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Chapter 7 - Inside the Cell Learning Objectives: Students should be able to …  Describe the structure and function of individual cell components.  Explain what molecular "zip codes" are and how they function.  Describe the structural and functional importance of the cytoskeleton.  Explain the dynamic nature of the cell. Lecture Outline I. Bacterial and Archaeal Cell Structures and Their Functions A. A revolutionary new view (Fig. 7.1) 1. Bacterial cells are highly organized, with an array of distinctive structures found among millions of species. B. Prokaryotic cell structures: a parts list 1. The chromosome is organized in a nucleoid. a. Bacterial DNA is inside a chromosome, which contains genes. b. In order to fit within the nucleoid, the chromosome is supercoiled. (Fig. 7.2) c. Some bacterial cells have additional DNA molecules called plasmids that carry genes that help cells adapt to unusual circumstances. 2. Bacterial ribosomes are the sites of protein synthesis. 3. Many bacterial species have internal photosynthetic membranes that convert solar energy into chemical energy. (Fig. 7.3) 4. Bacterial organelles perform an array of tasks. 5. Bacteria contain protein filaments that make up a simple cytoskeleton. 6. The plasma membrane separates life from nonlife. 7. Some bacteria have flagella that are used to power movement. 8. The cell wall protects the bacteria from osmotic stress. (Figs. 7.4 and 7.5) II. Eukaryotic Cell Structures and Their Functions A. The benefits of organelles 1. Eukaryotic cells are compartmentalized by membrane-bound organelles. a. Compartmentalization separates incompatible chemical reactions. b. Compartmentalization increases efficiency inside the cell in two ways:

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(1) It allows for the maintenance of high concentrations of reactants. (2) It clusters enzymes and reactants together, thus shortening the diffusion distance. 2. Prokaryotic versus eukaryotic cells (Table 7.1) a. Eukaryotic chromosomes are inside a membrane-bound nucleus. b. Eukaryotic cells are usually larger than prokaryotic cells. c. Eukaryotic cells have extensive amounts of internal membrane. d. Eukaryotic cells feature a diverse and dynamic cytoskeleton. B. Eukaryotic cell structures: a parts list (Fig. 7.6) 1. Nucleus (Fig. 7.7) a. The nucleus is the largest organelle in the cell. b. It is enclosed by a double membrane called the nuclear envelope. c. It has a nuclear envelope that is supported by the nuclear lamina. d. It contains the genetic information of the cell, DNA. e. It contains the nucleolus, the site of rRNA synthesis and ribosome assembly. 2. Rough endoplasmic reticulum (Fig. 7.8) a. The rough endoplasmic reticulum (ER) is a network of membrane-bound sacs and tubules. b. The ER has ribosomes bound to the cytoplasmic surface on which secreted and transmembrane proteins are made. c. It contains enzymes in the lumen that fold and modify proteins after they are synthesized on bound ribosomes. 3. Smooth endoplasmic reticulum (Fig. 7.9) a. The smooth endoplasmic reticulum is a portion of the ER that does not have ribosomes attached. b. It contains enzymes that are involved in the synthesis of lipids, detoxifying harmful substances and storing calcium ions. c. The ER (smooth and rough), the Golgi apparatus, and lysosomes make up the endomembrane system, which is the primary center for protein and lipid synthesis. 4. Golgi apparatus (Fig. 7.10) a. The Golgi apparatus consists of flattened membrane sacs called cisternae.

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b. It has polarity: a cis side that receives proteins from the rough ER and a trans side that ships proteins to their final destination. 5. Ribosomes (Fig. 7.11) a. Ribosomes are found in the cytosol. b. They are composed of two subunits: large and small. c. They are molecular machines that synthesize proteins. 6. Peroxisomes (Fig. 7.12) a. Peroxisomes are centers for oxidation reactions. b. They generate hydrogen peroxide as a by-product of these reactions. c. They contain an enzyme, catalase, that converts hydrogen peroxide into water and oxygen. d. Plants have special peroxisomes called glyoxosomes that convert the products of photosynthesis into a storable sugar. 7. Lysosomes (Fig. 7.13) a. Lysosomes are involved in solid-waste processing and material storage. b. They receive material destined for hydrolysis via three mechanisms: (Fig. 7.14) (1) Phagocytosis: cellular eating (2) Autophagy: the delivery of damaged organelles to lysosomes for recycling (3) Receptor-mediated endocytosis: targeted ingestion of extracellular molecules, some of which are destined for the lysosome (Fig. 7.15) c. Lysosomes have a proton pump in their membrane that keeps the lumen acidic. d. They contain digestive enzymes, called acid hydrolases, that work best in acidic conditions to hydrolyze macromolecules. 8. Vacuoles (in plant cells) (Fig. 7.16) a. Vacuoles occupy most of the volume of plant cells. b. They act as a storage depot for water, ions, and sometimes proteins. c. They may contain noxious substances that protect the plant from predators. 9. Mitochondria (Fig. 7.17) a. Mitochondria are the sites of ATP synthesis.

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b. They have two membranes. (1) The outer membrane is smooth. (2) The inner membrane contains folds called cristae. (3) The mitochondrial matrix is inside the inner membrane. c. Mitochondria contain some of their own circular DNA. d. They make their own ribosomes. e. They can divide independently of cell division. 10. Chloroplasts (Fig. 7.18) a. Chloroplasts convert the energy in sunlight into the chemical energy in sugar. b. They have two membranes. (1) The outer membrane is smooth. (2) The inner membrane is also smooth. (3) The inner membrane is filled with a series of flattened sacs, called thylakoids, that are stacked in grana. (4) Thylakoids are surrounded by stroma, the fluid filling the inner membrane. c. Chloroplasts have some of their own DNA and can divide independently of nuclear division. 11. Cell walls (Fig. 7.19) a. Algae, fungi, and plant cells have cell walls. b. Cell walls are composed of carbohydrate rods and fibers running through a stiff polysaccharide matrix. 12. Cytoskeleton (Fig. 7.20) a. The cytoskeleton is a system of protein filaments. b. It provides structural support to the cell. c. It facilitates many types of cellular movement. III. Putting the Parts into a Whole A. Structure and function at the whole-cell level (Table 7.2) 1. Examples (Fig. 7.21) a. Pancreatic cells are specialized for secreting digestive enzymes. They are packed with ER and Golgi apparatus, the organelles that manufacture secreted proteins. (Fig. 7.21a) b. Testis cells are specialized for making testosterone, a steroid hormone. They have an extensive smooth ER network. (Fig. 7.21b)

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c. Leaf cells are specialized for absorbing light and manufacturing sugars. They contain a large number of chloroplasts. (Fig. 7.21c) d. Potato tuber cells are specialized for storing sugars. They contain a large storage vacuole. (Fig. 7.21d) B. The dynamic cell 1. Light and electron microscopes allow us to see the shapes and locations of organelles inside a cell. 2. Differential centrifugation allows us to isolate and study the functions of individual organelles (see BioSkills 11 in Appendix A). 3. Studies involving green fluorescent protein and confocal microscopy allow us to study how all of the organelles in a cell act together (see BioSkills 10). IV. Cell Systems I: Nuclear Transport A. Structure and function of the nuclear envelope 1. The nucleus is enclosed by a double membrane called the nuclear envelope. (Fig.7.22a) a. The outer nuclear membrane is continuous with the rough ER. b. The space between the inner and outer membranes is continuous with the lumen of the rough ER. 2. Nuclear pores penetrate the nuclear envelope and connect the cytoplasm to the nucleoplasm. (Fig. 7.22b) a. Nuclear pores consist of 50 different proteins called the nuclear pore complex. b. Molecules travel into and out of the nucleus through the nuclear pores. (1) rRNA and ribosomal subunits are made in the nucleolus but are functional in the cytoplasm. (2) mRNA and tRNA are made in the nucleus but function in the cytoplasm. (3) Nucleotide triphosphates—enzymes involved in DNA replication, transcription, and so forth—are made in the cytoplasm but function in the nucleus. B. How are molecules imported into the nucleus? 1. Researchers studying viral proteins noticed that changing a single amino acid could disable the protein’s ability to enter the nucleus. 2. This observation led to the hypothesis that proteins destined to be imported into the nucleus contain a nuclear localization signal. 3. Experiments using a protein called nucleoplasmin (involved in chromosome assembly) revealed the nature of the nuclear localization signal. (Fig. 7.23) a. What portion of the molecule targets it to the nucleus?

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(1) Experimental design: Researchers used enzymes called proteases to separate the tail region of nucleoplasm from the head region. They labeled each with a radioactive atom and injected them into different living cells. (2) Results: The researchers found that only the tail regions were transported into the nucleus. (3) Conclusion: The tail region contains the nuclear transport “zip code” tag. b. Further experiments demonstrated that a 17-amino-acid stretch of the nucleoplasm in the tail region made up the nuclear localization signal. Follow-up studies showed that other proteins have nuclear localization signals that interact with proteins called importins and exportins, which act as delivery trucks. V. Cell Systems II: The Endomembrane System Manufactures and Ships Proteins A. Studying the pathway through the endomembrane system (Fig. 7.24) 1. George Palade studied pancreatic cells that secreted a large volume of proteins in order to understand the role of the endomembrane system in the production and processing of secreted proteins. 2. Hypothesis: The rough ER and Golgi apparatus form an endomembrane system that directs the production and secretion of specific proteins. 3. Experimental design: Palade used the pulse-chase technique to label newly synthesized proteins and visualize them over time. a. Palade exposed cells to a brief “pulse” of radioactively labeled amino acid (leucine). b. Then he gave the cells a large amount of unlabeled amino acid (the “chase”). c. After varying amounts of time, he killed the cells and examined them under the electron microscope (see BioSkills 9 and 10). 4. Results: These experiments demonstrated that the proteins pass from the rough ER to the Golgi apparatus to secretory granules and are ultimately secreted outside the cell. (Fig. 7.25) B. Entering the endomembrane system: the signal hypothesis 1. Günter Blobel hypothesized that proteins destined to be secreted have a signal in the first few amino acids that functions as an address tag directing them to the ER. 2. Researchers found that when secreted proteins are synthesized in a test tube without the ER, they are about 20 amino acids longer than the same protein that is secreted by cells.

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a. When the researchers added the ER to their test tubes, the synthesized proteins were the same length as the endogenous proteins. b. The sequence of 20 amino acids is located on the N-terminus (the beginning) of the protein. It has been named the ER signal sequence. 3. Recent studies have documented the mechanism by which proteins with signal sequences are received by and enter into the rough ER. (Fig. 7.26) a. A ribosome synthesizes the signal sequence, which then binds to a signal recognition particle (SRP) in the cytoplasm. b. The ribosome, new polypeptide, and SRP all bind to a protein receptor on the surface of the rough ER. c. After the binding to the rough ER, the synthesis of the polypeptide is completed, the signal sequence is removed, and there are two possibilities for the polypeptide: (1) The polypeptide may be transferred to the lumen of the ER so that it can be processed and ultimately packaged into an organelle or secreted from the cell. (2) It may be integrated into the rough ER membrane so that it can be processed and shipped to the plasma membrane. d. What happens to proteins when they are in the rough ER? (1) Proteins are folded into their tertiary and quaternary structures with the help of chaperone proteins. (2) Other enzymes modify proteins by adding carbohydrate groups (glycosylation). (Fig. 7.27) C. Moving from the ER to the Golgi 1. Palade and colleagues hypothesized that vesicles bud off of the ER, move through the cytoplasm to the nearby Golgi apparatus, fuse with the cis face of the Golgi apparatus, and dump their contents inside. 2. Studies using electron microscopy combined with differential centrifugation confirmed this hypothesis and demonstrated that distinct types of vesicles shuttle materials through the Golgi. D. What happens inside the Golgi apparatus? 1. Recent studies have shown that the cisternae are constantly regenerated by the fusion of vesicles with the cis face and disposed of as vesicles bud off the trans face. 2. The function of the Golgi is well understood.

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a. Cisternae have a different set of enzymes at each stage of maturation, which catalyze different parts of the glycosylation reactions. b. Existing sugar groups on proteins are modified, phosphorylated, or even removed, while new sugar groups may be added. E. How do proteins reach their destinations? 1. Once proteins are manufactured and processed through the ER and Golgi, they must be sent to the appropriate location or organelle within the cell. 2. Studies involving lysosomal enzymes reveal that these proteins are tagged with specific carbohydrate groups (mannose-6phosphate) acting as molecular zip codes that target the proteins to the vesicles destined for the lysosome. (Fig. 7.28) 3. Proteins that are to be secreted are packaged into vesicles destined for the plasma membrane, where they will fuse and dump their contents via a process called exocytosis. 4. Proteins that are synthesized in the cytoplasm also have zip codes directing them to mitochondria, chloroplasts, or other destinations. a. The arrays of proteins produced in a cell are sorted via distinctive zip codes. b. These molecular addresses allow proteins to be shipped to the compartment where they function. VI. Cell Systems III: The Dynamic Cytoskeleton (Table 7.3) A. Actin filaments (Fig. 7.29) 1. Actin filaments are long, fibrous polymers of globular protein called actin. a. Actin resembles two strands twisted together. b. Actin has polaritya plus end and a minus end; microfilaments grow at the plus end. 2. Microfilaments form a matrix that helps define the cell’s shape. (Fig. 7.29a) 3. Actin filaments are also involved in several types of cell movement that are facilitated by the action of myosin binding to actin filaments, causing them to slide across one another. (Fig. 7.29b) a. Cell crawling: Extension of actin filaments in one part of the cell forms pseudopodia that move the cell in a given direction. b. Cytokinesis: Actin filaments form a ring beneath the plasma membrane of a dividing cell; contraction of this ring pinches the cell in two. c. Cytoplasmic streaming: Actin filaments sliding across one another direct the movement of cytoplasm in plant and fungal cells.  2011 Pearson Education, Inc.


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B. Intermediate filaments (Table 7.3) 1. Intermediate filaments can be composed of any one of six different proteins. 2. Intermediate filaments (nuclear lamins) form a dense network on the inside of the nuclear envelope that maintains the shape of the nucleus. 3. Intermediate filaments also form a flexible skeleton between the nucleus and the rest of the cell that helps the nucleus stay in place. C. Microtubules 1. Microtubules are composed of tubulin dimers that polymerize to form a hollow tube that has polarity (a plus end and a minus end). 2. Microtubules are essential for mitosis. a. Microtubules move and separate chromosomes during mitosis. b. Centrosomes (made up of centrioles in animals) or microtubule organizing centers (in plants) organize the microtubules used in mitosis. (Fig. 7.30) 3. Microtubules act as "railroad tracks." (Fig. 7.31) a. Ronald Vale and colleagues studied how vesicles move throughout the cell by using the extruded cytoplasm of a squid giant axon. (1) They found that vesicle transport occurred along a filamentous track in the cytoplasm and that vesicle transport requires the presence of ATP. (2) They found that vesicle transport was abnormal when microtubule-disrupting drugs were added to the preparation. (3) The researchers concluded that vesicle transport was occurring along microtubules and required the energy from the hydrolysis of ATP. 4. A motor protein generates motile forces. a. Vale went on to identify the means by which a vesicle moves along a microtubule. (1) Kinesin is a motor protein that contains three major regions: a head region with two globular pieces, a tail, and a stalk that connects the head to the tail. (2) The globular pieces on the head contain microtubule binding sites as well as ATP binding sites; the tail region can bind the vesicle. (Fig. 7.32a) (3) When the globular pieces bind and release ATP, they undergo a conformational change.

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(4) The two globular head regions alternate between binding ATP and binding to the microtubule. (5) This alternation results in the two globular head segments actually acting as “feet” as they “walk” down the microtubule. (Fig. 7.32b) D. Flagella and cilia: moving the entire cell 1. How are cilia and flagella constructed? (Fig. 7.33) a. Cilia and flagella have nine pairs of microtubules that surround two individual microtubules. This “9 + 2” structure is called an axoneme. (Fig. 7.34a) b. The axoneme attaches to the cell at the basal body, a structure identical to a centriole. c. Electron microscopic studies revealed that the nine microtubule pairs are connected by motor proteins called dynein, and the center microtubules are connected to the nine doublets by protein spokes. (Fig. 7.34b) 2. What provides the force required for movement? a. Dynein hydrolyzes ATP and changes shape, thus “walking” along in a manner similar to that of kinesin. b. This walking causes the microtubules within the cilia or flagella to slide past one another. c. However, this sliding is limited because the whole structure is anchored to the center microtubules by the protein spokes. d. This constrained movement results in the bending of the cilia or flagella, thus creating movement. (Fig. 7.35) Chapter Vocabulary To emphasize the functional meanings of these terms, the list is organized by topic rather than by first occurrence in the chapter. It includes terms that may have been introduced in earlier chapters but are important to the current chapter as well. It also includes terms other than those highlighted in bold type in the chapter text. plasma membrane morphology phylogeny chromosome prokaryote eukaryote gene nucleoid plasmids ribosomes

cytoplasm flagella cell wall glycolipids nucleus nuclear envelope nuclear lamina nucleolus rough endoplasmic reticulum (RER)  2011 Pearson Education, Inc.

lumen smooth endoplasmic reticulum Golgi apparatus cisternae cytosol perixosomes glyoxysomes lysosomes autophagy


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phagocytosis receptor-mediated endocytosis early endosome late endosome endocytosis pinocytosis endomembrane system vacuoles mitochondria cristae mitochondrial matrix chloroplast thylakoids grana stroma differential centrifugation n

nuclear pores nuclear pore matrix nuclear localization pulse-chase experiment ER signal sequence signal recognition particle glycosylation glycoprotein exocytosis microfilaments actin filaments motor protein cytokinesis cytoplasmic streaming cell crawling nuclear lamins

microtubules dimers microtubule organizing center centrosome centrioles kinesin cilia axoneme basal body dynein centrioles kinesin cilia axoneme basal body dynei

Lecture Activities Case Study: Asbestosis Estimated duration of activity: 15+ minutes Case studies are an excellent way to increase student interest in biology. This exercise may be done completely in class (if class or a discussion section can meet in a computer lab), or it may be started in class and finished as an out-of-class assignment. It may also be assigned as homework and discussed during the next class session. This case study guides students to investigate the important roles that lysosomes play in human cells and to understand the consequences of lysosomal dysfunction. Procedure: 1. After dividing the students into groups, hand out the first part of the case study; ask them to brainstorm and make a list of questions about the case. 2. Have each group come up with one or two questions that will be assigned to each group member for part 1 (see the following part descriptions). 3. After the lists are complete (this should take about 10 minutes), give the groups part 2; have students add to their lists and revise their questions from part 1. 4. Repeat for parts 3 and 4. By the end of the class period, each group should have formulated a list of questions that can be divided among the group members.

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5. Group members must then find the answers to their questions. As information sources, encourage them to use the Internet (reputable, referenced sources only), their textbook, other textbooks, scientific or medical journals, and so on. You may want to have them bring their information to the next class, allowing groups to meet again to finish the assignment. 6. Alternatively, students may report to each other by e-mail (or on a class website) and then write individual responses to the assignment. 7. As a third alternative, you may choose to do this exercise quickly as a class. In this case, you may provide all the answers to the brainstorming group questions. This approach allows the students to reach a conclusion by the end of class but does lose the self-directed research aspect of the exercise. Part descriptions:  Part 1: Chuck hasn’t been feeling well lately. He is often out of breath, his chest feels tight, and he isn’t eating much. But, worst of all, he is constantly coughing up mucus.  Part 2: Chuck has worked for American/Atlantic Construction Company for 25 years. They are renovation specialists who restore old office buildings. Chuck is on the team that removes the old asbestos-containing insulation in the buildings, replacing it with asbestos-free insulation. Chuck likes his job, but he hates the protective suits he must wear while removing the old insulation. He much preferred the early years with the company, when they didn’t have to wear all that stuff! The company says the suits are protection against asbestos. Chuck doesn’t understand the big fuss about asbestos. He can’t see it, so how could it possibly hurt him?  Part 3: Chuck goes to the doctor and describes his symptoms. The doctor listens to his chest and says he can hear a crackling sound when Chuck breathes. He also has Chuck breathe into an instrument and then comments that Chuck has very low tidal volume. Last, the doctor orders chest X-rays and, after reviewing them, tells Chuck that he has found bilateral calcified plaques in the lower quadrant of the lungs as well as several irregular opacities in the same regions.  Part 4: You are a health-care representative for the union that Chuck belongs to. Chuck is overwhelmed by medical bills and is contacting you to see whether he has a valid case to claim this condition on the company’s worker’s compensation program. Chuck has not yet gotten a diagnosis from his doctor, but he hopes that you can help him figure out what is going on and what caused this problem. He has heard that you are really nice and might be able to explain to him what is happening. Compose an e-mail to Chuck covering these questions: What is wrong with Chuck? Which specific organ is affected by this ailment? What is happening in those cells? What caused this ailment? What are the treatment and prognosis for this ailment? Do you think this is a valid claim for worker’s compensation? Do you think the company was at fault, or was Chuck? Internet resources: www.mayoclinic.com/health/asbestosis/DS00482

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www.nlm.nih.gov/medlineplus/ency/article/000118.htm Think, Pair, and Share Estimated duration of activity: 20–25 minutes Toward the end of Chapter 7, pose the following question to the students to Think about in preparation for the next class. In the next class, have them form groups, or Pair with each other, and discuss their thoughts on the question. Then, ask each group to Share their thoughts with the entire class. The question is: Eukaryotic cells are generally about 1000 times the size of prokaryotic cells. What are the structures and mechanisms that evolved in eukaryotic cells that enabled them to become so much larger than prokaryotic cells? Tell the students there are at least two major differences between the two types of cells that account for their size difference. Here are the answers that should come out by the end of the discussion: 1. Prokaryotes have only one membrane surrounding each cell. This limits the size of the cell because the cell’s internal volume cannot be so large that the force of diffusion is unable to move a molecule from the outside of the cell to the center of the cell. If the distance from the cell surface to the center of the cell becomes too large, molecules will not be able to diffuse into the center of the cell because diffusion is a local force that cannot move molecules great distances. 2. Eukaryotic cells, in contrast, have evolved many internal membranebound organelles. All of those membranes count as part of the total surface area of the cell. Therefore, the distance from one membrane to another is never so great as to prevent the force of diffusion from moving a molecule. 3. The first two answers are part of the one major difference the students need to identify. The other difference is how molecules are moved around in the eukaryotic cell—packaged in vesicles traveling on the fibers of the cytoskeleton. This is directed motion, powered by the hydrolysis of ATP. Thus, the expenditure of energy allows the cell to overcome the limitations of the force of diffusion. Exercise objectives:  Review the relevant portions of Chapter 7 that cover the internal structure of prokaryotic and eukaryotic cells.  Compare and contrast those structures.  Come up with ideas that address the question.  Participate in class discussions that further the entire class’s understanding of the topic. Procedure: 1. Ask students to review Chapter 7 and compare eukaryotic cell structures with prokaryotic cell structures. 2. Ask students to think about the question and then write down their responses, issues, and additional questions that are relevant. 3. Ask students to bring their written ideas to class and then form groups to discuss their ideas. At the end of the class period, collect each student’s written ideas. The written ideas should be evaluated in a  2011 Pearson Education, Inc.


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formative way, as should anything collected from this exercise. The evaluation should be just a check mark to indicate that the exercise was done. Provide students with helpful comments to consider for the next time this type of exercise is attempted. 4. The groups must discuss each person’s idea(s), refine the ideas, and then write down the answers the group is most comfortable with. Collect these ideas for a formative assessment. The discussion should be limited to 10–15 minutes. 5. The groups should then informally share their ideas with the rest of the class. After each group has spoken, say something like, “What does everybody think about the other groups’ ideas? Are any of the ideas really good? Are there any ideas we can develop further?” Survey on the Think, Pair, and Share Activity Name (optional) _____________________ Course/section # _____________________ Date of the discussion: _____________________ 1. How much time did you spend on your own thinking about the question for discussion? 2. How much time did you spend discussing the question with your group? 3. How well did the group discussion go for you? Did you feel you made your opinion known? Did you feel your opinion was carefully considered by the group? 4. How well did you think the class discussion went? 5. Overall, how much did you get out of this exercise? 6. Any other comments? In-Class Demonstration: Pulse-Chase Experiment Estimated duration of activity: 5 minutes as you are lecturing, then 3–5 minutes to explain the demonstration This activity is rather elementary but will give the students a fun way to visualize how a pulse-chase experiment works. Because so many students are visual learners, role-playing demonstrations are often a fun and visual way to help them understand dynamic biological processes. Even the brightest students will at least appreciate the break from lecture. After or during an explanation of the pulse-chase experiment and its usefulness in visualizing molecule movement in a cell, perform the following demonstration. Purpose: Tell students they are going to create a pathway that you will be able to define without knowing it ahead of time (even the students won’t know the pathway because it is created as the demonstration progresses) and without watching the pathway directly.

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Instructions to students: Tell students that when they are handed a piece of paper (different-colored sticky notes work well), they must discreetly hand it to a nearby student of their choosing. The main rule is that each student must always hand every note they are given to the same nearby student. They must pass their note along only when they receive a new note. Instruct them to end the “pathway” after a reasonable number of students have become involved; the self-designated “end” person may accumulate the sticky notes. Instruct students to temporarily stop passing when you say “Data collection.” At that time, only the people holding pink notes should hold them up. You can then say “Resume” to indicate that they can start passing notes again. Logistics: Start the demonstration by handing a student in the front row a yellow note (it works better when a student or a teaching assistant does this, so the instructor can turn his/her back or simply lecture without paying attention to where the notes are going). Ask the students to wait several seconds before passing the note along. After they have given their note away, keep handing that first student yellow notes and have him/her pass them along. After the 10th note or so, begin handing the first student pink notes. After handing out five or six pink notes, switch back to yellow. (The pink is your “pulse” and the yellow is your “chase.”) When you “collect data,” record the position of the students holding pink papers. After several cycles of data collection, you should be able to map the pathway that the students have created. Analogies: The classroom represents the interior of the cell, and the students represent an organelle system (the endomembrane system or the cytoskeleton, for example). The sticky notes represent molecules: The pink notes are labeled molecules that form the pulse, and the yellow notes are the chase of unlabeled molecules. The data-collection periods represent the method researchers use to “stop” different samples in order to visualize where the label is at different times after the pulse has been initiated. Discussion Idea After discussing protein synthesis and modification through the endomembrane system, ask your students the following questions: How are proteins sorted into vesicles? How are those vesicles targeted to the appropriate destination? Then ask students to develop one or more hypotheses, and ask them what experiments they might perform to test their hypotheses. Describe the experimental design performed by LippincottSchwartz and colleagues as described in their 1997 paper in Nature (389: 81–85). Describe each experiment and review each data figure, pointing out the pertinent points. As you look at each figure, ask a student to summarize each experiment and record the data on the board. When all of the data have been recorded, ask the students to summarize the major findings of the paper. Then use their conclusions to segue into discussing Figure 7.28, the current model for how proteins are sorted into distinct vesicles and targeted to the appropriate destination. Note: This activity will work best in a classroom that is outfitted with computer projection and an Internet connection, or in a computer lab.

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Clicker Questions 1.

If you were a prokaryotic cell, you would be lacking _____. 1a. 2b. 3c. 4d.

a plasma membrane composed of phospholipids and proteins chromosomes that contain genetic information ribosomes to synthesize proteins mitochondria to generate ATP

Answer: 4d Section Reference: 7.1 Bloom’s Taxonomy: Level 3 Application 2.

Which of the following is a not considered a benefit of compartmentalization in eukaryotes? 1a. Chemical reactions are more efficient because substrates are more easily maintained at high concentrations within organelles. 2b. Chemical reactions that are incompatible can be segregated in different organelles. 3c. DNA is transcribed and translated at significantly higher rates because all of the genetic machinery is inside a single, membrane-bound nucleus. 4d. When the product of one reaction is the substrate for a second reaction, the enzymes that work together can be clustered together on internal membranes and result in greater speed and efficiency for both reactions.

Answer: 3c Section Reference: 7.2 Bloom’s Taxonomy: Level 2 Comprehension 3.

Why is the smooth endoplasmic reticulum unable to synthesize proteins? 1a. 2b. 3c. 4d.

It has no ribosomes. There is no supply of free amino acids that it can easily access. It stores calcium, which is known to inhibit protein synthesis. It has no DNA to direct the synthesis of proteins.

Answer: 1a Section Reference: 7.2 Bloom’s Taxonomy: Level 2 Comprehension  2011 Pearson Education, Inc.


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4.

Molecular “zip codes” direct molecules to specific destinations in the cell. How are these signals read? 1a. 2b. 3c. 4d.

They bind to receptor proteins. They enter transport vesicles. They bind to motor proteins. They are glycosylated by enzymes in the Golgi apparatus.

Answer: 2b Section Reference: 7.5 Bloom’s Taxonomy: Level 1 Knowledge 5.

What does a motor protein do in a cell? 1a. 2b. 3c. 4d.

Causes microtubules to “treadmill” Converts ATP into mechanical energy in the form of movement Triggers receptor-mediated endocytosis Aids in the transport of newly synthesized proteins from the endomembrane system

Answer: 2b Section Reference: 7.6 Bloom’s Taxonomy: Level 1 Knowledge

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Test bank biological science with masteringbiology 4th edition scott freeman