CONCEPTS OF BIOLOGY
miguel trigo morรกn
Maastricht 2014 Copyright ÂŠ trigomoran No part of this book may be produced in any form, by print, photoprint, microfilm, or other means without permision of the autor. Based in the Biology subject of Agronomic Engineering. Universidad PolitĂŠcnica de Madrid year 2008.
project diana concepts of biology was developed in the academie beeldende kunsten maastricht, during my erasmus semester 2014 miguel trigo moran
CONCEPTS OF BIOLOGY
history of research
simple & compound
calvin cycle 44
CELL The cell (from Latin cella, meaning “small room”) is the basic structural, functional and biological unit of all known living organisms. Cells are the smallest unit of life that can replicate independently, and are often called the “building blocks of life”. Cells consist of a protoplasm enclosed within a membrane, which contains many biomolecules such as proteins and nucleic acids. Organisms can be classified as unicellular (consisting of a single cell; including most bacteria) or multicellular (including plants and animals). While the number of cells in plants and animals varies from species to species, humans contain about 100 trillion (1014) cells. Most plant and animal cells are visible only under the microscope, with dimensions between 1 and 100 micrometres.
The cell was discovered by Robert Hooke in 1665. The cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that all cells come from preexisting cells, that vital functions of an organism occur within cells, and that all cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells.
cell membrane cytoplasm
single wall membrane enzyme complexes lysosome
starch grain thylakoids chloroplast animal cell 10
cell wal plasmodesma plasma membrane cytosol
outer membrane inner membrane cristae matrix mitochondria vegetal cell 11
All cells have a membrane that envelops the cell, regulates what moves in and out (selectively permeable), and maintains the electric potential of the cell. Inside the membrane, a salty cytoplasm takes up most of the cell volume. All cells (except red blood cells which lack a cell nucleus and most organelles to accommodate maximum space for hemoglobin) possess DNA, the hereditary material of genes, and RNA, containing the information necessary to build various proteins such as enzymes, the cellâ€™s primary machinery. There are also other kinds of biomolecules in cells. This article lists these primary components of the cell, then briefly describes their function. Membrane The cell membrane, or plasma membrane, surrounds the cytoplasm of a cell. In animals, the plasma membrane is the outer boundary of the cell, while in plants and prokaryotes it is usually covered by a cell wall. This membrane serves to separate and protect a cell from its surrounding environment and is made mostly from a double layer of phospholipids, which are amphiphilic (partly hydrophobic and partly hydrophilic). Hence, the layer is called a phospholipid bilayer, or sometimes a fluid mosaic membrane. Embedded 12
within this membrane is a variety of protein molecules that act as channels and pumps that move different molecules into and out of the cell. The membrane is said to be â€˜semipermeableâ€™, in that it can either let a substance (molecule or ion) pass through freely, pass through to a limited extent or not pass through at all. Cell surface membranes also contain receptor proteins that allow cells to detect external signaling molecules such as hormones. Ribosomes The ribosome is a large complex of RNA and protein molecules. They each consist of two subunits, and act as an assembly line where RNA from the nucleus is used to synthesise proteins from amino acids. Ribosomes can be found either floating freely or bound to a membrane (the rough endoplasmatic reticulum in eukaryotes, or the cell membrane in prokaryotes).
Lysosomes and Peroxisomes
Lysosomes contain digestive enzymes (acid hydrolases). They digest excess or worn-out organelles, food particles, and engulfed viruses or bacteria. Peroxisomes have enzymes that rid the cell of toxic peroxides. The cell could not house these destructive enzymes if they were not contained in a membrane-bound system.
Vacuoles store food and waste. Some vacuoles store extra water. They are often described as liquid filled space and are surrounded by a membrane. Some cells, most notably Amoeba, have contractile vacuoles, which can pump water out of the cell if there is too much water.
Centrosome, the cytoskeleton organiser
The vacuoles of eukaryotic cells are usually larger in those of plants than animals.
The centrosome produces the microtubules of a cell â€“ a key component of the cytoskeleton. It directs the transport through the ER and the Golgi apparatus. Centrosomes are composed of two centrioles, which separate during cell division and help in the formation of the mitotic spindle. A single centrosome is present in the animal cells. They are also found in some fungi and algae cells. Golgi apparatus Process and package the macromolecules such as proteins and lipids that are synthesized by the cell. 13
ribosome golgi body nuclear pore nuclear envelope nucleus cytoplasm cromatin (wavy) smooth endoplasmic reticulum rough endoplasmic reticulum
Mitochondria and Chloroplasts, the power generators
A cell’s information center, the cell nucleus is the most conspicuous organelle found in a eukaryotic cell. It houses the cell’s chromosomes, and is the place where almost all DNA replication and RNA synthesis (transcription) occur. The nucleus is spherical and separated from the cytoplasm by a double membrane called the nuclear envelope. The nuclear envelope isolates and protects a cell’s DNA from various molecules that could accidentally damage its structure or interfere with its processing.
Mitochondria are self-replicating organelles that occur in various numbers, shapes, and sizes in the cytoplasm of all eukaryotic cells. Mitochondria play a critical role in generating energy in the eukaryotic cell. Respiration occurs in the cell mitochondria, which generate the cell’s energy by oxidative phosphorylation, using oxygen to release energy stored in cellular nutrients (typically pertaining to glucose) to generate ATP. Mitochondria multiply by binary fission, like prokaryotes. Chloroplasts can only be found in plants and algae, and they capture the sun’s energy to make ATP through photosynthesis.
During processing, DNA is transcribed, or copied into a special RNA, called messenger RNA (mRNA). This mRNA is then transported out of the nucleus, where it is translated into a specific protein molecule. The nucleolus is a specialized region within the nucleus where ribosome subunits are assembled. In prokaryotes, DNA processing takes place in the cytoplasm.
Endoplasmic reticulum The endoplasmic reticulum (ER) is a transport network for molecules targeted for certain modifications and specific destinations, as compared to molecules that float freely in the cytoplasm. The ER has two forms: the rough ER, which has ribosomes on its surface that secrete proteins into the ER, and the smooth ER, which lacks ribosomes. The smooth ER plays a role in calcium sequestration and release. 15
Genetic material Two different kinds of genetic material exist: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Cells use DNA for their long-term information storage. The biological information contained in an organism is encoded in its DNA sequence. RNA is used for information transport (e.g., mRNA) and enzymatic functions (e.g., ribosomal RNA). Transfer RNA (tRNA) molecules are used to add amino acids during protein translation. Prokaryotic genetic material is organized in a simple circular DNA molecule (the bacterial chromosome) in the nucleoid region of the cytoplasm. Eukaryotic genetic material is divided into different, linear molecules called chromosomes inside a discrete nucleus, usually with additional genetic material in some organelles like mitochondria and chloroplasts (see endosymbiotic theory). A human cell has genetic material contained in the cell nucleus (the nuclear genome) and in the mitochondria 16
(the mitochondrial genome). In humans the nuclear genome is divided into 46 linear DNA molecules called chromosomes, including 22 homologous chromosome pairs and a pair of sex chromosomes. The mitochondrial genome is a circular DNA molecule distinct from the nuclear DNA. Although the mitochondrial DNA is very small compared to nuclear chromosomes, it codes for 13 proteins involved in mitochondrial energy production and specific tRNAs. Foreign genetic material (most commonly DNA) can also be artificially introduced into the cell by a process called transfection. This can be transient, if the DNA is not inserted into the cellâ€™s genome, or stable, if it is. Certain viruses also insert their genetic material into the genome.
History of research 1632
Antonie van Leeuwenhoek teaches himself to make lenses, constructs simple microscopes and draws protozoa, such as Vorticella from rain water, and bacteria from his own mouth.
Robert Hooke discovers cells in cork, then in living plant tissue using an early compound microscope. He coins the term cell (from Latin cella, meaning “small room”) in his book Micrographia (1665), in which he compared the cork cells he sees through his microscope to the small rooms monks lived in.
Theodor Schwann and Matthias Jakob Schleiden elucidate the principle that plants and animals are made of cells, concluding that cells are a common unit of structure and development, and thus founding the cell theory.
Rudolf Virchow states that new cells come from pre-existing cells by cell division (omnis cellula ex cellula).
The belief that life forms can occur spontaneously (generatio spontanea) is contradicted by Louis Pasteur (1822– 1895) (although Francesco Redi had performed an experiment in 1668 that suggested the same conclusion).
Ernst Ruska builds the first transmission electron microscope (TEM) at the University of Berlin. By 1935, he has built an EM with twice the resolution of a light microscope, revealing previously unresolvable organelles.
Watson and Crick made their first announcement on the double helix structure of DNA on February 28.
Lynn Margulis published Symbiosis in Cell Evolution detailing the endosymbiotic theory. 17
ROOTS In vascular plants, the root is the organ of a plant that typically lies below the surface of the soil. However, roots can also be aerial or aerating (growing up above the ground or especially above water). Furthermore, a stem normally occurring below ground is not exceptional either (see rhizome). Therefore, the root is best defined as the non-leaf, non-nodes bearing parts of the plant’s body. However, important internal structural differences between stems and roots exist.
The first root that comes from a plant is called the radicle. The four major functions of roots are: 1 · Absorption of water and inorganic nutrients 2 · Anchoring of the plant body to the ground and supporting it 3 · Storage of food and nutrients, 4 · Vegetative reproduction. In response to the concentration of nutrients, roots also synthesise cytokinin, which acts as a signal as to how fast the shoots can grow. Roots often function in storage of food and nutrients. The roots of most vascular plant species enter into symbiosis with certain fungi to form mycorrhizae, and a large range of other organisms including bacteria also closely associate with roots. 21
branch point lateral root incipient lateral root
root hairs coping
Early root growth is one of the functions of the apical meristem located near the tip of the root. The meristem cells more or less continuously divide, producing more meristem, root cap cells (these are sacrificed to protect the meristem), and undifferentiated root cells. The latter become the primary tissues of the root, first undergoing elongation, a process that pushes the root tip forward in the growing medium. Gradually these cells differentiate and mature into specialized cells of the root tissues. Over time, given the right conditions, roots can crack foundations, snap water lines, and lift sidewalks. At germination, roots grow downward due to gravitropism, the growth mechanism of plants that also causes the shoot to grow upward. In some plants (such as ivy), the “root” actually clings to walls and structures. Growth from apical meristems is known as primary growth, which encompasses all elongation. Secondary growth encompasses all growth in diameter, a major component of woody plant tissues and many nonwoody plants. For example, storage roots of sweet potato have secondary growth but are not woody. Secondary growth occurs at the lateral meristems, namely the vascular cambium and cork cambium.
The former forms secondary xylem and secondary phloem, while the latter forms the periderm. In plants with secondary growth, the vascular cambium, originating between the xylem and the phloem, forms a cylinder of tissue along the stem and root. The vascular cambium forms new cells on both the inside and outside of the cambium cylinder, with those on the inside forming secondary xylem cells, and those on the outside forming secondary phloem cells. As secondary xylem accumulates, the “girth” (lateral dimensions) of the stem and root increases. As a result, tissues beyond the secondary phloem (including the epidermis and cortex, in many cases) tend to be pushed outward and are eventually “sloughed off” (shed). At this point, the cork cambium begins to form the periderm, consisting of protective cork cells containing suberin. In roots, the cork cambium originates in the pericycle, a component of the vascular cylinder. The vascular cambium produces new layers of secondary xylem annually. The xylem vessels are dead at maturity but are responsible for most water transport through the vascular tissue in stems and roots. 23
Adventitious Arise out-of-sequence from the more usual root formation of branches of a primary root, and instead originate from the stem, branches, leaves, or old woody roots. They commonly occur in monocots and pteridophytes, but also in many dicots, such as clover (Trifolium), ivy (Hedera), strawberry (Fragaria) and willow (Salix). Most aerial roots and stilt roots are adventitious. In some conifers adventitious roots can form the largest part of the root system. Aerating roots Roots rising above the ground, especially above water such as in some mangrove genera (Avicennia, Sonneratia). In some plants like Avicennia the erect roots have a large number of breathing pores for exchange of gases. Tuber Various types of modified plant structures that are enlarged to store nutrients. They are used by plants to survive the winter 24
or dry months, to provide energy and nutrients for regrowth during the next growing season, and as a means of asexual reproduction. There are both stem and root tubers. Corm Short, vertical, swollen underground plant stem that serves as a storage organ used by some plants to survive winter or other adverse conditions such as summer drought and heat. Taproot Very large, somewhat straight to tapering plant root that grows downward. It forms a center from which other roots sprout laterally. Plants with taproots are difficult to transplant. The presence of a taproot is why dandelions are hard to uprootâ€”the top is pulled, but the long taproot stays in the ground, and resprouts.
LEAF A leaf is an organ of a vascular plant, as defined in botanical terms, and in particular in plant morphology. Foliage is a mass noun that refers to leaves as a feature of plants. Typically a leaf is a thin, flattened organ borne above ground and specialized for photosynthesis, but many types of leaves are adapted in ways almost unrecognisable in those terms: some are not flat (for example many succulent leaves and conifers), some are not above ground (such as bulb scales), and some are without major photosynthetic function (consider for example cataphylls, spines, and cotyledons).
differ from typical leaves in their structures and origins. Examples include phyllodes, cladodes, and phylloclades. According to Agnes Arber’s partial-shoot theory of the leaf, leaves are partial shoots. Compound leaves are closer to shoots than simple leaves. Developmental studies have shown that compound leaves, like shoots, may branch in three dimensions. On the basis of molecular genetics, Eckardt and Baum (2010) concluded that “is is now generally accepted that compound leaves express both leaf and shoot properties.”
Conversely, many structures of non-vascular plants, or even of some lichens, which are not plants at all (in the sense of being members of the kingdom Plantae), do look and function much like leaves. Furthermore, several structures found in vascular plants look like leaves but are not totally homologous with leaves; they 27
Typically leaves are flat and thin, thereby maximising the surface area directly exposed to light and promoting photosynthetic function. Externally they commonly are arranged on the plant in such ways as to expose their surfaces to light as efficiently as possible without shading each other, but there are many exceptions and complications; for instance plants adapted to windy conditions may have pendent leaves, such as in many willows and Eucalyptus. Likewise, the internal organisation of most kinds of leaves has evolved to maximise exposure of the photosynthetic organelles, the chloroplasts, to light and to increase the absorption of carbon dioxide. Most leaves have stomata, which open or narrow to regulate the exchange of carbon dioxide, oxygen, and water vapour with the atmosphere. In contrast however, some leaf forms are adapted to modulate the amount of light they absorb to avoid or mitigate excessive heat, ultraviolet damage, or desiccation, or to sacrifice light-absorption efficiency in favour of protection from herbivorous enemies. Among these forms the leaves of many xerophytes are conspicuous. For such plants 28
their major constraint is not light flux or intensity, but heat, cold, drought, wind, herbivory, and various other hazards. Typical examples among such strategies are so-called window plants such as Fenestraria species, some Haworthia species such as Haworthia tesselata and Haworthia truncata and Bulbine mesembryanthemoides. The shape and structure of leaves vary considerably from species to species of plant, depending largely on their adaptation to climate and available light, but also to other factors such as grazing animals (such as deer), available nutrients, and ecological competition from other plants. Considerable changes in leaf type occur within species too, for example as a plant matures; as a case in point Eucalyptus species commonly have isobilateral, pendent leaves when mature and dominating their neighbours; however, such trees tend to have erect or horizontal dorsiventral leaves as seedlings, when their growth is limited by the available light.
Other factors include the need to balance water loss at high temperature and low humidity against the need to absorb atmospheric carbon dioxide. In most plants leaves also are the primary organs responsible for transpiration and guttation (beads of fluid forming at leaf margins). Leaves can also store food and water, and are modified accordingly to meet these functions, for example in the leaves of succulent plants and in bulb scales. The concentration of photosynthetic structures in leaves requires that they be richer in protein, minerals, and sugars, than say, woody stem tissues. Accordingly leaves are prominent in the diet of many animals. This is true for humans, for whom leaf vegetables commonly are food staples. Correspondingly, leaves represent heavy investment on the part of the plants bearing them, and their retention or disposition are the subject of elaborate strategies for dealing with pest pressures, seasonal conditions, and protective measures such as the growth of thorns and the production of phytoliths, lignins, tannins and poisons. 30
Vascularised leaves first evolved following the Devonian period, when carbon dioxide concentration in the atmosphere dropped significantly. External leaf characteristics (such as shape, margin, hairs, etc.) are important for identifying plant species, and botanists have developed a rich terminology for describing leaf characteristics. These structures are a part of what makes leaves determinant; they grow and achieve a specific pattern and shape, then stop. Other plant parts like stems or roots are non-determinant, and will usually continue to grow as long as they have the resources to do so. Classification of leaves can occur through many different designative schema, and the type of leaf is usually characteristic of a species, although some species produce more than one type of leaf. The longest type of leaf is a leaf from a palm, measuring at nine feet long. The terminology associated with the description of leaf morphology is presented, in illustrated form, at Wikibooks
SIMPLE & COMPUND LEAVES
apex margin netted vein midrib
base petiole stipule axial bud
internode sheet cataphyll
apex I leaflet pedicels
cotyledon mibrid roots
petiole base 31
Leaves are normally extensively vascularised and are typically covered by a dense network of xylem, which supply water for photosynthesis, and phloem, which remove the sugars produced by photosynthesis. Many leaves are covered in trichomes (small hairs) which have a diverse range of structures and functions.
regulation of gas exchange, secretion of metabolic compounds, and (in some species) absorption of water.
A leaf is a plant organ and is a collection of tissues in a regular organisation. The major tissue systems present are
Is usually transparent (epidermal cells lack chloroplasts) and coated on the outer side with a waxy cuticle that prevents water loss. The cuticle is in some cases thinner on the lower epidermis than on the upper epidermis, and is generally thicker on leaves from dry climates as compared with those from wet climates.
The epidermis, which covers the upper and lower surfaces The mesophyll tissue inside the leaf, which is rich in chloroplasts (also called chlorenchyma) The arrangement of veins (the vascular tissue) These three tissue systems typically form a regular organisation at the cellular scale. Epidermis The epidermis is the waxy outer layer of cells covering the leaf. It forms the boundary separating the plantâ€™s inner cells from the external world. The epidermis serves several functions: protection against water loss by way of transpiration, 32
Most leaves show dorsoventral anatomy: The upper (adaxial) and lower (abaxial) surfaces have somewhat different construction and may serve different functions.
The epidermis tissue includes several differentiated cell types: epidermal cells, epidermal hair cells (trichomes) cells in the stomate complex; guard cells and subsidiary cells. The epidermal cells are the most numerous, largest, and least specialized and form the majority of the epidermis. These are typically more elongated in the leaves of monocots than in those of dicots. Is covered with pores called stomata, part of a stoma complex consisting of a pore surrounded on each side by chloroplast-containing guard cells, and two to four
cuticle upper epidermis palisade mesophyll chloroplast moist air space spongy mesophyll
lower epidermis cuticle guard cells stoma
parenchyma xylem sclerenchyma phloem vascular bundle 33
subsidiary cells that lack chloroplasts. Opening and closing of the stoma complex regulates the exchange of gases and water vapor between the outside air and the interior of the leaf and plays an important role in allowing photosynthesis without letting the leaf dry out. In a typical leaf, the stomata are more numerous over the abaxial (lower) epidermis than the adaxial (upper) epidermis and more numerous in plants from cooler climates. Mesophyll Most of the interior of the leaf between the upper and lower layers of epidermis is a parenchyma (ground tissue) or chlorenchyma tissue called the mesophyll (Greek for “middle leaf”). This assimilation tissue is the primary location of photosynthesis in the plant. The products of photosynthesis are called “assimilates”. In ferns and most flowering plants, the mesophyll is divided into two layers: – An upper palisade layer of tightly packed, vertically elongated cells, one to two cells thick, directly beneath the 34
adaxial epidermis. Its cells contain many more chloroplasts than the spongy layer. These long cylindrical cells are regularly arranged in one to five rows. Cylindrical cells, with the chloroplasts close to the walls of the cell, can take optimal advantage of light. The slight separation of the cells provides maximum absorption of carbon dioxide. This separation must be minimal to afford capillary action for water distribution. In order to adapt to their different environment (such as sun or shade), plants had to adapt this structure to obtain optimal result. Sun leaves have a multi-layered palisade layer, while shade leaves or older leaves closer to the soil are single-layered. – Beneath the palisade layer is the spongy layer. The cells of the spongy layer are more rounded and not so tightly packed. There are large intercellular air spaces. These cells contain fewer chloroplasts than those of the palisade layer. The pores or stomata of the epidermis open into substomatal chambers, which are connected to the air spaces between the spongy layer cells.
These two distinct layers of the mesophyll are absent in many aquatic and marsh plants. Even an epidermis and a mesophyll may be lacking. Instead, for their gaseous exchanges they use a homogeneous aerenchyma (thin-walled cells separated by large gas-filled spaces).
A vein is made up of a vascular bundle. At the core of each bundle are clusters of two distinct types of ducts (tubes): 路 Xylem Ducts that bring water and minerals from the roots into the leaf.
Their stomata are situated at the upper surface. Leaves are normally green, due to chlorophyll in plastids in the chlorenchyma cells. Plants that lack chlorophyll cannot photosynthesize optimally. Photosynthesis can still be performed utilizing other pigments such as carotenes and xanthophylls.
路 Phloem Ducts that usually move sap, with dissolved sucrose, produced by photosynthesis in the leaf, out of the leaf. A sheath of ground tissue made of lignin surrounding the ducts. This sheath has a mechanical role in strengthening the rigidity of the leaf.
Veins The veins are the vascular tissue of the leaf and are located in the spongy layer of the mesophyll. The pattern of the veins is called venation, and is typically characterized by hierarchical structures with abundant closed loops. They were once thought to be typical examples of pattern formation through ramification, but they may instead exemplify a pattern formed in a stress tensor field.
The xylem typically lies on the adaxial side of the vascular bundle and the phloem typically lies on the abaxial side. Both are embedded in a dense parenchyma tissue, called the pith or sheath, which usually includes some structural collenchyma tissue.
12 NADP +
12 NADP + 12 H+
12 NADP +
18 ADP + 18 Pi
18 ADP + 18 Pi 60hv
PHOTOSYNTHESIS Photosynthesis is a process used by plants and other organisms to convert light energy, normally from the sun, into chemical energy that can be later released to fuel the organisms’ activities. This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water – hence the name photosynthesis. In most cases, oxygen is also released as a waste product. Most plants, most algae, and cyanobacteria perform photosynthesis, and such organisms are called photoautotrophs. Photosynthesis maintains atmospheric oxygen levels and supplies all of the organic compounds and most of the energy necessary for life on Earth. Although photosynthesis is performed differently by different species, the process always begins when energy from light is absorbed by proteins called reaction centres that contain green chlorophyll pigments. In plants, these proteins are held inside organelles called chloroplasts, which are most abundant in leaf cells, while in bacteria they are embedded
in the plasma membrane. In these light-dependent reactions, some energy is used to strip electrons from suitable substances such as water, producing oxygen gas. Furthermore, two further compounds are generated: reduced nicotinamide adenine dinucleotide phosphate (NADPH) and adenosine triphosphate (ATP), the “energy currency” of cells. In plants, algae and cyanobacteria, sugars are produced by a subsequent sequence of light-independent reactions called the Calvin cycle, but some bacteria use different mechanisms, such as the reverse Krebs cycle. In the Calvin cycle, atmospheric carbon dioxide is incorporated into already existing organic carbon compounds, such as ribulose bisphosphate (RuBP). Using the ATP and NADPH produced by the light-dependent reactions, the resulting compounds are then reduced and removed to form further carbohydrates such as glucose.
The first photosynthetic organisms probably evolved early in the evolutionary history of life and most likely used reducing agents such as hydrogen or hydrogen sulfide as sources of electrons, rather than water. Cyanobacteria appeared later, and the excess oxygen they produced contributed to the oxygen catastrophe, which rendered the evolution of complex life possible. Today, the average rate of energy capture by photosynthesis globally is approximately 130 terawatts, which is about six times larger than the current power consumption of human civilization. Photosynthetic organisms also convert around 100â€“115 thousand million metric tonnes of carbon into biomass per year. In the light reactions, one molecule of the pigment chlorophyll absorbs one photon and loses one electron. This electron is passed to a modified form of chlorophyll called pheophytin, which passes the electron to a quinone molecule, allowing the start of a flow of electrons down an electron transport chain that leads to the ultimate reduction of NADP to NADPH. In addition, this creates a proton gradient across the chloroplast membrane; its dissipation is used by ATP synthase for the concomitant synthesis of ATP. 38
The chlorophyll molecule regains the lost electron from a water molecule through a process called photolysis, which releases a dioxygen (O2) molecule. Not all wavelengths of light can support photosynthesis. The photosynthetic action spectrum depends on the type of accessory pigments present. For example, in green plants, the action spectrum resembles the absorption spectrum for chlorophylls and carotenoids with peaks for violet-blue and red light. In red algae, the action spectrum overlaps with the absorption spectrum of phycobilins for red blue-green light, which allows these algae to grow in deeper waters that filter out the longer wavelengths used by green plants. The non-absorbed part of the light spectrum is what gives photosynthetic organisms their color (e.g., green plants, red algae, purple bacteria) and is the least effective for photosynthesis in the respective organisms.
LIGHT-INDEPENDENT REACTIONS The light-independent reactions of photosynthesis are chemical reactions that convert carbon dioxide and other compounds into glucose. These reactions occur in the stroma, the fluid-filled area of a chloroplast outside of the thylakoid membranes. These reactions take the light-dependent reactions and perform further chemical processes on them. There are three phases to the light-independent reactions, collectively called the Calvin cycle: carbon fixation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration.
These dark reactions are closely coupled to the thylakoid electron transport chain as reducing power provided by NADPH produced in the photosystem I is actively needed. The process of photorespiration, also known as C2 cycle, is also coupled to the dark reactions, as it results from an alternative reaction of the Rubisco enzyme, and its final byproduct is also another glyceraldehyde-3-P.
Despite its name, this process occurs only when light is available. Plants do not carry out the Calvin cycle by night. They, instead, release sucrose into the phloem from their starch reserves. This process happens when light is available independent of the kind of photosynthesis ,C3 carbon fixation, C4 carbon fixation, and Crassulacean Acid Metabolism; CAM plants store malic acid in their vacuoles every night and release it by day in order to make this process work. 39
Calvin cycle The Calvin cycle, Calvin–Benson–Bassham (CBB) cycle, reductive pentose phosphate cycle or C3 cycle is a series of biochemical redox reactions that take place in the stroma of chloroplasts in photosynthetic organisms. It is also known as the light-independent reactions.
set of reactions is also called carbon fixation. The key enzyme of the cycle is called RuBisCO. In the following biochemical equations, the chemical species (phosphates and carboxylic acids) exist in equilibria among their various ionized states as governed by the pH.
The cycle was discovered by Melvin Calvin, James Bassham, and Andrew Benson at the University of California, Berkeley by using the radioactive isotope carbon-14. It is one of the light-independent reactions used for carbon fixation.
The enzymes in the Calvin cycle are functionally equivalent to most enzymes used in other metabolic pathways such as gluconeogenesis and the pentose phosphate pathway, but they are to be found in the chloroplast stroma instead of the cell cytoplasm, separating the reactions.
Photosynthesis occurs in two stages in a cell. In the first stage, light-dependent reactions capture the energy of light and use it to make the energy-storage and transport molecules ATP and NADPH. The light-independent Calvin cycle uses the energy from short-lived electronically excited carriers to convert carbon dioxide and water into organic compounds that can be used by the organism (and by animals that feed on it). This 40
They are activated in the light (which is why the name “dark reaction” is misleading), and also by products of the lightdependent reaction. These regulatory functions prevent the Calvin cycle from being respired to carbon dioxide. Energy (in the form of ATP) would be wasted in carrying out these reactions that have no net productivity.
ribulose 1,5 - biphosphate ADP carbon dioxide
ATP RuBisCo carbon fixation
ribulose 5 - phosphate CALVIN CYCLE regeneration of ribulose
ATP reduction 1,3 phosphoglycerate
NADP+ inorganic phosphate 41
FLOWER A flower, sometimes known as a bloom or blossom, is the reproductive structure found in flowering plants, plants of the division Magnoliophyta, also called angiosperms. The biological function of a flower is to effect reproduction, usually by providing a mechanism for the union of sperm with eggs. Flowers may facilitate outcrossing (fusion of sperm and eggs from different individuals in a population) or allow selfing (fusion of sperm and egg from the same flower). Some flowers produce diaspores without fertilization (parthenocarpy). Flowers contain sporangia and are the site where gametophytes develop. Flowers give rise to fruit and seeds. Many flowers have evolved to be attractive to animals, so as to cause them to be vectors for the transfer of pollen.
In addition to facilitating the reproduction of flowering plants, flowers have long been admired and used by humans to beautify their environment, and also as objects of romance, ritual, religion, medicine and as a source of food. A stereotypical flower consists of four kinds of structures attached to the tip of a short stalk. Each of these kinds of parts is arranged in a whorl on the receptacle. The four main whorls (starting from the base of the flower or lowest node and working upwards) are as follows: 路 Calyx The outermost whorl consisting of units called sepals; these are typically green and enclose the rest of the flower in the bud stage, however, they can be absent or prominent and petal-like in some species. 43
petals sepal receptacle peduncle
· Corolla The next whorl toward the apex, composed of units called petals, which are typically thin, soft and colored to attract animals that help the process of pollination.
wherein the structure one sees in the innermost whorl is called a pistil. It may consist of a single carpel or a number of carpels fused together. The sticky tip of the pistil, the stigma, is the receptor of pollen.
Collectively the Calyx and Corolla form the Perianth (see diagram). Androecium (from Greek andros oikia: man’s house): the next whorl (sometimes multiplied into several whorls), consisting of units called stamens.
The supportive stalk, the style, becomes the pathway for pollen tubes to grow from pollen grains adhering to the stigma.
Stamens consist of two parts: a stalk called a filament, topped by an anther where pollen is produced by meiosis and eventually dispersed.
The relationship to the gynoecium on the receptacle is described as hypogynous (beneath a superior ovary), perigynous (surrounding a superior ovary), or epigynous (above inferior ovary).
· Gynoecium The innermost whorl of a flower, consisting of one or more units called carpels. The carpel or multiple fused carpels form a hollow structure called an ovary, which produces ovules internally.
The four main parts of a flower are generally defined by their positions on the receptacle and not by their function. Many flowers lack some parts or parts may be modified into other functions and/or look like what is typically another part.
Ovules are megasporangia and they in turn produce megaspores by meiosis which develop into female gametophytes. These give rise to egg cells. The gynoecium of a flower is also described using an alternative terminology
In some families, like Ranunculaceae, the petals are greatly reduced and in many species the sepals are colorful and petal-like. Other flowers have modified stamens that are petal-like, the double flowers of Peonies and Roses are mostly
Flowers show great variation and plant scientists describe this variation in a systematic way to identify and distinguish species. Specific terminology is used to describe flowers and their parts. Many flower parts are fused together; fused parts originating from the same whorl are connate, while fused parts originating from different whorls are adnate, parts that are not fused are free. When petals are fused into a tube or ring that falls away as a single unit, they are sympetalous (also called gamopetalous.) · Petals may have distinctive regions The cylindrical base is the tube, the expanding region is the throat and the flaring outer region is the limb. A sympetalous flower, with bilateral symmetry with an upper and lower lip, is bilabiate. Flowers with connate petals or sepals may have various shaped corolla or calyx including: campanulate, funnelform, tubular, urceolate, salverform or rotate. Referring to “fusion,” as it is commonly done, appears questionable because at least some of the processes involved may be non-fusion processes. 46
For example, the addition of intercalary growth at or below the base of the primordia of floral appendages such as sepals, petals, stamens and carpels may lead to a common base that is not the result of fusion. Many flowers have a symmetry. When the perianth is bisected through the central axis from any point, symmetrical halves are produced, forming a radial symmetry. These flowers are also known to be actinomorphic or regular. When flowers are bisected and produce only one line that produces symmetrical halves the flower is said to be irregular or zygomorphic, e.g. snapdragon or most orchids. Flowers may be directly attached to the plant at their base (sessile—the supporting stalk or stem is highly reduced or absent). The stem or stalk subtending a flower is called a peduncle. If a peduncle supports more than one flower, the stems connecting each flower to the main axis are called pedicels. The apex of a flowering stem forms a terminal swelling which is called the torus or receptacle.
INFLORESCENCES An inflorescence is a group or cluster of flowers arranged on a stem that is composed of a main branch or a complicated arrangement of branches. Morphologically, it is the part of the shoot of seed plants where flowers are formed and which is accordingly modified. The modifications can involve the length and the nature of the internodes and the phyllotaxis, as well as variations in the proportions, compressions, swellings, adnations, connations and reduction of main and secondary axes. Inflorescence can also be defined as the reproductive portion of a plant that bears a cluster of flowers in a specific pattern.
A flower that is not part of an inflorescence is called a solitary flower and its stalk is also referred to as a peduncle. Any flower in an inflorescence may be referred to as a floret, especially when the individual flowers are particularly small and borne in a tight cluster, such as in a pseudanthium.
The stem holding the whole inflorescence is called a peduncle and the main stem holding the flowers or more branches within the inflorescence is called the rachis. The stalk of each single flower is called a pedicel. The fruiting stage of an inflorescence is known as an infructescence. 47
FRUIT In botany, a fruit is a part of a flowering plant that derives from specific tissues of the flower, one or more ovaries, and in some cases accessory tissues. Fruits are the means by which these plants disseminate seeds.
In common language usage, “fruit” normally means the fleshy seed-associated structures of a plant that are sweet or sour and edible in the raw state, such as apples, oranges, grapes, strawberries, bananas, and lemons.
Many of them that bear edible fruits, in particular, have propagated with the movements of humans and animals in a symbiotic relationship as a means for seed dispersal and nutrition, respectively; in fact, humans and many animals have become dependent on fruits as a source of food.
On the other hand, the botanical sense of “fruit” includes many structures that are not commonly called “fruits”, such as bean pods, corn kernels, wheat grains, and tomatoes.
Fruits account for a substantial fraction of the world’s agricultural output, and some (such as the apple and the pomegranate) have acquired extensive cultural and symbolic meanings.
mitosis: new sporophyte
mature sporophyte with sporangiums
fecundation: sperm + eggs
diploid (2n) haploid (n)
A sporophyte is the diploid multicellular stage in the life cycle of a plant or alga. It develops from the zygote produced when a haploid egg cell is fertilized by a haploid sperm and each sporophyte cell therefore has a double set of chromosomes, one set from each parent. All land plants, and most multicellular algae, have life cycles in which a multicellular diploid sporophyte phase alternates with a multicellular haploid gametophyte phase.
The resulting meiospores develop into a gametophyte. Both the spores and the resulting gametophyte are haploid, meaning they only have one set of chromosomes. The mature gametophyte produces male or female gametes (or both) by mitosis. The fusion of male and female gametes produces a diploid zygote which develops into a new sporophyte. This cycle is known as alternation of generations or alternation of phases.
In the seed plants, the Gymnosperms and flowering plants (Angiosperms), the sporophyte phase is more prominent than the gametophyte, and is the familiar green plant with its roots, stem, leaves and cones or flowers. In flowering plants the gametophytes are very reduced in size, and are represented by the pollen and the embryo sac. The sporophyte produces spores (hence the name) by meiosis, a process also known as â€œreduction divisionâ€? that reduces the number of chromosomes in each spore mother cell by half.
FUNGI A fungus is any member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds (British English: moulds), as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from plants, animals, protists, and bacteria. One major difference is that fungal cells have cell walls that contain chitin, unlike the cell walls of plants and some protists, which contain cellulose, and unlike the cell walls of bacteria. Mycology has often been regarded as a branch of botany, even though it is a separate kingdom in biological taxonomy. Genetic studies have shown that fungi are more closely related to animals than to plants. Abundant worldwide, most fungi are inconspicuous because of the small size of their structures, and their cryptic lifestyles in soil, on dead matter, and as symbionts of plants, animals, or other fungi.
Since the 1940s, fungi have been used for the production of antibiotics, and, more recently, various enzymes produced by fungi are used industrially and in detergents. Fungi are also used as biological pesticides to control weeds, plant diseases and insect pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, that are toxic to animals including humans. The fruiting structures of a few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significant pathogens of humans and other animals. Losses of crops due to fungal diseases (e.g. rice blast disease) or food spoilage can have a large impact on human food supplies and local economies.
fla g e lu m ts
g o m y c et
io p zo o s ores w
it h o
64 z o osp ores w
as po os
a s c o y c ets
b a sidio m y c ets
The Chytridiomycota (chytrids), Zygomycota (bread molds), Ascomycota (yeasts and sac fungi), and the Basidiomycota (club fungi). Placement into a division is based on the way in which the fungus reproduces sexually. The shape and internal structure of the sporangia, which produce the spores, are the most useful character for identifying these various major groups. There are also two conventional groups which are not recognized as formal taxonomic groups (ie. they are polyphyletic); these are the Deuteromycota (fungi imperfecti), and the lichens. The Deuteromycota includes all fungi which have lost the ability to reproduce sexually. As a result, it is not known for certain into which group they should be placed, and thus the Deuteromycota becomes a convenient place to dump them until someone gets around to working out their biology.
Unlike other fungi, the lichens are not a single organism, but rather a symbiotic association between a fungus and an alga. The fungal member of the lichen is usually an ascomycete or basidiomycete, and the alga is usually a cyanobacterium or a chlorophyte (green alga). Often the fungal partner is unable to grow without the algal symbiont, making it difficult to classify these organisms. They will be treated here as a separate group, but it should be realized that they are neither single organisms, nor a monophyletic group. It should also be noted that some organisms carry the name of mold or fungus, but are NOT classified in the Kingdom Fungi. These include the slime molds and water molds (Oomycota). The slime molds are now known to be a mixture of three or four unrelated groups, and the oomycetes are now classified in the Chromista, with the diatoms and brown algae.
At another time, they were placed in the Mastigomycotina as the class Chytridiomycetes. Also, in an older and more restricted sense (not used here), the term "chytrids" referred just to those fungi in the order Chytridiales. Here, the term “chytrid” will refer only to members of Chytridiomycota. The chytrids have also been included among the Protista, but are now regularly classed as fungi. Chytrids are one of the early diverging fungal lineages and are saprobic, degrading refractory materials such as chitin and keratin, or acting as parasites. Their membership in kingdom Fungi is demonstrated with chitin cell walls, a posterior whiplash flagellum, absorptive nutrition, use of glycogen as an energy storage compound, and synthesis of lysine by the α-amino adipic acid (AAA) pathway. 66
There are approximately over 750 chytrid species distributed among 7 orders. There has been a significant increase in the research of chytrids since the discovery of Batrachochytrium dendrobatidis, the casual agent of chytridiomycosis. Chytridiomycota reproduces with zoospores, making it unusual among the Fungi. For most members of Chytridiomycetes, sexual reproduction is not known. Asexual reproduction occurs through the release of zoospores (presumably) derived through mitosis. The methods of sexual reproduction for those members of Chytridiomycetes in which it is known. It is generally accepted that the resulting zygote forms a resting spore, which functions as a means of surviving adverse conditions. In some members, sexual reproduction is achieved through the fusion of isogametes (gametes of the same size and shape).
olpidium endobiontic parasitism sporangium formation
haploid zoospores meioesporangium germination
isogamy K! & R!
plantozigot n + n
resistant sporangium n + n infection II 67
allomyces macrogynus cistes haploid zoospores resistant sporangium zoosporangium
vegetative diploid phase: sporophyte ciste
gametangiums: â™‚ â™€
K! vegetative haploid phase 2n zygote
This group includes the notable plant pathogens Synchytrium. Some algal parasites practice oogamy: a motile male gamete attaches itself to a nonmotile structure containing the female gamete. In another group, two thalli produce tubes that fuse and allow the gametes to meet and fuse. In the last group, rhizoids of compatible strains meet and fuse. Both nuclei migrate out of the zoosporangium and into the conjoined rhizoids where they fuse. The resulting zygote germinates into a resting spore. Sexual reproduction is common and well known among members of the Monblepharidomycetes. Typically, these chytrids practice a version of oogamy: the male is motile and the female is stationary. This is the first occurrence of oogamy in kingdom Fungi. Briefly, the monoblephs form oogonia, which give rise to eggs, and antheridia, which give rise to male gametes. Once fertilized, the zygote either becomes an encysted or motile oospore, which ultimately becomes a resting spore that will later germinate and give rise to new zoosporangia. Upon release from the germinated resting spore, zoospores seek out a suitable substrate for growth using chemotaxis or
phototaxis. Some species encyst and germinate directly upon the substrate; others encyst and germinate a short distance away. Once germinated, enzymes released from the zoospore begin to break down the substrate and utilize it produce a new thallus. Thalli are coenocytic and usually form no true mycelium (having rhizoids instead). Chytrids have several different growth patterns. Some are holocarpic, which means they only produce a zoosporangium and zoospores. Others are eucarpic, meaning they produce other structures, such as rhizoids, in addition to the zoosporangium and zoospores. Some chytrids are monocentric, meaning a single zoospore gives rise to a single zoosporangium. Others are polycentric, meaning one zoospore gives rise to many zoosporangium connected by a rhizomycelium. Rhizoids do not have nuclei while a rhizomycelium can. Growth continues until a new batch of zoospores are ready for release. Chytrids have a diverse set of release mechanisms that can be grouped into the broad categories of operculate or inoperculate. 69
Approximately 1060 species are known. They are mostly terrestrial in habitat, living in soil or on decaying plant or animal material. Some are parasites of plants, insects, and small animals, while others form symbiotic relationships with plants. Zygomycete hyphae may be coenocytic, forming septa only where gametes are formed or to wall off dead hyphae. Is a phylum of fungi. The name comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. Zygomycetes exhibit a special structure of cell wall. Most fungi have chitin as structural polysaccharide, while zygomycetes synthesize chitosan. This is the deacetylated homopolymer of chitin. Chitin is built of Î˛-1,4 bonded N- acetyl glucosamine. Fungal hyphae grow at the tip. Therefore, specialized vesicles, the chitosomes, bring precursors of chitin and its synthesizing enzyme, chitin synthetase, to the outside of the membrane by exocytosis. 70
sexual reproduction sporangium
The enzyme on the membrane catalyzes glycosidic bond formations from the nucleotide sugar substrate, Uridine diphospho-N-acetyl-D-glucosamine. The nascent polysaccharide chain is then cleaved by the enzyme chitin deacetylase. The enzyme catalyzes the hydrolytic cleavage of the N-acetamido group in chitin. After this the chitosan polymer chain forms micro fibrils. These fibers are embedded in an amorphous matrix consisting of proteins, glucans (which putatively cross-link the chitosan fibers), mannoproteins, lipids and other compounds.
rhizopus stolonifer haploid vegetative mycelium
aplanaspores (n) zygospore germination
K!+ R!* M!
gametangia and suspending
+ progametangiums -
The Fungi imperfecti or imperfect fungi, also known as Deuteromycota, are fungi which do not fit into the commonly established taxonomic classifications of fungi that are based on biological species concepts or morphological characteristics of sexual structures because their sexual form of reproduction has never been observed; hence the name “imperfect fungi.” Only their asexual form of reproduction is known, meaning that this group of fungi produces their spores asexually. The Deuteromycota (Greek for “second fungi”) were once considered a formal phylum of the kingdom Fungi. The term is now used only informally, to denote species of fungi that are asexually reproducing members of the fungal phyla Ascomycota and Basidiomycota. There are about 25,000 species that have been classified in the deuteromycota and many are basidiomycota or 72
ascomycota anamorphs. Fungi producing the antibiotic penicillin and those that cause athlete’s foot and yeast infections are imperfect fungi. In addition, there are a number of edible imperfect fungi, including the ones that provide the distinctive characteristics of Roquefort and Camembert cheese. Other, more informal, names besides Deuteromycota (“Deuteromycetes”) and fungi imperfecti, are anamorphic fungi, or mitosporic fungi, but these are terms without taxonomic rank.
Ascomycota is a Division/Phylum of the kingdom Fungi that, together with the Basidiomycota, form the subkingdom Dikarya. Its members are commonly known as the sac fungi. They are the largest phylum of Fungi, with over 64,000 species. The defining feature of this fungal group is the “ascus”, a microscopic sexual structure in which nonmotile spores, called ascospores, are formed. However, some species of the Ascomycota are asexual, meaning that they do not have a sexual cycle and thus do not form asci or ascospores. Previously placed in the Deuteromycota along with asexual species from other fungal taxa, asexual (or anamorphic) ascomycetes are now identified and classified based on morphological or physiological similarities to ascus-bearing taxa, and by phylogenetic analyses of DNA sequences. 74
The ascomycetes are a monophyletic group, i.e., all of its members trace back to one common ancestor. This group is of particular relevance to humans as sources for medicinally important compounds, such as antibiotics and for making bread, alcoholic beverages, and cheese, but also as pathogens of humans and plants. Familiar examples of sac fungi include morels, truffles, brewer’s yeast and baker’s yeast, dead man’s fingers, and cup fungi.
R! – meiosis young ascus mature ascus diploid phase
spores liberation a π K! – karyogamy budding and growth II
conidia formation ascus
blastic Before the recognition of the fungal kingdom, the sac fungi were considered to be a class, not a phylum. The original collective term for these taxa was “Ascomycetes”, which was first coined in the 1800s for a rankless nonlichenized taxon that possessed asci. The names Ascomycota, Ascomycetes, and others with the same root are based upon the term “ascus”. “Ascomycetes” was soon used to include lichenized taxa, and became the standard term, at the class level, for all ascus-bearing species, just as the term “Basidiomycetes” became used for their basidium-bearing counterparts. 76
Elevation of the taxonomic rank of the Ascomycetes resulted in the names Ascomycetae, Ascomycotina, and finally Ascomycota. Together, the Ascomycota and the Basidiomycota form the subkingdom Dikarya. The more familiar term, Ascomycetes, is still loosely used, e.g. at fungal forays it is often said of a fungus, such as Peziza, “It is an ascomycete, not a basidiomycete” in reference to their sexual reproductive mode. The terms are further abbreviated to “ascos” and “basidos”, which are not officially sanctioned technical names.
Basidiomycota is one of two large phyla that, together with the Ascomycota, constitute the subkingdom Dikarya (often referred to as the â€œhigher fungiâ€?) within the kingdom Fungi. More specifically the Basidiomycota include these groups: mushrooms, puffballs, stinkhorns, bracket fungi, other polypores, jelly fungi, boletes, chanterelles, earth stars, smuts, bunts, rusts, mirror yeasts, and the human pathogenic yeast Cryptococcus. Basically, Basidiomycota are filamentous fungi composed of hyphae (except for yeasts), and reproducing sexually via the formation of specialized club-shaped end cells called basidia that normally bear external meiospores (usually four).
(discussed below) can be recognized as members of this phylum by gross similarity to others, by the formation of a distinctive anatomical feature (the clamp connection - see below), cell wall components, and definitively by phylogenetic molecular analysis of DNA sequence data.
These specialized spores are called basidiospores. However, some Basidiomycota reproduce asexually in addition or exclusively. Basidiomycota that reproduce asexually 77
A typical basidiomycete cycle
Unlike higher animals and plants which have readily recognizable male and female counterparts, Basidiomycota (except for the Rust (Pucciniales)) tend to have mutually indistinguishable, compatible haploids which are usually mycelia being composed of filamentous hyphae. Typically haploid Basidiomycota mycelia fuse via plasmogamy and then the compatible nuclei migrate into each otherâ€™s mycelia and pair up with the resident nuclei. Karyogamy is delayed, so that the compatible nuclei remain in pairs, called a dikaryon. The hyphae are then said to be dikaryotic. Conversely, the haploid mycelia are called monokaryons. Often, the dikaryotic mycelium is more vigorous than the individual monokaryotic mycelia, and proceeds to take over the substrate in which they are growing. The dikaryons can be long-lived, lasting years, decades, or centuries. 78
The monokaryons are neither male nor female. They have either a bipolar (unifactorial) or a tetrapolar (bifactorial) mating system. This results in the fact that following meiosis, the resulting haploid basidiospores and resultant monokaryons, have nuclei that are compatible with 50% (if bipolar) or 25% (if tetrapolar) of their sister basidiospores (and their resultant monokaryons) because the mating genes must differ for them to be compatible. However, there are many variations of these genes in the population, and therefore, over 90% of (monokaryons) are compatible with each other. It is as if there were multiple sexes.
stipe dikaryotic mycelium 3: fruiting
basidiospores dikaryotic mycelium 2: growth
mycelium 1: monokaryotic