



Describe the function of the coelom, and the importance of the fluid within. [Comprehension]



Describe the importance of the third embryonic tissue layer (i.e., protostome vs. deuterostomes). [Comprehension]



Describe segmentation and its importance in animal evolution. [Comprehension]



Explain how a hydrostatic skeleton works. [Comprehension]



Describe an advantage of cephalisation and its evolution is correlated with that of bilateral symmetry. [Comprehension]



List and describe three major evolutionary changes in animals. [Comprehension]



Describe two differences between sponges and all other metazoans and explain why sponges are included in the same group as Metazoans. [Comprehension]



Describe filter feeding (used by sponges). [Comprehension]



Define key terms (Cnidarians): gastrovascular cavity, polyps, medusae, extracellular/intracellular digestion, nerve net, budding, external fertilization. [Knowledge]



Describe the function of the lophophore and the flame cell system. [Comprehension]



Define key terms: ganglion, ocelli, phanrynx, parasite, proglottid. [Knowledge]



Describe tapeworm morphology in terms of how it reflects a parasitic lifestyle.

[Comprehension]



Define key terms eutely, circulatory vessels, parthenogenesis. [Knowledge]

 

Compare eutely with cleavage in mammals (e.g., mice). [Comprehension, Analysis] Define key terms (mollusks): visceral mass, muscular foot, radula, mantle, mantle cavity, gills, haemolymph, sinuses, hermaphrodite, torsion. [Knowledge]

211



Describe the major features of the arthropod and mollusc body plans, identifying the three regions of the mollusc body. [Comprehension]



Compare and contrast the nervous systems of gastropods, bivalves, and cephalopods, relating the nervous system to the organism’s lifestyle. [Comprehension]



Describe the locomotion of a squid. [Comprehension]



Compare and contrast, briefly, an open-circulatory system and a closed circulatory system.

[Comprehension]



Discuss the advantages/disadvantages of internal vs. external fertilization. [Comprehension]



Define key terms (annelids): septum, metanephridia, parapodia, setae. [Knowledge]



Explain how annelids use the coelom as a hydrostatic skeleton. [Comprehension]



Comment on the advantages and disadvantages of the exoskeleton (including ecdysis/moulting) and how the exoskeleton can be modified for different environments (e.g., marine vs terrestrial). [Comprehension]



Describe environments favourable to external and internal fertilization. [Comprehension]



Define key terms (arthropods): exoskeleton, haemocoel, haemolymph, thorax, abdomen, chelicerae, pedipalps, cephalothorax, book lungs, spinnarets, carapace, mandibles, maxillae, antennae, tracheal system, malphigian tubules. [Knowledge]



Describe changes to body segmentation in arthropod evolution. [Comprehension]



Describe, briefly, the nervous system & eyes of most arthropods. [Comprehension]



Describe at least one specialization of appendages in crustaceans. [Comprehension]



Explain why class Insecta is considered the most successful animals. [Comprehension]



Describe the insect body plan, the tracheal system, and how insects excrete nitrogenous wastes. [Comprehension] Describe at least two different modifications of insect mouthparts to accommodate different modes of feeding. [Comprehension]





Describe how insects deal with fertilization in a terrestrial environment. [Comprehension]

212



Define and describe instars, pupa, limited metamorphosis, incomplete metamorphosis, complete metamorphosis. [Knowledge, Comprehension]



Describe two adaptations that allowed a water-to-land transition in protostome evolution.

[Comprehension]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 5.

This chapter contains a considerable amount of detail and new vocabulary, which can be overwhelming for students. Instructors should be explicit regarding the amount of detail, and breadth of information that they expect students to know. We recommend picking a few key learning objectives and concentrating on these. Much of this information is in other chapters.

6.

Because of the large amount of new vocabulary within Chapters 26 and 27, students can lose sight of general hierarchical patterns, for example, the three germ layers, two types of body symmetry, and classification based on embryo development. However, together these form a nested hierarchy with organisms grouped according to evolutionary history.

7.

Students may not realize the wealth of diversity within the arthropods, and that in addition to insects, crustaceans and many other organisms are classified within this phylum.

WHAT CAN I DO IN CLASS? Students may become overwhelmed with the number of different categorizations introduced in this chapter (diploblastic vs. triploblastic, deuterostome vs. prototome, bilateral vs. radial). It helps to have students try to arrange these comparative groups into a simple yes/no hierarchy. Animals can be subdivided into those without defined tissues or nerves (sponges) and those with defined tissues and nerves (all others). Of those organisms with defined tissues, which have radial symmetry and which are bilaterally symmetrical? Of those animals that exhibit bilateral symmetry, during development do they experience spiral cleavage and development of the gut to the anus (protostomes = ‘mouth first’) or do they exhibit radial cleavage and development of the anus to the gut (deuterostomes = ‘mouth second’) This can be done in small groups that then come together to report their hierarchies. Potentially, a generalised phylogenetic tree showing shared characteristics could be constructed as a class (See Fig. 26.6). [Stumbling Block 2] Compare eutely (seen in some protostomes) to cleavage in a human embryo. Unlike mammalian cleavage, eutely is a form of development where growth is achieved through a cessation in cell division and an increase in cell size. Early cleavage in mammals (Chapter 39) involves progressive cell divisions with no overall increase in volume; thus, with each cell division, cells become progressively smaller.

Hermaphroditism is common among invertebates. Brainstorm: what selective advantages might this characteristic offer and in which environments might it be most useful? This can be used to tie in concepts from Chapter 38 (Animal Reproduction). [Stumbling Block I] In terms of sheer species numbers, insects are the dominant form of life on Earth. Ask: What has contributed to their success? Why are insects smaller in size relative to vertebrates, plants, etc.? [Stumbling Block I, II]

ADDITIONAL LINKS TO OTHER CHAPTERS

213

Chapter 42:



Gas exchange (tracheal system).

Chapter 43:



Excretion of nitrogenous wastes and osmoregulation is discussed in much more detail.

Clicker questions:

1.

You are trying to classify a newly discovered organism that meets all criteria for an animal.

With respect to embryonic development, how could you determine whether it was a protostome or a deuterostome.

F. Look at the germ layers; if it is triploblastic it is a deuterostome.

G. Look at the germ layers: if it is triploblastic it is a protostome.

H. Look at the embryonic cleavage; if it is radial it is a protostome.* I. Look at the embryonic cleavage; if it is spiral it is a protostome.

This question reviews differences in protostome and deuterostome embryonic events. Both deuterostomes and protostomes are triploblastic.

2. Which embryonic layer contributes to muscles of the body wall in most metazoans?

F. ectoderm G. endoderm H. mesoderm* I. mesoglea

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WHAT OTHER RESOURCES ARE AVAILABLE? 

Radial vs spiral cleavage. Simple animation showing a rotated embryo, exhibiting each type of cleavage. Bill Wasserman. http://www.luc.edu/faculty/wwasser/dev/radspirl.htm

215

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… o

Chordates are deuterostomes that share characteristic features that are found at some point during development. In particular evolution of the jaw, limbs, wings, amniotic egg and other adaptations for terrestrial lifestyle within the subphylum Vertebrata profoundly changed the face of life on Earth.

LEARNING OBJECTIVES Students should be able to:



Define key terms (echinoderms): water vascular system, oral/aboral surface, tube feet, ampulla, test. [Knowledge]



Describe why echinoderms are considered bilaterally symmetrical although many of them are round. [Comprehension]



List the characteristics of protostomes and deuterostomes. [Knowledge]



Describe how tube feet are used in attachment to substrates. [Comprehension]



Explain why acorn worms are hemichordates, and not chordates. [Comprehension]



Describe the 4 characteristic morphological features of chordates. [Comprehension]



List the 3 subphyla of chordates. [Knowledge]



Considering the structure of a urochordate, describe why they would be included in phylum Chordata. [Comprehension]



Differentiate between invertebrate chordates and vertebrate chordates, providing an example of each. [Comprehension]

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

Describe the role of the notochord in invertebrate chordates. [Comprehension]



Describe the advantages of muscle segmentation in conjunction with a notochord.

[Comprehension]



Describe, briefly, the relationship between the brain and the dorsal hollow nerve cord of chordates. [Comprehension]



Describe the structure and function of gill (pharyngeal) slits, their original role, and the structures they give rise to in fishes and mammals. [Comprehension]



Define key terms (vertebrates): bone, cartilage, cranium, vertebrae, axial skeleton, pectoral girdle, pelvic girdle, appendicular skeleton, neurocrest cells. [Knowledge]



Describe how the neural crest cells contribute to unique vertebrate structures. [Comprehension]



Describe the advantages of a backbone. [Comprehension]



Describe, in general, the evolution of a hypothetical cephalochordate to a chordate.

[Comprehension]



Explain how duplication of the Hox gene could have contributed to the evolution of vertebrate diversity. [Comprehension]



Describe two general features that contributed to vertebrate evolutionary success.

[Comprehension]



Describe how the earliest vertebrates fed without jaws. [Comprehension]



Describe the evolution of the jaw. [Comprehension]



Describe how evolution of jaws changed how/what vertebrates ate and how this affected their lifestyle. [Comprehension]



Define: electroreceptors, lateral line system, swim bladder. [Knowledge]



Provide one reproductive adaptation of Chondrichthyans and one adaptation of bony fishes that improves swimming efficiency. [Knowledge]



Describe four lines of evidence suggesting that tetrapods evolved from fleshy-finned fishes (Osteopiformes). [Comprehension] Describe animal adaptations to terrestrial life with respect to prevention of water loss, respiration, structural elements and fertilization. Comprehension]



217



Describe characteristics of amphibians that allow them to use their skin as a major site of gas exchange. [Comprehension]



Describe three key features that allowed amniotes to become completely terrestrial.

[Comprehension]



Explain how evolution of the amniotic egg was crucial in the complete transition to a terrestrial lifestyle of tetrapods. [Comprehension]



Describe one feature of crocodilians that is homologous to those of birds and one feature that is analogous to those of mammals. [Comprehension]



Describe three skeletal features associated with bird flight, identifying those absent in flightless birds. [Comprehension]



Describe adaptations that make/made flight possible in birds and pterosaurs. [Comprehension]



Describe, briefly, the three hypotheses to explain the evolution of flight in birds.

[Comprehension]



Describe the characteristic features of mammals (that distinguish them from other vertebrates). [Comprehension]



Compare and contrast the reproductive strategies of monotremes, marsupials and placentals.

[Comprehension, Analysis]



Describe briefly three examples of convergent evolution among mammals. [Comprehension]



Describe how tooth morphology can be used to determine diet of a mammal. [Comprehension]



Describe the key adaptations that distinguish humans from non-human primates, apes.

[Comprehension]



Describe characteristics that distinguish Homo erectus from its ancestors. [Comprehension]

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

Describe the two hypotheses (African Emergence Hypothesis and Multiregional Hypothesis) of the relationship of H. sapiens with Neanderthals, and the evidence supporting each.

[Comprehension]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

This chapter contains a considerable amount of detail and new vocabulary, which can be overwhelming for students. Instructors should be explicit regarding the amount of detail, and breadth of information that they expect students to know. We recommend picking a few key learning objectives and concentrating on these. Much of this information is in other chapters.

2.

The taxonomic names in this chapter (e.g., Agnathans, Gnathostoma, Tetrapoda) can cause difficulties (and anxieties) for students. It is helpful to break down these words to their Latin or Greek roots/word origins.

3.

Students sometimes miss the link between the evolution of jaws and the evolution of a more active lifestyle. Jaws allowed efficient feeding at a level that was able to maintain higher levels of activity.

4. Because this chapter ends with human evolution, students may interpret this as an evolutionary progression (which it is not; evolution is not progressive nor directional).

Reviewing phylogenies (Chapter 19) can help to reinforce that recently evolved does not mean ‘the best’.

5. Chordates are grouped according to four (sometimes 5) characteristics that an organism must show at some point during their development. This is sometimes difficult for students as they cannot picture the developmental progression of some of the chordates, particularly the urochordates and cephalochordates. It is also confusing that within the chordates there are invertebrates and vertebrates. Often students will ‘want’ to classify all organisms within chordates as vertebrates.

WHAT CAN I DO IN CLASS? Before beginning this chapter, ask students to brainstorm (in small groups or as a class), what features of aquatic vertebrates are adaptive to their aquatic environment and what features of terrestrial vertebrates are adaptive to their terrestrial environment. Students can come up with the changes necessary for the water-toland transition of tetrapods, looking at the skeletal/support system, gas exchange, reproduction, etc. These can also be related to changes in plants with their invasion of the terrestrial habitat. [Stumbling Block III, 4] Students may have difficulties understanding why urochordates and cephalochordates, which look very different to their generalized vision of a chordate are categorized as chordates. It is helpful to visually demonstrate the characteristic chordate features in these organisms, as well as vertebrates – it is most helpful if these diagrams are shown side-by-side. [Stumbling Block 6] The book does not go into great detail as to what anatomical and physiological features make sharks great predators. Assign groups of students to find out what these features are. [Stumbling Block 3] It is helpful to walk students through diagrams depicting the evolution of jaws from gill arches and the evolution of limbs from the fleshy-fins of fish (Osteolepiformes). If possible you could show students the section on the evolution of jaws in Evolve (History Channel). [Stumbling Block 3]

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ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 34:



Mechanoreceptors (lateral line system) and electroreceptors of fishes.

Chapter 38:



Evolution of the amniotic egg was crucial in the complete transition of tetrapods to a terrestrial life.

Chapter 41:



Spiral valve in elasmobranchs is used to increase digestive surface area; more detailed information on nutrition can be found in this chapter.

Chapter 42:



More information on requirements of a respiratory membrane, internalization of respiratory surfaces, etc.

Chapter 48:



Loss of frog biodiversity through habitat fragmentation can be explored more in this chapter.

Clicker questions:

1.

Which one of the following key adaptations allows amniotes to occupy terrestrial habitats?

A. Production of carbon dioxide as a metabolic waste product.

B. An unshelled egg protected by jellylike material.

C. A dry skin largely impermeable to water.* D. A lightweight skeleton with hollow bones.

E. Feathers/fur providing insulation against cold weather.

This question reviews adapations to survive in a terrestrial environment.

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2.

Which of the following is not a characteristic of all chordates?

SSS. TTT. UUU. VVV.

Notochord Segmented nervous system.

Dorsal hollow nerve cord Pharyngeal gill slits.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Shubin, N. 2008. Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body. Pantheon. 240 p.



DVD set that looks at biological and behavioural adaptations. Evolve. The History Channel.



Ruvinsky I and Gibson-Brown JJ. 2000. Genetic and developmental bases of serial homology in vertebrate limb evolution. Development 127:5233-5244.



Gillis JA, Dahna RD, Shubin NH. 2009. Shared developmental mechanisms pattern the vertebrate gill arch and paired fin skeletons. 106(14): 5720-5724.

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

In animals, tissues (often with several specialized cell types) are organized into organs and organs organized into organ systems. Organs within a system are dedicated to a major physiological process. Because they are able to maintain an internal environment, animals are able to inhabit a wide variety of environments.

LEARNING OBJECTIVES Students should be able to:



Define key terms (general): anatomy, physiology, homeostasis, interstitial/extracellular fluid, stem cells, tissue, organ, organ system. [Comprehension]



Describe the four basic tissue groups and their roles: epithelial, connective, muscle and nervous. [Comprehension]



Describe structure and role of extracellular matrix (ECM), anchoring junctions, tight junctions, and gap junctions. [Comprehension]



Define (epithelial tissue): cilia, microvilli, basal lamina, basement membrane, stem cells (link to other chapters), glands. [Knowledge]



Draw the patterns of cellular arrangement in epithelia. [Comprehension]



Compare and contrast the three common shapes of epithelial cells with respect to their shape, function, and location. [Comprehension]



Compare and contrast endocrine glands and exocrine glands in terms of structure and function. [Comprehension]



Define (connective tissue): collagen, fibronectin, elastin, fibroblasts, mesenteries, tendons, ligaments, chondrocytes, osteocytes, osteoblasts, osteoclasts, osteon, adipocytes, leukocytes, erythrocytes, haemoglobin. [Comprehension]

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

Describe the six major types of vertebrate connective tissue (loose, fibrous, cartilage, bone, adipose, blood). [Comprehension]



Define (muscle tissue): actin, myosin, intercalated disk. [Comprehension]



Compare and contrast the three types of muscle tissue (skeletal, cardiac, and smooth).

[Comprehension]



Define (nervous tissue): neurons, glial cells, cell body, dendrites, axons, axon terminals.



Draw a typical neuron, labelling the nucleus, dendrites, cell body, axon, and axon terminals.



List 5 of the 11 vertebrate organ systems. [Knowledge]



List three functions of the organs/organ systems of animals. [Knowledge, Comprehension]



Define (homeostasis): negative feedback, set point, positive feedback. [Comprehension]



Explain how homeostasis is a dynamic process. [Knowledge]



Describe negative feedback, including the roles of the following components: sensor, integrator, effector, and response. [Comprehension]



Compare and contrast thermoregulation in humans, dogs, snakes, and insects. [Comprehension, Analysis]



Explain how positive feedback does not result in homeostasis. [Comprehension]



Differentiate between positive and negative feedback loops. [Comprehension, Analysis]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1. The dynamic nature of homeostasis (i.e., processes can go beyond a set point and then drop to an appropriate value) may be difficult for some students to comprehend. Examples and discussions of the different systems involved may help with this.

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2. Each organ system has a major role it performs for the body (e.g., circulatory system – move essential materials around the body, remove wastes from tissues; integumentary system – mechanical protection), but these systems do not work in isolation.

3. Many of the words in this chapter are new to students, but the root of scientific words is consistent for a specific tissue/organ/system. For some, it may be useful to get students to find the Latin or Greek definition of the word.

WHAT CAN I DO IN CLASS? The Why it Matters section describes homeostasis in meerkats (and some of their daily activities). Instructors could ask students to brainstorm examples of Canadian animals, the challenges they face, and how various systems are involved in physiology and behaviours in homeostasis. [Stumbling Block III, 1] Loss of bone mass is a consequence of ageing and may lead to osteoporosis, in which bones are quite brittle and can break more easily than those of a younger person. Assign students (or groups of students) to find out what treatment for osteoporosis involves. Then ask them to relate what they have found to question 1 in the Questions for Discussion (pg. 781): Astronauts lose bone mass during space travel. Why do you think this happens?

Brainstorm why negative feedback mechanisms are more prominent in animals than are positive feedback mechanisms.

You may wish to draw comparisons between negative feedback mechanisms in homeostasis to what occurs in regulation of enzyme activity via feedback inhibition (Chapter 4).

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 8:



Cell communication

Chapter 43:



Homeostasis (including osmoregulation, thermoregulation) is discussed in much more detail.

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Clicker questions:

1. Negative feedback is best described as A. a process in which an environmental stimulus triggers a system to shut down.

B. a process in which an environmental stimulus triggers a response that compensates for changes in the internal/external environment. * C. a process in which there is a response to change in the internal/external environment that adds to the change.

D. a process whereby the environmental stimulus is repeated.

This question may help students to differentiate between positive and negative feedback.

2. Sarah takes a medication that blocks her neurons’ ability to be stimulated by glutamate’s chemical signal. What part of her neuron is likely affected by the medication? Modified from test bank question.

A. Axon terminals B. Axon body C. Dendrites* D. Axon hillock E. Cell body

WHAT OTHER RESOURCES ARE AVAILABLE? 

George Wolf talks about animal homestasis in an engaging manner. http://www.5min.com/Video/Animal-Homeostasis-151425325 .

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Most multicellular animals have a nervous system. Hundreds to billions of neurons (depending on the animal) compose the nervous system and work together carrying electrical messages that control every aspect of the body. Messages are carried in the form of action potentials and the rate of conduction and strength of each message is affected by various physical and chemical factors.

2.

Neurons are connected to one another and other body tissues via chemical or electrical synapses.

LEARNING OBJECTIVES Students should be able to:



Identify and describe the function of each component of a neuron: dendrite, cell body, axon, axon hillock, and terminal. [Knowledge]



Describe the four components of neural signalling (reception, transmission, integration, and response). [Comprehension]



Describe the roles of the three functional classes of neurons (afferent/sensory, efferent/motor, interneurons). [Comprehension]



Describe components of a typical neuronal circuit and how these circuits combine to form networks, and ultimately the nervous system [Comprehension, Analysis]



Differentiate between the peripheral nervous system (PNS) and the central nervous system (CNS) in terms of the neurons of which they are composed. [Knowledge]



Describe the role of glial cells, identifying three types of these cells and their locations.

[Comprehension]

226



Draw a chemical and an electrical synapse, identifying the following components where applicable (neuronal communication): presynaptic cell, postsynaptic cell, gap junction, synaptic cleft, vesicle, neurotransmitter, chemical receptors, voltage-gated channels [Comprehension]



Differentiate between electrical synapses and chemical synapses in terms of their function and the speed with which they transfer messages. [Comprehension]



Define key terms (signal conduction): membrane potential, anions, excitability, resting potential, action potential, depolarized, threshold potential, hyperpolarized, refractory period, voltage-gated ion channels, propagation. [Knowledge]



Describe differences between voltage-gated Na + channels and voltage-gated K+ channels.

[Comprehension]



Describe the purpose of the Na+/K+ pump in neurons. [Comprehension]



Explain how and why membrane potential changes during an action potential.

[Comprehension]



Describe the ionic events that occur during the depolarization, repolarization and hyperpolarization stages of an action potential. [Comprehension]



Describe the all-or-nothing principle of an action potential and its implications. (E.g., What happens if threshold is not reached? What does this mean in terms of message propagation?)

[Comprehension]



Compare and contrast graded potentials and action potentials, and their relationship.

[Comprehension, Analysis]



Describe how nerve impulses move by propagation, including changes in action potential magnitude and involvement of ion channels. [Comprehension]



Describe, with reference to ion channels, how myelin increases the rate of conduction.

[Comprehension]



Describe, making reference to ion channels, the importance of a refractory period, in relation to impulse direction, and how it is created. [Comprehension, Analysis]



Describe, making reference to resistance, how the rate of conduction is affected by the diameter of the axon. [Comprehension]



Describe conduction of an action potential across a chemical synapse. [Comprehension]



Describe the postsynaptic events initiated by both direct and indirect neurotransmitters.

[Comprehension]

227



Name and describe the effects of at least two neurotransmitters. [Comprehension]



Describe integration and summation at the postsynaptic neuron and their relationship with action potentials. [Comprehension]



Compare and contrast excitatory postsynaptic potential (EPSP) and inhibitory postsynaptic potential (IPSP), including why each is considered a graded potential. [Comprehension, Analysis]



Differentiate between temporal and spatial summation. [Comprehension]



Describe, using at least one example, how brain evolution within various vertebrates was affected by natural selection. [Comprehension]



Describe, briefly, how the brain and spinal cord are protected. [Comprehension]



Differentiate between white matter and grey matter in terms of their structure and location within the spinal cord. [Comprehension]



Describe the role of grey matter in reflexes. [Comprehension]



Describe, briefly, how the brain integrates sensory information and formulates compensating responses. [Comprehension]



Diagram the relationships between the CNS and the components of the PNS, including reference to the afferent and efferent systems. [Comprehension]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 5.

Students may confuse neural signalling and cell signalling, particularly because some of the terms for the components involved are the same, and there are some similarities in the processes at a general level. Students may also experience difficulties integrating cell signalling with neural signalling. E.g., A hormone bound to a receptor on a nerve cell initiates a signalling pathway, which leads to changes in the presynaptic terminal and facilitates or inhibits neurotransmitter release.

6.

When discussing the functional classes of neurons, students may get confused because afferent and efferent sound very similar. Instructors may need to explicitly identify, through spelling and drawing relationships with the spelling and the roles of the two types of neurons. For example, efferent neurons carry responses to effectors. Efferent can be associated with the word “exit” (“e” for efferent and exit) because the message is leaving (exiting) the neuron soma. Afferent can be matched with “arrive” (“a” for afferent and arrive) because sensory messages are arriving at the cell.

Knowledge of these terms (efferent and afferent) will also facilitate understanding of other body systems (e.g., cardiovascular) where they are also used as directional descriptions.

7.

Students have difficulties understanding the importance of the electrochemical gradient in the creation of a resting potential. They tend to understand an electrogradient or a chemical gradient separately, but combining the two leads to confusion. Describing the resting potential as a balance between the

228

concentrations and charges of the available ions can help. We strongly recommend that you do not address the Nernst or Goldman equations in first year.

8.

With regards to resting potential (e.g., -70 mv for many cells), students tend to think that the intracellular environment is literally negative. They need to be reminded that the potential is relative to the extracellular environment. The intracellular portion is simply less positively charged than the extracellular space. Show students the difference between ionic concentrations (Na +, K+ and Cl-) both within and outside the cell.

9.

Many students tend to think of depolarization as the potential becoming more negative (greater than 70 mv) instead of less (less than -70 mv). It can help to describe this process as minimizing the potential difference between the inner and outer environment of the neuron.

10. Students have difficulties understanding saltatory conduction. Many think the impulse literally jumps or skips over the myelinated sections and this increases the rate of travel.

WHAT CAN I DO IN CLASS? Likening electrical flow to the flow of water is a very useful visual image. For example for conductance and resistance relative to axonal diameter, use the analogy of a plumbing pipe. Water, like electricity, takes the path of least resistance (the easiest route). Draw a diagram of a pipe that ends at a T intersection. To the right is a large diameter pipe and to the left a small diameter pipe. Which direction is most of the water (aka electricity) most likely to flow?

Remind students that potential is a relative term that compares the intracellular environment to the extracellular environment. Resting potential is when the intracellular space is less positively charged compared to the extracellular space. Instructors could show this by using an example and then asking students to work in groups to compare the charges on either side of the membrane. (Students would simply need to add the charges on either side.) [Stumbling Block 3, 4] Students may be interested to know the mechanism by which Botox™works. This highly purified neurotoxin (produced by the bacterium Clostridium botulinum) prevents release of the neurotransmitter acetylcholine that induces muscle contraction. Vesicles containing acetylcholine cannot bind with the membrane of presynaptic neuron, and thus acetylcholine is not released into the synapse and cannot stimulate a muscle contraction. This results in flaccid paralysis, and regions that have received injections of the toxin will not be able to contract … thus, no wrinkles! The disease tetanus, caused by another clostridial toxin, also acts on neurons but blocks release of GABA or glycine from inhibitory interneurons that normally signal the end of muscle contraction.

The motor neurons continue to release acetylcholine, resulting in spastic paralysis (constant contraction of muscle).

Show students a figure of a myelinated section of the nervous system. Ask them to discuss in groups and determine what is missing from these neural membranes (i.e., Na + and K+ channels). Ask: Why are myelinated sections not longer? (Hint: What could happen to the message?) Students should recognize that the message would degrade with distance, eventually falling below the threshold point. Interruptions of the myelin at the Nodes of Ranvier offer a point where the action potential can (and must) be restored (or it will disappear).

[Stumbling Block 6] Discuss the similarities of some symptoms of multiple sclerosis with difficulties seen in babies when learning to walk. Loss of myelin in multiple sclerosis (the signal never makes it to legs) and incomplete formation of myelin in infants (start to walk around 10 months of age) both interfere with walking signals.

ADDITIONAL LINKS TO OTHER CHAPTERS

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Chapter 2:



Features of cells.

Chapter 5:



Active transport, exocytosis

Chapter 34:



A basic grasp of the nervous system is required to understand and conceptualize the basics of the sensory systems.

Clicker questions:

1.

When an impala (a deer-like animal from Africa, not a car) attempts to run away from a pack of wild African dogs, what division of its autonomic nervous system would dominate?

A. Central nervous system.

B. Parasympathetic nervous system.

C. Sympathetic nervous system.* D. Cerebellar nervous system.

E. Somatic nervous system.

230

2.

The nervous system plays a role in A. Receiving information from external and internal environments.

B. Responding to information from external and internal environments.

C. Processing of information from external and internal environments.

D. All of the above (A-C) are correct.* E. None of the above (A-C) is correct.

3.

From which axon would you expect the fastest action potential propagation?

A. An unmyelinated axon with a small diameter.

B. A myelinated axon with a small diameter.

C. A myelinated axon with a large diameter.* D. Axon myelination and diameter do not affect action potential propagation rate.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Interactive action potential animation. http://outreach.mcb.harvard.edu/animations/actionpotential.swf

231

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Senses allow animals to detect and interact with our environment (both abiotic and biotic).

2.

Essentially, all animal senses work by the same basic mechanism, sensory transduction, whereby something in the environment (e.g., light, smell, sound, etc.) stimulates the appropriate receptor, and provides information about the animal’s environment.

LEARNING OBJECTIVES Students should be able to:



Define: sensory receptors, sensory transduction. [Knowledge]



Describe the five main types of sensory receptors (mechanoreceptors, photoreceptors, chemoreceptors, thermoreceptors, nociceptors), the types of stimulus that each detects (how they act in sensing the environment), and the locations where each might be found in a human. [Comprehension]



Explain the importance of sensory systems for an animal. [Comprehension]



Explain why humans should be said to have more than five senses. [Comprehension]



Describe, briefly, how the CNS processes information from sensory receptors, explaining how intensity of a stimulus can be detected. [Comprehension]



Describe the phenomenon of sensory adaptation and its importance to survival.

[Comprehension, Analysis]



Describe how pain detectors are nonadapting and the importance of this in survival.

[Comprehension]



Define key terms (mechanoreception): propioception, statoliths, lateral line system, vestibular apparatus, otoliths, stretch receptors, tympanum, cochlea, oval window, basilar membrane, Eustachian tube. [Knowledge]

232



Describe the impact of receptor density on sensitivity to touch. [Comprehension]



Describe how the lateral line system functions in the schooling behaviour of fish.

[Comprehension]



Describe, briefly, two of the different types of proprioceptors (e.g., statocysts, lateral line system, vestibular apparatus) and how they function. [Comprehension]



Describe the location and general function of the vestibular apparatus and stretch receptors.

[Comprehension]



Describe how statoliths and otoliths are analogous (i.e., have similar function).

[Comprehension]



Describe how fish, which don’t have external ears, always know where the fisherpeople are.

[Comprehension]



Describe, briefly, how hearing is similar in humans and grasshoppers, listing analogous components of each system. [Comprehension]



Define key terms (photoreception): ocellus, single-lens eyes, compound eyes, ommatidia, accommodation, retina, fovea, blind spot. [Knowledge]



Differentiate between rods and cones and their respective functions in photoreception.

[Comprehension]



Describe why clearly defined foveas are typically lacking in mammals and birds specialized for night vision. [Comprehension]



Describe the three parts of a photoreceptor. [Comprehension]



Draw and label a photoreceptor. [Knowledge]



Describe how the simplest eye differs from image-forming eyes. [Comprehension]



Describe why compound eyes are good at detecting motion. [Comprehension]



Describe, briefly, why some invertebrates and vertebrates are able to see colour and how colourblindness can result in such animals. [Comprehension]



Describe how the optic chiasm affects image transmission. [Comprehension]



Describe the adaptive value of binocular vision. [Comprehension]



Define key terms (chemoreception): gustation, olfaction, pheromones. [Knowledge]

233



List environmental factors about which chemoreception can provide information. [Knowledge]



Differentiate between taste and smell. [Analysis]



Describe the basic structure of a taste bud. [Comprehension]



Explain why some tastes evoke pleasure, whereas others cause revulsion. [Comprehension]



Describe how olfaction is used in communication. [Comprehension]



Describe, briefly, how thermoreceptor and nociceptor structures differs from those of mechanoreceptors and chemoreceptors. [Comprehension]



Describe two roles of thermoreceptors. [Comprehension]



Discuss how nociceptors function in protection, commenting on their nonadaptive nature.

[Comprehension]



Describe the two outcomes of nociceptor stimulation, in terms of CNS activation.

[Comprehension]



Describe how animals use electrical and magnetic information. [Comprehension]



Describe why a magnetic navigational system would be advantageous for an animal.

[Comprehension]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

Sensory adaptation may be confused by students to represent evolutionary adaptation. Although sensory adaptation may have an evolutionarily adaptive value, it refers to a reduction in the effect of a repeated stimuli on a sensory receptor.

2.

This chapter has a considerable amount of new vocabulary that is introduced in discussing the different receptor types (and their components) in different organisms. We recommend that instructors approach this chapter in a comparative way. E.g., students could prepare a table comparing proprioception in different generalized groups of animals (e.g., aquatic invertebrates, fish, birds, terrestrial mammals, etc.). Instructors should frequently remind students that the underlying basis of sensory perception is similar for all the receptors discussed: information from the environment (internal or external) is received, processed, and responded to.

234

WHAT CAN I DO IN CLASS? Ask students (perhaps using a clicker question), whether visual or olfactory information is better at stimulating memories. This could lead to a short discussion of where signals from each are sent (e.g., some olfactory signals are sent to the limbic system, which functions in the autonomic (involuntary) nervous system.

Often humans integrate visual and proprioceptive information to provide positional information. Ask students to stand up and stand on one foot and count to 10 slowly. Ask them how difficult this is. Then ask them to close their eyes, and repeat the exercise. Again, ask how difficult this is – particularly relative to when they had their eyes open. Ask: What types of sensory receptors are they using in each case?

Discuss: What are some redundancies in animal sensory systems? What would be advantages to these redundancies? What would be advantages to sensory adaptation? [Stumbling Block 1] Homing pigeons, among other organisms use magnetoreceptors to detect the earth’s magnetic field and determine their direction/location. Ask: What do you think would happen to a homing pigeon if you strapped a magnet to its head? To emphasize the commonality of life, you may want to bring up the fact that there are examples of bacteria that also use magnetoreception (referred to as magnetotaxis) to orient their direction.

[Stumbling Block II]

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 17:



The sensory system allows us to interact with our environment (both internal and external) and has great evolutionarily adaptive value. Even small developments of sensory systems (e.g., appearance of eyespots compared to no way of sensing light) could have had major effects on fitness.

Chapter 33:



Sensory receptors process information via the neural pathways (and associated action potentials) described in Chapter 33.

Chapter 41:



Includes information about the Archer fish, which “shoots” its prey with a targeted stream of water. Students can consider how the fish is able to sense its prey.

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Clicker questions:

1.

If two fruit flies landed on you, one on your face, near your lips, and the other on the back of your leg, which one would you most likely detect by touch receptors?

A. The fly on my face.* B. The fly on my leg.

C. Both would be detected equally.

D. Neither, as humans lack touch receptors in these areas.

This question relates to the relative spacing/density of the mechanoreceptors of the skin and the related sensitivity.

2.

Sensory input from eyes and ears travels in neurons to the brain. Why then can the different stimuli be perceived as light and sound, respectively? Modified slightly from Test Bank.

A. Light receptors are stimulated much more strongly than sound receptors.

B. Light receptors are stimulated much more frequently than sound receptors.

C. The physical location of the receptors differs, ensuring a different ‘sense’ will be perceived in the brain.

D. Information from each type of receptor is sent to a different part of the brain.* E. The process of sensory reception in light receptors differs substantially from that of sound receptors.

Although the basics of sensory reception are similar, information from different receptors may be sent to different regions of the brain for processing.

WHAT OTHER RESOURCES ARE AVAILABLE? 

 

The archerfish in action! http://www.youtube.com/watch?v=GhMi9Hw_wZ0 (from Absolutely Wild Visuals) or http://www.youtube.com/watch?v=fhBZ40jIo4Q (Our Wild World).

Fang J. Snake infrared detection unravelled.

Nature. March 14, 2010. doi:10.1038/news.2010.122 Gracheva E, Ingolia N, Kelly Y, Cordero-Morales J, Hollopeter G, et al. 2010. Molecular basis of infrared detection by snakes. Published online 14 March 2010.

236

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Behaviour and developmental events are affected by chemical messengers, hormones, which are secreted by endocrine glands in response to cues from the internal and/or external environment.

2.

Hormones of the endocrine system are another form of internal communication (the nervous system is another). They are released by endocrine glands and can effect change in cells/glands that are considerably far away in the body.

LEARNING OBJECTIVES Students should be able to:



Define: endocrine gland, exocrine gland, hormone, target cell, paracrine regulation, autocrine regulation, amplification. [Knowledge]



Differentiate between endocrine glands and exocrine glands. [Comprehension]



Describe, briefly, neuroendocrine signalling. [Comprehension]



Describe components of a typical neuronal circuit. [Comprehension]



Describe why paracrine and autocrine regulation are not considered part of the hormone signalling system. [Comprehension]



Describe the four major types of cell signalling in the endocrine system: classical endocrine signalling, neuroendocrine signalling, paracrine regulation and autocrine regulation.

[Comprehension]



Draw a simple diagram illustrating hormone origin, transportation, and effects on target cells differentiating the four major types of cell signalling within the endocrine system.

[Comprehension, Analysis]



Describe the four classes of hormones/local regulators (i.e., amine hormones, peptide hormones, steroid hormones, and fatty acids). [Comprehension]

237



Describe how secretion of most hormones is regulated. [Comprehension]



Explain how very small amounts of hormone are able to produce such large effects.

[Comprehension]



Describe three mechanisms by which hormone action can be controlled. [Comprehension]



Summarize, briefly, the response produced by hormones that bind surface membrane receptors. [Comprehension]



Summarize, briefly, the response produced by hormones that bind to intracellular receptors.

[Comprehension]



Describe the main difference between hormones that bind to receptor proteins on the plasma membrane and those that bind to receptors inside the cell. [Comprehension]



Describe, using an example, how target cells may respond to more than one protein.

[Comprehension]



Describe, using an example, how the same hormone may have different consequences on different target cells. [Comprehension]



Describe, using an example, how different animals may have different responses to the same hormone. [Comprehension]



Name and list the locations of four types of endocrine cells/glands, and their products in humans. [Knowledge]



Distinguish between tropic and nontropic hormones. [Analysis]



Provide one example each of a hormone that alters: mood, behaviour, cognitive abilities, physical performance, development, and health. [Comprehension]



Describe, briefly, how blood glucose levels are maintained. [Comprehension]



Discuss the role of hormones in invertebrates, in particular, metamorphosis. [Comprehension]



Relate the variety of roles of hormones in animals to those of plant growth regulators (plant hormones). [Analysis]

238

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

Students tend to confuse the terms endocrine and exocrine. Exocrine glands have ducts to deliver secretions directly to target locations; endocrine glands do not have such ducts.

2.

Some understanding of membrane transport/selective permeability (as discussed in Chapter 5) is necessary to understand how hormonal signals are received. Hormones binding to membrane receptor are going to be hydrophilic; those binding to a receptor inside the cell are typically hydrophobic.

3.

Table 35.1 is a summary of the major endocrine glands and their hormones in humans. While this can be useful to show the variety of different glands and their products, the amount of information can be overwhelming for students. (Moreover, this list is not exhaustive, as organs with other primary functions (e.g., the kidney) can also produce hormones.) We recommend that instructors be clear with expectations regarding what (if anything) students are expected to know from this table and suggest, depending on course curriculum, that instructors choose a few of these at most to focus on.

WHAT CAN I DO IN CLASS? The “Why It Matters” uses the example of a moulting moth larva and its transformation to the adult stage of its life cycle. Ask: How does the larva know when to begin moulting? What are the internal/external cues?

How is hormone release triggered by these cues?

Ask: If hormones are produced in one area and delivered to a location not close by in the body, how are the effects of the hormone controlled? (see Chapter 8, Cell communication) That is, how do they only act on the cells that they should be acting on? These questions can remind students that specific cells will have specific receptors for these hormones (to control the action of the hormones).

You may want to concentrate on a single endocrine gland and follow through all products and their actions, emphasizing connections between material covered in previous chapters. (Alternatively, different endocrine glands could each be assigned to a small group of students to carry out this kind of analysis.) This will provide students with an opportunity to integrate concepts from throughout the course. [Stumbling Block III] The hormones involved in a ‘Fight-or-Flight’ response are discussed within this chapter. These could be explicitly linked to material in Ch. 33 and Ch. 34. [Stumbling Block III] Bisphenol A has been in the news quite a bit over the past several years since it was identified as an endocrine disruptor chemical (EDC). These are compounds that interfere with the production of hormones or hormone activity. Such chemicals have been linked to health-associated risks, such as reduced fertility, feminization, and increased risk of some conditions and cancers. Student groups could be assigned an endocrine disruptor and find information about their uses, regulations, routes of exposure, etc. [e.g., dioxin, polychlorinated biphenyls (PCBs), DDT (which is highly persistent in the environment and slow to degrade – see Chapter 47, biomagnification), diethylstilbesterol, and plasticizers such as bisphenol A. Some act as hormone-mimics (e.g., phytoestrogens, such as genistein found in soy-based products), while others act as endocrine blockers; all can have profound effects on wild populations. Ask: why do endocrine disruptors work the way they do? Why are even small amounts in the environment potentially harmful for some organisms?

More information: EDCs have their greatest effect during embryogenesis and perinatal development (during organ and neural system development), but can have other consequences that affect animal

239

populations. For example, raptors such as bald eagles and peregrine falcons exposed to DDT were unable to produce eggshells (that would withstand the weight of the parent during incubation). As a result, populations suffered. Other EDCs may have feminizing effects and interfere with normal reproductive function. These affect wildlife through male reproductive organ abnormalities, reductions in male fertility, alteration of gender ratios (i.e., decreasing numbers of males), increased incidence of reproductive cancers (prostate, ovarian, mammary), and altered female reproductive development (earlier onset of puberty and subsequent early reproductive senescence, and fertility issues.) The impact of EDCs is extensive as they can affect future generations despite no direct exposure – research suggests may be able to alter/reprogram gene expression without changes to DNA sequence.

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 5:



Differences in chemical structure of different hormone types determines whether they can easily pass through the selectively-permeable membrane of a cell.

Chapter 8:



Signal transduction; amplification of effects (i.e., an activated receptor activates a series of proteins, which in turn activate a larger number of proteins, etc.)

Chapter 15:



Regulation of gene expression.

Chapter 20:



Similarities of peptide hormones between invertebrates and vertebrates, evolutionary history observed through unity of shared characteristics.

Chapter 32:



Negative feedback.

240

Chapter 43:



Endocrine regulation is involved in osmoregulation and thermoregulation.

Chapter 48:



Endocrine disruptors and severe consequences on population sizes.

Clicker questions:

1.

Neural activity involves transmission of information via ________; in contrast, endocrine activity involves transmission of information via ________?

A. Electrical events; hormone transport to target tissues.* B. Hormone transport; hormone release in body fluids.

C. Electrical events; hormone transport through electrical signals.

D. Hormone transport; hormone transport to target tissues.

Modified from Test Bank. Reinforces idea that both the nervous system and the endocrine system work in information transmission.

2.

The target tissues for steroid hormones do not have receptors on the membrane surface for these hormones because the hormones A. can enter the cell by simple diffusion.

B. alter the membrane potential of the cell, leading to cellular responses.

C. are soluble in the lipid bilayer.* D. are transported against their concentration gradient by active transporters in the cell membrane.

Modified from Test Bank. This question links membrane permeability/transport (Ch. 5) and cell communication (Ch. 8) concepts with this chapter. [Stumbling Block 2]

3.

Hormone A binds to intracellular receptors in its target tissue. As a result of Hormone A, the target tissue is now sensitive/responsive to Hormone B. The action of Hormone A was to A. Decrease mRNA for Hormone A receptors.

B. Increase receptor sites for Hormone B.* C. Increase receptor sites for Hormone A. D. Increase mRNA for Hormone A receptors.

Taken from Test Bank. Stumbling Block 2.

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4.

Which of the following hormones enter cells and have the primary action to increase or decrease mRNA production?

A. Steroid and phospholipid hormones.

B. Thyroid and peptide hormones.

C. Peptide and phospholipid hormones.

D. Steroid and thyroid hormones.*

Taken from Test Bank. Students will need to know the hydrophilic/hydrophobic nature of the hormones listed above. Hydrophobic hormones that enter cells to increase/decrease mRNA production bind to receptors within the cell. [Stumbling Block 2].

WHAT OTHER RESOURCES ARE AVAILABLE? 

Images http://www.epa.gov/endo/pubs/edspoverview/whatare.htm



National Institute of Environmental Health Sciences – National Institutes of Health website with several informative pdfs on endocrine disruption, clinical trials, etc, as well as educatorspecific lessons that could be modified for an introductory biology class. http://www.niehs.nih.gov/health/topics/agents/endocrine/



Summary of papers examining changes in sex ratio and feminization in the U.K., and the Great Lakes watershed. ehp.niehs.nih.gov/docs/2005/113-10/EHP113pa686PDF.PDF



http://ehp.niehs.nih.gov/docs/2005/113-10/ss.html

242

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

The muscles and skeleton provide a support system for the body and its movements.

LEARNING OBJECTIVES Students should be able to:



Define key terms (skeletal muscle): skeletal muscle, muscle fibre, myofibril, (thick filament, thin filament), actin, myosin (head, tail, crossbridge), tropomyosin, troponin, A bands, H zone, M line, I bands, Z line, sarcomere, T (transverse) tubule, sarcoplasmic reticulum, action potential, neuromuscular junction, acetylcholine, tetanus, slow muscle fibres, myoglobin, fast muscle fibres, motor unit. [Knowledge]



Describe the composition and arrangement of skeletal muscle. [Comprehension]



Describe the sliding filament mechanism of muscle contraction. [Comprehension]



Describe the role changing Ca2+ levels in the sarcoplasmic reticulum and cytosol in muscle contraction. [Comprehension]



Explain what is meant by the crossbridge cycle in muscle contraction. [Comprehension]



Describe what occurs for a contracting muscle to relax. [Comprehension]



Describe the relationship of tension produced in a muscle fibre to frequency of action potentials. [Comprehension]



Describe the role of myoglobin in muscles. [Comprehension]



Compare and contrast the composition and actions of slow muscle fibres, anaerobic fast muscle fibres and aerobic fast muscle fibres. [Comprehension, Analysis]



Describe the muscles of invertebrates. [Comprehension]

243



Describe how insect flight muscles provide high frequency wing beats without inducing tetanus. [Comprehension]



Define key terms (skeleton) hydrostatic skeleton, exoskeleton, chitin, endoskeleton, axial skeleton, appendicular skeleton, bone, red marrow, yellow marrow, synovial joint, ligament, cartilaginous joint, fibrous joint, fulcrum, agonist, antagonistic pairs, extensor muscle, flexor muscle. [Knowledge]



Describe how the muscles of annelids act upon the hydrostatic skeleton in movement.

[Comprehension]



Describe variations of the hydrostatic skeleton in sea anemones, annelids, echinoderms, and the vertebrate penis. [Comprehension]



Explain how some organisms/parts of organisms can achieve movement without support of skeletal elements. [Comprehension]



Describe the composition and role of an exoskeleton in non-vertebrates. [Comprehension]



Compare and contrast hydrostatic skeletons, exoskeletons and endoskeletons. [Comprehension]



Describe, using an example, the composition and role of the endoskeleton in a nonvertebrate. [Comprehension]



Explain why bones of the vertebrate endoskeleton can be considered organs. [Comprehension]



Describe how the vertebrate skeleton and its associated muscles work to produce movement. [Comprehension]



Describe an example of a vertebrate muscle-bone interaction optimized for specific movements. [Comprehension]



Describe, using examples, the different types of joints in vertebrate skeletons. [Comprehension]



Correctly identify the fulcrum in a diagram of vertebrate muscle, bone, and joint.

[Comprehension]



Describe the action of antagonistic muscle pairs in movement, including the arrangement of the muscles and action of each. [Comprehension]

244



Relate the factors that would affect the performance of an elite athlete (including aspects of the nervous system, nutrition, gas exchange, thermoregulation). [Analysis, Synthesis]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

Neural signals are an important part of muscle contraction. If students do not understand what an action potential is (see Chapter 33), they may have difficulty understanding aspects of the skeletal muscle events.

WHAT CAN I DO IN CLASS? Visual images (including figures from the text, such as Fig. 36.5) and physical models will be valuable in helping students understand the events that occur in muscle contraction at different levels (e.g., molecular, macro).

Ask students if there are limits to how large muscles can get. Bones? Students may have fun with looking at whether creatures such as Godzilla are biomechanically possible. Christiansen (2000) looked into the biomechanics of whether the “new” Godzilla (1998 movie) was biomechanically plausible, and compared this version to the “classic” Godzilla of Japanese movies. (See reference in Resources.) [Stumbling Block III]

ADDITIONAL LINKS TO OTHER CHAPTERS The muscles and skeleton are necessarily involved in many other animal systems, and concepts discussed in the Animals section (and other chapters).

Chapter 2



Cytoskeleton (actin)

Chapter 6



Cellular respiration (muscles require high levels of ATP)

Chapter 33



Nervous system

Chapter 34



Sensory systems

Chapter 35



Hormonal control of Calcium/phosphate deposition in bones

245

Chapter 37



Circulation of blood

Chapter 41



Animal nutrition

Chapter 42



Gas exchange (muscles need O2, removal of CO2)

Chapter 43



Thermoregulation is key in optimal performance of muscles

Clicker questions:

1.

Joe visits the hospital suffering from uncontrollable muscle spasms. Which of the following could have led to this state?

A. Acetylcholine release at the synaptic cleft of the muscle cell is blocked.

B. Calcium uptake is increased at the sarcoplasmic reticulum.

C. Calcium uptake is blocked at the sarcoplasmic reticulum.* D. Cellular respiration is slowed down, and low levels of ATP are available in muscle fibres.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Could an organism such as Godzilla exist (i.e., scaled up versions of small things)?

Christiansen P. 2000. Godzilla from a Zoological Perspective. Mathematical Geology 32(2): 231-245.

246

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

In animals, the circulatory system allows distribution and collection of nutrients, gases, wastes, etc., throughout the body. The heart plays a primary role in the circulatory system of many, but not all animals.

LEARNING OBJECTIVES Students should be able to:



Define key terms (general terms): circulatory system, lymphatic system, open circulatory system, closed circulatory system, haemolymph, heart, blood, arteries, capillaries, veins, aortic arch. [Knowledge]



Compare and contrast the open circulatory system to the closed circulatory system of animals, indicating which types of animals possess each system. [Comprehension]



Describe the evolutionary trends of vertebrate circulatory systems from a single-circuit to a double-circuit system. [Comprehension]



Compare and contrast the hearts of fish, amphibians, reptiles and mammals. [Comprehension]



Draw a simple diagram showing the circulation in heart and lungs of a mammal, indicating the different structures, circuits, and oxygenated and deoxygenated blood. [Comprehension]



Define key terms (blood and components): plasma, haemocytes, erythrocytes, leukocytes, platelets, plasma proteins (albumins, globulins, fibrinogen), haemoglobin, erythropoietin, fibrin. [Knowledge]



Describe how the composition of blood varies between animals (e.g., nematodes vs. arthropods vs. mammals). [Comprehension]



Describe the possible roles of haemocytes in animals. [Comprehension]

247



Describe the nature and roles of the major plasma proteins (albumins, globulins, fibrinogen).

[Comprehension]



List and describe the roles of ions present in blood plasma. [Knowledge, Comprehension]



Describe the origin of, and steps in maturity of erythrocytes in humans. [Comprehension]



Explain how a blood clot is formed, and the purpose of making one. [Comprehension]



Define key terms (heart): systemic circuit, pulmonary circuit, cardiac cycle, systole, diastole, neurogenic heart, myogenic heart, sinoatrial (SA) node, pacemaker cells, atrioventricular (AV) node, Purkinje fibres, electrocardiogram (ECG/EKG), blood pressure (systolic, diastolic). [Knowledge]



Draw a cut-away view of the human heart, labelling the atria, valves, ventricles, septum, aorta, pulmonary arteries, pulmonary veins, inferior vena cava, and indicating where blood is deoxygenated vs. oxygenated. [Comprehension]



Describe how blood is pumped through the mammalian heart, including the role of contraction and relaxation of atria and ventricles, and valves. [Comprehension]



Describe coronary circulation. [Comprehension]



Describe electrical control of the cardiac cycle in mammals, relating this to the structure and function of cardiac muscle. [Comprehension]



Correctly identify steps in the cardiac cycle as shown in an ECG. [Comprehension, Application]



Define key terms (blood vessels, blood flow): precapillary sphincter, arteriole (sphincter and muscles), blood-brain barrier, venule, cardiac output, baroreceptors, [Knowledge]



Compare and contrast arteries, veins and capillaries in terms of structure, relating this to their different functions. [Comprehension]



Describe how veins and venules serve as blood reservoirs, in addition to conduits.

[Comprehension]



Describe the three main regulators of blood pressure. [Comprehension]



Explain how O2 and CO2 concentrations influence cardiac output. [Comprehension]

248



Explain briefly how hormones contribute to regulation of blood pressure. [Comprehension]



Describe local controls that increase flow of blood to regions of the body undergoing increased metabolic activity. [Comprehension]



Define key terms (lymphatic system): lymph, lymph ducts, lymph capillaries, lymph vessels, lymphoid tissues/organs (spleen, thymus, tonsils, lymph nodes). [Knowledge]



Describe the three major roles of the lymphatic system. [Comprehension]



Draw a simple diagram showing the human lymphatic system, labelling the various components, tissues and organs. [Comprehension]



Relate the circulatory system to the lymphatic system. [Analysis]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

Students have a tendency to believe that humans are higher organisms (i.e., we are more evolved, rather than just more recently evolved), and thus the structures of our body must be “better”. This can translate into an assumption that the mammalian heart is the pinnacle of circulatory system perfection. However, the animal circulatory system is highly adapted to the environment and the lifestyle that an organism occupies. The open circulatory is well-suited a lifestyle with limited activity, whereas high-activity lifestyles require the continual replenishment of nutrients and oxygen that only the high pressure of a closed circuit can offer. For example, within the same phylum, most molluscs have an open circulatory system, whereas the cephalopods possess closed circulatory systems that match well to their active lifestyles (e.g., food acquisition).

WHAT CAN I DO IN CLASS? A comparative approach, looking at open circulatory systems versus closed circulatory systems in relation to organism lifestyle is highly recommended. Assign groups of students specific animals (e.g., a non-cephalopod mollusc, a cephalopod, organisms that lead fairly sedentary lives, organisms that lead highly active lives) and ask them to energetic/metabolism and oxygen needs and relate this to the organism’s circulatory system (i.e., open or closed). Many think that regardless a closed circulatory system would be ideal. It is good to remind students that adaptations do not come about because are wanted, as well as asking them to consider the energetic costs of building and maintaining a closed circulatory system. [Stumbling Block I, III, 1]

249

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 34:



Baroreceptors are a type of mechanoreceptor.

Chapter 35:



Hormones regulate blood pressure.

Chapter 36:



The heart is made of cardiac muscle.

Chapter 42:



Gas exchange and the circulatory system are intimately tied together.

Chapter 44:



The circulatory system plays a role in immune system function.

Clicker questions:

1.

Which of the following statements is correct concerning an open circulatory system?

A. It is more efficient than a closed system.

B. It contains two circulatory systems.

C. Hemolymph and interstitial fluids mix together.* D. Blood is contained in blood vessels.

Taken from Test Bank. This question can be used to prompt discussion regarding differences between open and closed circulatory. [Stumbling Block 1]

2.

Which of the following would NOT be likely to pass easily through capillary walls?

A. Carbon dioxide.

B. Erythrocyte* C. Water D. Glucose

Taken from Test Bank.

3.

The main fore that moves blood throughout the system of blood vessels is A. Venous blood pressure B. Valve action C. Arterial blood pressure* D. Smooth muscle action

[Stumbling Block 1]

WHAT OTHER RESOURCES ARE AVAILABLE?

250



Images of cork oat (including harvest of cork): http://www.forestryimages.org/browse/subthumb.cfm?sub=7071&start=1



Wigel D, Jürgens G. 2002. Stem cells that make stems. Nature 415(6873): 751-754.

251

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

As in plants, bacteria, fungi, and all other life, reproduction ensures the transfer of genes (as allowed by natural selection) and thus, there is a strong drive to reproduce, and considerable time and resources are devoted to reproductive processes.

LEARNING OBJECTIVES Students should be able to:



Differentiate between asexual reproduction and sexual reproduction, genetic makeup of offspring, and environments in which they might be favoured (advantageous).

[Comprehension]



Define key terms (asexual reproduction): asexual reproduction, fission, budding, fragmentation, parthenogenesis. [Knowledge]



Describe when offspring by parthenogenesis can be genetically identical to the parent and when they are not. [Comprehension]



Define key terms (sexual reproduction): egg, sperm, meiosis. [Knowledge]



Define key terms (sex cell formation): gametogenesis, germ cells (compare to somatic cells), fertilization, testes, ovaries, spermatogenesis, oogenesis, spermatogonia, oogonia, spermatocytes, oocytes, sperm/spermatozoa, egg/ova, acrosome, polar body, vitelline coat/zona pellucida. [Knowledge]



Describe the characteristic feature that distinguishes eggs from sperm. [Comprehension, Analysis]



Describe how sperm and eggs are specialized for their purposes (i.e., for travel (movement?), early embryo development, respectively). [Comprehension]



Describe how eggs of insects, amphibians, reptiles, including birds prevent their eggs from dessication. [Comprehension]

252



Describe why bird eggs would be larger than mammalian eggs. [Comprehension]



Describe the advantages and disadvantages of external fertilization and internal fertilization.

[Comprehension]



Describe how internal fertilization makes terrestrial life possible (the benefits of internal fertilization). [Comprehension]



Describe the basic steps in fertilization. [Comprehension]



Describe a gametic barrier to hybridization and its advantages in species that shed their eggs and sperm into aquatic environments. [Comprehension]



Describe two mechanisms that help to prevent polyspermy (fast block & slow block).

[Comprehension]



Define (embryonic development): oviparous, viviparous, ovoviviparous, uterus, eutherian, metatharian. [Knowledge]



Differentiate between the three patterns of embryonic support (ovipary, vivipary, ovovivipary) and the animals in which they are common/occur, and any advantages.

[Comprehension]



Define hermaphroditism, commenting on the frequency of self-fertilization in hermaphrodites. [Knowledge]



Describe an advantage to the fact that most hermaphroditic individuals don’t fertilize themselves.[Comprehension]



Distinguish between simultaneous and sequential hermaphroditism, providing an example of each. [Comprehension]



Define and describe ovulation, menstrual cycle, cryptic ovulation, corpus luteum, [Knowledge, Comprehension]



Describe how ovulation (ovarian cycle) and the menstrual/uterine cycle are coordinated in human females. [Comprehension]



Describe advantages of delayed fertilization (e.g., in sea turtles) or delayed implantation (e.g., seals, kangaroos). [Comprehension]



Describe the roles and levels of gonadotropin-releasing hormone (GnRH), folliclestimulating hormone (FSH), luteinizing hormone (LH), estrogen, progesterone, and inhibin in the ovarian cycle. [Comprehension]

253



Describe what happens to the uterine lining in mammals that do not experience menstruation. [Comprehension]



Label diagrams of the reproductive organs of a human male and female with the following terms where appropriate: ovary, oviduct, uterus, urethra, cervix, vagina, anus, bladder, testis, epididymis, scrotum, penis, vas deferens, prostate gland, seminal vesicles. [Knowledge]



Describe the role of Sertoli cells and Leydig cells in sperm production (spermatogenesis).

[Comprehension]



Describe the role of the secretions of the seminal vesicles, prostate, and bulbourethral glands in male fertility. [Comprehension]



Describe hormonal regulation of reproduction in the male and the negative feedback systems that control hormone levels. [Comprehension]



Describe the role of the acrosome reaction in fertilization and human chorionic gonadotropin (hCG) in implantation. [Comprehension]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

Students confuse unfertilized eggs with eggs that reptiles (including birds) lay that are fertilized. (They do so similarly with seeds of plants, believing these to be unfertilized). It may help to point out what the egg has – shell (a seed usually has a hard coat as well) and ask how sperm would fertilize the egg if it needed to (thankfully it doesn’t; it would have difficulty penetrating the shell).

2.

There are many factors that students may not be aware of in reproduction. It may be good to focus on water to land transition in discussing some aspects. In water how can an organism ensure that the eggs are going to meet the ‘right’ sperm (i.e., from same species)? On land how do you ensure that eggs and sperm won’t dry out (similarly for the embryo)?

WHAT CAN I DO IN CLASS? Limpets are an interesting reproductive example. (See Chapter 10 “Why it matters” – the first limpet to settle on a surface is female, with layers of additional limpets differentiating to be males. If the female dies, the next limpet changes sex.) Students are often shocked by this different, but not unique, type of reproductive strategy … and the fact that the sex of a limpet can change!

Reproduction is important! Indeed some animals’ existence seem very short culminating in a mass reproductive effort. Ask students to think about the effort that goes into successful reproduction. (E.g., Finding a mate, ensuring your genes are passed on. Protect your investments!)

Controlling reproduction (i.e., inhibiting or promoting) is important to humans and to other species.

Knowledge of animal reproduction can help with conservation efforts as well as minimizing or maximizing the chances of pregnancy in humans, which may make some of this material relevant to students. If appropriate, you could have an in-class discussion about the reproductive aspects of political/legal/medical policies in different countries.

254

Discuss: What factors could have led to the evolution of sexual reproduction? Does the evidence suggest it evolved once, or did it evolve several times? What are some advantages of sexual versus asexual reproduction?

Some species of organisms, e.g., Daphnia are capable of both sexual and asexual reproduction. What would be an advantage of maintaining the capability of both forms of reproduction?

Interesting discussion topic/example: How do plants exploit animals to effect pollination and dispersal of seeds? Are there examples of animals exploiting plants to achieve reproduction? There are many examples of plants exploiting animals in reproductive strategies, but we hear about the reverse situation less often. A classic example of a mutualism is between Ficus (fig) plants and pollinating wasps. This species of wasps deposit eggs in fig ovules, which are consumed by wasp larvae. The plant does gain benefit from the pollination, while the wasp larvae have a rich food source from the fig ovules. This links to life history traits (Chapter 45) and interspecific interactions (Chapter 46).

The penises of Drosophila have spines (spikes and hooks). In the search to figure out what these did, Canadian evolutionary biologist Dr. Michal Polak and colleagues found that laser ablation of these structures doesn’t affect fly behaviour, and the male is still allowed to mount; however, the male cannot stay in position. The spikes are like Velcro for reproduction. (Consult Quirks and Quarks podcast.)

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 17:



Sexual selection.

Chapter 35:



Endocrine system – hormones that act on the reproductive system.

Chapter 40:



Animal behaviour/mates as resources

Chapter 45:



Trade-offs and life history strategies.

255

Chapter 46:



Interspecific interactions (e.g., for pollination)

Clicker questions:

1.

On an unexplored island you find a salamander population of all females that produce offspring from unfertilized eggs. This form of reproduction is A. Oogenesis B. Parthenogenesis* C. Fragmentation D. Viviparity E. Embryogenesis

2.

Viviparity would be advantageous and selected for (over oviparity and asexual forms of reproduction) in which of the following circumstances?

A. Warm environment with low ova production by females.

B. Cold environment with low ova production by females.* C. Hot environment with high ova production by females.

D. Mild environment with low ova production by females.

Addresses fact that the different reproductive strategies are good in different environments. Viviparity requires energy, but protects offspring from external environment.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Gray RH, Kigozi G, Serwadda D, Makumbi F, et al. 2007. Male circumcision for HIV prevention in men in Rakai, Uganda: a randomized trial. The Lancet 369(9562): 657-666.



Shaving a Fly with a Laser. Quirks and Quarks. January 16, 2010. http://www.cbc.ca/quirks/archives/09-10/qq-2010-01-16.html o Polak M and Rashed A. 2010. Microscale laser surgery reveals adaptive function of male intromittent genitalia. Proc R Soc B 277(1686): 1371-1376.



Douglas W. Yu, Jo Ridley, Emmanuelle Jousselin, Edward Allen Herre, Stephen G. Compton, James M. Cook, Jamie C. Moore, and George D. Weiblen. 2004. Oviposition strategies, host coercion and the stable exploitation of figs by wasps. Proc Biol Sci. 271(1544): 1185–1195.



Indirect evidence for the earliest sexual reproduction. The Earliest Sex. Quirks and Quarks.

April 12, 2008. http://www.cbc.ca/quirks/archives/07-08/apr12.html o Droser ML and Gehling JG. 2008. Synchronous aggregate growth in an abundant new Ediacaran tubular organism. Science. 319(5870): 1660-1662.

256

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Events during early embryo development set the stage for the patterning, growth, and morphology of the animal for the remainder of its life. Although early embryo development may vary slightly among animals, much of the process is highly conserved.

LEARNING OBJECTIVES Students should be able to:



Describe two different ways each that a developing embryo can be protected and parents can feed their developing offspring. [Knowledge, Comprehension]



Define key terms (embryology): zygote, yolk, polarity (animal vs vegetal pole), cleavage, gastrulation, organogenesis, morula, blastula, blastomeres, blastocoel, gastrula, primary cell layers (ectoderm, endoderm, mesoderm), archenteron, cell induction, selective cell adhesions, cell determination, cell differentiation. [Knowledge]



List the six mechanisms primarily under genetic control that accomplish development in animals. [Knowledge]



Describe the adult tissues that derive from each of the embryonic tissue layers.

[Comprehension]



Provide two examples of genetic control of development. [Knowledge]



Distinguish between invagination and involution during gastrulation. [Comprehension]



Describe how the amount of yolk present in reptilian/avian eggs affects gastrulation.

[Comprehension]



Draw a diagram showing formation of the epiblast, hypoblast and blastocoel. [Comprehension]



Describe the contribution of the two layers (epiblast and hypoblast) to the embryo.

[Comprehension]

257



Describe what results from the primitive streak. [Comprehension]



Define and describe the functions of the extraembryonic membranes (yolk sac, chorion, amnion, allantois). [Knowledge, Comprehension]



Describe the features and explain the evolutionary importance of the amniotic egg.

[Comprehension]



Describe the main differences in development of protostomes and deuterostomes.

[Comprehension]



Define key terms (organogenesis): apoptosis, neurulation, neural crest cells, somites.

[Knowledge]



Draw a rough sketch of neural tube development in vetebrates, labelling the notochord, neural plate, neural crest and neural crest cells. [Comprehension]



List the 5 basic steps in vertebrate eye development. [Knowledge]



Draw a blastocyst, identifying/labelling the blastocoel, inner cell mass, trophoblast, and describing what each gives rise to. [Comprehension]



Explain why the eggs of placental mammals contain very little yolk and have only a vestigial allantois, but a well-developed chorion. [Comprehension]



Describe the umbilicus and what is passed via the umbilicus. [Comprehension]



Define parturition. [Knowledge]



Differentiate between altricial and precocial species. [Comprehension]



Describe the positive-feedback mechanism involved in milk production. [Comprehension]



Describe, briefly, the location of SRY and its role in mammalian sex determination.

[Comprehension]



Describe a developmental change each in humans and butterflies that occurs some time after birth or hatching. [Comprehension]



Describe what happens during induction, where it occurs, and its role in cell determination.

[Comprehension]

258



Define key terms (development): cell lineage, fate mapping, pattern formation, maternaleffect genes, segmentation genes, pair-rule genes, homeotic genes, homeodomain. [Knowledge]



Explain how gene expression is related to cell determination and cell differentiation.

[Comprehension]



Explain what maternal-effect and homeotic genes are, and what they do. [Comprehension]



Describe the importance of the highly conserved nature of the Hox genes in invertebrates and vertebrates and plants. [Comprehension, Analysis]



Describe, in general terms, the importance of apoptosis in invertebrate and vertebrate development. [Comprehension]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

There is a considerable amount of detail provided on cleavage and gastrulation. For this and other material (e.g., human gestation), students may be tempted to memorize details rather than looking at the common events and themes across organisms. As well, these commonalities may be lost in the details within the text. Students will benefit from a focus on learning objectives matched to course curriculum goals.

2.

It should be pointed out to students that in mammalian development, growth is achieved through cell division, and that up to a certain point, with each subsequent division, cell size decreases. (See Figure 39.8) The term cleavage may be confusing to students – in this context, it represents the cell division in the early embryo where typically the volume of the overall zygote may still be limited. Thus every cell division results in two smaller (cleaved) cells.

3.

This chapter integrates material introduced in Chapter 26, when protostomes are discussed. It is a good idea to revisit the differences between protostome and deuterostome early development that leads to their classification.

4.

During differentiation all genes are maintained in the descendant cells (except in cases of enucleation).

Students may confuse this and think that a cell becomes different through loss of other genes. It is good to remind students that these cells replicate by mitosis and in mitotic division the daughters are genetically identical to the parent cell.

259

WHAT CAN I DO IN CLASS? Relate material on genetic developmental processes to cell material covered earlier in text (cell-cell adhesion, differentiation, and gene expression (e.g., Chapter 15). [Stumbling Block III] Discuss: What are the risks of genetic testing through chorionic villus sampling and amniocentisis? Is one method safer or more accurate than the other? How does an expecting woman choose?

Emphasize the purpose behind early cleavage and gastrulation. Cleavage is amazingly fast – in frogs can produce more than 30 000 cells in less than 48 hours. Cytoplasmic determinants (e.g., proteins, transcription factors, mRNA) are typically found at certain location within the egg; because of the progressive division of the egg cytoplasm during cleavage, certain determinants are sequestered to specific cells of the resulting blastocyst.

During gastrulation massive movements of cells take place, establishing the distinct germ layers, the primordial gut.

Pharyngeal slits (gill arches) are developmentally homologous among the vertebrates and give rise to the gills in fish. Ask: What features do these form in humans? Relate the function of some of these structures to those of the gills. (Link to Chapter 20) [Stumbling Block I] In the chapters on homeostasis (Chapters 32 and 43) it is noted that negative feedback mechanisms are much more common in animals than are positive feedback mechanisms. Ask: What then, is an advantage to a positive feedback mechanism in milk production? [Stumbling Block III] Work with Xenopus and Caenorhabditis elegans has significantly increased our knowledge of developmental biology. Ask students to brainstorm about why these might be such good developmental models. Ask students what would happen if apoptosis did not occur correctly in an embryo? C. elegans is of great use in studies of apoptosis in developmental processes. This organism has a set number of cells (1090 somatic cells) of which a specific number (131) undergo apoptosis during development. By manipulating two genes, Ellis and Horvitz (1986), found survival of cells that would normally die via programmed cell death. These genes are conserved in mice and allowed study of disruption of these so-called suicide genes in mammals, which revealed that different genes are involved in apoptosis of different body parts (e.g., digit separation, brain formation).

Students can refer to the Purple Pages (F-37) for information about C. elegans. [Stumbling Block I] Students may be interested to learn that the homeobox of Hox genes is found in vertebrates and invertebrates, but also in plants. This provides an opportunity to show the commonalities of multicellular life on earth, as well as stressing the importance of genes that we know are highly conserved. [Stumbling Block II] There is much controversy over the use of human embryonic stem (ES) cells, but many people do not know the appearance of the embryo at the point in development when ES cells are accessible. In fact, many students are surprised when shown a picture of what a blastocyst looks like, having imagined the embryo to be a fully formed baby in miniature. Ask students to point out what part of the embryo (could be clicker question with labelled blastocyst) contains the ES cells. Ask them what characteristics these cells would have to be to be so useful? Students could debate the use of ES cells or draft guidelines for the ethical use of ES cells.

ADDITIONAL LINKS TO OTHER CHAPTERS Chapter 8, 9:



Apoptosis.

Chapter 10

260



Mitotic cell division.

Chapter 20:



Developmental homologies.

Clicker questions:

1.

Once fertilization occurs, there is a brief period (depending on the organism) during which the genes of the zygote are not yet active, but cell division and developmental processes proceed. What would be the primary director of such activities?

A. mRNA and proteins (cytoplasmic determinants) carried by the sperm.

B. The nucleus of the developing zygote.

C. The zygote’s environment.

D. mRNA and proteins (cytoplasmic determinants) carried in the egg.*

This question addresses the reason for the size disparity between sperm and egg. Sperm are motile and designed for travel (much of the cytoplasm is removed during the maturation process), whereas eggs typically are not motile and bring a considerable volume of cytoplasm that is packed with materials the early zygote can use. Stumbling Block 1

2.

During cleavage in the early zygote A. Cell division occurs and the mass of the zygote increases.

B. Cell division occurs and the mass of the zygote does not increase.* C. The mass of the zygote increases, but no cell division occurs.

D. The mass of the zygote does not increase, and no cell division occurs.

Stumbling Block 2.

3.

During cellular differentiation, cells become specialized for specific roles. These specialized cells would A. Contain all the genetic material present in the nucleus of the one-celled zygote.* B. Contain only genetic material relevant to the role of these cells.

C. Contain genetic material relevant to the role of these cells and with each cell division less of the material unrelated to their function.

Stumbling Block 4.

4.

Gastrulation in animal embryos A. Establishes a layer of yolk for the embryo’s nourishment during development.

B. Establishes precursor organs where organogenesis will take place.

C. Ensures correct positioning of cells in the developing embryo and formation of embryonic germ layers.* D. Involves development of the embryonic germ layers, but no cellular movement.

Stumbling Block 1.

WHAT OTHER RESOURCES ARE AVAILABLE? 261



Ellis HM and Horvitz HR. 1986. Genetic control of programmed cell death in the nematode C. elegans. Cell 44(6): 817-829.



Cool MRI images of frog zygote undergoing cleavage. Lee, S-C, Mietchen D, Cho J-H, Kim Y-S, Kim C, Hong KS, Lee C, Kang D, Lee W, Cheong C. 2007. In vivo magnetic resonance microscopy of differentiation in Xenopus laevis embryos from the first cleavage onwards.

Differentiation 75: 84-92.



Animation on cytoplasmic determinants. Cytoplasmic Factors. 2006. HHMI BioInteractive. http://www.hhmi.org/biointeractive/stemcells/cytoplasmic_factors.html



Creating Embryonic Stem Cell Lines. 2006. HHMI http://www.hhmi.org/biointeractive/stemcells/creating_lines.html



Newt Limb Regeneration. 2006. HHMI. http://www.hhmi.org/biointeractive/stemcells/newt_regen.html



Relating changes in organisms to developmental switches. Gene Switch. 2005. HHMI http://www.hhmi.org/biointeractive/evolution/gene_switch.html. Also, Paintbrush Gene.

2005. HHMI. http://www.hhmi.org/biointeractive/evolution/paintbrush_gene.html

262

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Behavioural traits are adaptive (and thus the result of evolution and have some genetic component).

While some behaviours are innate, others are learned; most have both a genetic and an environmental component. Animal behaviours include everything from feeding preferences to defensive actions.

LEARNING OBJECTIVES Students should be able to:



Define key terms (instinctive and learned behaviour): ethology, instinctive behaviour, learned behaviour, fixed action patterns, sign stimuli, imprinting, classical conditioning, unconditioned stimulus, conditioned stimulus, operant conditioning, operant, reinforcement, insight learning, habituation. [Knowledge]



Describe how to determine if a behaviour is learned or instinctive. [Comprehension]



Provide an example of a learned behaviour and an instinctive behaviour. [Knowledge, Analysis]



Describe how a parasite could exploit sign stimuli of another species to their own benefit.

[Comprehension]



Describe, providing an example, how instinctive behaviours are genetic in nature, but can be modified. [Comprehension, Analysis]



Differentiate between an instinctive behaviour and a learned behaviour, and an unconditioned stimulus and a conditioned stimulus, providing examples of each.

[Comprehension]



Describe, using an example, how a behaviour has a genetic component and an environmental component. [Comprehension]



Describe the influence of nerve connections in behaviour. [Comprehension]

263



Describe an example where the structural and neural connections of sensory systems can allow beneficial behaviours. [Comprehension]



Describe how hormones have a role in behaviour, referring to changes in gene expression and developmental changes. [Comprehension]



Describe how the genetic consequences of a behaviour can affect the environment of an organism. [Comprehension]



Define key terms (communication): signaller, receiver, ritualized, pheromones, tactile signals, language, syntax, symbols. [Knowledge]



List the different sensory modalities (i.e., senses) that can be used by animals producing signals, describing examples of two different modalities. [Knowledge, Comprehension]



Compare and contrast the honeybee “round dance” and “waggle dance”. [Comprehension]



Describe how behavioural interactions between signaller and receiver can affect reproductive output. [Comprehension]



Explain what is meant by “although language is communication, not all communication is language”. [Comprehension]



Define key terms (space, migration): kinesis, taxis, phototaxis, piloting, compass orientation, navigation, migration. [Knowledge]



Describe factors affecting habitat selection. [Comprehension]



Compare and contrast home range and territory. [Comprehension]



Compare and contrast the three categories of way-finding mechanisms (piloting, compass orientation, navigation). [Comprehension]



Describe an example of migration by a particular animal, including the reasons for the journey(s). [Comprehension]



Define key terms (mating): mating system, monogamy, polygamy, polyandry, promiscuity, polygynous, handicap hypothesis. [Knowledge]



Describe the conditions that would lead to monogamy, polygamy, and/or promiscuity.

[Comprehension]

264



Define key terms (social behaviour, kin selection): dominance hierarchy, alpha (dominant), subordinate, kin selection, altruism, reciprocal altruism, haplodiploidy. [Knowledge]



Describe different types of social behaviours exhibited by animals. [Comprehension]



Describe kin selection and the relationship to altruistic behaviours. [Comprehension]



Explain why the evolution of cooperative behaviour is a challenging concept to understand.

[Comprehension]



Describe the phenomenon of haplodiploidy in eusocial insects. [Comprehension]



Describe how the ultimatum game has revealed differences between human and chimp approaches to fairness. [Comprehension]

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 1.

Students often want to attribute all behaviour to learned behaviour and sometimes fail to take into consideration the genetic nature of behaviour and the genetics that allow learning of a behaviour.

2.

The term imprinting is used here to describe a behaviour, while earlier in the text imprinting was introduced as a genetic concept (‘genomic imprinting’, Chapter 12). While behavioural imprinting has a genetic component it is not necessarily related to imprinted genes. Students may require clarification on this.

WHAT CAN I DO IN CLASS? Behaviour has its roots in genetics just as any structural feature does. Similarly, like other traits, some aspects of behaviour have a larger environmental component, whereas others are affected less by the environment. Ask: If behaviour has adaptive value, just as structural traits do, what does this mean in terms of the basis of behaviour and natural selection? Are particular behaviours adaptive in all environments? (Just as with other traits, adaptations are not universally adaptive; what works in one environment may be detrimental in another.)

[Stumbling Block 1] Much behaviour is linked to maximizing reproductive success, but animals are not consciously seeking to outreproduce their neighbours. Ask students how natural selection acts to ‘produce’ animals that maximize their reproductive success.

Honest signals: Female zebra finches are attracted to male zebra finches with the brightest orange cheeks, while female blue-footed boo, male bluebirds with the strongest blue colour win the territories. These signals are all linked to the health and resources that an individual has (zebra finches – orange colour is related to a healthy immune system, etc.) Ask: Why would these ‘honest signals’, that cannot be faked (by the individual themselves), be selected for? How would you test that they were honest signals?

ADDITIONAL LINKS TO OTHER CHAPTERS

265

Chapter 17:



Natural selection is the only evolutionary agent that produces adaptations.

Chapter 35:



More detailed look at hormones, which have a role in behaviour; their role can underscore the genetic nature of many behaviours.

Clicker questions:

1.

Kin selection is a form of natural selection in which A. Shared alleles for altruism are perpetuated if the helper produces more offspring than the relatives it aids.

B. Shared alleles for altruism are perpetuated if the assisted animals produce more offspring than the helped could have produced without help.

C. Group members sacrifice their own reproductive success to help individuals that are not their direct descendants.

D. Individuals help relatives only if they are likely to return the favour in the future.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Stutchbury B. 2010. The Bird Detective: Investigating the Secret Lives of Birds. Harper Collins Canada.



Wittemyer G, Douglas-Hamilton I, Getz WM. 2005. The socioecology of elephants: analysis of the processes creating multitiered social structures. Anim Behav 69(6):1357-1371.



Thorpe WH. 2008. The Learning Abilities of Birds. 2008. The learning abilities of birds. Ibis 93(2): 252-296.



Honest signals, no deception! Fading Bluebirds. Quirks and Quarks. May 28, 2005. http://www.cbc.ca/quirks/archives/04-05/may28.html

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

All organisms share some requirements for essential elements, and face similar challenges in obtaining nutrients, although processes and mechanisms can vary.

266

LEARNING OBJECTIVES Students should be able to:



Define key terms: trace nutrient, essential element. [Knowledge]



Define key terms (plant nutrition): macronutrients, micronutrients, hydroponic culture, chlorosis, phytoremediation. [Knowledge]



Define key terms (animal nutrition): undernutrition, malnutrition, overnutrition, essential amino acids, essential fatty acids, vitamins, essential minerals. [Knowledge]



Explain how macronutrients differ from micronutrients. [Comprehension]



List the commonly absorbed forms of essential elements carbon, hydrogen and oxygen. [Knowledge]



Explain how hydroponic culture allows one to determine the essential nutrients required by a plant. [Comprehension]



Describe the four characteristics demonstrated by plants that are deficient in one or more required elements/nutrients. [Comprehension]



Describe the process of phytoremediation. [Comprehension]



Compare and contrast undernutrition and overnutrition, using examples.

[Comprehension]

267



Describe the importance of vitamins and inorganic elements in the animal diet.

[Comprehension]



Describe two types of vitamins important for humans, including source(s), function(s), and the effects of chronic deficiency. [Comprehension]



Describe what makes certain amino acids, fatty acids or minerals “essential” in animal nutrition. [Comprehension]



Explain why, considering the protein requirements of humans, a vegetarian must be careful in choosing foods. [Comprehension]



Compare and contrast the functions of, and deficiency-related issues for calcium, iron, and magnesium in plants and animals. [Comprehension, Analysis]



Define key terms (soil): humus, horizon, topsoil, subsoil, soil solution, cation exchange, acid precipitation. [Knowledge]



Explain how characteristics of soil (particle size, water availability, mineral availability) are important in plant nutrition. [Comprehension]



Define key terms (obtaining and absorbing nutrients): (plants) mycorrhiza, stele, nitrogen-fixing bacteria, nitrification, root nodule, bacteroid, leghemoglobin, nitrogenase; (animals) fluid feeders, suspension feeders, deposit feeders, bulk feeders.

[Knowledge]



Describe three ways that plants can obtain nitrogen from soil. [Comprehension]



Describe the steps in formation of a root nodule in a legume by nitrogen-fixing bacteria (e.g., Rhizobium). [Comprehension]



Compare and contrast the four major feeding types of animals. [Comprehension]



Define key terms (animal digestive processes): enzymatic hydrolysis, gastrointestinal tract, peristalsis, bile, carnivore, herbivore, sphincter, anus, salivary glands, lysozyme, esophagus, gastric glands, chief cells, mucus cells pyloric sphincter, chyme, duodenum, intestinal villi, microvilli, brush border, chylomicrons, hepatic portal vein, cecum, appendix, rectum, gastrin, secretin, cholecystokinin (CCK), glucosedependent insulinotrophic peptide (GIP), insulin, -melanocyte-stimulating hormone (-MSH), leptin.. [Knowledge] 268

269



Compare and contrast intracellular digestion, extracellular digestion. [Comprehension]



List and describe the five major steps in digestion that occur in animals possessing a digestive tube (GI tract). [Knowledge, Comprehension]



Compare and contrast digestion in annelids, insects, birds and mammals.

[Comprehension, Analysis]



List and describe the components of the mammalian digestive system. [Knowledge, Comprehension]



Explain how the length of the mammalian digestive system varies with feeding strategy. [Comprehension]



List and describe the four major layers of the gut in mammals. [Comprehension]



Describe, briefly, the events that occur as food enters the digestive system of mammals through the mouth, moving through the stomach, small intestine, and large intestine. [Knowledge, Comprehension]



List and describe the key enzymes involved in digestion of carbohydrates, proteins, fats and nucleic acids in humans. [Knowledge, Comprehension]



Describe two mechanisms involved in regulation of the digestive process.

[Comprehension]



Define key terms (variations in obtaining nutrients): bladderwort, parasitic plant, haustorial root, mycoheterotrophic plant, epiphyte, ctenidial lamellae, bioluminescent lure. [Knowledge]



Describe at least two variations in obtaining nutrients demonstrated by plants.

[Comprehension]



Describe at least two different variations in obtaining nutrients/feeding strategies demonstrated by animals. [Comprehension]



Relate challenges of obtaining nutrients in animals to those faced by plants. [Analysis]

270

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Much of human health is related to human nutrition. A thorough understanding of the problems with nutrition, we may be able to help people at risk of malnutrition, and those facing other problems with nutrition (metabolism, role in diseases, etc.).



Plant nutrition is of vital importance to crops, and thus is an important focus of crop science.



Bioremediation (including phytoremediation) has potential value in dealing with mitigating pollution, toxic waste and other types of contamination in the environment, without some of the disadvantages of traditional containment and disposal methods.

WHY SHOULD STUDENTS CARE? 

Much of human health is related to human nutrition. Students may be interested in some issues in humans, such as obesity and diabetes.



Vegetarians/vegans face unique challenges in obtaining the requirements for essential amino acids.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 143. Students may fail to see the common challenges faced by all organisms (plants, animals, fungi, bacteria) in obtaining nutrients. Part of this may stem from a lack of ability to relate to plants.

Understanding the aspects of nutrition shared by plants and animals, as shown in this chapter, highlights the unity of life, helping students view some of the similarities between diverse organisms.

144. Table 41.1 is a comprehensive summary of the essential elements of plants and animals, including known functions, deficiency symptoms, and source (for humans). While this can be useful to highlight shared and unique nutritional requirements, the size of the table, and amount of information displayed can be daunting to students. We recommend that instructors be clear with expectations regarding what (if anything) students are expected to know from this table.

145. If students do not have a good understanding of the biochemistry behind the nature of biological macromolecules, or enzymatic reactions, they are likely to encounter difficulties with some concepts in this chapter.

271

146. Animal digestion is described in great detail and this may lead students to memorize material without thinking about the major concepts. Depending on your curriculum, you may wish to focus on only some of these concepts, or, alternatively, work through the digestive process in an explicit fashion, taking care to link to animal physiology and metabolism to help students put the details into a larger context.

147. It can be confusing to face exceptions to what is the norm (e.g., Many people will agree that a defining feature of plants is the ability to photosynthesize, yet there examples of non-photosynthetic plants described in Section 41.7 - Variations in obtaining nutrients). However, this is a great opportunity to remind students that organisms face similar challenges, but display a wide variety of adaptations that have been favoured by natural selection.

WHAT CAN I DO IN CLASS? The digestive enzyme amylase is introduced in the “Why it Matters” section of this chapter, highlighting the role of amylase in humans/mammals. Levels of amylase production vary with AMY1 gene copy number, and societal and diet differences. As this chapter does include both plant and animal nutrition, it is relevant to discuss amylase enzymes produced in plants. Indeed, there is considerable research of the -amylases in plants because of agricultural (e.g., germination of cereal grains) and industrial (e.g., brewing) importance (see review

by Mitsui and Itohb, 1997). A demonstration or assignment could involve finding the nucleic acid sequence of various amylase-encoding genes in animals and plants, and comparing them (e.g., using BLAST analysis: http://blast.ncbi.nlm.nih.gov/ ). [Stumbling block 1] A pre-test or review of material from the Purple Pages (pages F-17 – F-34) and Chapter 4 may be useful prior to discussion of essential elements and aspects of digestion involving enzymes. If discussing fermentation (e.g., in hoatzins, termites), review of Chapter 6 (Section 6.7a) may also be helpful. [Stumbling block 3] Table 41.1 can be used in class, or in small groups, to highlight the common aspects of plant and animal nutritional requirements. Instructors can make copies of this table, and students can colour-code (e.g., using highlighters), portions of the table that reflect common and divergent aspects of nutrition between plants and animals. [Stumbling block 1, 2] In a pair or small group activity, have students to identify major differences in the digestive process between animals like insects, sponges, flatworms (Dugesia vs. others), hoatzins, and humans. (The pairs or small groups can be assigned a type of animal, and asked to identify unique aspects of digestion, with the larger group coming together to integrate all the information and decide what the major differences are.) You could also (or alternatively) have students compare digestion by making a table showing comparisons of digestion between different animals. [Stumbling block 4] If you are teaching a course with a strong human emphasis, you may want to engage in a class discussion regarding the problems of undernutrition vs. overnutrition in humans, relating social and biological factors to these issues. (E.g., Why are obesity researchers interested in leptin?)

There are many examples of coevolution and symbioses (ranging from mutualistic to parasitic) in which the relationship is based upon nutrition – e.g., mycorrhizae, nitrogen-fixing bacteria and legumes, parasitic plants, parasitic animals, microbes in the rumen of animals (e.g., cows). (Not all of these are discussed in Chapter 41, but students can be encouraged to seek further information about them.) Instructors can link this with material discussed in Chapter 46. [Stumbling block 1, 5] Clicker questions:

Which of the following is NOT required by both plants and animals?

WWW.

carbon.

272

XXX. YYY. ZZZ. AAAA.

iron. calcium. nitrogen.

All of the above are required in both plants and animals.*

This question highlights the common needs shared by plants and animals. [Stumbling block 1] Animals must obtain some amino acids from the diet. Plants BBBB. CCCC. DDDD. EEEE.

synthesize their own essential amino acids.* do not use amino acids. also must obtain some amino acids (from the soil). break down macronutrients to micronutrients, including amino acids.

Students must consider differences in the nutritional requirements of plants and animals.

[Stumbling block 1] Which of the following symbiotic relationships is NOT mutualistic?

FFFF. GGGG. HHHH. IIII. JJJJ.

mycorrhizal fungi and vascular plants.

Rhizobium or Bradyrhizobium bacteria and legumes.

Dodder and host plants. * microorganisms in the rabbit cecum, and rabbits.

All of the above are mutualistic.

Students would have to know the actions of the various partners in the potential answers in order to be able to correctly determine the parasitic relationship of dodder and host plants as compared to the benefits for the symbiotic partners in the distractors. [Stumbling block 5]

273

WHAT OTHER RESOURCES ARE AVAILABLE? 

Mitsuia,T. and Itohb, K. 1997. The α-amylase multigene family. Trends in Plant Science 2(7): 255-261.



Oklahoma State University hosts a number of tutorials/activities for the human digestive system and digestion of macronutrients : http://www.okstate.edu/hes/nsci/nutrition/NSCI2114/digestion.htm

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Plants and animals have adaptations involved in exchange of oxygen and CO 2 that allow them to survive in a variety of environments that pose challenges to exchange of gases.

LEARNING OBJECTIVES Students should be able to:



Define key terms (general): partial pressure, Fick’s equation of diffusion, ventilation, perfusion, buffer, external gills, internal gills, countercurrent exchange, tracheae, spiracles, lungs, positive pressure breathing, alveoli, negative pressure breathing.

[Knowledge]



Explain how gas exchange by simple diffusion varies between plant leaves and animals such as flatworms. [Comprehension]



Describe the limitations of gas exchange by simple diffusion. [Comprehension]



Explain why larger animals required adaptations providing specialized respiratory surfaces. [Comprehension] 274



Describe the purpose of buffers in the blood system. [Comprehension]



Compare and contrast ventilation and perfusion in animal gas exchange.

[Comprehension]



Explain why respiratory surfaces must be wet to work effectively. [Comprehension]



Compare and contrast water and air as respiratory media, considering the advantages and drawbacks of each. [Comprehension]

275



Compare and contrast the structures of external and internal gills, listing an example of an organism that uses each. [Knowledge, Comprehension]



Describe the tracheal system used by insects in gas exchange. [Comprehension]



Compare and contrast negative pressure breathing and positive pressure breathing, listing an example of an animal that carries out each. [Knowledge, Comprehension]



Describe countercurrent exchange in birds. [Comprehension]



Define key terms (mammalian lungs): pharynx, larynx, trachea, bronchi, bronchioles, pulmonary capillaries, interstitial fluid, cilia, diaphragm, pleura, intercostal muscles, tidal volume, vital capacity, residual volume, hemoglobin (used in this chapter)/haemoglobin, bicarbonate, carbonic acid, carbonic acid anhydrase.

[Knowledge]



Describe how the mammalian respiratory system filters, moistens and warms the air that enters the system. [Comprehension]



Describe mammalian lung ventilation. [Comprehension]



Describe the movement of the rib cage and diaphragm during inhalation and exhalation, indicating the muscles involved in each movement. [Comprehension]



Correctly interpret a graph showing a haemoglobin-O 2 dissociation curve, identifying levels of O2 saturation of haemoglobin. [Application]



Describe the role of haemoglobin in oxygen exchange and transport. [Comprehension]



Describe the movement of CO2 in gas exchange of animals. [Comprehension]



Describe the role of pH in gas exchange in animals [Comprehension]



Relate the challenges of gas exchange in animals to those faced by plants. [Analysis]



Relate gas exchange in animals to the circulatory system of animals. [Analysis]

276

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Gas exchange is vital for life processes. Many organisms (nearly all eukaryotes) require oxygen for cellular respiration. Plants also require CO 2 for photosynthesis.

WHY SHOULD STUDENTS CARE? 

Gas exchange is vital in life processes.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 148. The inclusion of both plant and animal gas exchange processes highlights the unity of life, and the common nature of challenges faced by all organisms, but this can be difficult for students to integrate.

149. Fick’s equation may be daunting to some students. We recommend, if possible, trying to explain the constraints on diffusion in general terms.

150. The term cuticle is used to describe the outer waxy layer of the shoot in plants, but also the chitinous coating of arthropods. (Both are mentioned in this chapter and may be confusing for students.)

151. If students do not have a good understanding of the chemistry of oxygen and CO 2, or of enzymatic reactions, they are likely to encounter difficulties with some concepts in this chapter.

WHAT CAN I DO IN CLASS? The “Why it Matters” section introduces the importance of O2 and CO2 in an animal and in plant photosynthesis. Instructors can have students brainstorm other specific examples where gas exchange is important in particular organisms.

When discussing the diffusion of gases (particularly O 2), it may be necessary/helpful to refer to Chapter 2 (surface area to volume constraints in cell size) and Chapter 5 (membrane transport). [Stumbling block 2] Aspects of plant gas exchange are discussed (briefly) in Chapters 7 and 28. Students may wonder how large trees (with trunks/branches covered in bark) and tiny seedlings are able to exchange gases. Gas exchange in plants is not limited to stomata; lenticels (in woody tissues) and root hairs can also allow gas exchange.

Ask students: How can plants survive without development of specialized organs for gas exchange? (They can consider distance gases must diffuse, respiration rates, regions of plants exposed to air, etc.)

The challenges of plant and animal life moving from an aquatic environment to a terrestrial one may have been discussed previously. You may wish to explore this in the context of respiratory media, and have students consider the adaptations for gas exchange in a terrestrial environment that would have been advantageous for plants and animals.

277

The animal circulatory system is discussed in Chapter 37. This is necessarily important in gas exchange in larger animals (such as mammals). Instructors may wish to combine these chapters, or review sections therein.

Activity: In groups, ask students to take a piece of paper and fold it in such a way that they have the same amount of exposed surface area, but in the smallest volume/space possible. This can be used to talk about adaptations that increase surface area (of particular importance in any structure involved in gas exchange).

The text mentions that CO2 can act as a narcotic poison. Carbon monoxide is dangerous, as it can bind to haemoglobin at a higher affinity than can oxygen. If there are high levels of CO, carbon monoxide poisoning can occur, as not enough oxygen is delivered to tissues by the haemoglobin.

We recommend working through the processes of oxygen uptake/transport (Fig. 42.11) and CO 2 exchange (Fig. 42.13) in mammals in some detail, if instructors expect students to understand the events and reactions that occur.

There are examples of animals living in high altitudes that have adaptations to maximize oxygen delivery in these lower-oxygen conditions. Llamas and other animals living in these environments produce a form of haemoglobin with a higher affinity for oxygen than what is produced in lower-altitude animals, enabling the haemoglobin to bind to oxygen even at low pressures (see Storz 2007). This can be related to natural selection in Chapter 17.

Ask students how humans are able to cope with high-altitudes (e.g., mountain climbing). (There are ways of acclimating to high altitudes … and we can also bring along oxygen in canisters.) Some of these strategies are used by elite athletes to increase their endurance and oxygen carrying capacity.

Haemoglobin is discussed in this chapter. It may be worth mentioning/reviewing the role of myoglobin in muscles. Myoglobin has some similarities to haemoglobin, but is smaller, and has a higher affinity for O 2. Ask students why myoglobin levels are high in animal muscles.

Adaptations are present in deep-diving mammals, like Weddell seals, that must hold their breath for long periods of time. These seals have much more blood (for their body weight) than we do, can lower the heart rate during a dive, show very efficient circulation, and have more myoglobin in muscles that can store oxygen for use during dives.

278

Clicker questions:

Plants and animals both KKKK. LLLL. MMMM. NNNN.

use haemoglobin to transport oxygen to tissues. require oxygen to carry out cellular respiration.* require CO2 to carry out carbon fixation reactions. have specialized respiratory organs involved in gas exchange.

Many students have the misconception that plants only use CO 2. [Stumbling block 1] How does a shortage of iron in the diet affect animal gas exchange?

OOOO. less oxygen can be bound by haemoglobin for transport to tissues.* PPPP. less CO2 can be removed from tissues by the blood plasma.

QQQQ. the blood pH levels are increased to dangerously high levels.

RRRR. None of the above; iron levels do not significantly affect gas exchange in animals.

Relates the structure of haemoglobin to nutrition. [Stumbling block 4] WHAT OTHER RESOURCES ARE AVAILABLE? 

How stuff works – gas exchange in plants video: http://videos.howstuffworks.com/hsw/14762-simply-science-gas-exchange-inplants-video.htm



How stuff works – animal gas exchange animation: http://health.howstuffworks.com/adam-200022.htm



Storz, J.F. 2007. Haemoglobin function and physiological adaptation to hypoxia in high-altitude mammals. Journal of Mammalogy 88: 24-31.



Hooker, S.K., Baird, R.W., and Fahlman, A. 2009. Could beaked whales get the bends?: Effect of diving behaviour and physiology on modelled gas exchange for three species: Ziphius cavirostris, Mesoplodon densirostris and Hyperoodon ampullatus.

Respiratory Physiology & Neurobiology 167: 235-246

279

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Animals have adaptations that allow them to regulate their internal environments, including osmotic pressure and temperatures so that these remain within the animal’s range of tolerance.

LEARNING OBJECTIVES Students should be able to:



Define key terms: homeostasis, osmoregulation, excretion, thermoregulation.

[Knowledge]



Describe how aqueous environments differ from terrestrial environments in terms of water, solutes, and temperature ranges. [Comprehension]



Define key terms (osmoregulation): osmosis, water balance, osmole, osmotic pressure, osmolality, hyperosmotic, hypoosmotic, isoosmotic, osmoconformer, osmoregulator, solvent, excretion, metabolic water, nitrogenous wastes (ammonia, urea, uric acid), osmoregulation, protonephridia, metanephridia, Malpighian tubules, nephron, kidney . [Knowledge]



Describe osmosis and its importance in animals. [Comprehension]



Explain how osmotic concentration is described (as osmolality). [Comprehension]



Compare and contrast osmoconformers and osmoregulators. [Comprehension]



Compare and contrast ammonia, urea and uric acid, including the types of animals that excrete nitrogenous wastes in each form. [Comprehension]

280



Explain why most invertebrates that spend their entire lives at sea are typically osmoconformers, while freshwater and terrestrial invertebrates are osmoregulators.

[Comprehension]



Describe at least two different ways that marine invertebrates can respond to variations in environmental osmotic concentrations. [Comprehension]



Describe how freshwater osmoregulators such as flatworms maintain internal hyperosmocity. [Comprehension]



Compare and contrast protonephridia, metanephridia, and Malpighian tubules.

[Comprehension]



Explain why the osmotic concentration of body fluids must be maintained in organisms with hydrostatic skeletons. [Comprehension]



Define key terms (mammalian urinary system): renal cortex, renal medulla, renal artery, renal vein, collecting ducts, renal pelvis, ureter, urinary bladder, urethra, Bowman’s capsule, glomerulus, proximal convoluted tubule, loop of Henle, distal convoluted tubule, peritubular capillaries, juxtamedullary nephrons, cortical nephrons, afferent arteriole, efferent arteriole, aquaoporin, transport epithelium, osmolyte, chloride cells, trimethylamine oxide, salt gland. [Knowledge]



List and describe the major components of the mammalian urinary system.

[Knowledge, Comprehension]



Describe the functions of the different regions of mammalian, explaining the importance of the shape/size of each part and its location within the kidney (e.g. The upper portion of the loop of Henle is in the renal cortex and the lower part in the renal medulla - why is this important? What would be the potential physiological result if this component never entered the renal medulla?) [Comprehension]



Describe the processes involved in reabsorption and secretion in the nephron, indicating the importance of internal and external water and ionic concentrations in each process. [Comprehension]



Label a simple diagram of a nephron and collecting tubules of the human kidney, indicating relative osmolality of interstitial fluid in different areas, regions where active and passive transport occur, and where movement of water, ions and urea occur. [Knowledge, Comprehension, Application] 281



Describe at least three adaptations in terrestrial mammals that assist with water conservation. [Comprehension]



Compare and contrast kidney function in marine fishes to those of freshwater fishes/ amphibians, and reptiles (including birds). [Comprehension, Analysis]



Define key terms (thermoregulation): thermoreceptors, organismal performance, heat exchange (conduction, convection, radiation, evaporation), exothermic, endothermic, ectotherm, endotherm, thermal acclimatization, countercurrent heat exchanger, integument, warm receptor, cold receptor, hypothalamus, vasoconstriction, epinephrine, thyroid hormone, nonshivering thermogenesis, brown adipose tissue/brown fat, hypothermia, hyperthermia, epidermis, keratin, dermis, hypodermis, torpor, hibernation, estivation. [Knowledge]



Describe how extremely cold or hot temperatures can cause cell death.

[Comprehension]



Describe how thermoregulation allows animals to maintain optimal levels of organismal performance, relating to the cellular components and activities that occur in various activities (e.g., movement, digestion, etc.). [Comprehension]



Compare and contrast ectotherms and endotherms. [Comprehension]



Compare and contrast ectothermic mechanisms between invertebrates, fishes, and amphibians/reptiles (not including birds). [Comprehension]



Describe the major physiological and behavioural responses of mammals involved in thermoregulation. [Comprehension]



Describe the effects of hypothermia on a mammal. [Comprehension]



Describe the importance of skin (including the different layers) to birds and mammals in heat transfer. [Comprehension]



Describe at least two specialized unique responses that enhance thermoregulation in different animal species. [Comprehension]



Describe the phenomenon of daily torpor. [Comprehension]



Describe the advantages of hibernation and estivation for animals. [Comprehension] 282



Differentiate among torpor, hibernation and estivation, with respect to circumstances under which each would occur. [Comprehension, Analysis]



Relate the concepts of osmoregulation, excretion and thermoregulation to the structure and function of animal systems as discussed in Chapters 26, 27, 32-40.

[Analysis]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

As ice caps melt, more water is being added to the ocean. Decreased salinity may have an impact on marine organisms.



Animal physiologists, human physiologists are seeking to understand aspects of these processes that relate to disease conditions (e.g., kidney disease).



Osmoregulation and thermoregulation – Research into how animals living in extreme conditions maintain a healthy balance of internal constituents and temperature. This is coupled with research into strategies that may applied to help organisms (e.g. zoo animals, livestock) deal with environments outside the norm. This research is also important for the treatment of people experiencing hyperthermia or hypothermia.



Sports medicine / human performance research: understanding of efficient osmoregulation and thermoregulation can help athletes (and others) avoid potentially dangerous conditions. Development of sports drinks is based on research of osmoregulation and related items during exercise.



Research into the regulatory strategies of wild animals that over-winter in a static state (e.g. frogs) or hibernate (e.g. black bears). This work could be applied to human cryogenic research.

WHY SHOULD STUDENTS CARE? 

Students will likely be interested in thermoregulation and osmoregulation as they pertain to humans (e.g., effects of heatstroke, water intoxication).



Sports and health – aspects of osmoregulation/thermoregulation are very important under conditions where humans undergo exertion.

283

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 152. This chapter includes numerous new terms and details regarding many structures. Students may be overwhelmed by the level of detail, so clear expectations will be valuable in helping students focus on the key concepts in your course. Instructors are encouraged to choose learning objectives to match to those key concepts.

153. Osmoregulation/excretion processes involve some of the major concepts discussed in Chapter 5.

Students may be confused by the similar terms tonicity and osmolality (and osmolarity, if they have encountered it). Tonicity and osmolarity both compare the solute concentrations of solutions on either side of a membrane. Osmolality is a measure of the total concentration of all solutes (in osmoles per kg solute), whereas tonicity considers only the total concentration of solutes that cannot cross the membrane. Osmolality is the measurement of solute osmotic concentration per mass, whereas osmolarity is a measurement per volume of solvent.

154. If students have not covered material from the animal chapters in some detail, they may be unfamiliar with many of the terms, structures and concepts discussed in this chapter. That will make understanding these processes challenging, but an instructor can introduce selected (background) information as needed, provide time review, and direct students to use the textbook as a valuable reference source.

155. Systems do not operate in isolation, although we usually study/discuss them as though this were the case (in part, because of the complexity of such systems). Reminders of the interconnectedness of physiological systems (e.g., neural, sensory, endocrine, circulatory) are strongly recommended. Where possible, use examples that students have already encountered.

156. It can be easy to focus exclusively on the physiological adaptations to regulate temperature. Many animals also exhibit behavioural adaptations that are quite effective in thermoregulation.

WHAT CAN I DO IN CLASS? The “Why it Matters” introduction ties the challenges of regulating the internal environment to the major transition from water to land (which occurred in both plants and animals). This allows instructors to link material in this chapter to material from other chapters in a number of different ways (depending on the course curriculum and student background). For example, this material can easily be approached as part of the animal physiology section, but alternatively could be discussed in the context of the common adaptations of plants and animals transitioning to land from water, illustrating the common challenges faced by terrestrial organisms.

It may be helpful to review Chapter 5 (solute movement across membranes, osmosis). A quick pre-test (e.g., using end of chapter questions from Chapter 5 with clickers) may help identify concepts that require refreshing.

Reminders of terms used in discussing tonicity and osmolarity/osmolality are recommended. [Stumbling block 2] Integration: If spending significant amount of time on animal anatomy/physiology, you may wish to teach these concepts with those covered in the other animal chapters. Homeostasis is introduced in Chapter 32 (in an introduction to animal organization and physiology), the endocrine system (Chapter 35) is involved in regulation of the distal tubule and collecting duct in urine production, as well as in thermoregulation processes. Circulation (Chapter 37) is important in osmoregulation/excretion.

[Stumbling block 3]

284

Although only animals are discussed in this chapter, it should be noted that all organisms are affected by osmotic pressure, demonstrating the common challenges faced by all organisms. Plants, fungi, bacteria, etc. may not have the specialized organs present in animals, but many species (particularly halophytes, halophiles, and halotolerant plants/bacteria) have mechanisms to cope with osmotic pressure (even in saline environments). For example, cell walls in bacteria and plants are important to withstand high osmotic pressure within cells. The waxy plant cuticle is vital in keeping water within plant tissues. Some plants, bacteria and archaea can alter their internal osmolality by ion uptake or production of compatible organic solutes (e.g., glycine betaine). Instructors can provide examples of salt-tolerant plants (see Canadian Gardening article below in the Resources) and discuss how agricultural scientists are interested in increasing halotolerance in crop plants to help expand the available regions where they can be grown in the world (see Zhu, 2001).

(Also included in Chapter 5 – if already used, can revisit or expand upon this.) The importance of osmosis can be demonstrated by discussing some of the tragic cases of “water intoxication” (hyponatremia) that have occurred in recent years. The story of the death of Jennifer Strange after participating in a radio station contest (“Hold your Wee for a Wii”) may be familiar to some students, but hyponatremia has affected marathon runners, a toddler under the care of a babysitter later charged with murder, and a student who died after an American hazing incident, among others. (In discussing these incidents, ask students to consider what happens at a cellular level when too much water is present. Why are sodium levels important?) Students could be encouraged to find news articles discussing these cases (or others), and evaluating the scientific accuracy of the reports. Students could be put into small groups to brainstorm guidelines to prevent water intoxication for at-risk individuals. [Stumbling block 2]

Osmoregulation and excretion are processes that vary between animals and reflect the different environments/conditions in which particular animals live. Approaching these processes by looking at the challenges faced by these animals may help students understand the key concepts without simply resorting to memorization. Assign groups of students to brainstorm the challenges of animals living in: marine water, freshwater, intertidal zones; temperate terrestrial environments; desert environments. What types of osmoregulation/excretion occur in animals living in these environments? [Stumbling block 1] Filtration is one of the most important functions of the kidney. Students (individually or in small groups) can brainstorm the features of an ideal man-made filter to carry out the functions of the human kidney. (They should consider how liquid enters/exits the system, which components must be removed, which components can remain, etc.) What will some of the challenges be if researchers/biomedical engineers are developing an artificial kidney? Learning how dialysis machines work may help students answer these questions. [Stumbling block 1] Students may be interested in learning about the physiological challenges faced by hummingbirds.

Thermoregulation is a major challenge for these birds, which must expend considerable energy in flight, and consume adequate calories to sustain their activities. Hummingbirds are tiny, and thus have relatively small volume compared to surface area. Students can be asked (in an in-class discussion, or assignment where they must search the scientific literature for relevant information) how hummingbirds might be able to deal with these challenges. (These birds exhibit physiological and behavioural adaptations in thermoregulation - see Suarez and Gass 2002. Some enter torpor.) [Stumbling block 4, 5] Many parts of Canada can experience very cold weather in winter. Students can discuss the conundrum faced by endotherms in such conditions: they require considerable energy (food) to maintain body temperatures, but in the winter, food can be scarce! Time permitting, you can use an example of such an animal (e.g., black bears, wolves, deer), highlighting the particular challenges faced by the animal and related adaptations (or small groups of students can be assigned particular animals to research, reporting their findings back to the larger group).

You may wish to have students relate the daily/seasonal rhythms of animals to circadian rhythms discussed in Chapter 1. See Heller HC, and Ruby (2004). Ask: What factors would affect the rhythms experienced by such animals? Which physiological systems would work together in these rhythms? [Stumbling block 4]

285

Clicker questions:

An invertebrate that is an osmoconformer SSSS. does not expend energy to maintain osmolality within the cells.* TTTT. excretes excess water to maintain hyperosmocity within the cells.

UUUU. excretes urine that is hyperosmotic to the surrounding liquid environment.

VVVV. can live in more varied habitats than one that is an osmoregulator.

286

The kangaroo rat (Dipodymus) lives in the desert, and has which of the following adaptations?

WWWW. They produce urine that is extremely dilute.

XXXX. They have sweat glands covering the entire body, allowing efficient cooling.

YYYY. Specialized passages in the nasal cavities condense moisture from breath before it leaves the body.* ZZZZ. They eat large amounts of succulent plant material, obtaining most of their water in this way.

The kangaroo rat has several characteristics/behaviours that contribute to water conservation, but even if students do not know all of them, they may be able to deduce the answer by ruling out the distractors that are illogical.

Animals that are ectotherms AAAAA. can typically survive on much less food than endotherms.* BBBBB. must expend energy on heating tissues that could otherwise be used for growth, reproduction, etc.

CCCCC. are more successful than endotherms in inhabiting cold environments.

DDDDD. Two of the above are true.

This question highlights some of the trade-offs between ectothermy and endothermy. This could lead to a discussion of trade-offs (e.g., which environments would be more favourable to ectothermy). (The idea of fitness tradeoffs links to Chapter 17 - Microevolution: genetic changes within populations.)

Animal adaptations to assist with thermoregulation in the heat include EEEEE. dissipation of heat through blood vessels in large ears.

FFFFF. spreading saliva on fur, which evaporates and provides a cooling effect.

GGGGG. spreading of limbs.

HHHHH. seeking shade.

IIIII. All of the above. * [Stumbling block 5] WHAT OTHER RESOURCES ARE AVAILABLE? 

Canadian Gardening: Salt tolerant plants for Canadian soil http://www.canadiangardening.com/plants/perennials/salt-tolerant-plants-forsodium-laced-soil/a/20997

287



J-K Zhu. 2001. Plant salt tolerance. Trends in Plant Science 6: 66-71.



Almond CS, Shin AY, Fortescue EB, Mannix RC, Wypij D, Binstadt BA, Duncan CN, Olson DP, Salerno AE, Newburger JW, Greenes DS. 2005. Hyponatremia among runners in the Boston Marathon. N Engl J Med. 352(15):1550-6.



Coverage of Jennifer Strange trial: http://www.injuryboard.com/national-news/the-strange-case-of-jennifer-strange-.aspx



Joanna Gilbert – BiologyMad website, kidney animation http://www.biologymad.com/resources/kidney.swf



Kidney Health Australia - How kidneys work animation: http://www.kidney.org.au/flash/kidney_animation/kidneys.html



Musée de la nature et des sciences - Hummingbird thermoregulation: http://museevirtuel.ca/Exhibitions/Colibri/En/Hummingbird/The-Life-Of-TheHummingbird/thermoregulation.html



Suarez RK, Gass CL. 2002. Hummingbird foraging and the relation between bioenergetics and behaviour. Comp Biochem Physiol A Mol Integr Physiol.

133(2):335-43.



Heller HC, and Ruby NF. 2004. Sleep and circadian rhythms in mammalian torpor.

Annu Rev Physiol. 66:275-89.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Organisms have defence mechanisms against pathogens (disease-causing agents) that include physical barriers and immune responses.

2.

The human immune system includes innate (non-specific) and adaptive (specific) systems.

288

LEARNING OBJECTIVES Students should be able to:



Define key terms: immune system (innate/non-specific, adaptive/specific), immune response, vaccination. [Knowledge]



Describe the three lines of defence (i.e., physical barriers, innate and adaptive immunity) against invasion by pathogens in vertebrates. [Comprehension]



Distinguish between innate and adaptive immunity. [Comprehension]



Describe how the epithelium serves as a barrier for infection, and other physical barriers make parts of the human body hostile to potential pathogens. [Comprehension]



Define key terms (innate immunity): pathogen-associated molecular patterns (PAMPs), pattern recognition receptors (PRRs) phagocytosis, melanotic encapsulation, antimicrobial peptides, complement system, defensins, inflammation, monocytes, macrophage, cytokine, mast cells, histamine, neutrophils, chemokines, membrane attack complexes, RNA interference (RNAi), apoptosis, interferons, natural killer cells, lymphocyte, perforin, major histocompatibility complex (MHC) proteins. [Knowledge]

289



Describe how humans (and many other animals) recognize pathogens as “nonself”.

[Comprehension]



Describe how phagocytosis, melanotic encapsulation and production antimicrobial peptides act against possible pathogens. [Comprehension]



Explain how the inflammatory response leads to tissue healing. [Comprehension]



Define key terms (adaptive immunity): antigen, lymphocytes, B cells, T cells, thymus, antibody-mediated (humoral) immunity, cell-mediated immunity, memory cell, B-cell receptors (BCRs), T-cell receptors (TCRs), epitope/antigenic determinant, antibody, immunoglobulin (Ig), light chain, heavy chain, constant region, variable region, dendritic cell, class II major histocompatibility complex (MHC) proteins, antigenpresenting cell (APC), CD4+ T cell, helper T cell, plasma cells, memory B cells, clonal selection, agglutination, immunological memory, primary immune response, secondary immune response, active immunity, passive immunity, cytotoxic T cells, CD8+ T cell, memory cytotoxic T cells, monoclonal antibodies. [Knowledge]



Describe the structure of an antibody. [Comprehension]



List and describe the five different classes of antibodies in humans. [Knowledge, Comprehension]



Compare and contrast activation of T-cells and B-cells. [Comprehension]



Describe B-cell activation. [Comprehension]



Explain how bacterial toxins and bacterial cells can be cleared (i.e., removed) from the body via the antibody-mediated immune response. [Comprehension]



Describe, briefly, the phenomenon of immunological memory, including the responses involved. [Comprehension]



Describe the process of cell-mediated immunity. [Comprehension]

 

Explain how antibodies are useful tools in research. [Comprehension] Define key terms (malfunctions/failures in immunity): autoimmune disease, allergic reaction, immunological tolerance, autoimmune reaction, allergens, basophils, sensitize, anaphylactic shock. [Knowledge]

of

290



Provide an example of an autoimmune disorder resulting from a failure of immunological tolerance. [Comprehension]



Describe the events that occur in an allergic reaction. [Comprehension]



Describe, using examples, immune (or immune-like) defences in other organisms that differ from what occurs in humans (e.g., sharks, plants). [Comprehension]



Describe the mechanism of host entry shared by many bacteria, nematodes, and trematodes. [Comprehension]



Explain, using an example, how some pathogens can disguise themselves from the host immune system. [Comprehension]



Explain, using an example, how some pathogenic organisms work together symbiotically to evade the host defences. [Comprehension]



Identify and describe similarities between the immune system of animals to the defence systems in plants against pathogens. [Analysis]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Much research is devoted to human disease, understanding the immune response, and helping augment immunity.



Antibodies are important research tools, that are used in many techniques/assays (e.g., ELISA, antibody-tagging).



Autoimmune diseases are particularly challenging in terms of treatment, and research is needed to find effective new treatments.

WHY SHOULD STUDENTS CARE? 

Students are generally interested in human health (particularly those who have the goal of medical school), and the immune system plays a role in many disorders/diseases that students know (and may have experienced personally, or know someone affected by such conditions).

291

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 157. A lot of terminology is introduced in this chapter, with many types of blood cells listed and described, and lots of acronyms. (Again, instructors are strongly encouraged to limit themselves to courseappropriate learning objectives, and to direct student focus by explicitly stating their expectations. Do you expect students to know all the terms in immunology, or is your focus the general mechanisms involved?)

158. Although the physical barriers to infection are often not discussed to the same extent as the immune system, this is important in protection from pathogens. There are other physical barriers that provide protection as well as the epithelium (e.g., secretions such as mucous, wax, and antibacterial enzymes).

159. If students do not have a clear understanding of the structure and physiology of bacterial, and eukaryotic pathogens, some concepts may be difficult to understand. E.g., Pathogen-associated molecular patterns, discussed in 44.1c, include some of the common components of bacterial cell walls, and the text provides examples of such components of Gram positive and Gram negative bacteria, which will not mean much to students who have not explored Chapter 21 (Prokaryotes).

160. This chapter does indicate, briefly, that plants have defences, but this may not unseat student misconceptions that plants (and other non-vertebrates) do not possess sophisticated and varied means of preventing infection/parasitism. Chapter 31 provides a bit more detail regarding the chemical defence mechanisms found in plants; physical barriers to infection exist in plants in a fashion similar to the physical barriers present in animals (e.g., epithelium, waxy cuticle, etc.).

WHAT CAN I DO IN CLASS? The “Why it Matters” introduces disease, and tells the story of Edward Jenner and the development of vaccination. Instructors may wish to use short cases of diseases that have received recent media attention (i.e., the instructor finds the cases, or assigns students to do so). How do the pathogens gain entry to the host (breach the physical barriers)? Does the pathogen have ways of evading immune responses that we know of?

Are vaccines available?

A pre-test or review of Chapter 21 may be useful prior to discussing aspects of immunology relating to bacterial pathogens. [Stumbling block 3] Map the route that a typical human pathogen would have to take to successfully infect a host. (Instructors can assign different pathogens to different students, or groups: e.g., Salmonella as GI pathogen, Staphylococcus aureus infecting skin, Streptococcus pneumoniae as respiratory pathogen, Neisseria gonorrheae infecting uro-genital tract.)

Students should consider all three lines of defence against invasions. Depending on the background of your students (and how much time you are allotting to this topic), students could follow up on this, and identify the actual virulence mechanisms (at a general/basic level) the pathogens employ to evade host defences, linking Section 44.6 with earlier material in this chapter. [Stumbling block 2] As an individual or group assignment, have students prepare a comprehensive chart/diagram of the various blood cells discussed in this chapter, and how they are involved in particular immune responses. Encourage students to find ways to highlight important connections/commonalities/differences visually (e.g., using diagrams, colour-coding). These charts/diagrams can be shared with the larger class to help students see different ways of understanding what can appear to be a set of facts to memorize. [Stumbling block 1]

292

Ask: Are animals the only organisms with the ability to respond defensively to attack by parasites/pathogens?

Chapter 31 includes some information that instructors can bring into this topic (Section 31.3: Plant Chemical Defences), emphasizing the unity of life and challenges faced by various types of organisms. You can encourage students to consider the physical barriers of various organisms that could provide protection, and compare those to the physical barriers to infection present in animals. [Stumbling block 4, 2] Pathogens and host immune systems can be viewed as partners in an “coevolutionary arms race”. Ask: How does the host immune system exert selective forces on a bacterial pathogen?

Clicker questions:

All of the following are considered physical barriers to infection EXCEPT JJJJJ. epithelium.

KKKKK. lysozyme.

LLLLL. mucous.

MMMMM. cilia.

NNNNN. histamine.* OOOOO. PPPPP. [Stumbling block 2] Which of the following is FALSE regarding antibodies?

QQQQQ. They all have a Y-shaped structure.

RRRRR. Specificity is provided by the variable region.

SSSSS. They directly kill pathogens.* TTTTT. They are composed of light and heavy polypeptide chains.

Antibodies do not directly kill pathogens. They recognize antigens, and “tag” pathogens, so that macrophages/neutrophils, or the complement system, can more easily target them for destruction.

293

One reason breastfeeding is recommended is that UUUUU. it provides passive immunity to the baby. * VVVVV. it provides active immunity to the baby.

WWWWW. it provides memory B cells to the baby.

XXXXX. All of the above.

YYYYY. Only A and B. Antibodies from the mother can provide protection to an infant for the first few months of life, while developing adaptive immunological responses.

WHAT OTHER RESOURCES ARE AVAILABLE? 

The Biology Project at the University of Arizona has a problem set (with related tutorials) for basic concepts in immunology: http://www.biology.arizona.edu/immunology/tutorials/immunology/main.html



Bio-Alive - immunological animations: http://bio-alive.com/animations/immunology.htm



Howard Hughes Medical Institute (HHMI) has a number of animations, including: Antigen presentation and CTL, Cloning an Army of T Cells for Immune Defense (sic): http://www.hhmi.org/biointeractive/disease/antigen_ctl.html http://www.hhmi.org/biointeractive/immunology/animations.html

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Humans are subject to the same regulatory mechanisms that control the growth and size of natural populations of other organisms. Only in recent history has agricultural practice allowed humans to grow at unprecedented rates that would not naturally be supported.

2.

If we follow a population, we can see changes in its characteristics over time and space.

294

LEARNING OBJECTIVES Students should be able to:



Define ecology and the four levels of ecological organization (organismal, population, community and ecosystem ecology). [Knowledge]



Describe how ecologists can use field or lab studies to examine relationships among the components of an ecosystem. [Comprehension]



Define intraspecific, interspecific, and conspecific. [Knowledge]



Define the following population characteristics, noting what each tells us about a population: geographic range and habitat, population size, population density, population dispersion, age structure, generation time, sex ratio, reproducing proportion. [Knowledge, Comprehension]



Describe the difference between a geographic range and habitat. [Comprehension]



Describe one abiotic and one biotic factor that could influence species distribution.

[Comprehension]



Explain why population size is more informative compared to population density.

[Comprehension]

295



Describe the relationship between an organism’s size and its population density.

[Comprehension]



Describe three methods that are used to estimate population size and density, noting advantages and disadvantages of each. [Comprehension]



Describe two potential difficulties in accurately determining population size.

[Comprehension]



Predict, given a specific organism and its environment, which method would be most useful/feasible to determine its population size. [Comprehension]



Describe the three general dispersion patterns, noting what they tell us about the population of interest, and the frequency with which these patterns occur.

[Comprehension]



Predict, given a description of an organism (e.g., interactions between individuals of a population), the type of dispersion it most likely exhibits. [Application]



Describe how generation time and body size are related. [Comprehension]



Describe how the age structure of a population differs between a shrinking population, a zero-growth population and a rapidly growing population.

[Comprehension]



Describe how the relative pre-reproductive, reproductive and post-reproductive proportions of a population affect a population’s growth rate. [Comprehension]



Describe differences in the effects of altered sex ratios on a population’s size for species with different mating strategies. [Comprehension]



Define the following terms (population size): life table, cohort, age-specific mortality, age-specific survivorship, (age-specific) fecundity, immigration, emigration, r, N, exponential population growth, and per capita growth rate, rmax, K (carrying capacity), logistic growth. [Knowledge]



Describe the relationship between age-specific mortality and age-specific survivorship. [Comprehension]



Describe what a survivorship curve represents. [Comprehension] 296

297



Identify or draw, given general information (e.g., high juvenile mortality rate, steady adult mortality), the type of survivorship curve (type I, II, or III) a population would exhibit. [Comprehension, Application, Analysis]



Define life history, energy budget, passive vs. active parental care, semelparity (bigbang reproduction), and iteroparity (repeated reproduction). [Knowledge}



List the main life functions/activities an organism’s energy budget is divided among.

[Knowledge]



Describe three different ways that natural selection can maximize the energy budget of organisms. [Comprehension]



Describe how natural selection shapes life history traits. [Comprehension]



Describe the different trade-offs (e.g., fecundity vs. parental care; number of times to breed; age at first reproduction) in reproductive life history traits. [Comprehension]



Describe the effects of reproduction and the number of offspring to mortality and lifespan. [Comprehension]



Explain, with respect to life history, why spaying/neutering may be beneficial for your pet. [Comprehension]



Describe factors that can increase or decrease a population’s size. [Comprehension]



Describe the basic information necessary to determine a population’s size.

[Comprehension]



Provide the exponential and logistic growth equations and identify all terms in each.

[Knowledge, Comprehension]



Explain how the value of r changes when b>d, b<d, and b=d and its impact on population growth. [Comprehension]



Explain how the increase in population size can grow even when r remains constant.

[Comprehension]



Define rmax and the conditions under which it occurs. [Knowledge]

298



Describe the general relationship between rmax and generation time. [Comprehension]

299



Differentiate between the exponential and logistic growth models. [Comprehension]



Describe what is indicated by each part of an S-shaped population size curve (described by the logistic equation). [Comprehension]



Given an assumption of the logistic growth model, explain whether it is realistic or unrealistic. [Comprehension]



Explain why K (carrying capacity) is not static (i.e., why it can change). [Comprehension]



Explain why K is not the same for different species occupying the same geographic area. [Comprehension]



Describe how the environment can limit a population’s growth. [Comprehension]



Describe what happens to r as N approaches K. [Comprehension]



Describe two ways humans have increased the K (carrying capacity) of their environment. [Comprehension]



Differentiate between density-dependent and density-independent factors that limit population growth. [Comprehension]



Describe two examples each for density-dependent and density-independent factors that can impact population growth. [Comprehension]



Describe a limiting resource (each) for plants, sessile animals, and motile animals.

[Comprehension]



Differentiate between intrinsic and extrinsic controls of population growth.

[Comprehension]



Draw a generalized population growth curve for a population that suffers frequent population density-independent events. [Comprehension]



Define a time lag with respect to predator-prey population cycles. [Knowledge]



Describe how density-dependent and density-independent factors could act together to alter a population’s growth rate. [Comprehension]

300



Compare and contrast r- and K-selected species with respect to: age of sexual maturity, life span, number of offspring, amount of active parental care, tolerance of environmental changes. [Comprehension, Analysis]



Describe, briefly, the demographic transition model and what it represents.

[Comprehension]



Explain, with respect to humans, how age structure impacts population growth.

[Comprehension]



Explain how age structure of a human population can be used to determine allocation of resources for social/public services. [Comprehension]



Define population bomb. [Knowledge]



Explain an ethically sound method for control of human population growth.

[Comprehension]



Describe two ways that humans have avoided the effects of density-dependent regulation factors (altered K). [Comprehension]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Many populations (of a wide variety of organisms) are currently in crisis. Conservation plans to save these species are futile if we cannot estimate a population’s current size, as we can’t accurately determine if our conservation actions help, hinder or are neutral.



Human populations are subject to the same controls/regulating factors as natural populations.

Understanding population dynamics allows us to make better predictive measures for social/public works (e.g., building of schools, retirement homes, etc.).



A better understanding of population dynamics can be helpful in the control of disease (as discussed in the ‘Why It Matters’ introduction), social/public planning.



Information on population size and growth is extremely important in the management of living resources (e.g., fish stocks, trees, etc.)

301

WHY SHOULD STUDENTS CARE? 

Ecology is not just about “other” organisms, it includes and affects humans. Human populations are subject to the same controls/regulating factors as natural populations. Understanding population dynamics allows us to make better predictive measures for social/public works.



Information about population sizes, growth patterns and distribution allow us to create better conservation models and is important to good management of living natural resources, which are vital to our Canadian economy.



A better understanding of population dynamics can be helpful in the control of disease (such as discussed in the ‘Why It Matters’), social/public planning (e.g., building of schools, retirement homes, etc.)

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 161. Often students view ecology as a topic about non-human organisms. While humans are used to demonstrate demographic models in this chapter, it is important that students see that human populations can be analyzed using all the same criteria as other organismal populations. Instructors are encouraged to highlight that knowledge of population criteria is very important economically in terms of food production and availability.

162. Students may mix up the terms species and population. Thus, if you are referring to multiple populations of one species, they may think that you are referring to multiple species. By asking them to think about these terms, and continually bringing up their definitions, students should become familiar with the differential use of these terms.

163. Students may think that dispersion patterns are completely random, but they are entirely dependent on the inter-individual dynamics within a population, and can be affected by food availability, breeding patterns, etc. Even ‘random’ distribution patterns are random for a reason. Moreover, dispersion patterns depend on scale. Dispersion of individuals may appear random at a smaller scale, while appearing clumped at a larger scale.

164. Students are often overwhelmed by the mathematics of the models of exponential and logistic growth.

As shown in the text, try to concentrate less on solving basic math problems and focus students’ attention on the patterns that these models describe. For example, students can be asked to determine the effects on population growth if b>d,or if r is positive (i.e., they should understand what the different terms represent and what it means when their values change relative to one another). If knowing the equations are important to instructors, they should make this explicit and provide enough time in class (and possibly in labs) to go over these models.

165. The d that represents death rate is not the same d in the term dN/dt. (The second represents delta (i.e., “a change in”).

166. Students may not see the similarities between the exponential and logistic growth models (the latter is a derivation of the former, taking into account limits to population growth) and may simply memorize the equations and graphs that describe each. Instructors should be explicit in their explanation of the unrealistic nature of continued exponential growth and that the logistic growth model provides a more realistic picture of how a population will increase in size.

302

167. Population cycles represent deviations of population growth from the logistic model. Students often do not see population cycles as an extension of the concepts regarding population growth. In many cases, these are populations that may not reach their carrying capacity or only briefly do so.

168. When we use the term ‘strategy’ to discuss life histories (i.e., an organism’s life history strategy), students often define strategy as a deliberate choice. However, strategy in this respect does not reflect a conscious decision. Rather, a strategy is shaped by natural selection, not chosen by the individual that possesses them and represent tradeoffs between investments in growth, reproduction and maintenance. .

169. Students may have difficulty seeing how the absolute number of individuals added to a population increases over time even though the growth rate may remain the same.

170. With survivorship curves it is more important that students can, given a description of a life cycle match it to the appropriate survivorship curve, rather than memorizing which curve is identified as a Type I, II or III survivorship curve. Some students may forget that they x-axis represents percentage of maximum life span and believe it to be absolute number of years. This makes it confusing when survival curves of two organisms with very different lifespans are on the same graph.

171. Students have problem with density-independent (e.g., conditions of climate) affecting population size. As well they may have trouble differentiating between intrinsic and extrinsic density-dependent factors.

172. Students may not see that population biology is useful/applicable to humans. However, census data is information about human populations and is used to inform public works projects, as well as to direct money to health research.

303

WHAT CAN I DO IN CLASS? The “Why it Matters” introduction describes how population ecology was used to help solve an epidemiological problem. This is likely to catch student interest and show how ecology is important to humans.

It is also an opportunity to reinforce that humans are subject to the same pressures that are other populations of organisms. [Stumbling Block 1] Mark/recapture class activity: (works for medium to large-sized classes). This is a simulation of the type of mark/recapture study carried out by population biologists (e.g., butterflies – see textbook, small mammals, etc.). Cut into strips, two different colours of paper (e.g., white and red); make about 10% more strips than your expected class size. Of the two colours, one colour of paper should make up only around 10-20% of the total number of strips (this need not be exact). This will be the ‘marking’ strips. Place strips randomly into a number of bags (e.g., for ~ 500 students I use 4-5 bags). Get student volunteers to randomly distribute their strips to a section of the class. Volunteers and students shouldn’t ‘choose’ their strip colour. (I ask them to close their eyes, stick their hand in the bag and pick a piece of paper.) Ask students to record the colour of their strip of paper such that they’ll have that piece of information for the next class. Give students the following clicker question.

1.

Please choose the appropriate statement regarding the strip of paper you got/picked at the beginning of class: A. I got a white strip of paper!

B. I got a red strip of paper!

C. Er…paper?

This is equivalent to the first capture in a real mark/capture experiment.

Ask students to return their strips of paper after class.

In the next class repeat the distribution of the strips of paper. This time you’ll ask the students a few clicker questions.

2.

Please choose the appropriate statement regarding the strip of paper that you picked up at the beginning of the last class.

A. I got a white strip of paper.

B. I got a red strip of paper.

C. Er…paper?

This is to refresh students’ minds re: their paper choice on day one.

304

3.

When I walked into class today, I received/picked up: A. A white strip of paper.

B. A red strip of paper.

C. Er…paper?

The group of students with red paper is equivalent to the second capture in a real mark/recapture experiment.

4.

For those of you who had a red strip of paper today, what colour strip did you have last class?

A. I had a red strip of paper.

B. I had a white strip of paper.

The group of students who report that they also had red paper on each of the days represents those organisms from the second capture that had been marked in the first capture.

Provide students with the number of respondents for each of the following: the number of students who had received red strips (use numbers from clicker question 1), the number of students who received red strips in the second class (clicker question 3), the number of students who had red strips in both classes (clicker question 4). Ask students to use these numbers to determine an estimate of the population (class) size.

This exercise can be done sequentially in the same class; however, sometimes the period of time between the classes reinforces the idea that mark-recapture is a method done over a period of time. This exercise can be done with candies, etc., but you have to warn students not to eat the candies first! You can ask students if the size of ‘captured’ group (both the first and second captures) would affect their results? Should they aim to catch approximately the same numbers for both captures? What are some limitations to this study? How would you mark organisms in the wild? What are the assumptions of the mark-recapture method? [Stumbling Block 4] There are several online simulation exercises, including those in Cengage (see Population Ecology Virtual Lab) for students to work through (on their own time, or in a laboratory, with computer stations) relating to examples of the concepts explored in this chapter.

Ask students to consider how governments determine how many schools should be built in an area. What information would they require? [Stumbling Block 12] Extinction is within easy reach even if there are living members of a population. This chapter looks at small populations from the standpoint of having a lot of growth capacity (reduced competition for food, shelter, etc).

However, some populations may exhibit the Allee Effect, where population growth and population density show a positive relationship. Ask students to brainstorm the various ways that a small population could be detrimental. If a population becomes of becomes so small, members of the population may not be able to function in group defense. As well, sexually-reproducing organisms could have difficulties finding mates, which could lead to declines in population growth. The Allee Effect is a consideration when implementing conservation plans.

To get students thinking about tradeoffs between maintenance, growth and reproduction that can directly affect them, show them a public-service announcement asking them to spay or neuter their pet. In addition to reducing the onus on animal shelters, there are benefits to your pet. Spaying/neutering (gonadectomy) can increase a pet’s lifespan! (E.g., Kustritz, MVR, 2007) Part of this is likely linked to decreased reproductive effort. Castration of salmon has been shown to greatly increase life span (Robertson, 1961).

305

The life history of guppies (p1122) is a great example that incorporates several of the concepts covered in this chapter. It shows some experimental manipulations that can be done in natural settings and aspects that can be modified in the lab. It also shows similar findings for natural and lab-setting experiments.

Ask students what happens to organisms put in extremely high-density situations in terms of stress. Then ask students to predict what would happen to immune system function and rates of reproduction under such stress.

Clicker questions:

When scientists study an organism, they find that it generally shows a uniform dispersion pattern. This would imply that member of the population ZZZZZ. have no ecological interactions with each other.

AAAAAA. use resources that are patchily distributed.

BBBBBB. work together to escape from predators.

CCCCCC. may experience intraspecific competition for vital resources.* DDDDDD. cooperate in rearing their offspring.

Stumbling Block 3 regarding dispersion patterns

(from text p1139 #7). According to the logistic model of population growth, the absolute number of individuals by which a populations grows during a given time period EEEEEE. gets steadily larger as the population size increases.

FFFFFF. is highest when the population is at an intermediate size.* GGGGGG. gets steadily smaller as the population size increases.

HHHHHH. remains constant as the population size increases.

IIIIII. fluctuates on a regular cycle.

This question can help with Stumbling Block 4 and 5 as it points out general patterns in population growth that can be identified using the logistic model of population growth. It helps to guide students away from the notion that they are to memorize the logistic equation and merely be able to plug in numbers.

A population’s growth rate (r) remains constant over 10 years. This means that JJJJJJ. The absolute number of individuals added per year is the same.

KKKKKK. The absolute number of individuals added per year decreases because r does not increase.

LLLLLL. The absolute number of individuals added increases each year.

MMMMMM. It is impossible to predict the trend regarding the absolute number of individuals added each year.

ASKS SAME THING AS QUESTION ABOVE? This helps students to see that even if r remains constant, the number of new individuals per unit time will increase. [Stumbling Block 4 and 5]

WHAT OTHER RESOURCES ARE AVAILABLE? 306



Virtual Lab – Population Biology. How does competition affect population growth using P.aurelia and P. caudatum. http://www.biologycorner.com/worksheets/virtual_lab_population.html



Human Population Ecology: Demography . http://www.biologycorner.com/worksheets/demography.html



Interpreting ecological data: http://www.biologycorner.com/worksheets/interpreting_data.html



Exercise on capture/recapture technique http://www.biologycorner.com/worksheets/estimatepop.html



Kustritz MVR, 2007. Determining the optimal age for gonadectomy of dogs and cats. JAVMA 231(11): 1665-1675



Moore GE, Burkman KD, Carter MN et al. 2001Causes of death or reasons for euthanasia in military working dogs: 927 cases (1993-1996). J Am Vet Assoc 219: 209214.



Bronson RT. 1982. Variation in age at death of dogs of different sexes and breeds Am J Vet Res 43:2057-2059.



Michell AR. 1999. Longevity of British breeds of dog and its relationship with sex, size, cardiovascular variables and disease. Vet Rec 145: 625-629



Basanez and Ricardez-Esquinca. 2001. Models for the population biology and control of human onchocerciasis. Trends in Parasitology 17(9):430-438

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Communities are made up of populations of different species. The interspecific interactions between these different populations, in addition to the climate, history, and frequency of disturbance of the area, shape the community in terms of the combinations of species. Some species, are more important than others in determining the structure and species diversity of a community.

307

2.

Communities are formed through interspecific interactions. As such, they can occur wherever these interactions occur.

3.

Disturbance is a normal occurrence in communities, and can even be a precursor to a healthy community.

LEARNING OBJECTIVES Students should be able to:



Define key terms: niche, coevolution, interspecific vs. intraspecific interactions, coevolution, predation, herbivory, parasitism, competition, mutualism and commensalism. [Knowledge]



Summarize, providing an example for each, the different types of interspecific interactions and their effects on the species involved. [Knowledge, Comprehension, Analysis]



Explain what is meant by the term ‘coevolutionary arms race’, providing an example.

[Comprehension]



Define specialists and generalists in terms of diet. [Knowledge]



List two traits each of predators and herbivores that enable them to feed effectively.

[Knowledge]

308



Describe how, in defence, various prey can use each of the following: chemicals, size, vigilance, reduced movement, evasion, armour, aposematic displays and mimicry.

[Comprehension]



Discuss, in terms of adaptation, why it can be said that there is no perfect defence mechanism. [Comprehension]



Differentiate between the purposes of cryptic camouflage, aposematic displays and mimicry in defence. [Comprehension]



Distinguish between Batesian and Müllerian mimicry, in terms of the toxicity/danger of the model and mimic involved. [Knowledge, Analysis]



Explain why the success of Batesian mimicry is frequency dependent. [Comprehension]



Summarize the optimal foraging theory, describing potential costs/benefits in acquiring food. [Comprehension]



Explain why prey density can influence a predator’s food choice. [Comprehension]



Differentiate between the two main types of interspecific competition: interference and exploitative. [Comprehension]



Explain why competition is described as a “-/-” interaction even when there is a winner. [Comprehension]



Describe the competitive exclusion principle, providing an example (other than Paramecium). [Comprehension]



Distinguish between the fundamental and realized niches of a species, providing an example (other than barnacles). [Comprehension]



Identify, given an example, the fundamental and realized niches of the species involved. [Application]



Extend the competitive exclusion principle to explain resource partitioning.

[Comprehension, Analysis]



Evaluate the impact of resource partitioning on the number of species that can occupy a given area. [Comprehension, Analysis] 309



Compare and contrast the phenomena of resource partitioning and character displacement. [Comprehension, Evaluation]



Describe the information needed to identify character displacement. [Comprehension]



Describe how an organism’s different life stages can reduce intraspecific competition. [Comprehension]



Explain why commensalism, mutualism, and parasitism are all considered forms of symbiosis. [Comprehension]



Explain why commensalism is likely a rare interspecific interaction, whereas mutualistic relationships are common. [Comprehension]



Explain why parasitism can be considered a form of predation. [Comprehension]



Differentiate between endo- and ecto-parasites, brood parasitism, and parisitoids.

[Knowledge]



Explain the effect of brood parasitism on the fitness of the host and parasitic species. [Comprehension]



Describe why parasitoids could be useful in the control of agricultural pests.

[Comprehension]



Discuss how mutualistic relationships can make one of the partners more vulnerable to extinction. [Comprehension]



Describe how interspecific interactions, including competition, can affect the organization/structure, species richness, and function of a community.

[Comprehension]



Define the following terms: species richness, species diversity, relative abundance, and species evenness. [Knowledge]



Compare and contrast the interactive and individualistic hypotheses of community species assemblages in terms of species composition and equilibrium. [Knowledge, Analysis]



Explain why ecotones are typically species rich environments. [Comprehension] 310



Describe the factors considered when measuring a community’s species diversity.

[Knowledge, Comprehension]



Identify, given an example, the community with the highest species diversity.

[Comprehension, Evaluation]



Describe how measures of species richness and species evenness are used in conservation biology. [Comprehension]



Define the following terms: trophic level, primary producer, consumers (primary, secondary, and tertiary), omnivores, detritivores, and decomposers. [Knowledge]



Assign each of the trophic levels (from primary producer to tertiary consumer) one of the following labels: photoautotrophs, heterotrophs. [Evaluation, Analysis]



Explain how the activities of detritivores and decomposers are crucial to community function. [Comprehension]



Describe how an organism may occupy more than one trophic level. [Comprehension]



Explain why the term ‘food web’ is more accurate than ‘food chain’. [Comprehension]



Define: biological hotspot, community stability, keystone species and facilitator species. [Knowledge]



Describe how community stability is related to species diversity and food web complexity. [Comprehension]



Identify, given a food web, the flow of energy through the web, categorizing organisms according to the trophic level(s) they occupy. [Comprehension]



Describe how the importance of competition varies between r- and K-selected species. [Comprehension]



Describe how a keystone species could influence species richness and structure of a community. [Comprehension]



Describe the effects of mild, intermediate and frequent disturbance frequencies on species richness and diversity. [Comprehension]

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

Explain how species richness affects a community’s rate of recovery (resilience) following a disturbance. [Comprehension]



Define succession, primary and secondary succession, climax community and aquatic succession. [Comprehension]



Describe the events (i.e., changes in plant species) as succession proceeds.

[Comprehension]



Compare rates of changes in species composition and richness in early and late stages of succession. [Comprehension]



Describe what determines species composition in a climax community.

[Comprehension]



Compare the three main hypotheses (facilitation, inhibition, and tolerance) regarding how succession proceeds. [Comprehension]



Discuss hypotheses explaining the higher species richness in the tropics.

[Comprehension]



Describe why (and how) species richness changes with latitude. [Comprehension]



Describe the equilibrium theory of island biogeography and what it explains.

[Comprehension]



Describe the factors that affect the rate of immigration and extinction on an island.

[Comprehension]



Describe what happens, according to the equilibrium theory of island biogeography, to the number of species on an island once equilibrium is reached. [Comprehension]



Describe the effect of island size and distance from the mainland on immigration and extinction of colonizing species. [Comprehension]



Given a description of an island (i.e., size and distance from mainland), predict whether colonization and extinction levels will be high or low. [Comprehension]

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WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Because certain organisms have a greater impact on community diversity than other species, we need to understand communities better to better direct our conservation effort. Management policies need to consider the wealth of complex interactions within a community.



The evolution of mutualistic interspecific relationships means that some organisms are almost or completely dependent on the survival of another organism. Knowledge of such interactions will again, help us to better direct our conservation efforts.

WHY SHOULD STUDENTS CARE? 

Maintenance of biodiversity could prove helpful to human health in the form of as yet to be discovered compounds (e.g., plant secondary metabolites with pharmacologic properties).



Because certain organisms have a greater impact on community diversity than other species, we need to understand communities better to better direct our conservation effort. Management policies need to consider the wealth of complex interactions within a community.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 173. The idea of a coevolutionary arms race can be confusing for some students. They often see no limits to how far this ‘race’ can go. It helps to remind students that species typically interact with more than one species (e.g., as predator or prey), as well as their abiotic environment; all of these exert selective pressure. For example, cheetahs do not only hunt gazelles, and cheetahs are not the only predator/danger to gazelles. Moreover, a population does not get faster because it needs to, rather there are chance mutations involved. This can be tied into Chapter 17 (genetic variation; random nature of mutation, drift, and sometimes gene flow; non-randomness of natural selection) and Chapter 45 in terms of fitness tradeoffs and life history.

174. Communities are made up of different populations that interact. It may be helpful to remind students that each population comprises only one species. As well, students may interpret “different organisms” to merely imply different individuals. This can cause considerable confusion as they read text and participate in class.

175. Sometimes students have difficulty picturing and understanding why the success of Batesian mimicry relies on low frequency of the mimic as compared to the model.

176. Because of our lifestyles today in this country, students may not realize how much energy goes into obtaining food and that there is a cost/quality strategy.

177. When visualizing competition, sometimes students are only thinking of physical (interference) competition, rather than the more subtle effects of exploitative competition. As a result, they may have difficulty grasping the idea that competition can often be hard to see. We must see two different populations of organisms using the same resource and that resource must be limiting. Also, by the time we look at a system, competitive exclusion and resource partitioning may have occurred; it is

313

only when we look at each species in an environment where the other doesn’t exist that we can see that they use similar resources.

178. In both Chapters 45 and 46, models of populations and their interactions are discussed. Students often have difficulty with the idea that models can help us make predictions, but they don’t dictate what will actually happen. This may be that there is a level of discomfort with the idea that there are no perfectly predictable situations. It may help to discuss models as hypotheses of what could happen.

179. Calculating species diversity takes into consideration more than simply the number of species (species richness). Students may confuse the terms species richness and diversity.

WHAT CAN I DO IN CLASS? The “Why it Matters” introduction describes the situation in which an area (such as the tropics) supports more species than another area (e.g., temperate zones), then niches become very specialized and narrow.) Ask students why it is beneficial for niches to become narrowed? If they were not, what would this mean for many organisms? (More competition). How has natural selection reduced intraspecific competition in many species?

As well, for many organisms, different life stages occupy different niches, limiting intraspecific competition, as young use different food sources than adults (e.g., butterflies, beetles, wasps, etc.).

Communities can be found everywhere. Challenge students to find examples of communities that they may otherwise overlook (e.g., the digestive tract of human, the back of a beetle, the fur of sloths).

When discussing defences, ask students why chemical defences would be more common in plants, rather than animals. You could ask students to write down their answers on cue cards, collect them and the following class use the most common suggestions as answer choices to a clicker question.

In order to demonstrate, rather than tell students about the importance of mimic:model ratios (success of this strategy is dependent on the frequency of mimics versus model), you could get the class to perform an exercise. Hand out strips of two different pieces of paper (e.g., red and white), with considerably more of one colour (e.g., a 70/30 or 80/20 white/red split). Tell everyone that they all strongly resemble each other, but those with the red are toxic. If you are the predator and they are the prey (there has to be a less offensive way of putting this), then what’s the likelihood you’ll capture a prey that is edible vs. inedible  students will know the ratio of strips? What’s your strategy going to be – will it be to take the risk? What if individuals holding a red strip of paper are non-toxic? What will be the likelihood that you’ll catch something safe versus catching something dangerous? [Stumbling block 3] Before discussing competitive exclusion or resource partitioning, show, a graph, two organisms whose niche ranges almost completely overlap (e.g., similar to Fig. 46.12, but with only 2 boxes, the slightly smaller of which is within the larger). Ask students a clicker question that gets them to describe the interaction and predict the result of these two species interacting (e.g., competition – both will continue to compete for the resource; competition – one species will be outcompeted and leave the area or go extinct; competition – but they’ll learn to share the resource). Next, show a diagram indicating that two different organisms that have overlapping niches (i.e., use same resource, but not necessarily in the same way or to the same extent). Again, ask students to discuss (or ask a clicker question) the outcome of such a situation. These questions can lead to students suggesting ideas that closely resemble those of competitive exclusion and resource partitioning without using the exact terms (i.e., avoiding the jargon and the tendency to memorize).

Ask students to reflect and brainstorm what are some species that humans interact with. Challenge them to come up with at least 10, eight of which are not eaten (they can be consumed as food, but get students to come up with other uses). Ask students to classify these interactions using the terms from this chapter.

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Discuss: are humans specialists or generalists? Are most organisms specialists or generalists? Can species be specialists some of the time and generalists the rest of the time? What are some factors that can affect whether an organism is a specialist or a generalist?

Ask students to list some of the costs (including risks) of obtaining food. What are the benefits? When do the benefits outweigh the risks? Of interest might be a segment from Quirks and Quarks (Slime Mould Dining Decisions) from March 6, 2010 (see Other Resources). Researchers showed that even an organism with no brain can make decisions regarding food based on risk versus quality.

Students may view succession and its associated concepts as material to memorize. Link the material from this chapter regarding succession to concepts on life history traits of Chapter 45 and to adaptation in Chapter 17.

Ask students to come up with some differences in the life histories of early successional versus late successional species. It may be good idea to get students to first define the differences between primary and secondary succession and the types of disturbances that initiate primary (volcanic eruptions, earthquakes, glaciers, etc) and secondary succession (logging, fire, etc.).

Link the material on recovery and resistance to disturbance with food web complexity in Chapter 47. The species interactions we examine here are greatly simplified. Food webs, nutrient cycling, and biogeochemical cycles, which are discussed in Chapter 47, introduce complexity that students should be made aware of.

The Pisaster keystone species example is a good, but other examples of keystone species can be introduced. In 1995, wolves were re-introduced into the Greater Yellowstone Ecosystem. Ask students to make a list of species that might be in this ecosystem before the wolf re-introduction. Then ask them to discuss and determine possible effects on each. Typically, students suggest only those species directly affected by the organism in question, but with a bit of prompting may start to explore indirect and cascading effects. Sea otters are another example of a keystone species.

Simberloff and Wilson tested the Equilibrium Theory of Island Biogeography by exterminating all arthropods on mangrove islands. Divide students into groups, and assign them to sides of a debate the value of such experiments. Although Simberloff and Wilson were careful to use a fumigant that was not toxic to the trees themselves, do students agree with this type of experimentation? What are the benefits of such experiments?

Do the benefits outweigh the drawbacks.

Even if material from Chapter 48 is not covered (or not in great detail) in your course, it may be useful to relate the equilibrium theory of island biogeography to edge effects, habitat corridors and fragmentation discussed in Chapter 48. This provides students with the practical aspects of this concept.

Clicker questions:

Which of these best describes a species fundamental and realized niches, in terms of size and variability within a species?

NNNNNN. The realized niche is typically smaller than the fundamental niche; the realized niche does not differ among populations of the same species.

OOOOOO. The realized niche is typically larger than the fundamental niche; the realized niche can differ among populations of the same species.

PPPPPP. The realized niche is typically smaller than the fundamental niche; the realized niche can differ among populations of the same species.* QQQQQQ. The realized niche is typically larger than the fundamental niche; the realized niche does not differ among populations of the same species.

315

Use this to introduce the variability of realized niches and how they are dependent on what are the limiting resources within a specific area, as well as the other species that are present. This can also be used to discuss the fact that the same species assemblages are not always found together.

316

In the table below, the numbers of species and numbers of individuals of each species for five field sites were recorded. Which community has the greatest species diversity?

Hermit crab Neireid worms Brachyuran crab Gastropod (Nucella sp.)

Gastropod (Lottia sp.)

A. Eagle Beach

B. Sandy Bay*

C. False Creek

D. Corbett’s Point

E. Shelter Cove

3 9 6 120 12

30 30 30 30 30

0 15 15 0 120

0 135 15 0 0

15 120 0 15 0

This question addresses Stumbling Block 8.

Which of the following islands would you expect to have the highest rate of extinction?

RRRRRR. 5 km2, 5 km from the mainland.

SSSSSS. 5 km2, 10 km from the mainland.

TTTTTT. 10 km2, 5 km from the mainland.* UUUUUU.10 km2, 10 km from the mainland.

Alternate forms of this question include asking which island would have the lowest rate of extinction or the highest rate of immigration. This could lead into a discussion regarding what other factors would affect immigration and extinction rates.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Wolves, keystone species of the Yellowstone ecosystem, have been reintroduced. http://www.nwf.org/News-and-Magazines/National-Wildlife/Animals/Archives/ 2003/A-Top-Dog-Takes-Over.aspx



Wolves in Nature project at the Oregon State University. Discusses trophic cascades. http://www.cof.orst.edu/wolves/



Slime mould dining decisions. March 6, 2010. http://www.cbc.ca/quirks/archives/09-10/qq-2010-03-06.html#2 (Also available as a podcast.)

317



Jonsson M and Malmqvist B. 2003. Mechanisms behind positive diversity effects on ecosystem functioning: testing the facilitation and interference hypotheses.

Oecologia 134(4):554-559.



Bronstein JL. 2009. The evolution of facilitation and mutualism. J Ecol. 97(6): 11601170.



Conservation International’s website on biodiversity hotspots. http://www.biodiversityhotspots.org/Pages/default.aspx



HilleRisLambers R and Dieckmann. 2003. Competition and predation in simple food webs: intermediately strong trade-offs maximize coexistence. Proc. R. Soc. Lond 270: 2501-2508.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Ecosystems are the result of species interacting with each other and their abiotic environment.

Interactions within and between ecosystems result in energy flow as well as global nutrient cycles.

LEARNING OBJECTIVES Students should be able to:



Define key terms: energetics, grazing food web, detrital food web, gross primary productivity, net primary productivity, biomass, limiting nutrient, secondary productivity. [Knowledge]



Differentiate between the grazing and detrital food webs, identifying where the two are linked. [Comprehension]



Explain, briefly, why only a small percentage of solar energy is available for photosynthesis. [Comprehension]



Describe how energy is stored in primary producers, addressing the different forms of new biomass. [Comprehension]



Differentiate between an ecosystem’s net primary productivity and its standing crop biomass. [Comprehension] 318



Describe why productivity estimates are shown as changes in biomass, not energy.

[Comprehension]



Explain why mean annual primary productivity varies globally, taking into account factors that inhibit or promote primary productivity. [Comprehension]



Organize/group the following different types of ecosystems according to their productivity, from highest to lowest (hint – some will be the same): temperate deciduous forests, temperate grasslands, deserts, tropical rainforests, open ocean, near-shore ecosystems (both temperate and tropical), and open lake. [Knowledge]

319



Describe why an area that receives a lot of sunlight can still have low levels of productivity (e.g., desert). [Comprehension]



Describe why two ecosystems might have similar rates of net primary productivity, but large differences in their amounts of biomass. [Comprehension]



Differentiate between primary and secondary productivity. [Knowledge]



Define key terms (related to energy use): ecological efficiency, harvesting efficiency, assimilation efficiency, production efficiency, pyramid of energy, ecological pyramids, pyramid of biomass, pyramid of numbers, and biological magnification. [Knowledge]



Describe the three factors that determine consumers’ ecological efficiencies.

[Comprehension]



Discuss why low ecological efficiencies result in pyramids of energy, biomass, and numbers for ecosystems. [Comprehension]



Explain why vegetarianism can be said to be a better use of energy than the omnivorous lifestyle of many humans. [Comprehension]



Describe how turnover rates can influence the stability of an aquatic ecosystem’s food web when biomass of the primary consumers exceeds that of the primary producers. [Comprehension]



Explain why the highest trophic levels (top predators) of food webs are more susceptible to genetic drift and other random events (including habitat destruction).



Describe the effects of consumers on the rates of primary productivity.

[Comprehension]



Define trophic cascade (differentiating between direct and indirect effects) and biological magnification. [Comprehension]



Describe briefly how knowledge of trophic cascades and biological magnification can be used for conservation purposes. [Comprehension]



Explain why some chemicals that have not been used in the recent past (i.e., a long time) can persist in the environment and be found at high levels in some organisms.

[Comprehension]



Define key terms (nutrient cycling): biogeochemical cycles, hydrogeologic cycle, carbon cycle, nitrogen cycle, phosphorus cycle, generalized compartment model.

[Knowledge] 320



Compare energy flow through ecosystems to biogeochemical cycles in terms of depletion and abiotic/biotic reservoirs. [Comprehension]



Describe components of a generalize compartment model of nutrient cycling, commenting on where different trophic levels acquire their nutrients from, and the rate of material exchange between the different compartments. [Comprehension]



Define key terms (nutrient cycling): carbon sink, carbon fixation, nitrogen fixation, ammonification, nitrification, denitrification, [Knowledge]



Describe, briefly, the roles of different ecosystems in the hyrogeologic, carbon, nitrogen and phosphorus cycles. [Comprehension]



Describe how manipulation of the nitrogen cycle through the Haber Bosch process (and its resultant effects) altered the earth. [Comprehension]



Describe why nitrogen and phosphorus are limiting nutrients. [Comprehension]



Compare and contrast conceptual and simulation models in terms of their application to ecosystem studies and potential limitations/challenges. [Comprehension]



Illustrate a basic conceptual model of an ecosystem, identifying key areas where more information (i.e., through a simulation model) is required. [Comprehension]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Humans benefit greatly from the ‘free’ ecosystem services (e.g., nutrient recycling, carbon sequestering, water purification) provided to us by nature. These services are reliant on functional ecosystems and research devoted to understanding/maintaining these services.



Understanding energy flow and nutrient cycling within and between ecosystems allows us to model potential effects of human activity on the natural environment.



Human development (e.g., removal of trees, etc.) not only alters the biotic environment, but can also effect profound changes to the abiotic environment. In turn, these abiotic effects can further impact the biota. Through modeling we can predict, with some accuracy, the potential impact of such human activities and, ideally, avoid those activities that may have devastating effects.

321

WHY SHOULD STUDENTS CARE? 

Humans benefit greatly from the ‘free’ ecosystem services (e.g., nutrient recycling, carbon sequestering, water purification) provided to us by nature. These services rely on functional ecosystems.



Understanding how human development (e.g., removal of trees, etc.) not only alters the biotic environment, but can also effect profound changes to the abiotic environment is important to society.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 180. The 10% rule, as pointed out in the text, is a rule of thumb and there are variations in the efficiency of energy transfer between the different trophic levels of different ecosystems. More important than the low efficiency of energy transfer between trophic levels is where the remaining energy goes (i.e., what it is used for). Concentrating on this allows a tie-in to earlier chapters on cellular respiration, waste production, etc. (Can ask students to brainstorm.) Although calculations of energy transfer are not imperative, it would likely help conceptual understanding if students were asked to determine (before being told or having read this part of the text) how they would go about calculating the efficiency of transfer.

181. Students can be overwhelmed by the wealth of steps in the biogeochemical cycles. If you don’t want students to memorize these cycles make this quite explicit to them.

182. Most students are familiar with the term ‘greenhouse gases’, but may not understand the short and long-term consequences of accumulation of such gases and how it facilitates climate change.

183. If students are asked to read anything aside from the text on biomagnification, there may be reference to the terms bioaccumulation and bioconcentration. These are often, (incorrectly) used interchangeably. While students do not necessarily need to know the specific differences between these terms, they should be made aware that there are differences.

WHAT CAN I DO IN CLASS? The “Why it Matters” discusses the value of knowing more about ecosystems and the impact of human activity on them. Ask students what changes they think would make urban developments more compatible with the natural environment.

This chapter offers an excellent opportunity to link material from other chapters, including: bacteria, fungi, nitrogen fixation and mutualism (N cycle, mutualistic relationships between mycorhizzae and plant roots); carbon sinks (disruption of C cycle through human activities that release stored carbon from fossil fuels, etc.); carrying capacity (alteration of K via Haber Bosch process), etc. [Stumbling Block 2] Many vegetarians (and vegans) make the point that eating meat is an unsustainable activity that is harmful for the environment. Ask students to explain what this statement means. Students may not understand the crux of this point relates directly to trophic system and energy pyramids, as well as land use devoted to raising food for cattle, etc., and the pollution issues (the nitrogen cycle in particular) involved. Students could be divided into groups to debate the issue of whether eating meat is an unsustainable activity for humans. [Stumbling Block 1]

322

In small groups, students can research a chemical (e.g., dioxins, mercury, cadmium; you may want to add some pharmaceuticals to this list) to determine if it has been shown to biomagnify. Students should find out what anthropogenic use the chemical has and address whether it impacts any organisms that humans eat and what safe levels are for human consumption. You may want to address differences between the terms biomagnification (bioamplifcation), bioaccumulation and bioconcentration before students handle this task; students can be asked to comment on whether their chemical biomagnifies, bioaccumulates or bioconcentrates.

[Stumbling Block 3] The Virtual Biology Laboratory Ecology exercises provide simulation exercises for the carbon cycle looking at both short- and long-term changes. [Stumbling Block 2] Clicker questions:

Are species of top carnivores more rare than other animals?

VVVVVV. Yes because there’s simply not enough room for all of them.

WWWWWW. No, there’s approximately as many of them as there are less dangerous animals.

XXXXXX. Yes, because we killed a whole bunch of them.

YYYYYY. No, we just don’t see them because they stay well hidden.

ZZZZZZ. Yes, because they require a lot more food to keep them going than do other organisms* This can be used to introduce limits to the number of levels in a food web. Students may not realize that numbers of types of organisms found in the lower trophic levels far exceed those in highest trophic level. [Stumbling Block 1]

323

Vegetarianism is sometimes promoted as a more efficient way of eating. Why? AAAAAAA. You can lose weight by not eating meat.

BBBBBBB. Meat costs more than produce and thus vegetarianism is cheaper.

CCCCCCC. The nutrients and amino acids you get from plant matter are constructed differently than those in meat.

DDDDDDD. There is less energy loss between producers and consumers.* EEEEEEE. You can digest the nutrients from plants more efficiently than those from meat.

This also addressed Stumbling Block 1, but can also be used to address the nutrient input necessary to grow large tracts of land for cattle consumption (etc.) and its effects on nutrient cycling and organismal populations.

WHAT OTHER RESOURCES ARE AVAILABLE? 

Bob McDonald. 2008. It’s about the ice, not the bears. Article discussing climate policy and its role in conservation. http://www.cbc.ca/technology/quirks-blog/2008/05/its-about-the-ice-not-the-bears.html



Environmental Literacy Council. Background information on biogeochemical cycles and climate. http://www.enviroliteracy.org/subcategory.php?id=1



Ecosystem Valuation. Environmental Literacy Council. What are the services that the environment provides us with? http://www.enviroliteracy.org/article.php/1320.html



Abramovitz JN. 1998. Putting a Value on Nature’s ‘Free’ Services. World Watch Institute.

IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

While extinction is a natural part of the evolutionary process and there have periodically been mass extinction events, the current extinction event is occurring at an unprecedented rate and the demise of most of these species are almost entirely at the hands and actions of humans.

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LEARNING OBJECTIVES Students should be able to:



Define key terms: extinction, background extinction rate, mass extinctions.

[Knowledge]



Discuss how extinction is a natural evolutionary process. [Comprehension]



Provide potential reasons for two of the five past extinction events. [Knowledge]



Describe how extinction of the dinosaurs facilitated adaptive radiation of mammals.

[Comprehension]



Describe how mutualism may render one of the partner species more vulnerable to extinction. [Comprehension]



Explain why species on islands are particularly vulnerable to extinction.

[Comprehension]



Describe factors (e.g., reproductive rate) that compound the effect of large harvests of a species for human use (e.g., consumption) in terms of that species’ risk of extinction. [Comprehension]



Define key terms: introduced species, invasive species, exotic species, endemic species, ballast water, and resource use efficiency (RUE). [Knowledge]

325



Describe two ways in which new species can be introduced to an ecosystem through human activity. [Knowledge, Comprehension]



Describe the difference between an introduced species and an invasive species.

[Comprehension, Analysis]



Summarize/list the potential negative impacts of introducing a new species to an ecosystem. [Comprehension]



Describe ballast water and the dangers it poses to local populations. [Comprehension]



Explain why not all introduced species are (equally) successful. [Comprehension]



Explain briefly, why invasive plant species may be difficult to eradicate (e.g., RUE).

[Comprehension]



Describe two examples of invasive species, one animal and one plant, providing the history of the invasion.



Describe one example each of species introduction that was purposeful (e.g., for economic reasons) and one that was accidental.



Define bycatch and describe its potential consequences to commercial fisheries.

[Knowledge, Comprehension]



Describe the cascading ecological effect resulting from the removal (or reduced numbers) of a top predator. [Comprehension]



Describe how declining numbers and, ultimately, extinction of a species can result from a complex interaction of different factors. [Comprehension]



Summarize at least three different ways that humans can cause the extinction of other species, indicating where life history patterns can exacerbate a negative situation. [Comprehension]



Define key terms (species protection): International Union for the Conservation of Nature (IUCN), Committee on the Status of Endangered Wildlife in Canada (COSEWIC), Convention for International Trade in Endangered Species (CITES), extinct, extirpated, endangered, threatened, special concern, data deficient, designatable unit, and resilience. [Knowledge] 326



Describe IUCN’s role in conservation. [Comprehension]



Describe factors considered when COSEWIC determines the appropriate conservation status of a species. [Comprehension]



Describe the eligibility factors that must be met in order for a species’ status to be evaluated. [Comprehension]



Describe the impact of political borders on conservation efforts (e.g., migratory species, hitchhiking species). [Comprehension]



Differentiate between an extinct species and an extirpated species. [Comprehension]



Discuss whether the term ‘designatable unit’ is synonymous with the term species.



Describe the use and importance of Linnaean species naming and descriptions to CITES and conservation efforts in general.[ Comprehension, Analysis]



Discuss factors that can impede conservation efforts. [Comprehension]



Describe two examples where protection of a habitat is a successful conservation strategy. [Comprehension]



List the United Nations’ Millennium Developmental Goals. [Knowledge]



Describe how hunting can be compatible with conservation. [Comprehension]



Provide two examples of the resilience of a natural system. [Knowledge]



Discuss the ESA’s (the United States’ Endangered Species Act) position on the conservation of hybrids. [Comprehension]

WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Humans benefit greatly from the ‘free’ ecosystem services (e.g., nutrient recycling, carbon sequestering, water purification) provided to us by nature. These services are reliant on functional ecosystems, with their full complement of biodiversity. To replace these free services would require millions and sometimes billions of dollars in man-made instruments and projects.

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

Many medically useful compounds are derived from a wide variety of organisms (e.g., taxol from the Pacific yew tree is used in the treatment of ovarian, breast and lung cancers). There may be many as yet undiscovered plants/animals that may provide us with clues and compounds with which we could improve human health.



We are losing diversity at an unprecedented rate, sometimes (often) before species and whole communities can be accurately described. Conservation biology research is very important in understanding these species and their communities and how they function.



Many economic ventures are entirely reliant on healthy ecosystems and species populations (e.g., commercial fisheries, agricultural crops etc). Loss of/reductions in top predators (e.g., sharks) can have devastating effects worldwide on commercial fisheries. Declining bee numbers and species could have drastic negative consequences for commercial agriculture reliant on their pollination services.

WHY SHOULD STUDENTS CARE? 

Humans benefit greatly from the ‘free’ ecosystem services (e.g., nutrient recycling, carbon sequestering, water purification) provided to us by nature. These services rely on functional ecosystems. To replace these free services would require millions and sometimes billions of dollars in man-made instruments and projects.



The biodiversity around us is awe-inspiring and fascinating and has intrinsic aesthetic value.

Functional ecosystems provide recreational playgrounds for many people.



Although the world has experienced mass extinctions in the past, the current extinction event has precipitated almost entirely through human activities.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 184. Mass extinctions are rapid, geologically speaking. (This text lacks a figure depicting the time line for these extinction events.

Simple timeline: http://www.dailygalaxy.com/photos/uncategorized/2007/10/24/mass_extinction_timeline_2.gif; Interactive timeline at Discovery Channel: http://dsc.discovery.com/earth/wide-angle/massextinctions-timeline.html) Many people assume that these mass extinctions happened quickly, which they did – on a geological time scale. (In terms of geology, rapid is on the scale of millions of years.

This is one way in which these extinction events differ from the current one we’re experiencing, which is occurring on a scale of tens to hundreds of years. Because of the unprecedented rate of extinction (i.e., small time scale involved), this extinction event has the potential to be the largest event yet. Another defining feature of the current event is that unlike other extinction events this one is caused by the actions of one species, Homo sapiens (rather than dramatic changes in climate due to natural catastrophic events, plate tectonics, etc.).

185. Many people believe that extinction only occurs to weak, inferior species that are not able to adapt.

Remind students of the definition of adaptation in its evolutionary sense. Factors that can put a species at risk do not indicate that the species is inferior, only that it exists in a fragile state. Factors that increase a species risk of extinction are limited habitat, small population, and a narrow tolerance range (i.e., habitat, etc.).

186. It is not enough to simply decrease hunting pressures on some organisms to conserve them. Culling, via controlled hunting, can sometimes aid in conservation efforts. In order to make conservation

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efforts successful, there needs to be change at the level of the actual problem (e.g., polar bears – hunting is problematic, but loss of sea ice due to global warming is a much larger factor in their demise).

WHAT CAN I DO IN CLASS? Although this is the second last chapter, instructors may want to introduce this material much earlier in the course to spark students’ interest in the diversity and fragility of life. Students would also gain an understanding of the practical importance of ecology.

This chapter offers an excellent opportunity to tie in material from other chapters, including: 

Chapter 17 – small populations more vulnerable to the effects of genetic drift. Hunting, poaching, bycatch, habitat loss, etc., can all result in a genetic bottleneck.



Chapter 45 – a population can become too small to sustain itself (Allee effect). Criteria used by COSEWIC are population characteristics used by population biologists. Control of human population is related to numbers of reproductive age females. By providing these women with the means to control their own fertility, may be able to limit human population growth.



Chapter 46 – link to immigration/extinction rates of islands and fact that species on islands are more vulnerable to extinction, particularly due to human effects; mutualism can render one or both species involved highly susceptible to extinction; some species have a greater effect in maintaining biodiversity of a community – removal of a keystone predator or an apex predator can have dire consequences for species occupying lower trophic levels. Resilience of a species (rather than a community)

Ask students what makes an extinction event a mass extinction event. Extinctions must be global, occur for a large number and types of species (often affecting all genera within a family), and, geologically speaking, occur within a relatively short amount of time (e.g., a few million years). [Stumbling Block 1] Discuss in small groups or as a class: what is different about this extinction event compared to previous mass extinctions? Many people point to the five mass extinction events in the past as evidence that extinctions are normal (as, indeed, they are – 10% of species go extinct every million years, while greater than 50% of species go extinct every 100 million years). However, what makes the current extinction event different? This event is driven by the success of humans (i.e., increased population and many different environment) and their activities. Organisms of one species don’t necessarily follow political boundaries, and differences in conservation or even resource use can exacerbate loss of populations that are already small. Because of the dramatic change in the last 150-200 years in how humans live (particularly in developed nations), has resulted in habitat loss and degradation, particularly in areas where there is high biodiversity (e.g., tropical forest), through urban development, mass agricultural method, and our need for extensive resources to supply our lifestyle.

This has pushed the scale/rate of extinction to a much more rapid rate than those that occurred in the past (past events have taken millions of years).

Endangered and threatened populations have small (or rapidly decreasing numbers). Ask students: What are the risks for a population that is small or rapidly declining? (Link to Ch. 17 – genetic drift; Ch. 45 – Allee effect, etc.) Follow up question: Suppose that conservation strategies for one or more of these species were successful (e.g., white rhinoceros – not discussed in text) – what are some potential issues for these populations?

(Although numbers may have increased, a population, or potentially the entire species, may now have very low genetic variability) Ballast water has been the vector by which many invasive species have been introduced. Students could look up international measures to limit or minimize this effect and then debate or comment on how effective these measures are.

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In class or in small groups discuss: 1) Should gardeners and farmers be exempt from rules concerning the introduction of foreign species? Why? Why not? This could be set up as a classroom debate. Students should consider containment issues, as well as resource use. (p1231 of text) 2) In situations where the behaviour of one endangered species threatens the survival of other endangered species, how should authorities proceed? (p1231 of text) 3) Do students agree with the position of the U.S. ERA that resources should not be used to protect hybrids?

4) Is the public driven by emotion, rather than need when it comes to prioritizing conservation? How would students feel if they were told that a population of bacteria endemic to a specific area was declining? Do students agree or disagree with the idea that the stereotype of the shark as a cold, hunting machine has likely also interfered with its lack of gaining protection status? [There is an illustration of this human tendency to conserve animals not viewed as predators in a recent episode of the Simpsons! In the episode “The Squirt and the Whale”, (Season 21, Episode 19, originally aired on April 25th, 2010), Lisa Simpson faces a dilemma when trying to save whales at the expense of sharks.]

5) Human activities are putting many species in precarious situations. Why is the term ‘survival of the fittest’ (or if they can’t adapt then they shouldn’t survive) inappropriate for today’s extinction event?

6) As mentioned in the chapter, non-genetic gender determination in many species could be greatly disrupted by global warming. What are some potential consequences?

Disappearing ice pack has been linked to increased greenhouse gas emissions. In his article “It’s about the ice, not the bears”, CBC’s Bob MacDonald discusses the United States choice of action (or inaction) in 2008, after acknowledging that the polar bear is a threatened species. Although loss of sea ice (polar bear habitat) is directly related to the demise of polar bears, the U.S. opted for legislation that banned the import of polar bear products, not for forced reductions in greenhouse gas emissions. We recommend using this article to get students thinking about matching conservation measures to a species’ threat. Instructors could use clickers to survey student opinions. E.g., Ask: Legislation was designed to limit hunting of polar bears – do you agree with this? Students could work as groups to find other endangered or threatened organisms where conservation strategies may not align with the threat to the species.

Get students to investigate Canadian legislation that deals with conservation. What is the Canadian Species At Risk Act (SARA)? Does it complement current conservation efforts, and if so, how? How does it tie in to work done under COSEWIC? Gender determination disrupted by global warming (add as a LO) – could result in severe consequences in some areas one sex or the other could be completely eliminated. Global warming could lead to even more disastrous outcomes for specific species. (Ospina-Àlvarez and Piferrer, 2008) In her book, The Bird Detective, Canadian researcher Bridget Stutchbury reveals that understanding the behaviour of organisms is imperative to developing useful and successful conservation plans. Ask students to comment on this? How this could be done? Applied?

Ask students to create a list of what traits/life histories allow invasive species to take over (grow and reproduce more rapidly compared to native species). (See Kolar & Lodge, 2001) This could be linked to life history traits in Chapter 45.

WHAT OTHER RESOURCES ARE AVAILABLE?

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

Interactive mass extinction timeline. Discovery Channel. http://dsc.discovery.com/earth/wide-angle/mass-extinctions-timeline.html



Canadian researcher Dr. Amanda Vincent’s Project Seahorse. http://seahorse.fisheries.ubc.ca/index.html

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

Bob McDonald. 2008. It’s about the ice, not the bears. Article discussing climate policy and its role in conservation. http://www.cbc.ca/technology/quirks-blog/2008/05/its-about-the-ice-not-the-bears.html



Quirks and Quarks host Bob MacDonald highlights 2010, International Year of Biodiversity. http://www.cbc.ca/technology/quirks-blog/2010/01/ international_year_of_biodiver_1.html



Dr. Nancy Shackell, guest on Quirks and Quarks, discusses the ecological cascade of overfishing top predators. January, 9, 2010. http://www.cbc.ca/quirks/archives/09-10/qq-2010-01-09.html#2



Colautti RI and MacIsaac HJ. 2004. A neutral terminology to define ‘invasive’ species. Diversity Distrib. 10:135-141.



Kolar CS and Lodge DM. 2001. Progress in invasion biology: predicting invaders.

Trends in Ecol & Evol. 16(4): 199-204.



Occhipinti-Ambrogi A. 2007. Global change and marine communities: alien species and climate change.



Stutchbury, B. 2010. The Bird Detective. Harper Collins Canada.



Stutchbury B. 2007. Silence of the Songbirds. Harper Collins Canada.



Mann CC. May 2007. Jamestown: America, Found and Lost. National Geographic. http://ngm.nationalgeographic.com/2007/05/jamestown/charles-mann-text



Ospina-Alvarez N and Piferrer F. 2008. Temperature-dependent sex determination in fish revisted. Prevalence, a single sex ratio response pattern, and possible effects of climate change. PLoS ONE 3(7): e2837. Doi:10.1371/journal.pone.0002837.



Brief humourous look at the human tendency to preserve the cute and cuddly, and ignore the predators. The Simpsons, “The Squirt and the Whale” (Season 21, Episode 19, originally aired on April 25th, 2010)

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IF NOTHING ELSE, MY STUDENTS SHOULD LEARN… 1.

Artificial selection by humans has shaped the evolution of domesticated plants and animals.

2.

Molecular biology techniques allow us to study origins/paths of domestication, and to make drastic changes at the genetic level of certain domesticated organisms (through genetic engineering).

LEARNING OBJECTIVES Students should be able to:



Define key terms: domestication, agriculture, cultivation, indehiscence, dehiscence, gynodioecious, parthenocarpic, niche construction/ecosystem engineering, controlled burning, monoculture, haplotype, teosinte, solonaceous plants, cultivar, ploidy (including diploid, triploid, tetraploid, hexaploid, octaploid), autogamous, mitochondrial DNA (mtDNA), hallucinogenic, aquaculture, yield, irrigation, short tandem repeat (STR), founder population, phenolic compounds, ginsenosides, molecular farming, energy return on investment (EROI). [Knowledge]



Describe the developments over the past 40 years that have led to a reduction in the number of people who are starving/malnourished. [Comprehension]



Describe the “green revolution”. [Comprehension]



Describe the progression of how humans have changed compared to our ancient ancestors, in terms of how they gather foods and other materials. [Comprehension]



Describe how farmer ants carry out agriculture. [Comprehension]



Explain how tools of molecular genetics have provided information regarding domestication events. [Comprehension]

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

Describe the impact of indehiscence on cereal crops. [Comprehension]



Explain how asexual reproduction may speed the process of domestication.

[Comprehension]



Describe, using an example, how changes in habitat could to relate to domestication.

[Comprehension]



Describe how human behaviours may have assisted in domestication. [Comprehension]



Compare and contrast the possible uses of domesticated plants and domesticated animals. [Comprehension]



Explain why population declines of honeybees could have catastrophic impact, both ecologically and economically. [Comprehension, Analysis]



Describe the uses of domesticated cotton. [Comprehension]



Describe (briefly) the four different species of cotton in terms of origin and ploidy.

[Knowledge, Comprehension]



Describe the uses of the yeast Saccharomyces cerevisiae. [Comprehension]



Describe, in general terms, what genetic analyses of Saccharomyces cerevisiae strains have indicated in terms of the origin and uses of this organism. [Comprehension]



Describe the difference between wild species of rice (Oryza rufipogon, O. indica) and domesticated rice (O. sativa). [Comprehension]



Describe Einkorn wheat, and how this strain arose. [Comprehension]



Explain why lentils (Lens culinaris) were more difficult to domesticate than other grains (e.g., wheat, rice). [Comprehension]



Describe the events involved in domestication of the grape (Vitis vinifera), modern corn (Zea mays), and Lens culinaris, highlighting similarities and differences between them. [Comprehension, Analysis]



Provide examples of domesticated food plants in the Solonaceae family. [Knowledge]



Describe characteristics of domestic potatoes. [Comprehension] 334



Using an example, describe how artificial selection was carried out in the domestication process of that plant. [Comprehension, Application]



Describe the social repercussions of the “potato famine” of Ireland. [Comprehension]



Explain how Curcurbita species morphology illustrates the difficulty of applying the species concept. [Comprehension, Analysis]



List and describe the major sites of plant domestication, throughout the world (locations in both the New and Old World), providing examples of the most important plants domesticated at these sites. [Knowledge, Comprehension, Analysis]



Describe how interspecific communication between humans and dogs could have been selected for in domestication of dogs. [Comprehension]



Explain how the Atlantic Salmon (Salmo salar) is considered to be domesticated.

[Comprehension]



Compare and contrast the potential benefits and risks of aquaculture. [Comprehension, Analysis]



Describe, using both plant and animal examples, organisms that provide more than one use/crop for humans. [Comprehension]



Explain what is meant by “cultivated but not domesticated” organisms.

[Comprehension]



Describe how the domestication of plants and animals has affected the environment’s carrying capacity (K) for humans. [Comprehension]



Describe the balance of crop costs and yields, including major factors involved.

[Comprehension]



Compare and contrast the domestication of dogs and cats. [Comprehension, Analysis]



Describe the potential problems faced by farmers that can reduce crop yields.

[Comprehension]



Provide and describe (2 or 3) examples of important chemicals from plants.

[Knowledge, Comprehension]

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

Describe the possible conservation risks that exist with molecular farming, and how the use of tobacco plants may circumvent some of these risks. [Comprehension]



Describe what the energy return on investment (EROI) indicates, and why tracking EROI over time can be useful. [Comprehension]



Explain, using two or three examples, how human exploitation of other species has been involved in changes in society. [Comprehension]



Explain how DNA fingerprinting can be used to determine the origin and path of domestication of a particular species. [Comprehension]



Provide examples where recent developments in molecular biology (DNA technologies) has been involved in domestication. [Comprehension, Analysis]



Given a phylogenetic tree, determine relationships between different species/strains of a given organism. [Application]



Explain how domestication of another species by humans can be considered an example of evolutionary change.



Describe the negative consequences of domestication to biodiversity. [Comprehension]

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WHY IS THIS CHAPTER IMPORTANT TO SCIENTISTS? 

Human population reliance on livestock and plant crops means that there is a need to maintain/improve yields and quality of domesticated organisms. Many researchers are working on ways to do this through selective breeding and/or genetic engineering.



Some scientists are involved in research to track the evolution of domesticated organisms over history. (In addition to biologists, anthropologists and archaeologists are also interested in aspects of domestication over time.)



Conservation biologists have concerns about the impact of domesticated species on natural ecosystems and biodiversity.

WHY SHOULD STUDENTS CARE? 

As humans, we are reliant on livestock and plant crops for our food and many other materials.



Many students have domesticated animals as pets.



Domestication illustrates how artificial selection can lead to evolution.



Understanding the history of domestication provides insights into the development of humans from small groups of hunter–gatherers to the dense populations we see today.

WHAT ARE COMMON STUDENT MISCONCEPTIONS/STUMBLING BLOCKS? 187. Students will need considerable background in various biological topics to fully comprehend all of the topics in this chapter. (It combines aspects of evolution, molecular biology, organismal biology, ecology, conservation biology, etc.) Many specialized terms are used in this chapter without definitions; if students have not encountered them in a previous chapter, this can be a stumbling block. Instructors are likely going to have to help students “connect the dots” in this chapter, relating concepts to other chapters in the book, and possibly reviewing some concepts. (As always, careful selection – and dissemination - of Learning Objectives is advised.)

188. Many different types of organisms are discussed, with various species cited. Additionally, there are a number of different origins and geographic paths followed in plant and animal domestication described in this chapter (but some overlap, in certain cases). The wealth of details can be overwhelming to students, and instructors are likely to be asked “Do we have to memorize all these scientific names/places?”. Communication of clear guidelines in terms of the knowledge students are expected to gain from this chapter, such as the learning objectives, may help alleviate student anxiety.

189. It can be difficult for students to picture a time when human society was without agriculture.

190. Students often have trouble understanding that artificial selection leads to evolution (i.e., genetic change in a population over time). Try to emphasize that if the phenotype selected is genetic in nature then there will be a genetic change in the population if you are choosing for specific phenotypes.

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191. The difference between cultivation and domestication is not necessarily easy to understand. Explicitly defining these terms, with examples, is necessary to help students distinguish them.

192. Similarly, many people do not realize that through selective breeding, humans have caused genetic changes in domesticated organisms (i.e., genetic engineering is not the only way to change the genetic makeup of an organism).

WHAT CAN I DO IN CLASS? The “Why it Matters” introduction discusses the food requirements of humans, and how the “green revolution” led to a reduction in starvation/malnutrition (although did not eliminate hunger entirely). A discussion about developments in agriculture that led to an improved supply of food to (most of) the world’s population, and the potential drawbacks of some of these developments may be useful in highlighting the importance of this chapter’s topic.

This chapter touches on many biological concepts and techniques. Students may wish to review portions of Chapters 16, 17, 20 and 45. Instructors may want to supply definitions for some of the terms used in this chapter if students have not already encountered them already in previous chapters.

Students (individually or in groups) can be asked to find information about Norman Borlaug, credited as the “father of the green revolution”. (Borlaug passed away in Sept. 2009.) A discussion of Borlaug’s contributions, and some of the criticisms made against aspects of his work (and the green revolution in general) could provide context for later material in the chapter, and even the foundations for a debate.

Have students brainstorm to list the most important crop plants/livestock animals in different parts of the world. (You may need to prompt students to consider aspects beyond food – e.g., building, industrial and manufacturing materials, perfumes, drugs, textiles, drugs, entertainment.)

Using a large map of the world, assign individual students (or small groups) to show the origin of various crop plants (e.g., using cut-outs that resemble the plant/food and adhering them to the map). These plants could be ones mentioned in the textbook, or you could include a larger sampling that would require students do additional research outside the textbook. A discussion could follow to consider why certain regions of the world were the origin of so many important cultivated and domesticated species, and why this did not occur in other regions.

In class, work through complex figures like Figure 49.2, encouraging students to make observations of the figure, and explain how one interprets such representations of data (i.e., mtDNA relatedness, geographical locations). Ask: Why use mtDNA? How was the mtDNA data obtained? Analyzed?

Show actual examples of plants that are indehiscent vs. dehiscent ones. Demonstrate the difference in release of seeds. Ask students to think of other possible changes that humans would appreciate in plants that produce grains (e.g., larger grains, more seeds produced, etc.).

Monoculture is attractive to many governments (local and national) and they encourage their citizens to grow commercially viable crops (e.g., palm oil, soybeans). Often this involves burning down old growth forests and replacement of these plants with a uniform crop species. Diversity in the area declines dramatically and ecosystem function begins to falter, which can have national and international consequences. A debate could be held re: the pros and cons of monoculture. In order to get students started in a discussion, an instructor could provide some examples (You may want to note that there several commercially important seedless fruits/vegetables; because the fruits are seedless, they must be propagated asexually. This could be used to discuss the Irish potato famine as there was just one potato variety, and these were propagated vegetatively.

Some biologists also warn that commercial bananas are at high risk of extirpation, as such crops are genetically uniform increasing their vulnerability to insects and disease. (E.g., the Gros Michel banana was nearly wiped

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out by the Panama disease in 1960. Currently, the Cavendish, its successor is the most common commercially stocked banana.)

In discussing chemicals from plants used by humans, instructors can ask students about the benefits of plants producing such chemicals in nature. (In many cases, these compounds deter herbivores or insect pests.)

Cats vs. dogs? Get students to discuss the different characteristics of each animal that led humans to domesticate them.

Students may be interested in learning more about the origins of their pet cats and dogs. (See “other resources” for more information.)

Some people have “exotic pets”, such as sugar gliders, snakes, or tarantulas. Ask students whether to compare these to cats and dogs, in terms of domestication (previous or future) and characteristics of these organisms.

Quirks and Quarks recently interviewed Dr. Camilla Speller, from the Ancient DNA Lab in the Department of Archaeology at Simon Fraser University. Students can be encouraged to listen to the podcast (see link below, under “other resources”) and learn more from the “Related Links”. If students have questions from the readings, these can be discussed in class. This interview also points out the links between domestication and genetic bottleneck events (link to Chapter 17).

Assign students to determine or estimate costs and yields, as well as some of the complications/considerations faced by farmers of typical crops/animals in their province. This could involve not just research of published information, but students could attempt to interview local farmers or agriculture experts.

A class discussion on the future challenges in agriculture (e.g., biotechnology) can explore some of the concerns likely to be faced in the coming years in terms of feeding/supplying the world’s population, conserving biodiversity, etc.

Clicker questions:

Agriculture has been part of human society for FFFFFFF. most of human history.

GGGGGGG. about half of human history.

HHHHHHH. less than 1/10 of human history. * IIIIIII. only 50 years.

Agriculture (cultivation and domestication of crop plants, animals) is thought to have arisen approximately 12,000 years B.P.

The most common wheat varieties used to make flour today are very different from the wild varieties that appear to resemble the original ancestral wheat plants. Modern varieties are indehiscent and hexaploid. Modern wheat is an example of JJJJJJJ. evolution by natural selection.

KKKKKKK. evolution by artificial selection. * LLLLLLL. cultivation, but not domestication.

MMMMMMM. more than one of the above.

Stumbling Block 4.

Which of the following is an example of domestication (rather than cultivation)?

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NNNNNNN. Modern corn varieties grown today produce corn kernels in an ear. * OOOOOOO. In early agriculture, humans kept seeds of edible plant varieties and planted them so that the same plants would grow the next year.

PPPPPPP. Each year, Jo gathers the small wild strawberries that grow in the woods behind her cabin.

Artificial selection by humans has resulted in many organisms being reliant on humans for continued propagation, indicating domestication has occurred. Stumbling Block 5.

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WHAT OTHER RESOURCES ARE AVAILABLE?  Norman Borlaug Biography on Nobel Prize website: http://nobelprize.org/nobel_prizes/peace/laureates/1970/borlaug-bio.html 

Monoculture and its evolutionary consequences (How does evolution impact my life?): http://evolution.berkeley.edu/evolibrary/article/_0_0/agriculture_02



Wayne RK, Ostrander EA. 1999. Origin, genetic diversity, and genome structure of the domestic dog. Bioessays.21(3): 247-257.



Driscoll CA, Menotti-Raymond M, Roca AL, Hupe K, Johnson WE, Geffen E, Harley EH, Delibes M, Pontier D, Kitchener AC, Yamaguchi N, O'brien SJ, Macdonald DW. 2007. The Near Eastern origin of cat domestication. Science.

317(5837): 519-523.



CBC Quirks and Quarks Feb. 6 – Taming Turkeys http://www.cbc.ca/quirks/archives/09-10/qq-2010-02-06.html

(Scroll

down)

Appendix: Clicker Tips 

Find out which system is used/preferred at your institution. In most universities that are using CRS, it is possible to arrange for clicker use (where you can obtain a receiver and clicker, and arrange for students to obtain clickers through the bookstore or your computing services).

Students will need to know where to obtain the clickers, and the registration process involved.



Determine if you will use a laptop or classroom computer. (If it is the latter, will you have options to transfer files via internet, or USB drive?)



Practice using the system alone before implementing in class.



Let students know your expectations (see Duncan, 2005 for some examples/tips). We recommend explicitly discussing academic honesty, grading of clicker questions, weighting towards final grade. This can be done in the course outline and in class.



Find out help/support offered by your university. Is there a help line/email address for support from the company that makes the clickers/software?



Check to see if your classroom has a designated channel. Many schools will assign channels to rooms to avoid problems with nearby rooms using the same one.

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

Check to see if your clicker software allows you to easily add questions during lecture. This is helpful if you want to take advantage of a teachable moment.



When introducing clicker use for the first time, be aware that there will probably be some time needed for the initial troubleshooting. (If you can bring some helpers along to that class, they can help assist students.) We recommend using some fun (or, at least, low-risk) questions for students to answer when first trying out the clickers on higher-risk (e.g., for marks) questions.



If you will be showing clicker questions in PowerPoint (or Keynote), you may want to add visual cues (e.g., a different colour background) to differentiate clicker questions from other slides.  If some of your questions are for participation marks only, whereas others are awarded marks for participation and a right answer, you may want use a different coloured background or text for each type of question.



Keep notes about which questions worked well, which ones less so ( immediately after class is best). Over time, you can develop your own optimized bank of questions.

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