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CHAPTER 1 : THE SCIENCE OF BIOLOGY 1.0 Introduction Biology is the science devoted to the study of living objects. Two Greek words, bios (life) and logos (discourse), explain the term "biology" as meaning study of living creatures. Since life manifests itself in various forms i.e. plant and animal forms, biology is the study of both. The study of plants is termed as botany or plant biology, while the study of animals is called zoology or animal biology. Biology also comprises of the cellular basis of living things for the activities of life. It consists of energy metabolism and also of genetics which forms the basis of inheritance in organisms. Living things have been studied since primitive times. Primitive man had to find out what could be utilized for food, shelter and clothing, which plants would be useful as medicines and which animals he could use to get work done for him. The science of biology thus arose out of basic human needs. Biology also includes evolutionary relationships between organisms. Biology tells us about the routine activities of microorganisms, plants and animals and also the relation between their structures and functions. Many sub-divisions and special areas of biology exist but biology can conveniently be divided into two categories, (A) Practical and (B) Theoretical. A. Practical biology consists of plant breeding, medical science, wildlife management, agriculture. B. Theoretical biology consists of Physiology (the study of the functions of living things), Microbiology (the study of microscopic organisms), Biochemistry (the study of the chemical makeup of organisms), Ecology (the study of populations and their environment) and Taxonomy (categorization). C. PinkMonkey Online Study Guide-Biology D. 1.1 Practical Biology E. Introduction F. Living things are made up of cells which form the basic unit of life. The cell is, in turn, made up of molecules and atoms. The cell usually cannot be seen with the naked eye. Each cell performs certain functions. Some functioning cells come together organize to form a tissue. It is at this stage that the complex structuring of living things begins. A group of tissues, when organized, form organs such as the brain, the heart, etc. When a number of organs work together, they compose an organ system. So an organism is a composite union of various organ systems. The combination of several organisms is called population, which, in turn, forms a community, leading to the creation of a Biosphere. Figure 1.1 represents the structural complexity of the Biosphere. G. i) Metabolism H. An organism is basically made up of six basic elements: C, H, O, N, P and Ca. These make up about 96% of the weight of an organism. To keep life intact there is an exchange of chemical matter from cell to environment and environment to cell. Organic matter from the environment is absorbed by the cell and utilized for preparing energy. The energy thus prepared is used to perform the functions of the cell. Unlike in nonliving things, a number of physical and chemical changes take place in the body of the organism. The sum total of physical and chemical changes in an organism is called metabolism. Metabolism includes anabolism in which complex organic substances are built up and energy is stored, and catabolism in which the complex organic substances are broken down to release energy. These changes of conservation and release of energy continuously take place in the organism. This energy is basically in the form of chemical energy. Nonliving matter does not show this kind of exchange of energy. I. ii) Growth J. In metabolism we have seen that organic matter is collected from the environment and processed in the cell. In the process of growth, the cell organizes this material into its own structure. During growth the cell spends some amount of the energy created in the process of metabolism. Every organ has its own pattern of growth. This pattern depends upon the tissue of the organ. Growth of different organs leads to physical growth. Food is converted into organic matter which is then utilized for the growth of the body. Nonliving organisms do not show these characteristics. K. iii) Reproduction L. A living thing has the ability to procreate when it matures through the process of reproduction. There are differences in the reproductive functions of higher animals and lower animals. In lower animals (as in unicellular animals like amebas and bacteria), reproduction merely extends the process of growth. For instance, after maturity, a single bacterium splits into two bacteria, in six stages. This process is called asexual reproduction. In asexual reproduction only one parent is involved. So generally the produced cells are identical to the parent cell. In asexual reproduction, the rate of production of offspring is faster than in sexual reproduction. In higher or more complex organisms there is another type of reproduction called sexual reproduction. In sexual reproduction, two parents of opposite gender type are responsible for the formation of a new organism. During sexual reproduction, a new combination of genetic material (D.N.A.) occurs. This process is complex and takes more time than asexual reproduction. Nonliving things do not reproduce. M. PinkMonkey Online Study Guide-Biology N. iv) Responsiveness to Stimuli O. All living things are able to respond to stimuli in the external environment. Stimuli originate from different sources. P. a) physical: light, heat, temperature, sound. Q. b) chemical: acids and alkali. R. c) mechanical: friction, pressure. S. The body has specialized tissue or higher centers to detect stimuli, such as eyes for light, ears for auditory stimuli, the nose for olfactory stimuli, the tongue for taste, the skin for touch, etc. T. An organism must co-ordinate well to give an appropriate response to the stimuli from the environment. All systems of the body help in this co-ordination, like nerves from the nervous system, and certain chemical regulators called hormones from the endocrine system. This simultaneously produces an effect of co-ordination and acts as a sensing system. To respond to the stimuli, the organism has certain efferent units like muscles, glands, hair, etc. The process of response involves the use of energy. U. The responses are of two types: V. a) generalized, and W. b) protective. X. Protective responses help to promote survival and thus sustain life. A generalized response contribute to the behavior patterns of an organism. For certain classes, the response occurs with a definite pattern which is innate to the organism. Y. Nonliving things don’t respond to stimuli as living things do. Z. v) Evolution AA. Living organisms normally interact with the environment for their daily requirements. There are always changes going on in the environment. To adapt to these changes, there are genetic changes in the animal. The process of adaptation in a new generation animal in the population is called evolution. Evolution allows for changes in interactions between the organism and its environment. The evolved organism is more capable of adapting to changes in the environment. This adaptation in the organism leads to the formation of a new species and also newer organisms within the species. So with evolution, a new species is formed but certain characteristics from the previous generation remain intact. BB. vi) Ecology CC. Ecology is the study of the relationships between the environment and the organism, and between various organisms . Due to interaction with the environment, the organism and its environment continuously influence each other. Animate organisms can migrate to another place if the environment is not suited to their survival in a given region. For instance, frogs cannot live in water if there are too many crocodiles on their side of the pond. DD. Nonliving things cannot change their environment . EE. PinkMonkey Online Study Guide-Biology FF. 1.2 Scientific Methodology GG. Introduction HH. To study the sciences, including biology, a person must adopt a certain manner of thinking about questions, The methods used to answer questions about biology require a scientist to think about all the possibilities that could explain an observation. The scientist then refers to the research that other scientists and experts have done which might help him or her to better understand the problem. Then experiments are designed which will rule out all the possibilities exept one. If all possibilities exept one are ruled out, then the remaining possibility must be true explanation. Scientific method consists of the following steps. II. i) Observation JJ. The scientist objectively ( without forming opinions yet) observes a particular phenomenon in nature or in the labratory. A problem based on that observation is declared. The scientist then formulates the required steps to solve the problem. Because other scientists may also beworking on this same problem or similar problems, the scientist must use the library to read about what others have already discovered. This is necissary to help design experiments that have already been done by others. KK. ii) Hpothesis, Experimental Inference, and Analysis LL. This next step is to form a hypothesis, which is a simple statement that is either true or false. For example, a scientist may exept that water is necessary to keep houseplants alive. He might form the hypothesis, " water is necessary for houseplants to remain alive," which is either true or false. The perameters of the experiment would include houseplants with water, and houseplants without water. The experiment is repeated several times. In this case, the scientist could merely observe the state of the plant ( dead or alive). In other experiments, the hypothesis might require that actual measurements would be made, such as the height of the plant, the number of leaves formed, etc. MM. iii) Conclusion NN. Based on the outcome of the experiments and whether the hypothesis was found to be true or proven to be false, an inference is drawn,. In our example, the houseplants without water would turn brown and die, so the scientist would infer that water is necessary to keep houseplants alive. Therefore, our hypothesis that " water is necessary for houseplants to remain alive" would be supported ( i.e., not proven to be incorrect). This, and other experiments which show that water is necessary for discoveries are also discussed at scientific converences. OO. iv) Theory and Law PP. If many different experiments are performed which all support a hypothesis, then it is likely to actually be true. If most scientist have high confidence that a hypothesis to be true, then it is now considered to be a theory. Theories are hypotheses that sre assumed to be true. If a theory is tested and retested in many ways, and no evidence can be found that proves that it is not true, then it is eventually considered to be a fact of nature, and is referred to as a " law".. PinkMonkey Online Study Guide-Biology CHAPTER 2: THE CHEMICAL BASIS OF LIFE 2.0 Introduction As we have seen in the last chapter, biology is the study of the natural world - the living world around us. Formerly the biologist merely classified plants and animals according to their size, shape ( i.e. anatomy), their physiology and their existence in nature. Scientists later discovered the chemical and physical bases of living things. From their own study they realized that there is a chemical similarity between a plant cell and an animal cell. This leads us to the study of the chemical basis of life. PinkMonkey Online Study Guide-Biology 2.1 Structural Organization and the Chemical Basis of Life (A) Introduction The universe and living bodies are composed of matter which occupies space and possesses mass. Matter can exist in four forms -solid, liquid, gaseous and plasma. Matter is made up of basic substances called elements. There are over a hundred elements recognized by scientists today. An element is made up of identicle atoms. Calcium, Carbon, hydrogen, iron, sodium, etc. are some elements. i) Atoms Each element is made up of one particular kind of atom. Atoms are the smallest part of an element which do not share the properties of the element. An atom consists of 3 basic particles: a) Protons, which are positively charged and are present in the nucleus. b) Electrons, which are negatively charged and which rotate around the nucleus. c) Neutrons, which are present in the nucleus and which don’t have any electricle charge. A neutron has approximately the same mass as a proton. In the nucleus of the atom the proton and neutron are firmly attached to each other. The chemistry of the atom is dependent upon the number of protons and electrons in the atom. Protons and electrons are present in the same number in the atom, which leads to a neutral electrical charge in the atom. The nucleus of an atom is surrounded by shells or orbits of electrons. In the first orbit there are a maximum of 2 electrons. From the second shell to the last shell, every shell has a maximum of 8 electrons. When the final orbit of an atom is complete with electrons it becomes a stable atom. When there is a single electron or more missing in the last orbit of the atom, the atom becomes active allowing for a chemical reaction with another atom. During the reaction there is sharing or exchange of electrons. Atoms are most stable when they have a full outer shell. If they can, they will either share one or more electrons with another atom so that both atoms " think " they have full outer shells, or sometimes an atom that " needs " one or two electrons to have a full outer shell will actually take electrons another atom that has only one or two electrons in its outer shell; therefore, both atoms end up with full outer shells. ii) Molecules In biology we study molecules as part of molecular biology, molecular interaction, etc. Atoms combine chemically in a specific order to form molecules. For instance, two atoms of hydrogen combine with one atom of oxygen to form a single molecule of water. A molecule is the smallest particle of a substance existing freely yet retaining the characteristics of that substance. A collection of molecules forms a compound. Properties of the compound depend upon molecules and atoms present in the molecule. Consider this example: the molecular weight of the compound, water, is 18. This weight has been calculated taking into account the weight of its molecular components H and O. H2O H + H + O  1 +1+ 16  18 Some molecules are formed from atoms of the same element e.g. oxygen molecule (O2) is formed from 2 atoms of oxygen; ozone (O3) is formed from 3 atoms of oxygen. But, oxygen or ozone cannot be called a compound because in a compound we require atoms of different elements. When the compound is formed it contains different elements. These elements stay together by means of links between them. In scientific terminology this link is called a bond. There are various kinds of bonds. In a compound, when one atom of an element gives away an electron, this exchange creates a bond between these two elements. This is an ionic bond. This bond consists of an electromagnetic force which is formed due to exchange of charge [electron]; the atoms conducting the exchange are called ions. This eletromagnetic force attracts two opposite charges: a positive charge in the atom which gives away electrons and a negative charge in the atom which takes up electrons. This attraction force forms the ionic bond. A second important type of bond is called the covalent bond. Such a bond is formed when two atoms share one or more electrons with one another. For example (fig. 21), in water (H2O) 2 atoms of hydrogen share 2 electrons with oxygen. In ammonia 3 hydrogen atoms share one electron each with a single nitrogen atom. This leads to the formation of ammonia (NH3). Between atoms when one pair of electrons is shared, a single covalent bond is formed. When two pairs of electrons are shared a double covalent bond is formed. Click here to enlarge iii) Acids and Bases or Alkalis If a compound reacts with water and releases hydrogen ions (H+) ions then this compound is called an acid, and is said to be acidic in nature. For example, when hydrogen sulphide is mixed with water it releases hydrogen ions and the solution becomes one of sulphuric acid. Other chemical compounds when dissolved in water attract hydrogen atoms. These substances are called bases or alkalis. For example, when sodium hydroxide (NaOH) is mixed with water, sodium hydroxide attracts hydrogen ions from H2O, and (OH-) ions remain. So these substances that remove (H+) from water act as bases or alkalis. PinkMonkey Online Study Guide-Biology 2.2 Organic Compounds Many chemical compounds in living organisms are known as organic compounds' which contain C,H and O. In the earlier chapter we have seen that an organism is formed primarily from six elements: C, H, O, N, P, Ca. The study of organic compounds is called organic chemistry. (A) Carbohydrates There are plenty of organic compounds present in nature. All living things contain basically four types of organic compounds.Carbohydrates form the first category of organic compounds. For metabolism the organism requires energy. This energy is provided primarily by carbohydrates. Carbohydrates are basically composed of 3 elements, C, H, and O. The ratio of H to O is 2:1, as in a water molecule (H2O). There are types of carbohydrates according to the complexity of the carbohydrate molecule. Carbohydrates and usually taste sweet to humans are referred to as sugar. If a carbohydrate is made up from a single molecule it is called monosaccharide. When the carbohydrate is made up of 2 sugar molecules linked together it is referred to as a adisaccharide Carbohydrates which have more than 3 molecules are called polysaccharides. The general formula to represent the carbohydrate is Cx(H2O)y. Click here to enlarge Table I : Schematic Representation of Carbohydrates 1) Monosaccharides They are the simplest soluble sugar. Depending on the number of carbon atoms present, monosaccharides are further classified as: a) trioses (3 carbons) C3H6O3 e.g. glyceraldehyde b) pentoses  (5 carbons) C5H10O5 e.g. ribose and deoxyribose c) hexoses (6 carbons) C6H12O6 e.g. glucose Glucose C6H12O6 is a basic form of fuel in all living things. It is soluble in blood plasma and water and so it is transported by body fluids to all cells in the body. In cells it is metabolized and releases energy. Glucose is also the main product of photosynthesis and also an initiating material for cellular respiration. Figure 2.2 A molecular representation of glucose PinkMonkey Online Study Guide-Biology 2) Disaccharides: These carbohydrates contain two monosaccharides linked together and accordingly they are known as: (a) Disaccharide : contains two monosaccharides e.g. lactose, maltose, sucrose Maltose  Glucose + Glucose Sucrose  Glucose + Fructose Lactose  Glucose + Galactose Click here to enlarge (b) trisaccharide: containing 3 monosaccharides. e.g. raffinose (c) tetrasaccharide: containing 4 monosaccharide e.g stachyose 3) Polysaccharides General formula n (C6H10O5). These complex carbohydrates are formed by chains of at least ten monosaccharides. They are of two types: (a) Homoglycans: containing only one type of monosaccharide (e.g. glycogen, starch, cellulose, contain only glucose molecules). Starch is a very important polysaccharide because it is formed through a chain of hundreds or thousands of glucose units. Carbohydrates in plants are stored in the form of starches. Starch contained in energy rich food like rice, corn, and potatoes form part of the staple diet of most people. Starch Click here to enlarge A second important polysaccharide is glycogen. Glycogen also contains thousands of glucose chains; the difference from starch though is in its branching pattern. Glucose is stored in the human liver in the form of glycogen. Another important polysaccharide is cellulose. Cellulose is used primarily as a structural carbohydrate. It is also composed of glucose units, linked in a different orientation but the units cannot be released from one another except by a few species of organisms. Wood is formed from cellulose. Even the cell wall of all plants is made up of cellulose. Cotton and paper are also cellulose products. (b) Heteroglucans: contain more than one type of monosaccharide linked together (e.g. mucilage, gum etc.) 4) Proteins and its derivatives Proteins are the fundamental chemical compounds of the protoplasm indispensable for vital life processes. They are complex, large molecules each containing thousands of atoms. proteins contain nitrogen in addition to carbon, hydrogen and oxygen; they usually also contain phosphorus and sulfur. These compounds are polymers of unit structures called amino acids, represented chemically as: amino acid -NH2 is an amino group, - COOH is the carboxyl group, ,and R represents the variable chain forming different amino acids. There are 20 diferent of amino acids. The amino acids differ depending on the nature of the R group. Examples of. amino acids are valine, alanine, glutamic acid, tyrosine and histidine. Two molecules of amino acids are joined by the carboxyl group of one ammino acid with the amino group of the other by loss of one molecule of water. This process is called dehydration synthesis and the bond thus formed between two molecules is referred to as the peptide or peptide bond. Formation of dipeptide Click here to enlarge There are 3 types of proteins namely : (1) Simple proteins: like albumins and globulins formed by group of amino acids only. (2) Derived proteins: like proteose and peptones which are hydrolytic cleavage products of complex proteins. (3) Conjugated proteins: like nucleo proteins (Proteins + nucleic acid), lipoproteins (protein + lipid), or glycoproteins (protein + carbohydrates) which are formed by the combination of proteins with some non-protein molecule. This non-protein portion is called Prosthetic group. All living things require protein for survival. In fact an organism is constructed by means of proteins. All living things then, in any form - liquid, solid, or plasma - contain proteins. Protein is also seen as a supporting tissue with main tissue. Bone, tendons, muscle, cartilage, ligaments are all formed of protein. Enzymes are a specified class of proteins. Enzymes act as catalysts in chemical reactions of the body. They are not used up by the reaction, rather they remain chemically unchanged and available to catalyze succeeding reactions. PinkMonkey Online Study Guide-Biology 2. 3 Nucleotides And Nucleic Acid Every organism reproduces within its life span. This is accomplished through cell divisions and is regulated by many kinds of protiens. The information forsynthesizing unique proteins is located in the nucleus of the cell. It is called the genetic code which is the "blue print" for producing specific sequences of the amino acids in proteins. Thus the genetic code can regulate chemical reaction going on in the cell. Man’s queries into the nature of cells did not end with its discovery of general structures. In an attempt to understand the chemical make up and functional details of the cell he succeeded in discovering a substance called nucleic acid, made up of long chains of nucleotide units. (A) Nucleotide It is the structural unit of nucleic acid. Each nucleotide is composed of: (1) Pentose sugar (2) Phosphate group (3) One of four nitrogen bases attached to the pentose sugar. A nucleotide without a phosphate group is a nucleoside. (B) Nucleic acids They are complex, large biomolecules formed of many units called nucleotides. Nucleic acids are of two types : (1) DNA - Deoxyribonucleic acid and, (2) RNA - Ribonucleic acid The DNA of cells contains genetic information in a coded form, and is only present in the nucleus of the cellis formed from DNA, plus a few special organelles. RNA and is present in the cytoplasm and in the nucleus of the cell. DNA and RNA differ from one another in their components. DNA contains the pentose sugar, deoxyribose, while RNA contains ribose. There are also small differences in the types of nitrogen bases found in DNA and RNA. (The structure of DNA and its importance in the life of cells will be explained in the chapter "Genes and Molecular genetics" ,Chapter 7.) PinkMonkey Online Study Guide-Biology 2.4 Lipids Fats and their derivatives are collectively called lipids. Fats are compounds containing fatty acids and glycerol. They are composed of carbon, hydrogen and oxygen, but less oxygen than that in carbohydrates. Fatty acids are long chains of CH2 groups with terminal methyl and carboxyl groups with general formula CH3[CH2]n-COOH, while glycerol molecule contains a chain of three carbon atoms and has a formula C3H6O3. In the formation of fat, three molecules of fatty acids are combined with three-OH groups on one molecule of glycerol, with removal of 3 molecules of water which is represented as follows : Formation of Fat molecule There are mainly three types of lipids . the simple lipids, commonly known as fats and oils, the compound lipids such as phospholipids and glycolipids which on hydrolysis yield not only alcohol and fatty acids but also other compounds and derived lipids such as steroids which include cholesterol, Vitamin D, estrogen , testosterone, cortisol, etc. Lipids are practically insoluble in water but are soluble in organic solvents like chloroform, ether and benzene. Fats stored in cells are usually clear oil droplets called globules. Because fats do not dissolve in water, animals store fat in large clear globules in the cells of adipose tissue. The enzyme lipose breaks down fats into fatty acids and glycerol which can be furthur broken down to produce energy. PinkMonkey Online Study Guide-Biology CHAPTER 3 : CELL - THE BASIC UNIT OF LIFE 3.0 Introduction A cell is a microscopic, structural and functional unit of living organisms capable of independent existence. (e.g. Ameba). All living things are composed of cells. Some functioning cells come together to form a tissue and tissues collectively form organs. In more complex living organisms, organs work together for the purpose of survival as system. However, in all living organisms, the cell is a functional unit and all of biology revolves around the activity of the cell. Figure 3.1 Animal Cell The study of cell is impossible without the microscope. The first simple microscope was prepared by Anton Van Leewenhoek (1632-1723) who studied the structure of bacteria, protozoa, spermatozoa, red blood cells etc. The word ‘cell’ was first coined by Robert Hooke in 1665 to designate the empty honey-comb like structures viewed in a thin section of bottle cork which he examined. He was impressed by the microscopic compartments in the cork as they reminded him of rooms in a monastery which are known as cells. He therefore referred to the units as cells. In 1838, the German botanist Matthios Schleiden proposed that all the plants are made up of plant cells. Then in 1839, his colleague, the anatomist Theodore Schwann studied and concluded that all animals are also composed of animal cells. Schwann and Schleiden studied a wide variety of plant and animal tissues and proposed the "cell theory" in 1839. It stated that "all organisms are composed of cells." But still the real nature of a cell was in doubt. Cell theory was again rewritten by Rudolf Virchow in 1858. In his theory he said that all living things are made up of cells and that all cells arise from pre-existing cells. It was German biologist Schulze who found in 1861 that the cells are not empty as were seen by Hooke but contain a ‘stuff’ of life called protoplasm. During the 1950s scientists developed the concept that all organisms may be classified as prokaryotes or eukaryotes. For example, in prokaryotic cells, there is no nucleus; eukaryotic cells have a nucleus. Another important difference between prokaryotes and eukaryotes is that the prokaryotic cell does not have any intracellular components. Bacteria and blue- green algae come under the prokaryotic group, and protozoa, fungi, animals, and plants come under the eukaryotic group. 3.1 Modern cell theory Modern biologists have made certain additions to the original cell theory which now states that: 1. All organisms are made up of cells. 2. New cells are always produced from pre-existing cells. 3. The cell is a structural and functional unit of all living things. 4.The cell contains hereditary information which is passed on from cell to cell during cell division. 5. All cells are basically the same in chemical composition and metabolic activities. As the cells of different parts of an organism (such as epithelial cell, muscle cell, nerve cell, etc). vary in shape, size and internal structure, no cell can be described as a typical one. In spite of all these variations, they are all cells, showing certain common fundamental properties. Figure 3.2 Plant cell PinkMonkey Online Study Guide-Biology 3.2 Structure of cell Both prokaryotic and eukaryotic cells possess the basic features of a plasma membrane and cytoplasm. The plasma membrane is the outermost surface of the cell which separates the cell from the environment. The cytoplasm is the aqueous content within the plasma membrane. Plasma membrane : It is like any other membrane in the cell but it plays a very important function. It forms the border of a cell, so it is also called the cell membrane. It is primarily composed of proteins and phosphalipid. The phospholipids occur in two layers referred to as a bilayer. Protein is embedded within the lipid layer, or attached to the surface of it. The plasma membrane is elastic and very fluid because of protein and lipid. Normally the function of the plasma membrane is that of a gate-keeper. It allows certain important substances to enter and exit the cell. Cytoplasm and organelles : The cytoplasm is a semi-solid substance which is present in the cell and which gives structure, size, shape and foundation to the cell. It is enclosed by the plasma membrane. Within the cytoplasm are a number of microscopic bodies called organelles that perform various functions essential for the survival of the cell. Figure 3.2 Endoplasmic reticulum with the nucleus and the Golgi complex Endoplasmic reticulum (ER) : is one of the important organelles present in the cytoplasm. Endoplasmic reticulum is a series of membranes which extend throughout the cytoplasm in eukaryotic cells. In certain cases in ER there are submicroscopic bodies called ribosomes which are involved in production of protiens. Rough ER : In this kind of ER the ribosomes are presenton the surface.The endoplasmic reticulum is responsible for protein synthesis in a cell. Ribosomes are suborganelles in which the amino acids are actually bound together to form proteins. There are spaces within the folds of ER membrane are known as cisternae. Smooth ER : This type of ER does not have ribosomes. Another organelle is the Golgi body or Golgi apparatus (G.A.). The Golgi body is a series of flattened sacs usually curled at the edges. Proteins which have formed in ER are processed in G.A. After processing, the final product is discharged form the G.A. At this time the G.A. bulges and breaks away to form a dropline vesicle known as secretory vesicles. The vesicles move butward to the cell membrane and either insert their protien contents in the membrane, or release their contents outside the cell. There is another organelle which is related to the Golgi apparatus called the lysosome. The lysosome is derived from the Golgi body. It is a sac of enzymes in the cytoplasm, used for digestion within the cell. These enzymes break down particles of food taken into the cell and make the food product available for use. There are also cytoplasmic organelles called peroxisomes in the cell which produces the enzymes to degrade fatmolecules. Mitochondria : is another organelle of the cell. It is called the "power house of the cell" because it stores and releases the energy of the cell. The energy released is used to form ATP (adenosine triphosphate). Figure 3.3 A cross-section of a Mitochondrion Nucleus : Prokaryotic cells don’t have a nucleus but eukaryotic cells have a nucleus situated in the cytoplasm. The nucleus mainly contains DNA ( i.e., Deoxyribonucleic acid). DNA is organized into linear units called chromatin. Genes are the functional segments within the chromosome. Each chromosome consists of approximately 1,000,000 genes. The chromatin is coiled around nuclear protiens called histones. When chromatin is coiled, it forms chromasomes. Genes contain the coding for all the protiens in a cell of an animal or plant. The nucleus of the cell is surrounded by an outer membrane called the nuclear envelope. The nuclear membrane resembles the plasma membrane in its function. It is also a double layer membrane consisting of two lipid layers similar to those in the plasma membrane. Pores in the membrane allow the internal nuclear part to communicate with the cytoplasm of the cell. Prokaryotic cells don’t have a nucleus but they do possess DNA which exists freely in the cytoplasm. In bacteria a single looped chromosome consists of 4,000 genes.In plant cells, organelles called chloroplasts exist. Due to chloroplasts plants look green in color. The chloroplasts function in the process of photosynthesis. During this process, chloroplasts convert the energy in the sunlight into energy of carbohydrate molecules. Energy from the sun comes in the form of photons i.e. a package of energy which gets converted into carbohydrate energy. Chloroplasts consist of a green pigment called chlorophyll. Because chlorophyll molecules absorb most wavelenghths of light except green, they reflect green light and appear green to our eyes. chlorophyll is normally present in that area of a plant where sunlight can reach easily. For example, the leaves and stem of a plant are green. On the contrary, the roots don’t have chloroplast so they are not green. Cytoskeleton : is an interconnecting system of fibers and threads and interwoven molecules that give structure to the cell. The main component of the cytoskeleton are microtubules, microfilaments and intermediate filaments. They are all made up of proteins. Centriole : is another organelle present in the cell. It is cylindrical in shape and always occurs in pairs. Centrioles are involved in cell division. Vacuole :Another organelle seen in the plant cell is the vacuole. The vacuole forms about 75% of the plant cell. In the vacuole, the plant stores nutrients as well as toxic wastes. If pressure increases within the vacuole it can increase the size of the cell. In this case the cell will become swollen. If the pressure increases further the cell will get destroyed. Many cells have structures attached to them called Flagella or Cilia. Flagella are seen in the single-celled plant and protozoans, and cilia are commonly seen in animal cells. Flagella are long hairlike extensions that extend from the cell and help in locomotion. Animal sperm has flagella which permit locomotion. Cilia are shorter and more numerous than flagella. Rows of cilia move in waves to move the cell (prokaryotes like paramecia), or to move fluids around the cell (e.g., respiratory epithelial cells).These cells help in the removal of particles from the tract. Cell Wall : Plant cells possess a cell wall. It is a structure which is present outside the cell membrane. It is not very thick. In bacteria the cell wall is very thick and rigid: this gives shape to the bacteria. In a eukaryote cell, the cell wall is not identical in different animals. In fungi, the cell wall is made up of chitin which is a polysaccharide. In plant cell there is no chitin. Cell walls are composed of another polysaccharide called cellulose. The cell wall provides support to the structure to the cell. It also saves the cell from mechanical pressure.; it is not a selective (semipermeable) membrane like the plasma membrane. When bacteria enter the human body the cell wall this is recognized as a foreign substance in the body; this is how our immune system recognizes and destroys bacteria. 3.3 Movement through the plasma membrane The cell membrane separates the cell from the external environment. In order to communicate with the external environment for the purpose of survival (e.g., for the consumption of food, minerals etc.), there is movement in the cytoplasm and plasma membrane. This movement occurs through several mechanisms which are listed below: Osmosis : One method of movement through the membrane is osmosis. Osmosis is the movement of water. Osmosis often occurs across a membrane that is semipermeable. A semipermeable membrane allows only certain molecules to pass through while keeping other molecules out. Osmosis is really a type of diffusion involving only water molecules. Diffusion : Another method of movement through the membrane is diffusion. Diffusion is the movement of molecules from a region of higher concentration to one of lower concentration. This movement occurs due to molecules which constantly collide with each other. The total effectual momentum of the molecules is away from the region of high concentration to the region of low concentration. Diffusion is the random movement of molecules. The exchange of molecules (taking place from a higher concentration region to a lower concentration region) leads to the formation of concentration gradient. Diffusion phenomena can be seen by letting a drop of dye into water. The color of the dye gets diffused throughout the water. Facilitated diffusion : A third method is facilitated diffusion which occurs across the plasma membrane. This type of diffusion is very specialized. This occurs only in cases where specific proteins in the membrane permit only certain molecules across the membrane. These membrane proteins allow movement in the direction that diffusion would normally take from a region with a higher concentration of molecules to a region with a lower concentration of molecules. No energy use is required for facilitated diffusion. Active transport : A fourth method for movement across the membrane is active transport. When active transport takes place, a protein moves a certain substance across the membrane, usually from a region of lower concentration to a region of higher concentration. As you know this movement is against the concentration gradient, hence energy is required for this movement. Normally the cell gets its energy from ATP (adenosine triphosphate). For example, in cardiac muscles, active transport takes place. In these cells, sodium ions are constantly transported out of the cell. The cellular compartment is a region of high concentration of sodium ions. Buildup of electrically charged ions allows changes in voltage over the cell membrane which affects contraction of muscle cells. Endocytosis : This another mechanism of movement across the plasma membrane. In this type, a small patch of plasma membrane encloses particles or tiny volumes of fluid which are at or near the cell surface. The membrane enclosure then sinks into the cytoplasm and breaks off from the membrane, forming a vesicle that moves into the cytoplasm. When the vesicle contains particulate matter, the process is called phagocytosis. When the vesicle contains liquids or droplets of fluids the process is called pinocytosis. CHAPTER 4 : PHOTOSYNTHESIS 4.0 Introduction Energy is needed for existence as well as maintenance of life. Solar radiation is the unending source of energy for all forms of life on earth. However, living organisms can use only one form of energy for various life activities i.e. the biologically usable form of chemical energy. It is represented by the energy-rich organic compound called ATP (adenosine tri-phosphate). Photosynthesis is the only process in which the solar energy is trapped and converted into the chemical energy ATP. This process is described as photophosphorylation. This energy is stored in food molecules as food energy. In respiration, organic food is oxidized and the food energy is released as free energy and is made available for various cellular activities. In cells, the ATP molecules act as energy mediators. Organisms which can synthesize their own organic food from simple inorganic nutrients are called autotrophs or producers. These are mostly photosynthetic (e.g. green plants) which take energy from light. A few are chemosynthetic (e.g. certain soil bacteria) which obtain energy from chemicals. Photosynthesis is the most important and essential physiological process in green plants. This is because it is the primary source of organic food and ATP energy for all forms of life. It utilizes carbon dioxide and converts it into organic food (carbohydrates). It also releases oxygen into the atmosphere. In fact, oxygenic photosynthesis was responsible for converting the totally anaerobic atmosphere on earth into the aerobic atmosphere that exists today. 4.1 Chloroplasts Chloroplasts are green plastids. These are the special protoplasmic organelles present only in the green cells of plants. Chloroplasts act as photosynthetic apparatus. The entire process of photosynthesis is completed in each chloroplast. Hence these are the site of photosynthetic reactions. Leaves are specialized photosynthetic organs and hence, they contain the maximum number of chloroplasts in their mesophyll cells. Moreover the morphology and the anatomy of leaves are most helpful during photosynthesis for : (i) getting maximum absorption of sunlight, (ii) providing steady exchange of water to green cells, and (iii) allowing free exchange of carbon dioxide and oxygen. Ultrastructure of chloroplast The chloroplasts in higher plants are microscopic and mostly oval, spherical or discoid. Each chloroplast is bounded by two smooth and selectively permeable cytoplasmic membranes with an inter-membrane space. These are composed of lipo-protein subunits. Click here to enlarge The internal space of the chloroplast is filled with a colorless hydrophilic matrix called the stroma. A number of grana are suspended in the stroma. Each granum is a stack (compact bundle) of thylakoids. These are membrane-bound, flattened, disc-shaped vesicles. The thylakoid membranes are called grana lamellae. All grana are connected to one another by stroma lamellae (i.e. inter-grana lamellae or frets). The internal space of each thylakoid is called a fret channel. The thylakoid lamellae are composed of alternating layers of lipids and aqueous proteins. There is a layer of chlorophyll and carotenoid molecules situated between the protein and lipid layers. The chlorophyll molecules are arranged in such a way that their hydrophilic heads extend into the aqueous protein layer while the lipophilic tails are embedded in the lipid layer. The pigments are organized into numerous photosynthetic units called quantasomes. Each quantasome contains about 230 to 300 chlorophyll molecules. Quantasomes are capable of trapping light energy and converting it into chemical energy (ATP) during the photochemical reactions (light reaction) of photosynthesis. The grana also contain various co-enzymes and electron acceptors necessary for the process. Hence, grana are the site of the light reactions (phase-I) in photosynthesis. The stroma contains various enzymes required for the dark reaction( i.e., the biochemical reactions involving the reduction of carbon dioxide to form carbohydrates). Hence, stroma is the site of the dark reactions (phase-II) of photosynthesis. The "dark reactions" do not directly require light, but they do require energy produced from light during the light reactions. The grana thylakoids and the stroma lamellae together form an intricate internal membrane system in the chloroplast. This system is derived from the inner limiting membrane during the development of chloroplast. Pigments in photosynthesis : The most common photosynthetc pigments present in higher plants and green algae are: (i) Chlorophyll-a (blue-green) = C55H72O5N4Mg (ii) Chlorophyll-b (yellow-green) = C55H70O6N4Mg (iii) Carotenoids - Carotenes (orange-red) = C40 H56 (iv) Xanthophylls (yellow) = C40H56O2 For photosynthesis, these pigments can absorb and use light belonging to the visible spectrum only. Both chlorophyll-a and chlorophyll-b show maximum light absorption in the blue-violet and in the red regions of the visible range of wavelengths of light. Carotenoids absorb light in the blue and blue-green regions. They also protect the chlorophyll from undergoing photo-oxidation when exposed to very high intensity light. Chlorophyll-a is the essential pigment in photosynthesis, because only chlorophyll-a can utilize the absorbed light energy for the synthesis of chemical energy ATP. Other pigments act as accessory pigments. They collect the light energy and transfer it to chlorophyll-a for photosynthesis. Thylakoids in prokaryotes : In prokaryotes like cyanobacteria, purple bacteria, etc., thylakoids are present but they lie naked in the cytoplasm. Chloroplasts are absent. In prokaryotes, pigments are distributed uniformly on or in the lamellae. 4.2 Overall Equation of Photosynthesis Definition : Photosynthesis is the intracellular anabolic process, characteristic of the green cells of plants in which carbohydrates are synthesized from carbon dioxide and water in the presence of light and chlorophyll. In this process, light energy is converted into chemical energy and stored in carbohydrate molecules, while oxygen is liberated. The overall process of photosynthesis is represented by the following general chemical equation. 4.3 Primary Processes of Photosynthesis (The photochemical phase, light reaction or Hill reaction) Nature of light : As stated earlier, solar radiation is the only natural source of light for all organisms. Green plants can utilize light belonging to the visible spectrum only (Figure 4.2) for photosynthesis. This visible part of the electromagnetic spectrum from the sun is confined between wavelengths of 390 nm (violet) and 760 nm (red). Click here to enlarge Light is a form of energy. It appears to travel as a stream of discrete particles called photons. Each photon contains one quantum (unit) of light energy. The energy quantity of each type of light depends on its wavelength. Light with a shorter wavelength has greater energy; light with a longer wavelength has lesser energy. Rate of photosynthesis is measured in terms of the amount of carbon dioxide used (reduced) or oxygen released. It has been estimated that 8 quanta (photons) of light are required to reduce each molecule of carbon dioxide (or to release each molecule of oxygen) during photosynthesis (Emerson and Lewis, 1943). This is called the quantum requirement in photosynthesis. Light trapping systems : During the photochemical phase, light is trapped by the photosynthetic pigments present in the quantasomes of the grana thylakoids. These pigments are organized into two pigment systems called pigment system I (PS I) and pigment system II (PS II). (I) PS I is composed of the following pigment molecules: Chl-a 700 (P700) - one molecule - Reaction center Chl-a 683 - 200 molecules - Antenna chlorophyll Carotenoids - 50 molecules - Accessory pigments (II) PS II is composed of the following pigment molecules: Chl- a 680 - one molecule - Reaction center Chl- a 670 - 200 molecules - Antenna chlorophyll Chl- b - up to 200 molecules } Accessory pigments Carotenoids - up to 50 molecules In both the systems, all pigment molecules help in trapping light energy. However, all other molecules transfer their energy to the reaction center to be used for the photochemical reactions in photosynthesis. Photo-excitation of chlorophyll-a When a molecule of chlorophyll-a (acting as the reaction center) receives light energy in the form of photons (quanta), it becomes energy-rich and activated. This is called the excited state of chlorophyll. In this excited state, the chlorophyll-a expels one electron. With the loss of an electron, the chlorophyll-a develops a positive charge. This is called ionized chlorophyll-a. The expelled electron contains an extra amount of energy received from light. In other words, the energy-rich expelled electron represents light energy. This electron energy is used for the formation of ATP during photosynthesis. Photolysis of Water In the photosynthesis of green plants, water is used as a source of hydrogen required for the reduction of carbon dioxide to form carbohydrates. In this process, water is oxidized in presence of light and chlorophyll. Hydrogen is removed from water, and oxygen is released as follows : This is described as photolysis of water, or photochemical oxidation of water. This was first indicated by Van Niel (1931). It was demonstrated with the help of an experiment by R. Hill (1937). Hill suggested that during the photolysis of water, hydrogen combines with some hydrogen acceptor in the plant, while oxygen is released. (where A = unknown H-acceptor in plants). Later on, Arnon (1951) discovered this hydrogen acceptor to be a coenzyme called NADP (nicotinamide adenine dinucleotide phosphate). Substance A = NADP Similarly, Ruben, Kamen, et al. (1941) confirmed that the oxygen evolved during photosynthesis comes from the splitting of water only. They used heavy isotope of oxygen (O18) to demonstrate the fact as follows : HILL REACTION R. Hill (1937) suspended isolated chloroplasts in water in a beaker. He added some known hydrogen accepting compound (e.g. benzoquinone or ferric salt) to the water and exposed the beaker to the light. Immediately the oxidation of water took place and bubbles of oxygen were evolved. When the hydrogen acceptor in the beaker was examined, it was found to be reduced. (A = hydrogen acceptor) This is photolysis or the photochemical oxidation of water and is commonly called the Hill reaction. Photophosphorylation The formation of ATP molecules (chemical energy) from ADP and HPO in presence of light and chlorophyll-a during the photochemical phase of photosynthesis is called photophosphorylation or photosynthetic phosphorylation. More commonly, it is described as the conversion of light energy into chemical energy (ATP). (ADP = adenosine diphosphate) During the light reactions (the primary process or the photochemical phase), ATP formation takes place through two types of phosphorylation reactions. These are (1) non-cyclic photophosphorylation and (2) cyclic photophosphorylation The non-cyclic process involves both PS I and PS II. The cyclic process involves only PS I. (1) Non-cyclic photophosphorylation In the light reaction of photosynthesis, the formation of ATP from ADP and H3PO4 in presence of light and chlorophyll-a during the non-cyclic transfer of electrons is called non-cyclic photophosphorylation. Important features (1) It is the major pathway of the light reaction of photosynthesis. (2) It is a photochemical reaction. (3) It takes place in the grana of chloroplasts. (4) It requires participation of both PS I and PS II. (5) The transfer of electrons through the ETS is unidirectional or non-cyclic. (6) The non-cyclic process involves : (a) Photophosphorylation (ATP formation) (b) Photolysis of water (c) Formation of assimilatory power (ATP and NADPH2) (d) Liberation of oxygen The non-cyclic photophosphorylation takes place as follows. (a) Photoexcitation of PS I : The chlorophyll-a (P 700) of PS I is activated on receiving photons of light and so it expels electrons. As a result of this loss, it becomes ionized chl-a+. The electrons from PS I are first accepted by FRS (ferredoxin reducing substance) and are transferred to co-enzyme NADP via Fd (ferredoxin). NADP retains the electrons and is thus reduced. PinkMonkey Online Study Guide-Biology Figure 4.4 Diagrammatic representation of the non-cyclic process (Z scheme) b) Photoexcitation of PS II : Similarly, on receiving photons of light, the chl-a (680) of PS II also gets activated and expels electrons. As a result, it becomes ionized chl-a+. The high energy containing electrons from PS II are first accepted by an electron acceptor PQ (plastoquinone) and are then transferred along stet Electron Transport System consisting of plastoquinone, cytochrome b6, Cytochrome f and plastocyanin. Finally, the electrons are accepted by the ionized chl-a+ of PS I. In this way, ionized PS I comes back to the ground state and can again participate in the process. (c) Photolysis of water : The ionized chlorophyll-a+ of PS II is brought back to the ground state with the help of the electrons made available through the photolysis of water. (d) Formation of NADPH2 and liberation of O2 : During photolysis of water, oxygen is released as a by-product. The 2 NADP receive 4e- from PS I and 4H+ from the photolysis of water to form reduced coenzyme NADPH2 (e) Non-Cyclic electron transfer : In this process, the movement of electrons is considered to be non-cyclic, or unidirectional. This is because, the final electron acceptor is different from the initial electron donor. Initial electron donor Final electron acceptor In this way, the light-induced electron flow is maintained continuously in the non-cyclic manner from water to NADP as follows Because of the zig-zag path of the electrons (Figure 4.4), the non cyclic process is also called ‘Z’ scheme electron transport. (f) ATP formation : During the non-cyclic transfer of energy-rich electrons through the Electron Transport System from PS II to PS I, energy from the electrons is released. This is used for the formation of ATP from ADP and H3PO4. This is called non-cyclic photophosphorylation. End products of non-cyclic process and the assimilatory power : The end products are ATP, NADPH2 and O2. Of these, O2 is liberated from the green plants. ATP and NADPH2 are used in the following dark reactions (phase II) for carbon assimilation( i.e., reduction of CO2 to form carbohydrates). ATP and NADPH2 of light reaction are called ‘assimilatory power. PinkMonkey Online Study Guide-Biology (2) Cyclic photophosphorylation In the light reaction of photosynthesis, the formation of ATP from ADP and H3PO4 in the presence of light and chlorophyll-a during the cyclic transfer of electrons is called cyclic photophosphorylation. Important features (1) It is a part of the light reaction of photosynthesis. (2) It is a photochemical reaction and depends on light. (3) It takes place in the grana of chloroplasts. (4) It requires participation of PS I only. (5) The movement of electrons is cyclic. (6) The cyclic process involves only ATP formation. The various steps involved are as follows: (a) Photoexcitation of PS I : The reaction center of PS I (chl-a 700, i.e. P 700) is activated on receiving light energy in the form of photons. In this excited state, the chl-a of PS I expels an electron and becomes ionized chl-a. (b) Cyclic electron transfer : The energy rich electrons from the PS I are first accepted by FRS and transferred to Fd. From Fd, the electrons are transferred to Cytochrome. b6 (and not to NADP), Cytochrome. f and then to PC. From PC the electrons are finally accepted by the same ionized chl-a+ of PS I. On receiving the lost electrons, the chlorophyll-a+ comes back to the ground state and can again participate in the process. Figure 4.5 Diagrammatic representation of the cyclic process In this process, the initial donor and the final acceptor of electrons is the same chlorophyll-a of PS I. Hence, the movement of electrons is cyclic. (c) Synthesis of ATP : During the cycle transfer of the energy-rich electrons, there is loss of electron energy at each transfer. It is used at one such transfer for the formation of ATP from ADP and H3PO4 . This is called cyclic photophosphorylation. In the cyclic process, neither PS II or the photolysis of water are involved. Hence, NADPH2 is not formed and oxygen is not evolved. Products of the light reaction : From the foregoing account, it is very clear that the overall light reaction consists of the non-cyclic and the cyclic photophosphorylation reactions. The products of the light reaction (cyclic + non-cyclic) are ATP, NADPH2 and O2. As stated earlier, the oxygen is liberated from the green plants. ATP and NADPH2 are used in the following dark reactions (phase-II) for the reduction of cabon dioxide to form carbohydrates (carbon assimilation). Hence, these products of the light reactions (ATP and NADPH2) are called assimilatory power (Arnon). PinkMonkey Online Study Guide-Biology 4.4 Secondary Processes of Photosynthesis (Biochemical Phase, Dark Reactions) The second part or phase-II of photosynthesis is known as the dark reactions. This is because, the reactions in this phase do not require light. These reactions are thermo-chemical and depend on temperature. The dark reaction involves thermo-chemical reduction of carbon dioxide to form carbohydrates. This was first established by Blackmann (1905), hence it is also called Blackmann reaction. Presence of light is not necessary for the reduction of carbon dioxide. However, the dark reaction utilizes the products of light reaction (i.e., the assimilatory power (ATP and NADPH2) to reduce carbon dioxide into carbohydrates.) All the reactions in phase-II are completed in the stroma of the chloroplast. These are biochemical reactions in which every step is controlled by a specific enzyme. The reactions begin with the fixation of carbon dioxide, involve the utilization of the assimilatory power for the reduction of carbon dioxide and end with the formation of carbohydrate, which is the end product of photosynthesis. The details of the steps involved in the dark reaction (i.e., the complete path of carbon) were worked out by Professor M. Calvin (who received the 1961 Nobel Prize for the same) and hence, the dark reaction came to be called as Calvin cycle. Calvin cycle (C3 pathway) Important features (1) This is the major pathway for the fixation of carbon dioxide in green plants. (2) It represents phase-II, i.e., the dark reaction of photosynthesis. (3) It takes place in the stroma of the chloroplasts. (4) The reactions are enzyme-controlled and temperature dependent. (5) It was discovered by Professor M. Calvin and therefore called the Calvin cycle. (6) After the fixation of carbon dioxide, the first stable compound formed is 3-carbon phosphoglyceric acid (PGA). Hence it is also called the C3 pathway. The important events of the Calvin cycle can be studied under the following heads. (a) The first CO2 acceptor and fixation of CO2 : In the Calvin cycle, a 5-C pentose sugar, ribulose diphosphate (RUDP) acts as the first acceptor of CO2 . On entering the reactions of the Calvin cycle, CO2 first combines with 5-C RUDP (fixation of CO2) to form an unstable and unknown 6-C disphosphate compound. This compound immediately breaks into 2 molecules of 3-C phosphoglyceric acid (PGA). The enzyme carboxy dismutase catalyzes the reaction. Thus, 3-C PGA is the first stable compound formed in Calvin cycle. Hence, it is also called C-3 pathway. Click here to enlarge Figure 4.6 Diagrammatic representation of Calvin cycle Regeneration of RuDP is indicated by broken lines (b) Utilization of assimilatory power (or reduction of PGA). The 3-C PGA then undergoes reduction with the help of the assimilatory power to form 3-C phosphoglyceraldehyde (PGAL). NADPH2 provides the hydrogen and ATP supplies energy for the reduction. Enzyme triosephosphate dehydrogenase catalyzes the reaction. Some molecules of PGAL are converted into another triose phosphate called dihydroxyacetone phosphate (DHAP) in presence of enzyme triose phosphate isomerase. (c) Formation of sugars (end products of photosynthesis) : The 3-C triose phosphates( i.e., PGAL (3-C) and DHAP (3-C)) form 6-C hexose sugar fructose.1, 6 diphosphate in the presence of enzyme aldolase. Fructose diphosphate is then dephosphorylated first to fructose mono-phosphate and then to fructose (6-C) in the presence of enzyme phosphatase. Some fructose monophosphate molecules may be isomerized into glucose monophosphate by enzyme isomerase and then into glucose (6-C). The hexose sugars may be further converted to sucrose (C12H22O11) or to starch (C6H10O5)n and stored in storage cells. (d) Regeneration of the CO2 acceptor, RUDP : The 5-C RUDP is constantly required for the fixation of CO2 in the Calvin cycle. It is regenerated through another chain of reactions. Some molecules of triose phosphates and fructose mono phosphates are used from the Calvin cycle for the formation of RUDP. 4.5 Diversity in Photosynthetic Pathway Various experiments and investigations regarding the fixation of CO2 and the path of carbon during the dark reaction have indicated that there are a number of different pathways for CO2 fixation in green plants. These are 1. C3 Pathway (Calvin cycle) 2. C4 Pathway (H-S pathway or Hatch-Slack cycle) 3. CAM (Crassulacean acid metabolism) 1. The C3 pathway or Calvin cycle is the main pathway and is present in most green plants. Plants which follow the Calvin cycle are called C3 plants. 2. C4 Pathway (or Hatch-Slack pathway) : In some plants, the first stable product, after the fixation of CO2, is a 4-C dicarboxylic acid called oxaloacetic acid (OAA). Such plants are called C4 plants and the path of carbon (dark reaction) is the C4 pathway. It was first noticed by Kortschak (1964) in the photosynthesis of sugarcane leaves. However, details of the C4 pathway (i.e. the first CO2 acceptor, the first stable product, the complete carbon pathway, etc.) were worked out by Hatch and Slack (1966). Therefore, it is known as Hatch-Slack Pathway. C4 pathway is observed in many plants of family Gramineae (e.g. sugarcane, maize, some other monocot and some dicot plants). Anatomical peculiarities of C4 plants : Most of the C4 plants have a characteristic leaf anatomy and dimorphic chloroplasts. For example, (1) The leaf mesophyll consists of more or less compactly arranged cells. (2) It is not differentiated into palisade and spongy mesophyll as it is in C3 plants. (3) The vascular bundles (veins) in the leaf are surrounded by a distinct bundle sheath of radial enlarged parenchyma cells. (4) The chloroplasts in leaf cells are dimorphic( i.e., of two types): (a) Chloroplasts in the mesophyll cells are smaller and possess grana. (b) Chloroplasts in the bundle sheath cells are larger and without grana. This type of leaf anatomy in C4 plants is described as Kranz anatomy. Important steps in Hatch and Slack Pathway The various steps in C4 pathway are completed in two parts and in two different regions in the leaves. (a) First part reactions are completed in the stroma of the chloroplasts in mesophyll cells, and (b) Second part reactions are completed in the stroma of chloroplasts in bundle sheath cells. (a) Part - I (in mesophyll cells) (i) First CO2 Fixation: In the pathway, the first CO2 acceptor is the 3-C phosphoenol pyruvate acid (PEP). CO2 first combines with 3-C PEP to form 4-C OAA (oxaloacetic acid). As OAA is a dicarboxylic acid, this is also known as the dicarboxylic acid pathway. (ii) 4-C OAA may be converted into 4-C malic acid or 4-C aspartic acid and transported to bundle sheath cells. (b) Part - II (in bundle sheath cells) (i) In the chloroplasts of the bundle sheath cells, 4-C malic acid undergoes decarboxylation to form CO2 and 3-C pyruvic acid. (ii) Second CO2 fixation : The CO2 released in decarboxylation of malic acid combines with 5-C RUDP (ribulose diphosphate) to form 2 molecules of 3-C PGA as in the Calvin cycle. Further conversion of PGA to sugars is the same as in the Calvin cycle. (iii) The pyruvic acid produced in decarboxylation of malic acid is transported back to the mesophyll cells. Here it is converted into PEPC and again made available for the C4 pathway. These steps in the Hatch-Slack pathway in the mesophyll and the bundle sheath cells are schematically shown in the figure below. Thus, in the C4 plants, the initial few steps are different (typical of C4 pathway). However, later on the reactions are similar to the Calvin cycle (i.e., C3 pathway). Hence, C4 plants have both C4 and C3 pathways. Moreover, in C4 plants, CO2 fixation (i.e. carboxylation) occurs twice: first in the mesophyll cells (PEP + CO2) and then again in the bundle sheath cells (RUDP + CO2). For this reason, the C4 pathway is also called a dicarboxylation pathway. PinkMonkey Online Study Guide-Biology Click here to enlarge 3. CAM plants (Crassulacean acid metabolism) The CAM plants are mostly succulent xerophytes such as plants of families Crassulaceae, Euphorbiaceae, Cactaceae, etc. The stomata in these plants remain closed during the day. This helps to check transpiration and open them during the cool night for gaseous exchange. These plants are characterized by the presence of Crassulacean acid metabolism (CAM) involving night photosynthetic activity. This is a desert adaptation where stomata must remain closed during the day. The CAM plants have the dark reaction very much similar to the C4 plants ( i.e., they have both C4 and C3 pathways.) However, they differ from C4 plants because, in CAM plants, both pathways occur in mesophyll cells only. Moreover, C4 pathway occurs during the night when stomata are open (night photosynthetic activity) and C3 pathway is completed during day time when the stomata are closed. At night, atmospheric carbon dioxide is taken in through the open stomata. As in the C4 pathway, carbon dioxide combines with 3-C PEP to form 4-C OAA. This is then converted to malic acid and stored in the cells. Thus, organic acids accumulate in the dark. During the day, when stomata are closed and atmospheric carbon dioxide is not available, the 4-C malic acid undergoes decarboxylation to form carbon dioxide and 3-C pyruvic acid. Carbon dioxide thus released enters the Calvin cycle (C3 cycle) to form sugars. 4.6 Significance of Photosynthesis (1) It is the primary source of organic food and food energy (ATP) for all forms of life, either directly or indirectly. (2) Excess sugars produced in photosynthesis are either stored in the form of carbohydrates or used in the biosynthesis of other organic compounds. (3) In any ecosystem, green plants represent the most essential biotic components as they are the primary producers. (4) Photosynthesis helps to purify air and also maintain balance of oxygen and carbon dioxide in the ecosystem. (5) Oxygenic photosynthesis was responsible for converting the totally anaerobic condition on earth into aerobic atmosphere present now. (6) The fossil fuels (e.g. natural gas, coal, petroleum (oil), etc.) are all energy-rich materials of an organic origin. The energy stored in all these fuels is basically solar energy which was trapped and stored during photosynthesis in the geological past. CHAPTER 5 :CELLULAR RESPIRATION 5.0 Introduction All forms of life have one basic common requirement, and that is energy. Energy gives the capacity to do work. Organisms need energy for existence and maintenance of life. The cell is the basic structural and functional unit of an organism and it performs various metabolic and other vital activities. These activities need energy, i.e. biologically usable forms of chemical energy, such as the energy-rich organic compound called ATP (adenosine tri-phosphate). ATP molecules act as energy mediators in cells. For example, ATP undergoes a breakdown (hydrolysis) and provides energy for energy requiring reactions. On the other hand, ATP is synthesized by input of energy made available through some energy-yielding reactions in the cell. Figure 5 The solar energy that is trapped by green plants is converted into chemical energy during photosynthesis and is stored as food energy in carbohydrates and other organic food materials (e.g. fats, oils, organic acids, proteins, etc.) In cell metabolism, these energy-rich organic food materials are oxidized and the stored energy is released as free energy. This is utilized by the cell to perform various cellular activities. Part of the energy is lost as heat. In the cells, the process which supplies energy through oxidation of organic compounds is called cellular respiration. Definition : "Respiration is an intracellular process of oxidation-reduction reactions in which the complex organic food materials are broken down in a step-wise manner to form simpler end products, with the release of energy and carbon dioxide." It is basically an energy releasing and supplying process. The energy released in respiration is of two types : (a) Chemical energy, i.e. ATP. It is utilized for the cellular activities. (b) Heat energy. It is mostly lost. Depending upon the availability of oxygen as an oxidant, respiration is of two types : (1) aerobic respiration, in which oxygen in used in the respiratory break down of organic substrate, and (2) anaerobic respiration, in which oxygen is not used in the respiratory breakdown of organic substrate. 5.1 Ultrastructure and functions of Mitochondrion Mitochondria are the special protoplasmic organelles distributed in the cytoplasm of eukaryotic cells. Mitochondria contain the biochemical machinery involved in cellular respiration which take energy from breakdown of glucose and produce energy-rich ATP molecule which fuel the biochemecal reactions in the rest of the cell. Hence, mitochondria are described as the ‘power houses’ of cells. Mitochondria were first observed by Altmann (1894). Hogeboom (1948) discovered that mitochondria are the site of aerobic respiration. Ultrastructure (Figure 5.1) Mitochondria are microscopic and granular or cylindrical, Figure. 5.1 A mitochondrion in section Ultrastructure of a mitochondrion And are bound by two lipo-protein membranes called outer and inner membranes. These are separated from each other by the inter-membrane space. The outer membrane is smooth, while the inner membrane is highly folded. The folds are called cristae, and project into the inner space of the mitochondrion and appear finger-shaped in the section. The internal space of the mitochondrion (enclosed within the folded inner membrane) is filled with dense proteinaceous material and is called the matrix. It contains small ribosomes and mitochondrial DNA (DNA) invited in the replication of mitochondria. The matrix also contains all the enzymes required for the Kreb’s cycle reactions during the second phase of aerobic respiration. Structure of cristae membrane: The inner surface of the cristae membrane (i.e. the surface towards the matrix) is covered with numerous (infinite) stalked particles. These are called F1 particles, elementary particles or sub units. These particles project into the matrix. Each F1 particle has three parts, viz., the head piece, the stalk and the base piece. The respiratory chain is situated in the cristae membrane where the F1 particles are present. The chain consists of enzymes and co-enzymes which form the electron transport system (ETS) in the mitochondrion. These enzymes and co-enzymes of the ETS act as the electron acceptors in the aerobic respiration reactions oxidative phosphorylation). Functions of mitochondria (1) These are the sites of the phase-II reactions of aerobic respiration. (2) Kreb’s cycle reaction takes place in the matrix. (3) Terminal oxidation (utilization of O2 and formation of water) and oxidative phosphorylation (formation of ATP) take place in cristae membrane. (4)ATP molecules formed in aerobic respiration are stored in mitochondria and are supplied for cellular activities. Hence, mitochondria are the energy supplying power houses of cells. 5.2 An Overview of Cellular Respiration Respiration is of two types : aerobic and anaerobic respiration. (1) Aerobic respiration : "When free or molecular oxygen participates in the respiratory breakdown of organic substrate, it is called aerobic respiration." (In this process, free molecular oxygen acts as the final electron acceptor.) Aerobic respiration is represented by the following chemical equation. C6H12O6 + 6O2  6CO2 + 6H2O + Energy (2) Anaerobic respiration : "When the respiratory breakdown of organic substrate takes place without participation of free molecular oxygen, it is called anaerobic respiration." (In this process, free or molecular oxygen is not the final electron acceptor.) Anaerobic respiration is represented by the following chemical equation. C6H12O6  2C2H5OH + 2CO2 + Energy The process of respiration is completed in two phases. Reactions in Phase I are called glycolysis and are common to both types of respiration. Reactions in Phase II depend upon whether O2 is utilized or not. 5.3 Glycolysis (E.M.P. pathway = Embden - Meyerhof - Parnas Pathway) Important features (1) Glycolysis represents phase I of respiration. (2) This pathway is common to both aerobic and anaerobic respiration. (3) These reactions are completed in the cell cytoplasm (cytosol). Therefore, glycolysis is also called cytoplasmic respiration. (4) Glycolysis involves a series of reactions in which a molecule of 6-C glucose is broken down in a step-wise manner into two molecules of 3-C pyruvic acid. (5) Each step (reaction) is controlled by a specific enzyme and is reversible. (6) Reactions in the glycolysis are anaerobic in nature,( i.e. they do not require molecular oxygen). 6-C Glucose is the most commonly used organic substrate for respiratory breakdown because (i) It is most readily available. (ii) It is soluble and can be easily transported and supplied.. Reactions of glycolysis (EMP pathway) involve : (A) Phosphorylation of glucose (preparatory phase), isomerization to fructose-6-phosphate, and phosphorylation to fructose-I, 6-biphosphate. (B) Cleavage of Fructose 1, 6 diphosphate to 2 3-C PGAL. (C) Formation of 3-C pyruvic acid (end product of glycolysis). Various steps (intermediate reactions) in glycolysis are as follows. (A) Phosphorylation of glucose PinkMonkey Online Study Guide-Biology The initial steps in glycolysis involve the phosphorylation of glucose into an unstable fructose 1, 6-diphosphate for easy breakdown. This is called the preparatory phase of glycolysis during which 2 ATP are used. The reactions are as follows. (1) In the first step, 6-C glucose is converted into glucose-6-phosphate. One ATP is used in the reaction. (2) The next step involves isomerization of glucose 6-phosphate into Fructose 6-phosphate. (3) Fructose-6-phosphate is then phosphorylated to fructose-1, 6-diphosphate. This reaction utilizes one ATP. Thus, two ATP are used up in the preparatory phase. (B) Cleavage of fructose-1, 6 - diphosphate (4) The molecule of 6-C fructose-1, 6-diphosphate undergoes cleavage to produce two molecules of 3-C triose phosphates. One is 3-phosphoglyceraldehyde (3-PGAL) and the other is dihydroxy acetone phosphate (DHAP). The two triose phosphates can isomerize into each other. However, further reactions in glycolysis utilize only PGAL. Therefore, DHAP is first converted into PGAL. Thus, in all, two molecules of 3-PGAL are formed from the cleavage of one fructose-1, 6- diphosphate. (C) Formation of 3-C pyruvic acid Further reactions in glycolysis result in the conversion of 3-C PGAL into 3-C pyruvic acid through the following intermediate steps: (5) 3-PGAL is converted into 1, 3 diphosphoglyceric acid (1, 3 diPGA). This is an oxidation and phosphorylation reaction. It takes place in the presence of inorganic phosphate (P.) and co-enzyme NAD (nicotinamide adenine dinucleotide). The reduced co-enzyme NADH2 is formed in the process. (6) In the next step, 1, 3-diPGA undergoes dephosphorylation to form 3-phosphoglyceric acid (3-PGA). Phosphate removed from each diPGA is transferred to by ADP to form ATP. Two ATP molecules are formed at this step. (7) 3-PGA is transformed into 2-PGA. (8) In the next step, 2-PGA is converted into 2-phosphoenol pyruvic acid (2-PEP) with the loss of water (dehydration). (9) In the final step of glycolysis, 2-PEP is dephosphorylated to form 3-C pyruvic acid, which is the end product of glycolysis. The reaction produces 2 ATP. Thus, when a molecule of 6-C glucose undergoes the reactions in glycolysis (EMP pathway), the overall process may be represented as follows. However, 2#ATP are used up in the preparatory phase of glycolysis. Therefore the net gains of glycolysis are: Phase-II of Aerobic Respiration Phase-II of aerobic respiration comprises a series of enzymic reactions in which 3-c pyruvic acid (the end product of glycolysis) is broken down step-wise to form the end products of aerobic respiration, (i.e. CO2 , H2 O and ATP energy), inside the mitochondria. Phase-II involves the following two main sets of reactions: (1) The T.C.A. cycle (2) Terminal oxidation and oxidative phosphorylation (E.T.S. and the redox reactions). 5.4 The T.C.A. Cycle (Tricarboxylic#Acid#Cycle) The T.C.A. (Tricarboxylic acid) cycle represents the major set of reactions during Phase-II of the aerobic respiration. It is also called the citric acid cycle or Kreb’s cycle. These reactions involve the final breakdown of pyruvic acid to form the end products of aerobic respiration. The T.C.A. cycle reactions take place in the matrix of the mitochondria. Pyruvic acid is first converted into a 2-C compound called acetyl co-enzyme-A (Acetyl #Co-A). Click Here To Enlarge (i) Formation of 2-C Acetyl Co-A This is the initial step in Phase II of aerobic respiration. The reaction involves oxidation and decarboxylation of 3-C pyruvic acid to form 2-C acetyl Co-A. It in the cell cytoplasm and requires the presence of co-enzyme-A (Co-A) and NAD. It is catalyzed by complex enzymes. In this process, carbon dioxide is released and the reduced co-enzyme NADH2 is formed. The 2-C acetyl Co-A formed in the cytoplasm then enters the mitochondria and takes part in the Kreb’s cycle reactions (the TCA cycle). Thus, acetyl Co-A is the connecting link between glycolysis (in the cytoplasm) and Kreb’s cycle (in mitochondria). (ii) T.C.A. cycle (Kreb’s cycle) The Kreb’s cycle reactions occur in the matrix of mitochondria. All enzymes required for these reactions are present in the matrix. Each step is controlled by a specific enzyme and is reversible. The various steps in the T.C.A. Cycle are as follows: (1) Each molecule of 2-C acetyl Co-A that enters the T.C.A. cycle first combines with 4-C oxalo acetic acid (OAA), and a 6-C Citric acid is formed. One molecule of H2O is used in the reaction. Thus, the first product in Kreb’s cycle is citric acid, hence it is also called the citric acid cycle. As citric acid is a tricarboxylic acid (with 3-COOH groups), it is also called tricarboxylic acid (TCA) cycle. (2) In the next step, 6-C citric acid is first converted into 6-C -aconitic acid (deletion of H2O) and then into 6-C isocitric acid (addition of H2O). (3) The next reaction involves the oxidation of isocitric acid (by removal of hydrogen) to form 6-C oxalo succinic acid. NADH2 is formed in the process. (4) Decarboxylation of 6-c Oxalo succinic acid results in the formation of 5-c  -Ketoglutaric acid with the liberation of carbon dioxide. (5) -Ketoglutaric acid (5-C) then undergoes oxidation (by removal of hydrogen) and decarboxylation to form 4-C succinyl Co-A. The reaction is highly complicated and takes place in the presence of Co-A and NAD. NADH2 is formed and carbon dioxide is released. (6) 4-C Succinyl Co-A is hydrolyzed to succinic acid (4-C) in the next step. One molecule of H2O is used and Co-A is regenerated. The reaction is exergonic. Energy released is used for the formation of GTP (guanosine triphosphate) from GDP and inorganic phosphate. Subsequently, ATP is formed when GTP reacts with ADP GTP + ADP  ATP + GDP (Thus, there is the direct formation of one ATP when 5-C acid is converted to 4-C acid.) (7) In the next step, 4-C Succinic acid is oxidized (by removal of hydrogen) to 4-C fumaric acid in the presence of co-enzyme FAD (flavin adenine dinucleotide). A reduced FADH2 is formed. (8) Fumaric acid (4-C) is converted to another 4-C acid, malic acid, by the addition of H2O. (9) In the final step of the TCA cycle, 4-C Malic acid is oxidized (by removal of hydrogen) to 4-C Oxaloacetic acid. NADH2 is formed in the process. Thus, OAA is regenerated in the last step. It can combine withanother 2-c Acetyl Co-A to form Citric acid and participate in the TCA cycle again. During various steps of the Kreb’s cycle, oxidation of substrate takes place by the removal of an electron hydrogen ion from substrate. It is accepted at each step by a suitable co-enzyme such as NAD or FAD to form a reduced co-enzyme molecule, NADH2 or FADH2, respectively. The chart of the Kreb’s cycle indicates the result of the participation of only one molecule of pyruvic acid. It should be noted that 2 pyruvic acid molecules are formed at the end of glycolysis. Therefore, the final analysis of the Kreb’s cycle involving 2 pyruvic acids may be summarized as follows. (i) Total number of reduced co-enzyme molecules formed = 8#NADH2 and 2#FADH2 (ii) Total number of ATP formed directly (when 5 - C acid is converted to 4 - C acid) = 2#ATP (iii) Total number of CO2 molecules released = 6#CO2 (iv) Total number of H2O molecules utilized = 6#H2O 5.5 Electron Transport Chain This is the final part of the phase-II of aerobic respiration. As stated earlier, in respiration, oxidation of the substrate occurs by dehydrogenation (i.e., removal) of hydrogen atoms (2H) from the substrate. These are mostly accepted by NAD to form reduced co-enzyme NADH. In the aerobic respiration of a molecule of glucose (6-C), a total of, 10 NADH2 are formed, (2NADH2 in glycolysis + 8 NADH2 in Kreb’s cycle). At one step in Kreb’s cycle, hydrogen is accepted by FAD to form FADH2. total, 2#FADH2 are formed in the aerobic respiration of each glucose. Each molecule of reduced co-enzyme thus formed in aerobic respiration (glycolysis and Kreb’s cycle) is finally oxidized by the free molecular oxygen through a process called terminal oxidation. This involves participation of the respiratory chain, also called electron transport system (ETS). Click Here To Enlarge The respiratory chain (or the ETS) is present in the inner membrane of mitochondrion (i.e., in the cristae membrane). It consists of various enzymes and co-enzymes which act as electron carriers. The hydrogen ions (and the electrons of hydrogen) from the oxidized substrate pass through the ETS and finally react with free molecular oxygen to form water. The electron flow from the substrate(NADH2 or FADH2)to O2 (through ETS) is the source of energy for the formation of ATP. This is called oxidative phosphorylation. Transfer of hydrogen and electrons through ETS As stated earlier, the most common acceptor in respiration reactions is NAD. Thus, stet is transferred to Co-Q via-FMN (Flavin mononucleotide). At one step in Kreb’s cycle, hydrogen is accepted by FAD. From FAD, it is transferred to Co-Q. At Co-Q, the hydrogen undergoes ionization, i.e. it splits into electrons and protons. 2H  2e- + 2H+ Therefore, from Co-Q onwards, only the electrons are transferred through the ETS along the chain of the electron carrying molecules. The protons (H+) are transferred across the inner membrane into the intermembrane space. The first electron acceptor in the chain is cytochrome. b. It accepts the electrons from Co-Q and transfers them first to cytochrome C1, and then to cytochrome C1. From cytochrom C1, electrons are accepted by cytochrome oxidase. In the final step, cytochrome oxidase donates electrons to the free molecular oxygen. In other words, oxygen acts as the last electron acceptor in the respiratory chain (aerobic respiration). Oxygen receives 2 electrons through the ETS and 2 protons directly from the aqueous medium to form one molecule of water. 1/2O2 + 2 e- + 2H+ H2O (Terminal oxidation) Utilization of oxygen at the end of the ETS is the final step in aerobic respiration and is called terminal oxidation. fields marked (*) are mandatory Oxidative phoshorylation : As mentioned earlier, the electron flow from the substrate to oxygen through the ETS is the source of energy for the formation of ATP. Transfer of electrons by these enzymes results in the HT being pumped into the intermembrane space from oxidative phosphation. The buildup of HT in the intermembrane space yield a concentration gradient, such that HT flow back into the stroma through the membrane-bound protien enzymes, ATP synthase. The flow of HT through the synthase provides energy for the synthase to convert ADP to ATP. There is a progressive decrease in the level of electron energy as they flow along the Chain. This is given out as free energy. There are three sites in the ETS at which enough free energy is released. At each site, this energy is utilized to form ATP from ADP and iP (i.e. inorganic phosphate = H3PO4). Formation of ATP using the energy released during terminal oxidation is called oxidative phosphorylation. As can be seen in Figure 5.4 for the respiratory chain, each molecule of reduced co-enzyme NADH 2 produces 3#ATP through the ETS, while each FADH2 yields 2ATP through the ETS. The ETS reactions are oxidation-reduction (Redox) reactions. During the transfer of hydrogen/electrons through the chain, each carrier molecule is alternately reduced and oxidized. For example, when a carrier accepts hydrogen/electron it gets reduced. On the other hand, the reduced carrier is oxidized when it transfers the hydrogen/electron to the next carrier in the chain. There is a net flow of electrons through the ETS from more electronegative redox potential (i.e. from NADH2 or FADH2) to the more electropositive redox potential (i.e. to oxygen). Click Here To Enlarge Overall result of aerobic respiration Complete oxidation of one molecule of 6-C glucose through aerobic respiration (involving glycolysis, Kreb’s cycle, ETS, etc.) results in — (a) release of 6#CO2 (b) Utilization of 6#O2 and (c) Formation of 6#H2O. However, 6H2O are used up in Kreb’s cycle (involving 2 pyruvic acid molecules).  12 H2O formed - 6H2O used = 6H2O net gain Anaerobic respiration : An intracellular-oxidation of organic substrate (e.g. glucose) without utilization of free molecular oxygen (in the absence of oxygen). The oxidation is incomplete and results in the formation of either ethyl alcohol or lactic acid, carbon dioxide and energy (2#ATP). Important features 1. Complete process of anaerobic respiration takes place in the cell cytoplasm only. 2. Mitochondria are not involved. 3. Oxygen is not used. 4. Kreb’s cycle reactions, ETS or oxidative phosphorylation are not involved. 5. Phase-I consists of the same reactions of glycolysis (EMP pathway). found in aerobic respiration . 6. Phase-II consists of decarboxylation and reduction reactions converting the pyruvic acid into either ethyl alcohol with the evolution of Carbon Dioxide. The whole process may be summarized as follows : (1) Further anaerobic breakdown of pyruvic acid involves following two steps. After adding up the equations (1) + (2) + (3), the final overall equation for the anaerobic respiration is obtained as follows: The 2 NADH2 gained in glycolysis are used in the reduction of acetaldehyde to ethanol. 5.6 Fermentation Fermentation is of different types and takes place under anaerobic conditions mostly in saprophytic microorganisms like certain bacteria and fungi. However, it may also take place in higher organisms under certain conditions. The two most common types of fermentation are (1) alcoholic fermentation and (2) lactic acid fermentation. (1) Alcoholic fermentation : the type of fermentation in which ethyl alcohol is the main end product .This is very common in yeast (unicellular fungus) and also seen in some bacteria. Yeast cells release enzymes called zymase complex which bring about the fermentation. The reactions are similar to anaerobic respiration. (2) Lactic acid fermentation : The type of fermentation in which lactic acid is the end product. It is carried out by some bacteria (e.g. lactic acid bacteria), and also by animals (muscle glycolysis in animals, under oxygen deficiency, results in the formation of lactic acid this is whay we experience in muscle cramps, or "Charley horse"). Lactic acid bacteria can ferment milk sugar lactose (C12H22O11) to lactic acid. The process is extracellular. This brings about curdling of milk. Commercial application of fermentation : There are various kinds of fermentation carried on by different microorganisms. Many of these result in highly useful end products. Such useful microbial activity is used on large industrial scale to obtain the useful end products for the benefit of mankind. Some of the industrial products of the microbial fermentation activities are (a) antibiotics (b) vitamins (c) industrial alcohol (d) bakery products (e) some dairy products (f) tanning of leather (g) curing of tea and coffee (g) lactic acid (h) butric acid, (i) acetic acid etc. 5.7 Significance of Respiration (1) It is the energy releasing and supplying process in all living organisms. (2) It converts food energy into metabolically usable forms of chemical energy. (3) Respiration releases energy in a controlled and step-wise manner as a result of which most of the released energy is properly utilized for the cellular activities (e.g. metabolism, cell division, growth, etc.) Only a small part of energy is lost as heat. (4) In other words, respiration conserves energy very efficiently. Out of the total 673 Kcal energy released per molecule of glucose, 456 Kcal is conserved as 38 ATP molecules. (5) Various intermediate products of glycolysis and Kreb’s cycle are used for biosynthesis of other complex organic compounds in cell metabolism. (6) Carbon dioxide, required for photosynthesis by green plants, is replenished by carbon dioxide released in respiration. Similarly, oxygen required for respiration is replenished by oxygen released in photosynthesis. Thus, photosynthesis and respiration are complementary to each other and together help to maintain the balance of oxygen and carbon dioxide in nature. (7) Fermentation, which is a type of anaerobic respiration, is helpful in the industrial production of various useful products such as alcohol, antibiotics, vitamins, organic acids, bakery and dairy products, tanned leather, etc. SUMMARY - RESPIRATION (1) It is a characteristic process of every living cell. (2) It is an intracellular oxidation of organic compounds with release of carbon dioxide and energy. (3) In respiration, substrate is enzymatically broken down in a step-wise manner. (4) Phase-I is glycolysis (EMP pathway). It is completed in cell cytoplasm. These reaction involves further breakdown of pyruvic acid to form the end products of respiration. (6) Pyruvic acid metabolism can be aerobic or it can be anaerobic. (7) Phase-II of aerobic respiration is completed in mitochondria. The oxidation of substrate is complete and end products are 6CO2, 6H2O and 38 ATP for every molecule of glucose. (8) Phase-II of anaerobic respiration is completed in cytoplasm only. The end products are ethyl alcohol, carbon dioxide and energy. (9) Fermentation is an anaerobic respiration. It is commonly found in saprophytic microorganisms like bacteria and fungi. End products are sometimes very useful. Alcoholic fermentation and lactic acid fermentation are the two most common types. CHAPTER 6 : CELL DIVISION 6.0 Introduction The cell is the structural and functional unit of life. New cells arise from the preexisting ones. The process by which new cells are formed from the pre-existing cells is called cell division. In unicellular organisms, the cell division directly produces two individuals and thus, represents a type of reproduction (multiplication). In multicellular organisms, there are two types of cells; the somatic cells or the body cells (which form the body of the organism) and the reproductive cells (such as gamete-producing cells and-spore producing cells). The somatic cells divide by mitosis (equational division) and the reproductive cells divide by meiosis (reduction division). Mitosis helps in growth and development of an organism. Meiosis produces gametes in sexual reproduction and spores in asexual reproduction. All eukaryotic organisms, plants as well as animals, show great regularity as well as similarity in the cell divisions. Generally, a cell increases in size before dividing. This is mainly due to the synthesis of proteins, RNA and DNA. This is followed by division of the cell nucleus (karyokinesis) and finally the division of the cell cytoplasm (cytokinesis). All these events collectively form a cell cycle. PinkMonkey Online Study Guide-Biology 6.1 The Cell Cycle Click here to enlarge Figure 6.1 The Cell Cycle Definition : The cell cycle, also called generation time, is the sequence of events in the life of a cell. The cell cycle starts immediately after one cell division and ends with the completion of the next division. The cell cycle of eukaryotic cells is classified into (1) interphase (2) karyokinesis and (3) cytokinesis (Howard and Pelc, 1953). (1) Interphase : It is the preparatory phase during which the cell is metabolically very active and prepares itself for the division. Three important processes occur in interphase, viz. (a) replication of chromosomal DNA, synthesis of RNA and the basic nuclear proteins (histones) (b) synthesis of energy rich compounds which provide energy for mitosis and (c) in animal cells, division of the centriole. On the basis of DNA synthesis, interphase is subdivided into following three stages. fields marked (*) are mandatory G1 (Gap1) : It starts immediately after the previous division. Therefore G1 is called gap phase or first growth phase. Synthesis of proteins and RNA takes place. The cell grows in volume. S phase (Synthesis phase) : It is the period during which DNA synthesis occurs, i.e. replication of chromosomal DNA takes place. This results in doubling of the chromosomal threads. G2 (Gap 2) : It is the last part of interphase and occurs just before the new cell division. Hence G2 is called pre-division gap phase or second growth phase. It begins after completion of DNA synthesis in the S phase and ends when new division (karyokinesis) commences. During G2, synthesis of proteins and RNA takes place and the nuclear volume increases. (2) Karyokinesis : It is the division of the parent nucleus into daughter nuclei. (3) Cytokinesis : This is the division of the cytoplasm. It occurs after karyokinesis and divides the parent cell into daughter cells. Karyokinesis and cytokinesis together form the M phase (i.e. cell division). The total duration of a cell cycle varies greatly in different organisms and under different conditions, e.g. it may be as short as 20-30 minutes in the bacterium Escherichia coli or may take 12-24 hours as in most higher plants and animals. The time required for completion of each phase in the cell cycle varies greatly. In general, actual cell division (M-phase) occupies only a short span of the total cycle while the major span is occupied by the interphase. Normally, time duration of S and G2 phases is more or less equal. The duration of G1 is longer in cells which do not divide frequently, and is very short in cells which divide repeatedly in close succession. G0 stage : It is a stage during which cell cycle is arrested for an indefinite period. Significance of cell cycle 1. In multicellular organism, the 'cycling type' of cells (dividing cells) help in reproduction, growth and replacement of dead cells, healing of wounds, etc. 2. The interphase allows time for synthesis and growth of the dividing cell. 3. Properly controlled and regulated cell cycle results in normal and proportionate growth of organisms. 4. Loss of control over the cell cycle can lead to cancerous growth. Cancerous cells : For some reason, in some cells, if the control over the cell cycle is lost, then they start behaving abnormally. These cells divide repeatedly in an uncontrolled manner at abnormally high rates. As a result, they do not get enough time for growth and differentiation. Such cells mass together and form tumors in the body which may lead to cancer. The cancerous or malignant cells are those which show continuous and uncontrolled growth through repeated cell divisions at abnormally high rates. In the cancerous tissue, the metabolism of cells is disturbed and abnormal. The cells continue to move and crawl (grow) over one another, i.e., they do not show contact inhibition. The cancerous growth may remain localized or may spread to other parts of the body. 6.2 Mitosis Mitosis is the characteristic division of the body cells, hence called somatic division. It can be studied in the meristematic cells in root and stem tips of plants. Figure 6.2 Various stages in the mitosis of a plant cell Definition : "Mitosis is an equational division, dividing the mother cell into two daughter cells which are identical to each other and also to the original mother cell in every respect. In mitosis, the chromosomes of the mother cell are duplicated and distributed equally to the two daughter cells." The mitotic cell cycle consists of interphase and M-phase. Interphase is sub-divided into G1, S and G2 phases (as described earlier in the cell cycle). The M-phase consists of karyokinesis followed by cytokinesis. Interphasic nucleus : The nucleus increases in volume during interphase. At this stage, the nuclear membrane and nucleolus are prominently visible. The chromosomes appear to form a continuous network (nuclear reticulum or chromatin network) of very fine threads. DNA replication has taken place (S-phase) and chromosomes have doubled. Interphase ends as the karyokinesis begins. Karyokinesis : It involves a series of changes within the nucleus. This is a continuous process but, for convenience, it has been divided into four phases. These are (1) Prophase (2) Metaphase (3) Anaphase and (4) Telophase. The main features of the nuclear division during each phase are summarized below. (1) Prophase : During early prophase, the chromatin network becomes visible as it condenses into separate threads or chromosomes. At this stage, each chromosome appears as a very fine, long single thread, the chromonema and is it described as the monad. The nucleus envelope and nuclear are prominently visible. As the prophase progresses, chromosomes become shorter and thicker (due to the condensing of their coils). In each chromosome, the chromonema splits lengthwise into two identical threads or chromonemata (dyads). These are coiled round one another. Chromosomes become more distinct. Each chromonema becomes short, thick and is called a chromatid. At this stage, each chromosome is shorter, thicker and consists of two identical sister chromatids joined together by a spherical body called a centromere (kinetochore). By the end of prophase, the nuclear envelope and nucleolus disappear completely. The chromosomes remain distributed in the nucleoplasm. (2) Metaphase : Metaphase begins with the formation of a bipolar spindle body in the region of nucleoplasm (i.e. center of the cell). It consists of numerous spindle fibers. These are fine thread-like structures formed by the organization of proteins called tubulin into microtubules. There are two types of fibers in the spindle (a) Continuous fibers which extend from pole to pole and (b) Chromosomal fibers which extend from pole to the center (equator of the spindle). The chromosomes move and get arranged in a plane along the equator of the spindle. This results in the formation of the equatorial plate (metaphasic plate). The centromere of each chromosome in the plate is connected with both the poles by the chromosomal fibers. (3) Anaphase : During early anaphase, the centromere of each chromosome divides longitudinally into two. As a result, each chromosome is now completely divided into two identical halves (sister chromatids) called daughter chromosomes. The centromere of each daughter chromosome remains connected to the pole on its respective side by a chromosomal fiber. During late anaphase, the two groups of daughter chromosomes are pulled away from each other and start moving towards the opposite poles. Most probably, this movement is caused by the shortening of the chromosomal fibers. In each group, chromosomes appear 'V' or 'L' shaped as the centromeres are pulled towards the poles and the chromosomal arms trail behind. (4) Telophase : This is the last phase in karyokinesis. The two sets of daughter chromosomes reach the opposite poles. The chromosomes again become long and thin. A new nucleolus is organized. A Nuclear envelope is formed around each set of chromosomes. In other words, a daughter nucleus is organized at each pole in the parent cell. Each daughter nucleus has the same number of chromosomes as that of the mother cell. The spindle fibers also dissolve and disappear gradually. The two daughter nuclei are identical in structure and characters. They are also exact copies of the original parent nucleus. Cytokinesis : The division of the cell cytoplasm is called cytokinesis. It starts towards the end of telophase. In plant cells, cytokinesis usually begins with centrifugal formation of a cell plate along the equatorial plane which is followed by a new wall formation. This divides the mother cell into two equal daughter cells. In animal cells, cytokinesis takes place by the cleavage constriction of the cell cytoplasm. It begins peripherally and progresses centripetally. Figure 6.3 Aster and the mitotic apparatus in an animal cell Astral and Anastral mitosis. In the cell of higher animals and lower plants, the centriole is present just outside the nucleus. It plays a definite role in mitosis. During interphase, the centriole divides into two. The two centrioles then move to the opposite poles during prophase and later on help to organize the bipolar spindle body during the early metaphase. From each centriole at the pole, radiating fibers extend into the cytoplasm. These are called astral rays and form the aster (Figure 6.3). Astral mitosis : "The mitosis in which asters are formed from the centrioles is called astral mitosis." Anastral mitosis : The centriole is absent in the cells of the higher plants and some animals. In such cells, the astral rays and the asters are not formed at the poles of the spindle body during the metaphase. "The mitosis in which asters are not formed at the poles of the spindle body is called anastral mitosis." It is common in the higher plants. Mitotic apparatus : It is called achromatic figure and is jointly formed by the centrioles, asters and the spindle body. Significance of Mitosis (1) It is an equational division which maintains equal distribution of the chromosomes after each cell cycle. (2) The resulting daughter cells inherit identical chromosomal material (hereditary material) both in quantity (i.e., number) and quality (i.e., genetic make up or characters). (3) Mitosis maintains a constant number of chromosomes in all body cells of an organism. (4) It helps to maintain the equilibrium in the amount of DNA and RNA contents of a cell, as well as the nuclear and cytoplasmic balance in the cell. (5) Dead cells are replaced by newly formed cells through mitosis. It thus helps in the repair of the body. (6) It helps asexual reproduction, growth and development of organisms. SUMMARY - MITOSIS (1) It can take place in haploid as well as diploid cells. (2) Both the daughter cells formed through mitosis receive similar characters and number of chromosomes as that of the mother cell. (3) The original structure of the chromosomes remains unchanged in both the daughter nuclei. (4) Hence, it is an equational division and the resulting daughter cells are identical qualitatively and quantitatively. 6.3 Meiosis In the sexually reproducing organisms, two important phenomena regulate the number of chromosomes in the life cycle. These are meiosis and fertilization. Meiosis is the reduction division in which the diploid (2n) number of chromosomes is reduced to haploid (n) during gamete formation (or spore formation). Whereas, in fertilization, the two haploid gametes fuse to form a diploid zygote. In this way, the diploid condition is restored again in the life cycle. Click here to enlarge Figure 6.4 Meiosis-I (M-I, First meiotic division) Definition : "Meiosis is a special type of division characteristic of reproductive cells in which the diploid number of chromosomes is reduced to haploid in the daughter cells. In meiosis, chromosomes divide once while the nucleus (and in some cases the cytoplasm also) divides twice. Four haploid daughter cells result from one diploid mother cell. These differ from each other as well as from the mother cell." Homologous chromosomes : Sexually reproducing diploid organism develops from a diploid zygote (2n). The zygote is formed when haploid (n) male and haploid (n) female gametes fuse at the time of fertilization. Thus, the diploid individual receives two sets of chromosomes; one through the male gamete (paternal set) and the other through the female gamete (maternal set). For every chromosome in the paternal set, there is a similar looking chromosome present in the maternal set. Such similar chromosomes from paternal and maternal sets called homologous chromosomes. In this way, in both the sets, all chromosomes have their homologues. The meiotic cell cycle : It consists of the interphase, karyokinesis and cytokinesis. Interphase : It consists of G1, S and G2 phases and involves changes as described earlier in this chapter. The interphase nucleus : The nucleus enlarges during interphase. The chromosomes are not clearly visible being very thin and long threads. However, nucleus envelope and the nuclear are prominent. Karyokinesis in meiosis : It consists of two complete nuclear divisions : Meiosis-I and Meiosis-II. The time interval between M-I and M-II is called interkinesis. It is a reduction division during which a diploid nucleus divides into two haploid nuclei through separation of homologous chromosomes. Chromosomes are not duplicated in M-I. PinkMonkey Online Study Guide-Biology Figure 6.5 (A) Various stages in Meiosis--I The various events in M-I are classified into Prophase-I, Metaphase-I, Anaphase-I and Telophase-I. The important features in each phase are described in brief. Prophase-I : This is the longest phase in meiosis and involves some very important events. Prophase-I is sub-divided into five stages (a) Leptotene (b) Zygotene (c) Pachytene (d) Diplotene and (e) Diakinesis. (a) Leptotene (Leptonema) : Chromosomes become visible as long slender threads bearing numerous bead-like nucleosomes (chromomeres). These are arranged in a linear fashion along their lengths. The nuclear envelope and the nucleolus are prominently visible. The thin chromosomes are scattered in the nucleus. (b) Zygotene (Zygonema) : This phase is characterized by the pairing of homologous chromosomes. The homologous chromosomes (one paternal and the other maternal) from the two sets are attracted towards each other and form pairs. In each pair, the two homologues lie parallel to each other all along their lengths. This pairing is called synapsis (or syndesis or synizesis). During zygotene, chromosomes become shorter, thicker and more distinct. (c) Pachytene (Pachynema) : This is the most important stage in meiosis in which a recombination of characters (genes) takes place through a phenomenon called crossing over. The chromosomes become shorter, thicker and more distinct. Each chromosome has two sister chromatids joined by a centromere. Thus, each pair of homologous chromosomes at this stage consists of four chromatids (tetrad) and is called a bivalent. The paternal and maternal chromatids in each homologous pair are non-sister to one another. The non-sister chromatids are twisted round each other in relational coiling and take part in the crossing over. Figure 6.5 (B) Crossing over Crossing over : Crossing over is an important genetic phenomenon. It takes place between any two non-sister chromatids of a homologous pair. Crossing over consists of a mutual exchange of equal quantity (segments) of chromosomal material between two non-sister chromatids. It involves the following events: (a) The relationally coiled non-sister chromatids, which are taking part in crossing over, break simultaneously at the identical points (i.e. at homologous points); (b) the broken segments are of equal lengths; (c) the segments again join with the chromatids; (d) however, there may be an exchange of the segments between the non-sister chromatids, i.e. the maternal segment may join with the paternal chromatid and the paternal segment may join with the maternal chromatid. This is called crossing over; (e) In this process, the genes located on the segments are exchanged between the two chromatids. (f) Thus, crossing over results in the recombination of genes (characters); (g) Crossing over does not take place between sister chromatids. Significance of recombination (crossing over ) : (i) The gametes produced through meiosis receive a new combination of characters (genes). (ii) Therefore individuals with new combination of characters are produced in each generation. (iii) This forms the genetic basis for variations and plays important role in evolution. (d) Diplotene (Diplonema) : Two important events begin during diplotene; (I) the repulsion of homologous chromosomes and (II) terminalization. I. Repulsion : In each pair, the homologous chromosomes start repelling each other. As a result they begin to separate and uncoil. However, the non-sister chromatids involved in the cross-overs are held together at the points of crossing over. Each such points is called a chiasma where the separating chromatids form a cross-like #(x) figure. A homologous pair can show one or more chiasmata. II. Terminalization : The separation and uncoiling of the homologues begins at the centromeres and proceeds towards the ends. This causes progressive shifting of the chiasmata towards the ends of the chromatids. This is called terminalization of chiasma. (e) Diakinesis : This is the last phase of Prophase-I. Chromosomes are still in the pairs and in contact with each other by terminal chiasma. The chromosomes become shorter, thicker and more prominent. By the end of the Prophase-I, the nucleolus and nuclear envelope disappear completely and the pairs of chromosomes are seen distributed in the nucleoplasm. Metaphase - I : There is formation of a bipolar spindle body. It has two types of spindle fibers; (a) Continuous fibers extending from pole to pole and (b) Chromosomal fibers extending from pole to the equator of the spindle body. The homologous chromosomes, still in pairs, move towards the center of the spindle. These are arranged along the equatorial plane in such a way that the maternal homologues of all the pairs are facing one pole while the paternal homologues are facing the opposite pole. The chromosomal fibers connect the centromeres of all the homologues to the pole on their respective side. Each chromosome has only one centromere. Figure 6.5 (C) Various stages in Meiosis - II PinkMonkey Online Study Guide-Biology Figure 6.6 Simultaneous cytokinesis by cleavage constriction Centriole and aster : In animals, a centriole is present outside the nucleus. It divides into two during prophase-I and later on helps in the organization of the bipolar spindle as well as the asters (as in mitosis). Anaphase-I : The homologous chromosomes are pulled away from each other and finally separate completely (terminalization is completed). In other words, the sets of maternal and paternal chromosomes separate (segregate) and start moving towards opposite poles. This is due to the shortening of the chromosomal fibers. Telophase-I : The two sets reach the opposite poles. The chromosomes, each with two chromatids and one centromere, become thin and long. A nucleolus is organized. Each nucleus is haploid as it has received only one set of chromosomes. Hence M-I is called reduction division. Interkinesis : The time interval between M-I and M-II is called interkinesis. Meiosis-II (M-II or Second meiotic division) Second meiotic division is similar to mitosis i.e. it is an equational division in which there is duplication of the chromosomes. The two nuclei formed after M-I divide during M-II and produce four haploid nuclei. The various events in M-II are classified into Prophase-II, Metaphase-II, Anaphase-II and Telophase-II. Both the nuclei divide simultaneously and all the changes during each phase are similar in both. Prophase-II : The chromosomes again become shorter, thicker and distinct. Each chromosome has two sister chromatids joined by a centromere. The nuclear envelope and the nucleolus disappear by the end of Prophase-II. Metaphase-II : The bipolar spindle body is formed. Chromosomes are arranged along the equators in such a way that their chromatids are facing the opposite poles. The centromere of each chromosome is connected with both the poles by chromosomal fibers. In animals, centriole is present outside the nucleus and participates in the formation of bipolar spindle and asters. Anaphase-II : During early anaphase-II, the centromere of each chromosome divides longitudinally into two. Therefore each chromosome is divided into two halves (chromatids) or daughter chromosomes. During late anaphase-II, the two sets of daughter chromosomes are pulled away from each other and move towards the opposite poles. Telophase-II : The sets of chromosomes reach the opposite poles and a new nucleus is organized at each pole. In all, four daughter nuclei are formed. Each nucleus has half the number of chromosomes as compared to the original mother nucleus. These nuclei also differ from each other in the structure and characters of chromosomes. This is because of the crossing over during prophase-I. Cytokinesis : This is the division of the cell cytoplasm. It follows the nuclear division and may be successive or simultaneous. Figure 6.7 Zygotic Meiosis in some algae 6.4 Comparison Between Mitosis and Meiosis MITOSIS MEIOSIS 1. Occurs in somatic cells. 1. Occurs in reproductive cells. 2. Consists of only one nuclear division. 2. Consists of two nuclear divisions M-I and M-II. 3. Cytokinesis takes place only once. 3. May take place only once (simultaneous type) or twice (successive type). 4. Involves division of chromosomes. 4. Involves separation of homologous chromosomes in M-I and division of chromosomes in M-II. 5. Dividing cells can be haploid or diploid. 5. Dividing cells are diploid. 6. Does not involve either pairing of homologous chromosomes or crossing over. 6. Pairing of homologous chromosomes and crossing over occur during Prophase-I. 7. Two daughter cells are formed. 7. Four daughter cells are formed. 8. Number of chromosomes present in the mother cell is maintained in both the daughter cells. Therefore it is an equational division. 8. Diploid number of chromosomes is reduced to haploid in each daughter cell. Therefore it is a reduction division. 9. Original characters of the chromosomes are maintained in the daughter cells. 9. Chromosomal characters are altered due to "crossing over" causing recombination of genes. 10. Daughter cells are similar to each other and also to the original mother cell. 10. Daughter cells differ from each other as well as from the original mother cell. 11. Helps in growth and body repairs. 11. Helps in the sexual reproduction and regulation of chromosome number in the life cycle of sexually reproducing organism. SUMMARY : MEIOSIS (i) Meiosis occurs in reproductive cells only. (ii) It occurs in diploid cells. (iii) The karyokinesis of meiosis consists of two complete nuclear divisions called first meiotic division (Meiosis-I or M-I) and second meiosis division (Meiosis-II or M-II). (iv) M-I is reduction division involving separation of homologous chromosomes. (v) M-II is equational division like mitosis which involves duplication of chromosomes. (vi) The four daughter nuclei are haploid due to the reduction division (M-I). Moreover, they differ from each other in the characters of chromosomes due to ’crossing over’ during Prophase-I of M-I. (vii) Cytokinesis may be successive or simultaneous dividing the diploid mother cell into four haploid daughter cells. CHAPTER 7 : CLASSICAL OR MENDELLIAN GENETICS Definition : "Genetics is the study and understanding of the phenomena of heredity and variation." The term ’genetics’ was first coined by Bateson in 1906. In Latin, it means genesis or origination of organisms. Heredity is the transmission of characters from one generation to the next, i.e., from parents to their offspring. Because of heredity, the offspring resemble their parents. Heredity is the essence of self-reproduction. It is owing to heredity or self-reproduction that we commonly observe the phenomenon of "like begets like", i.e., a seed of mango develops into a mango tree, or the offspring of a dog is a puppy, and that of human beings is a human being only. Variations are the visible differences between the parents and the offspring, or between two offsprings of the same parents. An offspring receives all the characters from its parents and yet, an offspring is never an exact copy of its parents. Similarly, no two offsprings of the same parents are identical (exception : identical twins). In order to understand the principles of inheritance and to discover the reasons for the variations, Mendel began a systematic search during the second half of the nineteenth century. For this, Mendel experimented on garden pea plants and performed various crosses with great precision, care and objectivity. He carefully counted the plants resulting from such crosses and kept statistical records of successive generations with the accuracy of a mathematician. 7.1 Gregor Mendel Gregor Johann Mendel was born on July 22, 1822 in Moravia, Austria. He had his early education in a monastery in Brunn, Austria (now Brno in Czechoslovakia) and later studied science and mathematics at the University of Vienna. He graduated in 1840. Mendel returned to the monastery in Brno as a monk. He worked as a teacher of physics and natural science in a Higher Secondary School of Brno during 1854 to 1868. He was appointed abbot of the monastery in 1868 and held this post untill his death. Mendel carried out his legendary experiments on garden pea plants in the monastery garden from 1857 to 1865. He had a clear perspective and worked on the experiments with precision and thoroughness. He published his research paper containing his observations and conclusions in 1866 in the annual proceedings of the Natural History Society of Brunn. These conclusions are now known as Mendel’s Laws. This work is a classic in biology for its elegance and simplicity and ranks amongst the most outstanding biological contributions of all times. But unfortunately, this work failed to attract the attention of the biologists of that time. Hence, it went ignored for 35 years. One of the possible reasons for such neglect was the inability of the biologists of that time to understand and appreciate the statistical approach adapted by Mendel. Thus, Mendel was left bitterly disappointed, and died an unrecognized death in 1884. Sixteen years after Mendel's death, in 1900, Hugo de Vries (Holland), Karl Korrens (Germany) and Von Tschermark (Austria) independently arrived at similar conclusions as those of Mendel. De Vries rediscovered the research paper of Mendel and it was published again in 1901. The experiments on heredity of plants and animals since then have confirmed that Mendel's laws of heredity are applicable to other organisms as well. They form the basis of modern genetics. Hence, Mendel is called The Father of Genetics. ********** 7.2 Mendel’s Experiments on Sweet Pea Selection of the material : Mendel selected garden sweet pea (Pisum sativum) for his hybridization experiments for of the following reasons : (i) Plants are annual and easy to cultivate. (ii) Peas have many distinct, well-defined and easily observable morphological characteristics (traits). (iii) Flowers are bisexual and naturally self-fertilizing, but they can also be easily cross-fertilized. (iv) The offspring of cross-fertilized plants are fertile. (v) Flowers are sufficiently large for easy emasculation (removal of stamens) and artificial cross-pollination. Selection of characters (traits) : Mendel selected 14 different varieties of the pea and grouped them into seven pairs. Each pair was considered for a specific trait (characteristic) such as flower color or seed shape or stem length, etc. The two members of each pair showed contrasting forms of the chosen trait, ,e.g., in a pair selected for stem length, one variety had a tall stem (6-7 feet tall) while the other had a dwarf stem . These seven pairs of contrasting traits are shown in Table 1.1. Table 1.1 : Showing seven pairs of contrasting characters selected by Mendel BIOBIOBIO Sr. No. Characters Contrasting pairs (Allelic pairs) (Dominant) (RecBIOe) 1. Form of seed Round (R) Wrinkled(r) 2. Color of cotyledons Yellow(Y) Green(y) 3. Color of seed coat Colored(C) White(c) 4. Form of pod Inflated (I) Constricted(i) 5. Color of pod Green(G) Yellow(g) 6. Position of flower Axial(A) Terminal(a) 7. Height of plant (Length of stem) Tall(T) Dwarf(t) Nature and procedure of the experiments : Mendel had very clear concepts of what he was doing and what requirements were necessary if he had to arrive at the conclusions accurately and successfully. He realized the necessity of: (i) using pure breeding parent plants; (ii) considering only one character at a time during the breeding experiments; (iii) always keeping the generations separate; (iv) and using statistical and mathematical principles to compute the obtained results properly. Mendel conducted his experiments in three stages. . Stage-1 : It involved selecting a pair of parents with contrasting characters and obtaining each parent plant in pure condition ,i.e,. breeding true for the characters selected. For example, Mendel ensured that the plant selected for round seeds produced only round seeds on self-fertilization and the plant selected for wrinkled seeds produced only wrinkled seeds . Such pure, true-breeding parents were obtained by Mendel through repeated self fertilizing, generation after generation. Stage -2 : It involved crossing of the selected parents. Of the pair, one plant was used as the male parent and the other as the female parent. Pollen from the male was dusted on the stigma of the female parent for cross-pollination. Mendel conducted reciprocal crosses also. For example : in one cross, the round seeded variety was used as the male parent and the wrinkled seeded variety as the female parent, while in the reciprocal cross of the same parents, the wrinkled variety was used as the male parent and the round seeded variety as the female parent. This may be represented as follows : Male Parent Female Parent Cross - I Rounded seeded Wrinkled seeded Reciprocal Cross Wrinkledd seeded Rounded seeded Such a cross between two parents representing contrasting forms of a single character is called monohybrid cross and the offspring is called a hybrid. The hybrid represents the first filial generation or F1 generation. Stage - 3 : In the third stage, Mendel allowed each F1 hybrid to self-pollinate and produce the next, i.e., Second Filial generation or F2 generation. Mendel conducted a similar type of hybridization experiment separately for each of the seven pairs. He meticulously maintained a complete record of the actual number of each type of offspring in every generation (i.e., data of qualitative as well as quantitative results). Mendel observed that in each of these crosses, all the F1 hybrids resembled only one parent, while the character of the other parent was not seen in the F1 hybrid. For example, in a cross between round X wrinkled type, the F1 were all round seeds only. The wrinkled character was not seen. The character which appears in the F1 hybrid was termed dominant and the other as recessive by Mendel. Thus, in each of the seven pairs, one form is dominant and the other is recessive (See Table 1.1). The F2 progeny showed presence of both parental forms which always appeared in the ratio of 3 dominants : 1 recessive. This 3:1 F2 ratio was termed as the monohybrid ratio. Reasons for Mendel’s success: i. Mendel concentrated on the results of one trait at a time. ii. When the behavior of one trait was established, only then he considered two characters together. iii. He conducted a large number of crosses (2000-3000) to eliminate the chance factor and to obtain a valid and accurate explanation iv. Most of all, he actually counted the number of offsprings of each category and maintained accurate records for each generation in each experiment. v. However, luck played a major role in his success (though Mendel did not know this fact) in the selection of pea plants as well as in the selection of those particular seven pairs of contrasting characters. Because, luckily for Mendel, in each pair, one form of the character is completely dominant over the other. Moreover, these seven characters are present on seven different chromosomes in the pea plant. However, Mendel was unaware of this fact. In nature, there are several instances of incomplete dominance also. In such cases, the hybrid shows haracter intermediate between the two parents. For example, in snapdragon, when a parent plant with red flowers is crossed with another having white flowers, the F1 hybrids show pink flowers. Parents Red Flower X White Flower  F1 hybrid Pink Flowers 7.3 Terminology Used 1. Factor : A particle or unit in the organism which is responsible for the inheritance and expression of a particular character. 2. Gene : Mendel’s factor is now known as gene. A gene is a particular segment of a DNA molecule which determines the inheritance and expression of a particular character. 3. Alleles or Allelomorphs : Two or more alternative forms of a gene are called alleles or allelomorphs. For example in pea, the gene for producing seed shape may occur in two alternative forms: round (R) and wrinkled (r). Round and wrinkled forms of the gene are alleles of each other. Alleles occupy same locus on homologous chromosomes. 4. Dominant : Of the two alternating forms (allomorphs) of a trait, the one which appears in the F1 hybrid is called the dominant trait (Dominant Allele). 5. Recessive : Of the two alternating allomorphs of a trait, one which is suppressed (does not appear) in the F1 hybrid is called the recessive trait (recessive allele). 6. Genotype : The genetic make-up or genic constitution of an individual (which he/she inherits from the parents ) is called the genotype, e.g., the genotype of pure round seeded parent will be RR. 7. Phenotype : The external (morphological) appearance of an individual for any trait or traits is called the phenotype, e.g. for seeds, round shape or wrinkled shape is the phenotype. 8. Homozygous : An individual possessing (receiving from parents) identical alleles for a trait is said to be homozygous or pure for that trait, e.g. plant with RR alleles is homozygous for the seed shape. A homozygous always breeds true for that trait. 9. Heterozygous : An individual receiving dissimilar alleles for a trait is said to be heterozygous or impure for that trait, e.g. a plant with Rr alleles is heterozygous for the seed shape. Heterozygous is also called a hybrid. 10. Parent generations : The parents used for the first cross represent the parent (or P1) generation. 11. F1 generation : The progeny produced from a cross between two parents (P1) is called First Filial or F1 generation. 12. Inbreeding : When the individuals of a progeny (e.g. F1 generation) are allowed to cross with each other, it is called inbreeding. 13. F2 generation : The progeny resulting from self hybridization or inbreeding of F1 individuals is called Second Filial or F2 generation. 14. Monohybrid cross : The cross between two parents differing in a single pair of contrasting characters is called monohybrid cross and the F1offspring as the hybrid(heterozygous for one trait only). 15. Monohybrid ratio : The phenotypic ratio of 3 dominants : 1 recessive obtained in the F2 generation from the monohybrid cross is called monohybrid ratio. 16. Dihybrid cross : The cross between two parents in which two pairs of contrasting characters are studied simultaneously for the inheritance pattern. The F1 offspring is described as dihybrid or double heterozygous (i.e. with dissimilar alleles for two characters). 17. Dihybrid ratio : The phenotypic ratio obtained in the F2 generation from a dihybrid cross is called dihybrid ratio. In Mendelian experiments, this ratio is 9:3:3:1. 18. Homologues or Homologous chromosomes : The morphologically similar looking chromosomes in a diploid cell (one chromosome coming from the male parent and the other from the female parent) are called homologous chromosomes. They have identical gene loci bearing alleles. 19. 7.4 Law of Dominance 20. Unit characters : On the basis of his experiments and observations, Mendel concluded that the characters from parents to offsprings are transmitted in the form of some kind of hereditary units or particles called factors (now called genes). These factors determine the characters in the individual. For each factor representing a character there are two alternate forms called alleles. Mendel represented the allelic factors by appropriate alphabets. In each of the seven pairs selected by him, the dominant allele was represented by the capital alphabet and its recessive allele by the same but smaller alphabet (See Table 1.1) (e.g., Round seed = R, Wrinkled seed = r). 21. Table 1.2 Showing dominant and recessive characters in some plants and animals Examples Dominant Recessive Appearance of F1 hybrids PLANTS Sorghum (i) Pearly grain Chalky grain Pearly (ii) Awnless Awned Awnless Maize Full Endosperm Shrunken endosperm Full Rice Starchy endosperm Glutinous endosperm Starchy ANIMALS Rabbit Black coat white coat Black Mice Normal body size dwarf Normal Man (i) Brown eyes blue eyes Brown (ii) Short stature tall short 22. Law of dominance : In a hybrid union, the allele which expresses itself phenotypically is the dominant allele while the other allele which fails to express itself phenotypically is the recessive allele. The hybrid individual shows phenotypically only the dominant character. 23. The law of dominance is often described as Mendel’s first law of inheritance. 24. Dominance is seen in various characters in many plants and animals (See Table 1.2). But this is not of universal occurrence. There are many cases where dominance is incomplete or absent. 25. 7.5 Monohybrid Ratio 26. The phenotypic ratio of different types of individuals occurring in the F2 generation of the monohybrid cross is called the monohybrid ratio. In the Mendelian monohybrid experiments, this ratio was always 3:1( i.e., 75% is dominant and 25% is recessive). 27. For example, for one of his monohybrid crosses, Mendel selected true breeding homozygous parents showing contrasting characters for the height of the plant. He performed the experiment in three stages as described. The result obtained is shown in Figure 7.2 below. 28. 29. Figure 7.2 Tall x Dwarf Monohybrid cross showing the result obtained by Mendel According to Mendel, each sexually reproducing diploid organism possesses two 'factors' (genes) for each character; one factor is received (inherited) from male parent and the other factor is inherited from the female parent. These two factors for a particular character are called alleles or allelomorphs. When an offspring receives identical alleles from both parents, it is called homozygous, pure or true breeding for the character. On the other hand, when the offspring receives dissimilar alleles from two parents, it is called heterozygous, impure or a hybrid for that character. 30. The pure tall is crossed with the pure dwarf parent. According to Mendel, when the diploid individual (having both the alleles/factors) produces gametes, each gamete receives only one of the two factors/alleles of a character. No gamete receives both the alleles of a character. Thus, pure tall parent produces only one type of gametes, i.e. all the gametes possess only (T) factor for tallness. Similarly, all gametes produced by pure dwarf are of one type only and possess (t) factor. The fusion of (T) and (t) gametes (fertilization) results in the F1 offspring with (Tt) genotype. It is heterozygous or a hybrid. Its phenotype (external appearance) is tall because the factor for tallness (T) is dominant and expresses itself. The factor for dwarfness (t) is present in F1 hybrid but, being recessive, does not express itself (remains hidden). 31. Mendel allowed hybrids to self-fertilize or inbreed to raise F2 generation. The F1 hybrid has dissimilar alleles (Tt). Therefore, it will produce two types of gametes in equal number i.e. 50% gametes will have (T) factor and remaining 50% will have (t) factor. Since the pea flower is bisexual, it produces both male and female gametes. Thus, the F1 hybrid will produce two types of male gametes (T) and (t) in equal numbers. Similarly, there will be two types of female gametes (T) and (t) in equal numbers. During self fertilization, the fusion between these male and female gametes occurs at random. For example, each type of male gamete has an equal chance to fuse with either (T) or (t) female gametes and vice-versa. This chance fusion, between two types of male and two types of female gametes will produce a maximum of four combinations (genotypes) in the F2 progeny. This is shown in the checker board or Punnet’s Square (Figure 7.2). These four combinations fall into three categories of the genotypes as follows : 1 (TT), 2 (Tt) and 1 (tt) i.e. 32. 1 Pure tall : 2 Hybrid tall : 1 Pure dwarf 33. (TT) 2(Tt) (tt) 34. This is called 1:2:1 genotypic ratio of a monohybrid cross. However, phenotypically, the progeny shows 3 Tall and 1 Dwarf individuals (75% Dominant and 25% recessive characters) or 3:1 ratio. This is called monohybrid ratio or phenotypic ratio of a monohybrid cross. The result indicates that even though the recessive character was not seen in hybrid, it was present there and reappeared in pure form in 25% individuals of the progeny. This result also enabled Mendel to conclude that the two factors (alleles) come together in the hybrid but do not mix or fuse with each other. They simply remain together without diluting or contaminating each other. In other words, factors maintain their purity. As the gamete always receives only one factor (alleles) for a trait, it is always pure for the character. This is called purity of gametes. 7.6 Law of Segregation Mendel performed monohybrid crosses separately for each of the seven pairs of contrasting characters. In each such cross, he got similar results as described for the Tall x Dwarf cross. On the basis of the results obtained for the monohybrid crosses, Mendel formulated the law of segregation, also called Mendel’s second law of heredity. The law states that when a pair of alleles is brought together in hybrid union, the members of the allelic pair remain together without mixing, diluting or altering each other and separate or segregate from each other when the hybrid forms gametes. Thus, according to this law, when the hybrid tall (Tt) in the above experiment forms gametes, the factors T and t shall separate (segregate) and enter different gametes. As a result, the hybrid shall form two types of gametes; those with (T) factor and an equal number with (t) factor. Since each gamete will be pure for tallness or for dwarfness, the law is also known as the law of the purity of gametes. 7.7 Dihibrid Ratio Mendel established the law of segregation through monohybrid crosses involving only one pair of alleles at a time. However, in an organism, so many characters are present together and each character is represented by a pair of alleles. So, Mendel wanted to know, "Whether one pair of alleles affects or influences the inheritance pattern of other pairs of alleles in the organism or, each pair is inherited independently as if in a monohybrid cross?" To find the answers to these questions, Mendel performed dihybrid crosses. A cross between two pure, true breeding parents in which the inheritance pattern of two allelomorphic pairs is considered (studied) simultaneously is called a dihybrid cross. The phenotypic ratio obtained in the F2 generation of a dihybrid cross is called the dihybrid ratio. A dihybrid is an individual which is double heterozygous (i.e. heterozygous for two pairs of alleles). Mendel’s dihybrid cross : Mendel considered two characters in the pea plants simultaneously, e.g. cotyledon color (yellow / green) and seed shape (round / wrinkled). He selected one variety of pea which was pure (true breeding) for yellow round seeds and crossed it with another variety pure for green wrinkled seeds. All the F1 of this cross were yellow round seeds (green and wrinkled characters did not appear in F1 hybrids). Mendel anticipated this because, from the earlier monohybrid experiments he knew that yellow was dominant over green and round was dominant over wrinkled. P Yellow Round X Green Wrinkled  F1 Yellow Round Similarly, a cross between yellow wrinkled and green round also produced only yellow round seeds in F1 P Yellow Wrinkled X Green Round  F1 Yellow Round Moreover, the reciprocal crosses (interchanging male and female parents) also gave the same results. Further, when the F1 dihybrids were self-pollinated or inbred, the F2 generation was always the same, e.g. Click here for enlarge The analysis of F2 progeny showed four different kinds of phenotypes. These were (1) Yellow round (2) Yellow Wrinkled (3) Green round and (4) Green Wrinkled in the ratio of 9:3:3:1 respectively. It will be seen that out of these four types, two show the same combinations as the parents whereas the remaining two are new combinations (recombinants). The phenotypic ratio of 9:3:3:1 in the F2 progeny of a dihybrid cross is called the dihybrid ratio. Same results were obtained by Mendel using other pairs of alleles in different combinations. On the basis of these experiments and their results, Mendel formulated the law of independent assortment of characters and explained it as follows. 7.8 Law of Independent Assortment "When a dihybrid (or a polyhybrid ) forms gametes, (i) each gamete receives one allele from each allelic pair and (ii) the assortment of the alleles of different traits during the gamete formation is totally independent of their original combinations in the parents In other words, each allele of any one pair is free to combine with any allele from each of the remaining pairs during the formation for the gametes This is known as the Law of Independent Assortment of characters. It is also referred to as Mendel’s third law of heredity. Explanation of the law of independent assortment: The principle of independent assortment was explained by Mendel with the help of a dihybrid cross involving characters of cotyledon color (yellow / round) and seed shape (round / wrinkled). Mendel crossed a true breeding variety of pea having yellow cotyledons (YY) and round seeds (RR) with another true breeding variety having green cotyledons (yy) and wrinkled seeds (rr). The complete result of this cross is shown in the Figure 7.3 Thus, the yellow round parent has the genotype (YYRR) and the green wrinkled parent (yyrr). Since each parent is homozygous for both characters (color and shape), each will produce only one type of gametes. The (YYRR) parent will produce all (YR) type gametes and the (yyrr) will produce all (yr) type gametes. All F1 dihybrids resulting from the fusion of these gametes would be double heterozygous with (YyRr) genotype and appear yellow round. This indicated that in the dihybrid cross also in each pair, the alleles behaved exactly in the same way as in the monohybrid cross. Both the dominants (Y and R) expressed themselves in F1 while both the recessive alleles (y and r ) remained hidden. Types of gametes formed by F1 dihybrid: According to Mendel, during gamete formation by the F1 dihybrid, the alleles in both pairs Y-y and R-r first segregate from each other (Law of segregation). Each pair segregates independently of the pair. Then the alleles enter the gametes. A gamete can receive only one allele from each pair, i.e. Y or y and R or r. Similarly, a gamete that receives a factor (gene) for color must also receive factor for shape (a factor for every character must be present in each gamete). Thus, a gamete that receives Y for color may receive R or r for shape. This would result in (YR) and (Yr) types of gametes. Similarly, a gamete that receives y for color may receive R or r for shape. This would give (yR) and (yr) types of gametes. In other words, the F1 dihybrid would produce four types of gametes (YR), (Yr), (yR) and (yr) in equal proportions. This is the principle of independent assortment of characters. There will be four types of male gametes and four types of female gametes formed by the F1 dihybrid. During self-fertilization or inbreeding of the F1 dihybrids to produce an F2 generation, these male and female gametes can form maximum to dihybrid unions as shown in the Punnet’s Checker-board (Figure 7.3). These can be grouped into four kinds on the basis of phenotypic appearance. i.e. yellow round, yellow wrinkled, green round and green wrinkled in the ratio of 9:3:3:1 respectively. This is called the Phenotypic dihybrid ratio. In Figure 7.3, the 16 squares of the checker board are serially numbered for convenience. The squares represent the 16 possible combinations of the gametes which might result. The genotypes and the phenotypes of the F2 offspring are shown in the sixteen squares. A count of these squares shows the four kinds of phenotypes and their ratio in the F2 generation. Phenotypes Square numbers Total Yellow Round 1,2,3,4,5,7,9,10,13 ... 9 Yellow Wrinkled 6,8,14 ... 3 Green Round 11,12,15 ... 3 Green Wrinkled 16 ... 1 In the actual dihybrid cross of the above type, Mendel obtained a total of 556 seeds in the F2 generation. The actual number of seeds of each type was as follows. Phenotype Actual number obtained Yellow Round (Parental Combination) 315/556 Yellow Wrinkled (New Combination) 108/556 Green Round (New Combination) 101/556 Green Wrinkled (Parental Combination) 32/556 This gives approximately 9:3:3:1 ratio. Thus the actual results agree completely with the theoretical expectations. Method of calculating inheritance of each individual character (gene) Multiplication rule states that the probability of two or more independent events occurring together is the product of their individual probabilities. In the above mentioned dihybrid cross, the gene for shape (round/wrinkled) and the gene for color (yellow/green) are present together but are sorted independently (law of independent assortment). Calculation of F2 phenotypes in a dihybrid cross The multiplication rule applies to the probabilities of the phenotypes. For each gene, the monohybrid phenotypic ratio is 3:1 or ¾ : ¼ Thus, for the color gene the monohybrid phenotypic the ratio is 3 yellow : 1 green or ¾ yellow : ¼ green. And, for the shape gene, it is 3 Round :1 wrinkled or ¾ Round : ¼ wrinkled. Therefore, in the dihybrid cross, the total probability of the F1 phenotypes will be the product of the two monohybrid ratios. This is calculated as follows: Gene for Gene for Probabilities shape color of Phenotypes 7.9 Test Cross or Back Cross Test cross is a simple method devised by Mendel to verify the genotype of the F1 hybrid. When the F1 hybrid is crossed with the homozygous recessive parent, it is called a test cross. Since, the F1 is crossed back with one of the parents, it is also called a back cross. Test cross is also used for checking the correctness of Mendel’s law of segregation (using a monohybrid test cross) and the law of independent assortment of characters (using a dihybrid test cross). For example, (1) Monohybrid test cross : In a monohybrid cross of Tall x Dwarf, the F1 are all tall (Figure 1.1). Let us see what happens when this F1tall is test crossed with the homozygous recessive parent i.e. Dwarf with (tt) genotype. We aim to check and verify two things (i) determine the genotype of F1 Tall and (ii) check the correctness of the law of segregation. Thus, F1 tall is back crossed (test crossed) with the homozygous recessive dwarf parent and the progeny of the cross examined. We know that the recessive dwarf with (tt) genotype will produce only one type of gametes (i.e., all with (t) only). However, as regards the F1 tall, there can be two possibilities: a. If the F1 tall is homozygous with (TT) genotype, it shall produce only one type of gametes (i.e. all with (T) only). As a result, the progeny of the cross should be all tall. (T) x (t) = (Tt) Tall. b. If, on the other hand, the F1 tall is heterozygous with (Tt) genotype and, if Mendel's law of segregation of characters is correct, then the F1 should produce two types of gametes, (T) and (t) in equal proportion. The recessive dwarf parent produces only (T) type of gametes. The resulting test cross progeny should be 50% Tall and 50% Dwarf or in 1:1 ratio as follows: The results obtained in the actual test cross experiments completely agree with the theoretical expectations. Thus it is proved that F1 Tall is a heterozygous dominant (monohybrid) with (Tt) genotype and that the alleles segregate during gamete formation. (2) Dihybrid test cross : In the dihybrid cross of yellow round X green wrinkled the F1, dihybrid is a double heterozygous yellow round with (YyRr) genotype. It is test crossed with the double homozygous recessive parent,( i.e. green round with (yyrr) genotype). We aim to test the correctness of Mendel's law of independent assortment of characters. If the principle of independent assortment is correct, then as Mendel explained, the (YyRr) dihybrid should produce four types of gametes: YR, Yr, yR and yr in equal proportions. The recessive parent (yyrr) shall produce only one type of gametes i.e. yr type. It is expected that the maximum possible chance combinations between these gametes should produce four kinds of phenotypes in the ratio of 1:1:1:1 as follows. The actual numbers of these four types of offspring obtained in one of Mendel's test crosses were: Yellow round = 55, Yellow Wrinkled = 49, Green Round = 51 and Green Wrinkled = 52. This gives an approximate 1:1:1:1 ratio as per the theoretical expectations and thus, confirms the law of independent assortment of characters. Significance of back cross in plant breeding 1. It is a rapid method of improving a variety of crop. 2. It is an easier and quicker method of obtaining a desirable trait in a pure homozygous condition (true breeding trait). 3. Back cross is also use frequently in hybridization experiments because of its simple ratio. Moreover, this needs the analysis of fewer progeny. 7.10 The Concept of "Factor" The period in which Mendel conducted his experiments and drew his conclusions about the principles of heredity and variations, the world was totally ignorant about ’genes’ (as the units of heredity) and the ’chromosomes’ (as the carriers of hereditary units). Mendel believed that some definite hereditary units or particles represent the characters. He called these hereditary units ’factors’. Thus, tallness is due to a factor for tallness and dwarfness is due to the factor for dwarfness. Since tallness or dwarfness are two expressions or forms of the same character,(i.e. height), it is also understood that their factors also are two forms of the same gene. Such two factors representing different forms of the same character (or its gene) are described as alleles. We now know these ’factors’ as genes. The term ’gene’ was first coined by Johansen in 1909. Chromosomes were discovered by Strasburger in 1875. Now it is established that genes are definite units of the DNA molecule of each chromosome. Genes are present in a linear fashion on the chromosomes. Each chromosome carries several genes ’linked’ together in ’linkage groups.’ Hence, genes are not inherited individually as was thought by Mendel but are passed on to the next generation as ’linkage groups’ (i.e., as whole chromosomes). This fact alters Mendel’s principle of independent assortment. However, the principle of segregation remains unchanged even today. The studies on genetics have shown that genes influence certain biochemical reactions which in turn are responsible for the production of characters in organisms. However, a single character is not (always) produced by a single gene as believed by Mendel. On the contrary, several genes influence the same basic biochemical reaction and are responsible for the expression of a single character. SUMMARY : MENDEL’S LAWS OF INHERITANCE (1) Genetics is the study of the principles of heredity and variations. (2) Hybridization experiments using garden pea plants by Mendel, and his conclusions and explanations regarding the nature of inheritance of each character are commonly known as Mendelism. (3) Mendel established the phenomena of dominance and recessiveness through monohybrid experiments. (4) Mendel formulated the law of segregation of characters on the basis of the results of monohybrid crosses. (5) The law of independent assortment of characters was formulated by Mendel on the basis of the results of dihybrid crosses. (6) The monohybrid cross in Mendelian experiments gives a phenotypic ratio of 3 : 1 and genotypic ratio of 1:2:1 in the F2 generation. (7) The dihybrid cross gives the phenotypic ratio of 9 : 3 : 3 :1 and genotypic and genotypic dihybrid ratios are the products of their respective monohybrid ratios. (9) Mendel devised the test cross (back cross) method to verify the genotype of F1 hybrid as well as for testing correctness of his laws of heredity. (10) Mendel established the concept of ’factor’ which is now known as gene. CHAPTER 8:GENES AND MOLECULAR GENETICS 8.0 Introduction Mendel (1865) was the first to put forward clearly the idea of hereditary units, and referred to them as ’factors’. These were later named genes. In 1903, Sutton and Bovery postulated the chromosomal theory of inheritance and stated that the genes were located in the chromosomes. This was subsequently confirmed by the works of Morgan and others and is now accepted universally. Thus, it was established that the chromosomes are the carriers of the genetic material. The chemical of which the genes are composed is called the genetic material. Quest for the identification of the genetic material The nucleic acids were discovered by Meischer in 1869. In later years, it was also established that chromosomes are made up of proteins (histones and protamines) and nucleic acids (DNA). Now, the question was, which of these actually represented the genetic material? Was it the proteins or the DNA? The process of identification of genetic material began in 1928 and was successfully concluded in 1952. It was conclusively established that it is the DNA that contains the genetic material and not the proteins in the chromosomes. This fact could be established only through some brilliantly conceived and designed novel experiments. The most notable among these are: i. Experiments of Griffith (1928): Through his experiments, Griffith discovered the phenomenon of transformation (a special type of genetic recombination) in which the non-virulent strain of the bacterium Diplococcus pneumoniae was transformed into the virulent strain. Griffith’s experiments started the process of the identification of the genetic material. ii. Avery, Macleod and Mc Carty (1944) : repeated, elaborated and modified the transformation experiments of Griffith. They provided the first clear evidence the DNA is the genetic material and is responsible for the transformation in bacteria. They also gave evidence of the chemical nature of genes. iii. Lederberg and Zinder (1952) : confirmed the identity of DNA as the genetic material through a bacteriophage (vector), and the subsequent incorporation of the segment in the recipient DNA thereby causing transformation. iv. Hershey and Chase (1952) : confirmed that at least in the bacterial virus called T2-phage, DNA is the only genetic material. This fact has been universally accepted since then. v. Frankel - Conrai and Singer (1957) : established that in some viruses, RNA functions as the genetic material (and not the DNA). Table 8.1: Some additional historical events Year Scientists Discovery/Event 1909 Johannsen Coined the term "gene" 1924 Feulgen Showed that chromosomes contain DNA 1953 Waston and Crick Double stranded helical model for structure of DNA molecule 8.1 Packaging of Hereditary Material Structure of nucleus (A) in a prokaryotic cell and (B) in an eukaryotic cell As stated earlier, chromosomes are the carriers of the hereditary material. In cells, chromosomes are located in the nucleus. In prokaryotic cells (e.g., bacteria, cyanobacteria, etc.), organized nuclei are not present. As a result, the hereditary material occurs in the cell cytoplasm as a nucleoid (Figure 8.1-A) without the nuclear envelope. (a) Eukaryotic nucleus (Figure 8.1-B): In eukaryotic cells (e.g., all higher plants and animals), a well organized nucleus is present. It is bounded by a double membrane nuclear envelope with trilaminar structure. There are pores in the envelope. Internally, the nucleus is filled with nucleoplasm (nuclear sap) that is acidophilic and clear. The interphasic nucleus (i.e. the nucleus which is not in the stage of division) usually shows the presence of one dark, spherical body called nucleolus. The nucleoplasm also contains nuclear reticulum or chromatin network. It consists of very fine, long chromatin fibers. These represent the chromosomes at the interphasic stage. They become short, thick and distinct during cell division. fields marked (*) are mandatory (b) Structure of chromatin (Figure 8.2): The chromosomes are composed of nucleoprotein called chromatin. The chromatin fiber appears to have a structure like a ‘string of beads.’ According to the nucleosome-solenoid model proposed by Komberg and Thomas (1974), the beaded string is made of repeating units called nucleosomes (Figure 8.2A). Each nucleosome is a bead-like particle about 60 Ao high and 110 Ao wide. Click here for enlarge Figure 8.2. Nucleosome - solenoid model for the structure of chromatin In the nuclesome, the DNA double helix is wound around the core of eight histone molecules (octamer). The segments of DNA joining the ‘beads’ are called linker DNA. Each linker DNA has an average of one molecule of a histone protein (H1) attached to it. The thin, long and "beads-on-string" chromatin fiber is condensed and packed into a short and thick chromosome (metaphase chromosome) because of further coiling and "super coiling", wherein (1) the string of beads condenses and coils to produce a 100 Ao thick nucleosome fiber (2) the nucleosome fibre then supercoils to produce a 300-350 Ao thick solenoid fiber. A solenoid represents the structure of chromatin fiber in the metaphase chromosome. 8.2 The Structure of DNA Deoxyribonucleic nucleic Acid (DNA) is a highly complex megabiomolecule. The long chain molecule is formed of repeating units called nucleotides. Hence, it is described as the polynucleotide molecule. It consists of two polynucleotide antiparallel strands which are spirally coiled round each other along their lengths (Watson and Crick, 1953). (a) Chemical Components of DNA : The highly complex DNA molecule is composed of only three types of chemical components. These are (i) deoxyribose sugar, (ii) a phosphate, and (iii) nitrogen containing organic bases. i. Deoxyribose sugar : The sugar present in the DNA molecule is called deoxyribose sugar and hence the nucleic acid is called deoxyribonucleic acid (DNA). It is a pentose sugar (with 5 carbon atoms) having a pentagonal ring structure (Figure 8.3) ii. Phosphate (Figure 8.3) : The phosphate in the DNA is present as phosphoric acid (H3PO4). It has three reactive (-OH) groups of which two are involved in the formation of the sugar-phosphate backbone of each DNA strand. iii. The nitrogen-containing organic bases These are heterocyclic compounds containing nitrogen in their rings and therefore called nitrogenous bases. DNA contains four different bases called adenine (A), guanine (G) cytosine (C), and thymine (T). These are grouped into two classes on the basis of their chemical structure: (i) Purines (with a double ring structure) and (ii) Pyrimidines (with a single ring structure) (Figure 8.3) Nucleosides : In the molecules of nucleic acids (DNA and RNA), each pentose sugar molecule has one nitrogen base attached at carbon number 1. It may be either a purine or a pyrimidine base. Thus, a pentose sugar with the attached N-base forms a nucleoside. [Sugar + N-base] = Nucleoside. In DNA, the deoxyribose sugar has one of the four bases (A,G,T or C) attached. Therefore, the nucleosides in DNA are called deoxyribosides. [deoxyribose sugar + N-base] = Deoxyriboside Click here to enlarge Fig.8.3 Chemical components of DNA and the phosphodiester linkage Nucleotides : A nucleoside with a phosphate group attached to it is called a nucleotide. [Nucleoside + Phosphate] = Nucleotide A nucleotide is the basic unit or monomer in the structure of a nucleic acid molecule. Thus, a nucleotide is a nucleoside phosphate. In a nucleotide, the phosphate group is linked with the pentose sugar at carbon-5. In the DNA, each nucleotide is called deoxyribonucleotide. [Deoxyribose sugar + N-base + Phosphate] = Deoxyribonucleotide As there are four different bases (A,#T,#G and C) in DNA, there can be only four types of nucleotides in DNA. The nucleotides act as the building block molecules for the synthesis of the polynucleotide molecules. When two nucleotides are linked together, a dinucleotide (or dimer) results. Similarly, when many nucleotides are linked with each other in a linear fashion, the resulting chain, is referred to as a polynucleotide (polymer, or). For example, each strand of DNA molecule has many deoxyribonucleotides linked in a chain-like arrangement. Therefore, it is described as polynucleotide strand and DNA molecule as polynucleotide molecule. In the DNA polynucleotide strands, the nucleotides are joined with each other by ‘phosphodiester linkages’ (Figure. 8.3). In a phosphodiester linkage, the phosphate group present at the C-5 of the sugar of one nucleotide gets attached to the C-3 of the sugar of the next nucleotide in the chain. (b) The Watson-Crick model of the DNA double helix : The most widely accepted model for the structure of DNA molecule (Figure 8.4) was proposed by Watson and Crick in 1953 (who won the Nobel Prize for Medicine in 1962). According to their model, the DNA has the following structural characteristics. i. Molecule : The DNA molecule is a double helix (Fig. 8.4A). The molecule is formed by two antiparallel polynucleotide strands which are spirally coiled round each other in a right-handed helix. The two strands are held together by hydrogen bonds. The double stranded helical molecule has alternate major (or deep) and minor grooves. Click here to enlarge Figure 8.4. Structure of DNA (Watson and Crick model) (A) DNA double helix. (B) Detailed structure of the two strands. (C) C-5 and C-3 ends and antiparallel nature of strands (diagrammatic) ii. Structure of each strand (8.4 B) : Each strand is a long polynucleotide of deoxyribonucleotides. The backbone of the strand is formed by alternately arranged deoxyribose sugar and phosphate molecules which are joined by the phosphodiester linkages. Each sugar in the strand has one base horizontally attached to it at carbon-1. It can be any one of the four: A,#T,#G or C. These four N-bases can occur in any possible sequence along the length of a strand. iii. Complementary nature of the strands : The two strands are complementary to each other with regards to the arrangement of the bases in the two strands. For example, where adenine (a purine) occurs in one strand, thymine (a pyrimidine) is present in the corresponding position in the opposite strand and vice versa. Similarly, wherever guanine (a purine) is present in one strand, the other strand has cytosine (a pyrimidine) opposite to it and vice versa. Thus, in the double helix, purines and pyrimidines exist in base pairs, i.e., (A and T) and (G and C). As a result, if the base sequence of one strand of DNA is known, the base sequence of its complementary strand can be easily deduced. vi. Complementary base pairing : In each pair, the two bases of the opposite strands are joined by hydrogen bonds. A and T are joined by two hydrogen bonds, while G and C are joined by three hydrogen bonds. This is called complementary base pairing. The two strands are thus held together all along their lengths by these hydrogen bonds. v. Purine : Pyrimidine ratio : Because of the fixed or complementary base pairing in the DNA molecule, the total number of A is equal to the total number of T and the total number of G is equal to the total number of C. In other words, (A+G)= (T+C). Hence, purines: pyrimidines ratio is 1:1. vi. C-3 and C-5 ends of the strand : In each strand one end of the strand has one free phosphate group on carbon-5 of the sugar molecule. This is the end of the strand is called C-5 (or 5') end. The other end of the strand has a free -OH on carbon-3 of the sugar molecule. This is called C-3 (or 3') end of the strand (Figure 8.4c). vii. Antiparallel nature of strands: The two strands are oppositely oriented and hence are called antiparallel. This means, the 3' end of one strand is adjacent to the 5' end of the other strand (Fig. 8.4c) . This is because, the phosphate-sugar linkages run in opposite directions in the two strands. viii. Dimensions: The diameter of the DNA double helix is 20 Ao. The length of each complete spiral (turn or pitch) of the molecule measures 34 Ao. 10 pairs of nucleotides are present in each complete spiral. Therefore, each nucleotide in the strand occupies a distance of 3.4A0. (c) Circular DNA molecules : Chromosomes of most prokaryotes (e.g. bacteria, cyanobacteria,) are circular molecules of DNA. In bacteria, there is no organized nucleus. The bacterial nucleoid consists of a single circular DNA molecule (bacterial chromosome). The molecule has two complementary strands forming a covalently closed circle. Generally, the circular molecule is present in a highly folded and suspercoiled state (Figure 8.5A). This is expected because the diameter of a bacterial cell (e.g. Escherichia coli) is about 1-2 microns while the total length of the circular DNA is about 1100 microns. The circular molecule has 40-50 folds or looped domains. These folds are held in position by RNA molecules (RNA connectors) and some non-histone proteins associated with the bacterial chromosome. (Histones are absent in bacteria). The DNA segment in each loop is supercoiled independently. Because of this characteristic formation of loops as well as the supercoils within the loops, the large circular DNA molecule can be packed into a small bacterial cell. Otherwise, the relaxed and fully expanded circular molecule (Figure 8.5) would be too large (about 350 microns diameter) to be contained in the bacterial cell. The coils of the supercoiled circle can be relaxed by treatment with enzymes such as RNAse or DNAse. The uncoiling occurs due to a break (nick) in one or both the strands of DNA. In some viruses, e.g. certain bacteriophages, the circular DNA is single stranded. It becomes double stranded only during replication (replicatable form). Click here to enlarge Figure 8.5 8. 3 Replication Of DNA In Eukaryotes Definition: "The process by which DNA produces daughter DNA molecules which are exact copies of the original DNA is called replication of DNA." In eukaryotes, DNA is double stranded. The two strands are complementary to each other because of their base sequences. Semi-conservative method of DNA replication Important points: (i) This is the most common method of DNA replication. (ii) It takes place in the nucleus where the DNA is present in the chromosomes. (iii) Replication takes place in the S-phase (synthesis phase) of the interphase nucleus. (iv) The deoxyribose nucleotides needed for the formation of the new DNA strands are present in the nucleoplasm. At the time of replication, the two strands of DNA first separate. Each strand then acts as a template for the formation of a new strand. A new strand is constructed on each old strand, and two exactly identical double stranded DNA molecules are formed. In each new DNA molecule, one strand is old (original) while the other is newly formed. Hence, Watson and Crick described this method as semi-conservative replication. Click here to enlarge (A) An overall process of DNA replication showing replication fork and formation of new strands template and lagging template Click here to enlarge Figure 8.6 Stages in the semi-conservative method of DNA replication in eukaryotes The various steps involved in this process are summarized as follows: i. The mechanism of replication starts at a specific point of the DNA molecule. This is called the origin. ii. At the origin, the DNA strand breaks because of an incision (nick). This is made by an enzyme called incision enzyme (endonuclease). iii. The hydrogen bonds joining the two strands are broken by the enzyme. iv. The two strands start unwinding. This takes place with the help of a DNA unwinding protein. The two polynucleotide strands are thus separated. v. The point where the two strands separate appears like a fork or a y-shape. This is described as a replicating fork. vi. A new strand is constructed on each old strand. This takes place with the help of a small RNA primer molecule which is complimentary to the DNA at that point. Each old DNA strand acts as a template (site) for the construction of new strand. The RNA primer attaches itself to the old strand and attracts the enzymes which add new nucleotides. The deoxyribose nucleotides are present in the surrounding nucleoplasm. Appropriate nucleotides are selected from the nucleoplasm, and are attached by H-bonds to their respective complementary bases on the old strand. A new DNA strand is thus constructed opposite to each old strand. vii. The formation of new complementary strand always begins at the 3' end of the template strand (original strand) and progresses towards the 5' end (i.e in 3'  5' direction). Since the new strand is antiparallel to the template strand, it is obvious that the new strand itself is always developed in the, 5'3' direction. For this reason when the two original strands separate (then with respect to the origin of separation), one acts as 3'5' template while the other acts as 3'5' template. Of the two, the replication of 3'5' template begins first. Hence the new strand formed on it is called the leading strand. The other template (5'3') must begin replication at the fork and progress back toward the previously transcribed fragment. The new strand formed on it is called the lagging strand. viii. Replication of the lagging strand takes place in small fragments called Okazaki fragments. These are then connected together by the enzyme polynucleotide ligase. ix. Replication may take place in only one direction on the DNA helix (unidirectional) or in two directions (bidirectional). x. At the end of the process, two double stranded DNA molecules are formed from the original DNA molecule. xi. In each newly formed DNA, one strand is old while the other is new. Hence, it is described as semi-conservative replication. The semi-conservative nature of DNA replication was confirmed by Meselson and Stahl (1958) with the help of an experiment. They marked the DNA in Esherichia coli with heavy isotope of nitrogen (15N) and then traced it in the following generations of the E-coli progeny. It was demonstrated that every daughter DNA is an exact copy of the parent DNA and that each daughter DNA has one strand of the parent (old strand) and the other strand in newly formed. 8.4 Replication of Prokaryotic Chromosome Figure 8.7 Replicating circular DNA ( replication) The DNA of the prokaryotic chromosome replicates as a circular structure. It is a semiconservative as in the linear DNA of the eukaryotes. Replication begins a fixed point called the origin. In most prokaryotes, the DNA has only one ‘origin’ point. The uncoiling of the two strands of the circular molecule begins at the point of origin and progresses in opposite directions (bidirectional). This is helped by the enzyme called DNA gyrase. Simultaneously with the uncoiling of the original strands, a new complementary strand is being constructed on each strand. As a result, the circular DNA appears as the Greek letter  (theta) during replication (Figure 8.7). Hence this mode of replication is called  replication. Each newly forming strand also goes on helically coiling around its circular template strand (original strand). As a consequence, by the time the replication process is over, two complete double-stranded circular DNA molecules are formed. These are exact copies of the original molecule. Moreover each daughter molecule has one original (parental) and the other newly formed circular strands. 8.5 Plasmids In addition to the normal DNA chromosome, extrachromosomal genetic elements are often found in the cytoplasm of most bacterial species and in some species of eukaryotes. These elements are called plasmids. Plasmids are extrachromosomal circular DNA molecules (except the plasmid called Killer-Plasmid present in yeast cells, which is a double stranded RNA molecule). The DNA of all plasmids is double stranded supercoiled circular DNA molecule (Figure 8.8). These are capable of autonomous replication in the cytoplasm of the bacterial cell. Therefore, plasmids are also described as autonomously replicating ’minichromosomes’. A bacterial cell can have one to many copies of a plasmid. Plasmids represent extra genes. Some plasmids are called episomes. An episome is a plasmid with a dual ability to replicate, i.e. it can replicate autonomously in the cytoplasm like other plasmids or it can also integrate itself into the DNA of the bacterial chromosome and behave as part of the chromosome. Role of plasmids Many plasmids contain important and essential plasmid genes which are helpful under certain conditions. For example, a bacterial cell possessing R Plasmid develops resistance to certain antibiotics. Similarly, presence of some plasmids gives the bacterial cell the ability to produce toxins (toxigenicity), or the ability to use unusual chemical compounds as nutrients. Moreover, plasmids and episomes prove to be good vehicles for gene manipulations (genetic engineering). Figure 8.8 Bacterial cell showing a plasmid 8.6 RNA : Structure and Types Ribonucleic Acid (RNA) is another polynucleotide which occurs in the cells as non-genetic material, with the exception of some viruses. RNA is present in the nucleus as well as in the cytoplasm. General structure RNA molecule is single stranded and consists of nucleotides arranged in a long series. The single strand of RNA may be simple and straight, or it may be variously folded upon itself in certain regions. Structural components : RNA molecule has three primary components. 1. Ribose sugar (a pentose sugar), with a pentagonal ring structure 2. Phosphate, as phosphoric acid 3. Nitrogenous bases There are four kinds of nitrogenous bases found in RNA. Of those, two are purines and two are pyrimidines, as follows : Thus in RNA, uracil is present in place of thymine found in DNA. Structure of an RNA strand : The strand is made up of alternating molecules of ribose sugar and the phosphate. The nitrogen bases are attached to the sugar molecules in the strand and ’stick out’ laterally as in DNA (figure 8.9). A sugar, a N-base and a phosphate together form a ribonucleotide. A nucleotide without the phosphate is called ribonucleoside. RNA being single stranded, the nitrogen bases remain mostly unpaired. However, the strand may be folded upon itself in certain regions. In such folded regions, base pairing occurs between purines and pyrimidines as follows : Adenine = Uracil (two H-bonds). Guanine = Cytosine (three H-bonds). Nitrogen bases remain unpaired in the unfolded regions of the strand. Because of this variability in base pairing in different regions of the same strand, the total number of purines need not be equal to the total number of pyrimidines in RNA. Figure 8.9 General structure of RNA PinkMonkey Online Study Guide-Biology Table 8.2 : Difference between DNA and RNA Characters DNA RNA 1. Molecule Double stranded, helical Single stranded, straight or variously folded and twisted. 2. Pentose sugar Deoxyribose Ribose 3. Pyrimidine base Thymine Uracil 4. Complementary base pairing Always present and exists between A = T and G = C Normally absent, but may be present in twisted segments of a molecule. If present, pairing is between A = U and G = C 5. Ratio of Purines: Pyrimidines Always 1 : 1 Not necessarily 1:1 6. Replication Can replicate Cannot replicate Types of non-genetic RNA and their functions There are three types of non-genetic RNA. (1) mRNA or messenger RNA, (2) rRNA or ribosomal RNA and (3) tRNA or transfer RNA. fields marked (*) are mandatory (1) mRNA (Messenger RNA) : This is called messenger RNA because it carries information for protein synthesis from the DNA to the ribosomes in the cytoplasm (the site of protein synthesis). m-RNA constitutes about 3-5% of the total RNA. It is produced on the DNA strand. The process is called transcription. Hence, the base sequence of mRNA is complementary to that of the DNA strand. The bases on the mRNA strand are organized into triplets. Each triplet consists of a sequence of three consecutive bases (nucleotides) and is called a codon (code word). Each codon specifies one amino acid. The sequence of codons on the mRNA strand is called the mRNA language. It indicates the sequence of amino acids for the synthesis of a protein. It begins with the codon AUG (initiation codon or starting codon) and ends with either UAA, UAG or UGA (stop codons). The single-stranded mRNA molecule is always straight (Fig. 8.10) and therefore, base pairing is totally absent in mRNA. < Figure 8.10 m-RNA Role of # m-RNA in # protein # synthesis i. Represents the sequence of codons from the DNA strand (transcription). ii. Brings the sequence to the ribosomes (site of protein synthesis) in the cytoplasm. iii. Provides the sequence for the synthesis of specific protein from the amino acids with the help of t-RNA (translation). (2) rRNA (Ribosomal RNA) : r RNA forms about 80% of the total RNA. It is present in the ribosomes in the cell cytoplasm (site of protein synthesis) and hence called rRNA. The single-stranded molecule of rRNA is variously folded and twisted upon itself in certain regions (Figure 8.11). In such folded regions, complementary bases form pairs and are joined by hydrogen bonds. Role of rRNA in protein synthesis : The role of rRNA in protein synthesis is not yet very clearly known but it is known to complex with various protiens. The resulting structure is a ribosome, and this complex reads the coded sequence in mRNA to link amino acids together into particular protiens. i. It provides proper binding sites for the mRNA of the ribosomes. ii. It orients the mRNA in such a way that its nitrogen base triplets or codons are properly read or translated. iii. It also releases tRNA after the transfer of activated amino acid. iv. It protects the mRNA strand from the action of enzymes (nucleases). v. It protects the growing (nascent) polypeptide chain from proteolytic enzymes. (3) tRNA (Transfer RNA) : It is the smallest of all the types of RNA. About 10 to 20% of the total RNA of the cell is of this type. tRNA strand is folded upon itself forming loops. It results in either a clover leaf pattern or hair pin pattern (Figure 8.12). One end of the strand has guanine, while the other end carries the CCA combination of nitrogen bases. A triplet of nitrogen bases called anticodon is present on one of the loops. The anticodon pairs with the complementary codon on the mRNA molecule. The tRNA molecules carry amino acids to the mRNA during the process of protein synthesis. Each type of the amino acid is carried by a specific tRNA molecule. tRNA is synthesized on the DNA template. It has complementary base pairs in folded regions. Role of tRNA in protein synthesis i. tRNA carries the required specific amino acids from cell cytoplasm to the ribosome (site of protein synthesis). ii. Each type of amino acid is carried by a specific type of tRNA. iii. In the ribosome, tRNA helps to arrange the amino acids in their proper sequence for the synthesis of a protein. This is done with the help of the codons on the mRNA and the matching (complementary) anticodons on the tRNA (translation). iv. 8.7 The Genetic Code v. Some historical events 1954 Gamow : Suggested the triplet genetic code. 1958 Crick : DNA determines the sequence of amino acids in a polypeptide (Central dogma of molecular biology). 1961 Crick et al : Provided direct evidence for triplet code. 1966 Crick : Proposed the wobble hypothesis for the genetic code. 1967 Komberg and Sinsheimer : Synthesized single-stranded DNA in a bacteriophage. 1970 Khorana : Synthesized an artificial gene from DNA nucleotides. vi. The genetic code : DNA is genetic material and contains genetic information. The expression of a gene takes place through specific enzymes. Each gene produces a specific (one-gene one-protien hypothesis). In other words, formation of each specific protein is controlled by a particular gene. A gene is (almost always) a segment of DNA strand and so, the information for the formation of a protein is contained in the DNA strand. fields marked (*) are mandatory vii. Further, each protein is a long polypeptide chain molecule formed by joining amino acid molecules. From the cell pool, only 20 different types of amino acids are used for protein synthesis. viii. The sequence of the nitrogen bases in the DNA determines the sequence of amino acids in a protein molecule through the mRNA. This sequence is copied down by the mRNA (transcription). It is present on the mRNA strand in the form of coded language (cyptogram or mRNA language or genetic code). The mRNA bases (A, U, C and G) serve as the four alphabets of the coded language. ix. Codon : The smallest sequence of the nitrogen bases (nucleotides) on the mRNA which can specify one amino acid is called a codon . Each codon consists of three successive bases on the mRNA. x. Why should each codon in the genetic code consist of 3 bases (triplet codon) and not of one base each or 2 bases each? This is because there are 20 different amino acids which can be used in the synthesis of proteins in the cells. There must be at least one specific codon for each amino acid. Thus, there has to be at least 20 different codons in the genetic code. There are only four bases. A minimum of 3 bases per codon is necessary to have (a minimum of) 20 codes. xi. The wobble hypothesis (Crick, 1966) : The anticodon on tRNA is complementary to the codon on the mRNA as per the A = U, G = C base pairing rule. However, it has been observed that the 3rd base position may vary and yet still code for the same amino acid. For example, both codons TTA and TTG code for the amino acid, leucine. Thus, the third position is called the wobble position. xii. Thus, Crick’s (1966) wobble hypothesis explains the degeneracy of the genetic code at the third position of the codon. 8.8 The Central Theme of Protein Synthesis A protein is a long chain polypeptide. The chain molecule is formed by joining amino-acid molecules with peptide linkages. The sequence of amino acids in each type of protein is highly specific. The functional proteins form enzymes and hormones and control all metabolic and biochemical reactions and processes in cells. Any alteration in the sequence of amino acids in protein molecules can affect the function of that protien. Hence, bio-synthesis of proteins is a highly specific process. fields marked (*) are mandatory Click here to enlarge The main principle of protein synthesis. According to Crick (1958), DNA determines the sequence of amino acids in a polypeptide (protein) through mRNA. This is the main principle (central dogma) of protein synthesis. This involves transcription and translation. Components involved in protein synthesis : The process requires 1. The 20 types of amino acids that are specified by the genetic code. 2. DNA (to provide the base sequence). 3. The non-genetic RNAs (m-RNA, t-RNA and r-RNA). 4. Ribosomes (site of protein synthesis) and 5. Various enzymes (factors). Mechanism of protein synthesis As stated earlier, the mechanism of protein synthesis involves two main events namely (A) Transcription (B) Translation. (A) Transcription Transcription is the process of formation of mRNA on the DNA strand. It takes place in the presence of enzyme RNA Polymerase. One of the strands of DNA acts as a template for the formation of the same m-RNA in a series, one by one. Such ribosomes bound to the same mRNA strand are called polyribosomes or polysomes. The polypeptide chain formation in each ribosome is independent and the same as described above. (B) Translation In Translation one particular group gets transmitted from one Band of DNA to another Band of DNA. In this procedure the DNA polymer (enzyme) is used. Normally, 40% of protein synthesis occurs in this manner. SUMMARY : MOLECULAR GENETICS AND GENE EXPRESSION (1) DNA is the genetic material in almost all organisms. (2) Chromosomes carry genes. (3) The chromatin consists of DNA and two types of proteins (histones and non-histones). (4) During prophase of the cell division, DNA of the chromatin undergoes coiling, super coiling and folding and along with the associated proteins, forms highly a condensed and prominent chromosome (as seen during metaphase). (5) This is explained with the help of necleosome solenoid model (Komberg and Thomas, 1974). (6) DNA molecule has a double stranded, helical structure in which the two antiparallel polynucleotide strands are helically coiled round each other, and joined by hydrogen bonds (Watson and Crick). (7) DNA has the ability of self-replication. (8) RNA molecule is single stranded. It can not replicate. It is produced on DNA strand. (9) Non-genetic RNA is of 3 types and helps in protein synthesis. (10) In prokaryotes, the single circular chromosome has a circular DNA capable of replication. (11) Prokaryotes also possess plasmids and episomes. These are the extra chromosomal circular DNA which carry genes and are capable of self-replication. (12) Genetic information required to produce a protein is called the genetic code. It is present on the DNA in the form of the base sequence. It is transcribed on m-RNA and is then used for synthesis of protein in the ribosomes. (13) Genetic code is triplet. (14) Each triplet or codon on m-RNA specifies one amino acid. (15) In all, there are 64 codons in the genetic code of which 61 codons specify 20 different amino acids. (16) Three codons (UAA, UAG and UGA) do not specify any acid (stop codons). (17) AUG is the starting or initiation codon. (18) In protein synthesis, m-RNA provides the sequence of the arrangement of amino acids in form of the codon sequence. These are carried by the t-RNA and are arranged in the sequence with the help of matching anticodons on t-RNA. (19) After formation, the peptide chain is released with the help of release factors. CHAPTER 9 : BIOENERGY 9.0 Introduction Socio-economic development, standard of living, as well as the quality of life of any country largely and primarily depend on the availability and supply of energy. The availability and supply of energy come under great pressure because of increasing demands of the ever-increasing global population. This eventually leads to the problem of energy crisis. This is especially true for the developing countries like India. At present, the main conventional source of energy used all over the world is the ’fossil fuels’ (i.e. the huge deposits of plant and animal remains accumulated during the geological past and which serve as the main source of energy such as. petroleum (oil), natural gas, coal, derivatives of coal, oil shale, tar sands, etc.). However, fossil fuels are non-renewable and hence their deposits will eventually be exhausted. Therefore, alternative energy sources must be tapped and exploited to their full potential. Solar energy, nuclear energy, energy from tides, energy from wind, and hydroelectric energy are some of the alternative resources. However, one of the major renewable alternative sources is the bioenergy obtained from biomass. "Bioenergy refers to the various forms of energy (e.g. heat (fire), fuel, oil, biogas (methane), ethanol (alcohol), methanol, charcoal, oil gas, etc. ) generated from the biomass by using simple or complex biotechnological methods." "Biomass refers to all the living organisms as well as their products and wastes." "Biofuels are the combustible bodies of plants or combustible products derived from the biomass." Biofuels are a renewable resource of energy. The primary source of the energy stored in biomass is solar energy which is trapped by green plants during photosynthesis and stored as potential energy in organic molecules. Biofuels are obtained from the terrestrial biomass ( wood, forest litter etc.), aquatic biomass (algae and water weeds like water hyacinth, Pistia, Salvinia, Azolla, etc. ), various types of organic wastes (agricultural and industrial wastes, municipal and domestic wastes like sewage, garbage, animal drug, wastes from slaughter houses, etc. ). Plants that produce alcohol, oil and petroleum (petro-plants) also are a source of biofuels. Various methods and technologies which convert biomass into bioenergy fuels fall into two main categories. (1) The non-biological processes such as (a) direct combustion (b) conversion of biomass into liquid fuels such as fuel oil (e.g. by pyrolysis - a type of fertilization, liquefaction, etc. ) and (c)gassification.. (2) The biological process or bioconversion involves the conversion of biomass into bioenergy, fertilizer, food and chemicals through the biological action of micro-organisms. One of the important biofuels obtained through bio-conversion is natural gas, a biogas (methane). 9.1 Common Methods of Biogas Formation Methane is the main constituent (63%) of the biogas. (The other major constituent is carbon dioxide = 30%.) It is known by various names such as biofuel, sewerage gas, Klar gas, sludge gas, will-o-the wisp of marsh lands, fool’s fire, gobar gas, bio-energy and even fuel of the future. Biogas is often used for cooking and lighting purposes in the rural sector. It burns with a blue flame without smoke and is without odor.. Biogas is formed under anaerobic conditions when organic materials are converted into gases (fuel) and organic fertilizer (sludge) through microbial reactions . Similarly, fuel oil is produced from domestic wastes, agricultural wastes, forestry wastes, etc. by the process of pyrolysis (destructive distillation or decomposition of organic wastes in anaerobic conditions at high temperatures). 9.2 Raw Materials and Substrates Biogas can be produced from the biomass of plant origin (either terrestrial biomass or aquatic biomass) or animal origin (cattle dung, domestic sewage, organic manure, poultry, slaughter house and fishery wastes, etc. ). An enormous quantity of sugarcane wastes is produced in the sugar mills. Sugarcane bagasse and molasses are the two important wastes. Bagasse is the cellulosic material of sugarcane produced after the extraction of the sugar juice. It is used for the production of biogas, alcohols, single cell protein (SCP), etc. Sugarcane molasses contains about 50-55% fermentable sugars and hence is an important source for the production of liquid fuel, alcoholic beverages and animal feed. Similarly, straw, agricultural wastes, forest litter, aquatic weeds like water hyacinth, Pistia, Salvinia, etc., and cyanobacteria are also the common raw materials used for the production of biogas. 9.3 Producer Gas Figure 9.1 - A Producer Gas Generator Producer gas is a mixture of approximately 25% carbon monoxide, 55% nitrogen, 13% hydrogen and 7% other gases. It is obtained by burning coal or coke in the generators with a restricted supply of air, or by passing air and steam through a bed of red hot fuel. Producer gas is cheap and used as a fuel mainly in glass furnaces and metallurgical furnaces. It also serves as a fuel in gas engines to operate tractors, motor cars and truckso. It is also used as a source of nitrogen for the preparation of ammonia. However, produce 9.4 Methane As stated earlier in this chapter, the common raw materials used for the production of methane are biomass products such as human and animal wastes, agricultural, industrial and domestic residues. Cattle dung is the most common material used in most biogas plants. Stage Process involved Group of bacteria involved 1 Solubilization Hydrolytic fermentor bacteria (mostly anaerobic). 2 Acetogenesis Hydrogen - producing acetogenic bacteria (facultative anaerobic) 3 Methanogenesis Methanogens( i.e. methane producing anaerobic bacteria) Micro-organisms involved : Conversion of the biomass into biogas (methane) is a process called anaerobic digestion. It is completed in three stages. Breakdown of the biomass as each stage is done by a different group of bacteria as shown in the above table. fields marked (*) are mandatory Gobar gas plant (Figure 9.2) : As the biogas (gobar gas) production is an anaerobic process, it is carried out in an air tight, closed cylindrical concrete tank called a digester. In countries like India, domestic gobar gas plants use single digester tanks (Fig. 9.2). The tank has a concrete inlet basin on one side for feeding fresh cattle dung (gobar). There is a concrete outlet on the outer side for removing the digested sludge. The top of the tank serves as the gas tank. It has an outlet pipe for the gobar gas/ biogas. Figure 9.2 Domestic Gobar gas plant (Diagrammatic) Process : Fresh cattle dung is fed into the digester tank through the inlet and allowed to remain there. After about 50 days, a sufficient amount of gobar gas is accumulated in the gas tank. It is conducted through the outlet pipe and used for domestic purposes. The digested sludge (digested biomass) is removed from the tank and is used as fertilizer. The tank is again filled with fresh dung and the process is repeated. Uses (1) Gobar gas is mainly used for cooking and lighting in rural areas. (2) Also used in internal combustion engines to power water pumps and electric generators. (3) Used as a fuel in the fuel type refrigerators. There are certain advantages in using methane (gobar gas) as a source of energy : i. Methane is very insoluble, hence it separates very readily from the fermentor system. ii. It can be very easily collected, pressurized or liquified for storage. iii. It is readily combustible. Other advantages are : (a) Sludge is used as fertilizer. (b) It serves as a pollution free method for the disposal of human and animal wastes in rural areas. (c) The anaerobic process involved also eliminates pathogenic bacteria from the biomass. 9.5 Plants as Sources of Hydrocarbons Figure 9.3 Some latex-containing species of Euphorbis (petro-plants) (a) Introduction : There are certain species of flowering plants belonging to different families which convert a substantial amount of photosynthetic products into latex. The latex of such plants contains liquid hydrocarbons of high molecular weight (10,000da). These hydrocarbons can be converted into high grade transportation fuel (i.e. petroleum). Therefore, hydrocarbon producing plants are called petroleum plants or petroplants and their crop as petrocrop. Natural gas is also one of the products obtained from hydrocarbons. Thus, petroleum plants can be an alternative source for obtaining petroleum to be used in diesel engines. Normally, some of the latex-producing plants of families Euphorbiaceae, Apocynaceae, Asclepiadaceae, Sapotaceae, Moraceae, Dipterocarpaceae, etc. are petroplants. Similarly, sunflower (family Composiae), Hardwickia pinnata (family Leguminosae) are also petroplants. Some algae also produce hydrocarbons. (b) Euphorbia : Different species of Euphorbia (Fig. 9.3) of family Euphorbiaceae serve as the petroplants. Dr. M. Calvin (1979) was the first to collect the hydrocarbons from plants of Euphorbiaceae. He suggested that these can be the renewable substitute for the conventional petroleum sources. Latex of Euphorbia lathyrus contains fairly high percentage of terpenoids. These can be converted into high grade transportation fuel. Similarly the carbohydrates (hexoses) from such plants can be used for ethanol formation. (c) Sugarcane and sugar beet : Sugarcane (Saccharum officinarum - family Gramineae) is the main source of raw material for sugar industry. The wastes from sugar industry include bagasse, molasses and press mud. After extracting the cane juice for sugar production, the cellulosic fibrous residue that remains is called bagasse. It is used as the raw material (biomass) and processed variously for the production of fuel, alcohols, single cell protein as well as in paper mills. Molasses is an important by-product of sugar mills and contains 50-55% fermentable sugars. One ton of molasses can produce about 280 liters of ethanol. Molasses is used for the production of animal feed, liquid fuel and alcoholic beverages. Sugar beet (Beta vulgaris, family-Chenopodiaceae) is yet another plant which contains a high percentage of sugars stored in fleshy storage roots. It is also an important source for production of sugar as well as ethanol. Raising crops like sugarcane, sugar beet, tapioca, potato, maize etc. purely for production of ethanol is described as energy cropping, and the crops are called energy crops. Cultivation of plants (trees) for obtaining fuel/fire wood is described as energy plantation. SUMMARY : BIOENERGY (1) Energy obtained from any biomass is called bioenergy. (2) Various kinds of organic wastes of plant or animal origin, residues from agricultural industries, municipal and domestic wastes, aquatic weeds, etc. provide the biomass. (3) Biogas (methane) is a very common source of bioenergy. (4) Domestic biogas is mostly produced from cattle dung and hence called gobar gas. (5) Producer gas also represents an alternative source of energy. (6) Plants of family Euphorbiaceae, Apocynaceae, Asclepiadaceae, etc. produced liquid hydrocarbons. These form the source for formation of liquid fuel (petroleum). Hence, hydrocarbon producing plants are called petroplants. (7) Bioenergy is a very good alternative for conventional fossil fuels. ********** CHAPTER 10: BIOTECHNOLOGY 10.0 Introduction Definition : "Biotechnology is the industrial application of biochemistry, biology, microbiology, chemical engineering, genetic engineering etc. in order to make the best use of the capabilities of micro-organisms, cultured tissues, cells, etc. for the benefit of mankind." In other words, biotechnology is the use of living organisms or of substances obtained from them in industrial processes, using modern scientific and engineering principles. This is a comparatively recent branch of immense applied value even though use of microbial activity has been in practice since the early ages (e.g. formation of alcohol by fermentation process or formation of curd and other milk products). Yes, I wish to receive information about Toyota Products & Promotional Offers. *conditions apply During the past 2-3 decades, biotechnology has brought total revolution and sophistication in various fields such as medicine, agriculture, industrial microbiology etc. For example, genetic engineering has made it possible to map the whole genome of an organism, to make gene transfers, gene cloning, etc. Recombinant DNA technology has helped to develop growth hormones, interferon, vaccines against viral and malarial diseases, etc. In agricultural sciences, inter-generic crosses have become possible due to cell culture and protoplast fusion techniques. Cell culture techniques are also useful in the industrial production of essential oils, alkaloids, pigments, etc. Biofertilizers are non-toxic, biodegradable and produce a better yield of agricultural crops as compared to synthetic fertilizers (which are mostly non-biodegradable). Biotechnology has helped to increase the industrial production of alcohol, antibiotics, vitamins, hormones, antibodies etc. by developing new and more efficient strains of microorganisms. Biotechnology has helped not only in the disposal of domestic wastes but also evolved techniques to make use of the biomass as a source of bioenergy. 10.1 Fermentation Fermentation is a process very much similar to anaerobic respiration. It is a metabolic process in many micro-organisms and involves oxido-reduction reactions resulting in the breakdown of complex organic molecules into various end products with the release of energy. Fermentation is mostly extracellular and is brought about with the help of enzymes released by the micro-organisms. The end products or the various intermediate products (primary and secondary metabolites) of the fermentation activities of many micro-organisms are highly useful. Hence, micro-organisms have been commercially exploited by the fermentation industry. Thus, with reference to industrial microbiology, fermentation may be defined as "a process for the production of useful products through mass culture of micro-organisms." Micro-organisms involved in the fermentation industry : More than a million different micro-organisms are known to exist in nature. However, only a few hundred species are of commercial importance. Some of these species are listed below. Algae Chlorella sp., Spirulina sp:,etc. Bacteria Acetobacter lacti, Bacillus subtilis, Pseudomonas denitrificans, etc. Actinomycetes Streptomyces aureofaciens, S.griseus, Nocardia sp ;,etc. Fungi Aspergillus niger, Penicillium notatum, P. chrysogenum, Sacchromyces sp;,Gibberella fujikuroi, Fusarium moniliforme, etc. Fermenter : A fermenter is a vessel designed to carry out fermentation process, (i.e. the microbiological reactions under the controlled conditions). Hence, a fermenter is also called a bio-reactor. The fermenter allows long term operation in aseptic conditions. It has the necessary arrangements for adequate aeration, agitation, pH control, temperature control, sampling, harvesting, etc. Thus, it is very convenient for operation in the fermentation industry. Uses of fermentation 1. Useful intermediate products : The various intermediate compounds produced during fermentation activity are classified as primary and secondary metabolites. Some of the commercially important metabolites are (a) Primary metabolites, such as amino acids, proteins, carbohydrates, vitamins, acetone, ethanol, organic acids etc. and (b) Secondary metabolites such as antibiotics, toxins, alkaloids, gibberellins, etc. 2. Enzymes : Enzymes produced by the micro-organisms during fermentation include amylases, cellulases, invertase, esterase, lipase, protase, lactase, etc. 3. Microbial biomass: After the process of industrial fermentation is over, the exhausted cells of the micro-organisms (in the fermenter) serve as microbial biomass. It is also known as microbial protein or single cell protein (SCP). It is an important source of proteins. 10.2 Manufacture of Alcohol A primary industrial alcohol is ethanol, or ethyl alcohol (C2H5OH). Alcoholic fermentation is one of the oldest, best known and most important of industrial fermentations. In this process, ethyl alcohol is produced from carbohydrate materials (such as sugars) by yeasts. The process is extracellular. The overall biochemical change accomplished by the yeast is represented by the following equation. This ability of the yeasts to convert sugars to alcohol and other end products of value has been exploited a great deal by brewers, bakers, distillers, wine makers, chemical manufacturers, vinegar manufacturers, etc. Figure 10.1(A) A Tubular Tower Fermenter (B) Flow Chart of alcoholic fermentation Manufacture of ethyl alcohol (Fig. 10.1) 1. Raw materials used : Molasses are one of the commonest raw materials used in the manufacture of alcohol. This is because they are cheap and readily available in large quantities. 2. Micro-organism used : Selected strains of the yeast Saccharomyces cerevisiae are commonly employed for fermentation. This is because (a) they grow vigorously, (b) they have high tolerance for alcohol and (c) they have a high capacity for producing a large yield of alcohol. Steps involved in the process It is a large scale biotechnological process requiring large scale tubular tower fermenters (bio-reacters) (Fig. 10.1A) and involves the following steps. a. Preparation of the medium : Water is added to the molasses to bring down the sugar concentration to the desired level (usually 30 to 40 percent). A measured quantity of acid is then added so as to adjust the pH on the acidic side. b. Addition of yeast : After adjusting the desired temperature, a yeast ‘starter’ is allowed to be mixed thoroughly with the molasses ‘mash’ in the fermentation tank. PinkMonkey Online Study Guide-Biology c. Fermentation : Fermentation by the yeast process starts and soon becomes vigorous. A large quantity of carbon dioxide is evolved during the process. The gas (by-product of the alcohol industry) is collected, purified and used in various other industries. d. Separation of ethyl alcohol : Alcoholic fermentation is completed in about 48 hours. The fermented medium contains alcohol as well as other volatile constituents and unused constituents of the molasses. Therefore, separation of ethyl alcohol from other impurities is necessary. This is done by distillation. e. Purification : Finally, alcohol is purified with the help of rectifying columns and stored in bonded warehouses. Ethyl alcohol is also formed as one of the products of fermentation during the manufacture of alcoholic beverages such as beer, wine, whisky, rum and gin. Different types of alcoholic beverages are obtained by making use of the fermentation activity of different strains of yeast Saccharomyces as shown in the following table. Various products of alcoholic fermentation Beverage Substrate Micro-organism (Saccharomyces) Species/Strains Alcohol % 1. Wine Grape juice S. ellipsoideus 10-12% 2. Beer Cereals S. cerevisae 4-8% 3. Rum Black strap molasses ___________ 4. Whiskey Cereals 51-59% 5. Sake Starch (rice) Aspergillus oryzae, Lactobacillus and S. cerevisae 16% 6. Champagne Grape juice ___________ 12-13% 7. Brandy Wine ___________ 43-57% 10.3 Antibiotics Definition : "An antibiotic is the complex organic chemical substance which is produced as the secondary metabolite by one micro-organism and acts as a toxin against other micro-organisms; either inhibiting their growth or killing them." Figure 10.2 A stirred tank fermenter Historical account : Penicillin was the first antibiotic to be produced industrially. The credit for the discovery of penicillin goes to Sir Alexander Fleming (1929). He extracted it from Penicillium notatum under laboratory conditions. However, the remarkable chemotherapeutic effectiveness of penicillin was demonstrated by Ernst B. Chain and Sir Howar W. Florey during 1939-41. Fleming, Chain and Florey shared the Nobel Prize in 1945 for their contributions in the field of antibiotics. Selman Waksman (1942) coined the term "antibiotics". He also discovered streptomycin. Several thousand antibiotic substances have been discovered since then, although only a few are of chemotherapeutic importance for the cure of certain human diseases caused by bacteria, fungi and protozoa. Some common antibiotics, their microbial origin, and uses are listed in the accompanying table. Some antibiotics, their microbial source and uses Click here to enlarge Medium scale process of antibiotic production The process of antibiotic production basically involves fermentation of the medium by some specific micro-organism. Hence, (i) the medium should be ideal for the microbial action and (ii) the selected strain of the micro-organism should give the maximum yield. The fermentation process is carried out in a medium size sterilized stirred tank fermenter (Figure 10.2A). This is provided with a stirring device. 1. Medium : The fermentation medium is prepared as per the requirement. 2. Inoculum : The selected strain of the micro-organism is cultivated under aseptic conditions. This is used as the ‘seed’ or ‘inoculum’. 3. Fermentation : The medium and the inoculum are poured in the sterilized fermenter tank. The pH, temperature, etc. of the fermenting medium are regulated as per the specific requirements. The fermenting medium is constantly stirred and aerated. This increases the yield. 4. Recovery of the antibiotic : After the process is over, the fermented medium is filtered to remove the microbe. The filtrate contains the antibiotic. It is recovered using various methods, e.g. precipitation, redissolving, filtration, etc. Click here to enlarge Figure 10.3 Flow sheet for the medium scale production of an antibiotic 10.4 Vitamins Vitamins are the complex organic compounds essential for complete, normal and healthy growth. Absence of any vitamin from the body results in specific deficiency diseases. Vitamins are naturally synthesized by most green plants. All phototrophic micro-organisms produce vitamins either as primary metabolic products or as fermentation products. Animals and human beings do not produce all vitamins in their bodies and must obtain them from food. Vitamin B-12 - (Cyanocobalamine) : It is a compound containing cobalt. In nature, micro-organisms like Propionibacterium, Pseudomonas denitrificans, Streptomyces olivaceous, etc. synthesize vitamin B-12 from the medium containing cobalt-rich substrate (e.g. corn sugar, cane molasses, starch, etc.) Some of the micro-organisms present in the digestive system also produce vitamin B-12 in the natural process. Cyano-cobalamin is the most essential vitamin for human growth. Meat and fish are the main sources of vitamin B-12. Vitamin B-2 - (Riboflavin) : Cereals, green vegetables, brewer’s yeast, etc. are the most common sources of vitamin B-2. Riboflavin is essential for growth and reproduction in animals. The natural biological synthesis of riboflavin occurs during fermentation by the fungus Ashbya gossypii and by another micro-organism, Eremothecium ashbyii. In the biotechnological process for the commercial production of Cyano-cobalamin (vitamin B-12), genetically improved and highly efficient strains of Propionibacterium or Pseudomonase denitrificans are used. The common substrate used in the process is corn steep and glucose plus cobalt (5 ppm) As a result of the biotechnological application, now the improved strain of P. denitrificans can produce 50,000 times more vitamin B-12 than its original strain. This is one of the most outstanding examples of the application of biotechnology. Some vitamins and the effects of their deficiency are listed below Vitamins Deficiency diseases Retinol (Vit. A) Retardation of growth, dryness of skin, less resistance to infections and night-blindness. Thiamine (Vit. B1) Loss of appetite, gastrointestinal disorders, muscular weakness, low blood pressure etc. Riboflavin (Vit. B2) Inflammation of tongue, cracking of lips and corners of mouth, etc. Cyanocobalamine (Vit. B12) Pernicious anaemia which is accompanied by the degradation of the spinal cord. Ascorbic acid (Vit. C) Scurvy and brittleness of bones; gums bleed and teeth become loose. Calciferol (Vit. D) Causes rickets Phylloquinone and Farnoquinone (Vit. K) Delays the clotting of blood. SUMMARY : BIOTECHNOLOGY (1) Biotechnology is the use of living organisms or substances obtained from them in the industrial processes using scientific and engineering technology. (2) In the recent few decades, biotechnology has brought revolutions in medical, agricultural and industrial fields. (3) Fermentation of organic compounds by micro-organisms produces various useful products such as antibiotics, vitamins, alcohol, amino acids, proteins, carbohydrates, and enzymes. (4) Fermentation industry fully exploits this microbial activity. (5) By using improved and highly efficient strains of micro-organisms and employing modern biotechnological principles, the industrial yield of fermentation products has been increased by a great deal. (6) Fermentation activity of micro-organisms is also used for industrial production of alcohol, vitamins (e.g. cyanocobalamin (Vitamin B-12), riboflavin (Vitamin B-2), etc.) (7) Sophisticated and technologically modern bio-reacters (i.e. fermenter tanks) are used for the synthesis of fermentation products. CHAPTER 11 : EVOLUTION OF LIFE 11.0 Introduction Scientists have long tried to discover the origin of living organisms. Various observations about the varieties of plants and animals, the diversities in their structures and the reproductive patterns, lead to the concept of evolution. The process of evolution involves a gradual change of organisms generation after generation. Essentially it means that the present-day organisms have arisen from ancestors that were more simple in organization. Evolution involves changes in genetic composition of a population, generation after generation. Modification and development of a species takes place through hereditary transmission of slight changes (variation) from one generation to another. It results in new characteristics in a species, and the eventual formation of new species. Three main observations support the idea of evolution. a) The development of present organisms can be traced back to the organisms living in the past. The study of fossils reveals that fossils in successive strata of rocks show a gradual change from simple forms to complex forms of life. The geological time scale explains that the oldest rocks formed show the fossils of simple animals only. The rocks formed later show more complex forms of living organisms, and thus a gradual evolution of more complex living organisms from simple forms is suggested. The Proterozoic era shows fossils of invertebrate animals. Paleozoic era shows fossils of fishes and amphibians in the lower strata and reptiles in the upper strata. The Mesozoic era shows dominance of reptiles. Coenozoic era shows appearance of birds and mammals. The recent epochs show evolution of man. b) Another observation about the diversity in the structure of living organisms explains that there is unity in diversity of life. The animals show variations in their structures but the basic pattern of working is the same. There may be variations in the food and feeding habits, but the basic components of food are same. The proteins, carbohydrates and lipids are converted into aminoacids, monosaccharides and fatty acids, respectively. The biochemical changes during digestion are similar. The pattern of getting energy is basically the same. Similarly the nucleic acids which are involved in the inheritance of characters are similar in most of the organisms. The protein synthesis mechanism is also similar. Structures of many organs also suggest a common basic pattern, (e.g. the forelimbs of the frog, bird, horse, whale, bat and man have the same basic skeleton pattern). But necessities like running, flying, swimming, perching or grasping, variations result from various changes in shape. c) The unit of evolution is population : An individual may show adaptation and survive. But development of one fit individual will not result in evolution. The individuals may pass on their advantageous characters to their offspring. When the individuals with new characters interbreed in a population, the characters are spread amongst the population. The varieties in the population thus have common ancestors and thus in this way a gradual evolution of more fit individuals must have taken place. PinkMonkey Online Study Guide-Biology 11.1 Darwin’s Theory of Natural Selection Various hypotheses were suggested by scientists to explain the concept of evolution. As a result of many years of careful study and observations, Charles Darwin proposed his theory of evolution. He published a book The Origin of Species in the year 1859. He proposed that the new species came about by a process called ‘natural selection.’ While explaining his theory, Darwin gave an account of many basic facts and deductions and stated how natural selection operates and results in the evolution of a new species. (1) Over-production. Darwin reported that all organisms tend to increase in a geometric ratio provided there are no environmental checks. Lower animals produce a large number of eggs within 10 to 14 days. A female drosophila produces 200 eggs at a time. If all flies from these eggs survive and reproduce with the same rate, they may produce 200 million organisms within a period of 40 to 50 days. Amongst the higher animals also there is a rapid increase in number. A single pair of sparrows may produce as many as 275 million individuals in a span of 10 years. Even slow breeding animals like the elephant may theoretically give rise to 19 million descendants in a period of 750 years. (2) Population Stability. In spite of the high reproductive potential, the number of individuals in a species remains relatively constant, suggesting struggle for existence. (3) Struggle for Existence. There is an inevitable competition between the organisms for space, food, shelter, nesting sites, water, etc. This struggle takes place in three ways- a) Intraspecific struggle b) Interspecific struggle and c) Environment struggle a) Intraspecific struggle takes place between the individuals of the same species. This is often most severe and fatal, as the needs of the individuals of the same species are similar. b) Interspecific struggle takes place between the individuals of different species. In a community, some organisms feed on others. Both animals and plants are affected by this kind of struggle. c) Environmental struggle is the struggle of organisms against the physical environment. Organisms struggle against excess of moisture, drought, extreme heat or cold, lightning, volcanic eruptions, etc. (4) Genetic variations within a species. Animals and plants show variations in physical structure. Some of these variations are simply caused by external conditions (environmental), such as accidents, temperature, food abundance, etc. (e.g. animals look different when they are starving than when they are well fed). Such somatic variations die with the organism and not inherited. Thus, they have no effect on evolution. Heritable variations are called genetic variations. Such variations arising from changes in DNA are passed on within families and to the offspring from the parents, (e.g. parents with a larger stature body generally have larger children than parents with a small statured body). (5) Natural selection, or "survival of the fittest". Organisms struggle for existence. Those individuals who have favorable variations have better chances of living long enough to reproduce. They pass on their advantageous characters to the next generation. Thus, organisms with advantageous characters survive, while those which lack such variations perish. The advantageous characters are passed on to the offsprings generation after generation and the organisms become better suited for survival. Darwin described that nature selects such organisms, i.e. there is natural selection. Herbert Spencer referred to this as ‘survival of the fittest.’ (6) Environmental change. The physical environment changes continuously. There are seasonal changes in availability of moisture, light, severe heat or cold, etc. Mountain ranges are formed where there were no mountains before. Volcanoes erupt and cause changes in the environment. Similarly floods and fires convert plains and forests into temporary deserts. (7) Inheritance of adaptive characters. Because organisms are continually tested by their environment, their forms change to suit new conditions. New advantageous characters are inherited along newer generations and their cumulative effect results in an organism with new characters. (8) Origin of species. Darwin explained that favorable variations are passed on to the offsprings down the generations. After a certain period of time the organisms appear so different from the original species that ultimately a new species is evolved. The basic facts and deductions of Darwin’s theory are summarized as follows: 11.1 (A) Common Origin of Living Organisms There are numerous varieties of living organisms. But they show some basic similarities which suggest that a common early form of life gave rise to millions of species through the process of evolution. There is a great deal of evidence that proves that there is a common origin of all organisms. Figure 11.1 Connecting links (i) The study of comparative anatomy supports the claim of a common origin of organisms. Homologous organs are formed on the same basic plan though they may be modified variously to perform different functions. For example the forelimbs of a bird, bat, whale, horse and man are different in grass appearance and function but have the same basic pattern of skeleton. They must have a common ancestral structure which gave rise to different modifications . Homology is also seen in the structure of eye, brain, joint appendages of arthropods, etc. The basic similarity of vertebrate forelimb structures indicates inheritance from a common ancestor. It is thus evidence for evolution. Occurance of vestigeal organs such as vermiform appendix in man, vestigeal hindlimbs and pelvic girdle in snakes, reduced nictitating membrane in mammalian eye, etc. suggests that these organs were well developed in the ancestors. There are certain animals with intermediate characters between two major groups of animals. They are called connecting links. For example, lung fishes show common features of both fishes and amphibians, Seymouria (extinct) connect amphibia and reptiles. Archaeopteryx (extinct) connects reptiles and birds, and Prototheria (egg laying mammals) connects reptiles and mammals(fig.11.1). All these examples suggest common ancestors of the organisms. (ii) Embryological studies also suggest the common origin of the organisms. The early stages of development of the embryos of fish, salamander, tortoise, hen and man show peculiar similarity. Earlier stages are so similar that they cannot be differentiated. Only later stages show species-specific differences. The similarity of early embryos in closely related animals is an evidence of evolution. (iii) Fossils are the remains of organisms that lived in the past. A study of fossil record helps to build a historical sequence of biological evolution of complex organisms from simple ancestors. Fossil evidence shows that the horse has undergone considerable evolutionary change over a period of 60 million years (Figure 11.2). Adapting to life on the open plains, the horse evolved from a dog-sized, 5-toed browser to a large 1- toed grazer. The modern horse evolved from Eohippus through 14 distinct stages extending through the age of mammals and the age of man. Few important representative stages are Eohippus (Eocene), Mesohippus (Oligocene). Merychippus (Miocene), Pliohippus (Pliocene), and Equus (Pleistocence and recent epochs). Important structural changes during the evolution of horse are : 1. Increase in size from 11" (Eohippus) to about 60" (Equus). 2. Elongation of the 3rd digit, side toes are lost, and only the middle toe and splints of second and fourth digits remain in horses now. (3) Elongation of the head and neck so as that it can reach the ground. (4) The front teeth are modified as chisel-like cropping structure, molars elongated and became adapted for grinding. Thus, evolution of the horse, elephant, camel, etc. show that much can be learned from fossil records. Equus Merychippus Mesohippus Eohippus (Recent) (Miocene) (Oligocene) (Eocene) One toe Three toes Three toes Four toes Two splints Splint of 5 Figure 11.2 Evolution of horse (iv) A comparative study of physiology and biochemistry also supports the common origin for different organisms. The protoplasm of all organisms is more or less same in composition. The chromosomes of all organisms also show similarity in their chemical nature (i.e. nucleic acids and histones). Enzymes, hormones, the nitrogenous waste materials, hemoglobin, composition of blood plasma, types of antibodies and antigens etc. also demonstrate the relationship. 11.1 (B) Recombination as a Source of Variability In organisms which reproduce asexually, the offsprings are identical as they are formed by mitosis. However, in sexually reproducing organisms the offsprings differ from their parents in many respects. This is due to genetic recombinations. During gametogenesis, the homologous chromosomes exchange genes by the process of crossing over. This produces a new combination of genes. The process of fertilization brings together genetic material from two different cells, the sperm and the ovum, which differ in their characters. Thus genetic recombinations take place firstly by bringing together paternal and maternal chromosomes and secondly the by crossing-over mechanism. This process of genetic recombination results in new variations. If during such recombination process any advantageous characters develop, they are passed on to the offspring generation after generation and thus contribute to the evolution of better and strong organisms. 11.1 (C) Role of Selection The process of natural selection plays important role in the following processes. Figure 11.3. Industrial melanism, Biston betularia and its black form B carbonaria on tree trunk in (A) unpolluted area, and (B) polluted area (i) Variations. Variations result due to generic recombinations. If the variations are favorable, (i.e. if they are of some help or advantage), they are passed to the next generation. This can be best studied with reference to certain characters. Human complexion colors vary from almost black, through brown to white. These shades result because of difference in the amount of melanin developed in the skin. In tropical areas such as Africa, sunlight is intense, and melanin develops in the skin and screens out sun’s rays, yet adequate amounts of vitamin D can still be synthesizedin the skin. In the northern areas there is less sunlight. Less melanin is developed so that light can penetrate the skin and synthesize vitamin D. Therefore, humans in the north of the tropic countries tend to be lighter complected. Industrial melanism (Figure 11.3) is another example of favorable variations developed and selected. In the industrial areas of Britain, the soot released from numerous factories is deposited on the tree trunks which made them dark. The normal peppered moth, Biston betularia, has a grey body which more closely matches with the color of lichens on the bark of trees. Some moths have developed melanin. When such dark moths settled on dark tree trunks, they are not noticed by predators. But the original light-colored moths could be easily noticed and killed by their predators and thus diminished in number gradually. The darker variety of moth Biston carbonaria is at advantage in this environment. They escapes predators and survive and reproduce. Similar changes have been observed in nearly 100 other species of insects and spiders. Thus, selection plays an important role in choosing favorable variations. (ii) Adaptations. Any characteristic that is advantageous to an organism is referred to as an adaptation. Adaptations are genetically controlled traits that help an individual to survive and produce offspring in a particular environment. Evolution implies that the surviving species are more adaptive than the those that do not survive. Adaptations can be classified under three categories, structural, physiological and behavioral adaptations. The adaptations may also be described under the following heads when different environmental conditions are taken into consideration. They are described as cursorial adaptations (terrestrial adaptations especially for fast running), fossorial adaptations (subterranean adaptations shown by diggers), aquatic adaptations (shown by animals living in water), scansorial or arboreal adaptations (shown by animals living in or on trees), volant adaptations (shown by animals that can fly), cave adaptations and desert adaptations. Depending upon environmental pressures, animals adjust to the environmental changes. Adaptive features may result by the process of genetic recombinations or mutations. Organisms which show favorable variations can survive and reproduce their kind. Thus, the adaptive features are passed on to the offspring down through generations and in this manner new varieties develop. Selection plays important role in allowing the new variety to survive and thus, a new species evolves from the pre-existing simple species. The paleontological record proves how organisms must have adapted and evolved into more fit and successful individuals. Figure 11.4 Adaptive radiation in mammals Adaptive radiation produces bush-like pattern of evolution Living creatures show many adaptive features. For a fast running body shape, lengthening of the limbs, loss of digits and foot posture are modified. Burrowing animals show a spindle form body, sharp nails and teeth, and short, strong, broad limbs for digging burrows. Aquatic animals show streamlined shape of the body, aquatic respiratory organs (gills), fins as locomotory organs. Flying animals show a streamlined body form, pneumatic bones, feathers, wings, broad and strong sternum and pectoral girdle for muscle attachment, well-developed brain and sense organs, etc. Natural selection operates in micro-organisms also. In the laboratory, bacteria resistant to streptomycin were developed. Their adaptation of streptomycin resistance helped them to survive and reproduce. Similarly a large number of flies have developed resistance to insecticides. Continued exposure to DDT enables the flies to develop resistance. Prolonged application of DDT down the generations selects combinations of genes that provide greater and greater resistance. Thus, continuous genetic recombination and selection results in the establishment of adaptive characters. Similar adaptations which occur in unrelated groups is referred to as convergence, so that animals of different kinds look similar (e.g. fish and whale show convergence). However some animals of the same group show divergence and appear quite different from each other. Divergent evolution is also called adaptive radiation (Fig. 11.4). Animals show adaptations in the locomotory organs and appear different. For example, limbs are modified for walking (mammals) flight (in birds), and swimming (in whales). (iii) Reproduction. Variations resulting after recombinations or mutations may be favorable or unfavorable. Favorable mutations may be described as adaptations. With natural selection new adaptive characteristics get established in the population. Differential reproduction or natural selection Natural selection results not from direct struggle between organisms, but only from differential reproduction. An organism survives in an evolutionary sense by producing more offspring. Those that have more offspring will contribute greater percentage of genes to the gene pool than those that produce fewer offspring. Therefore, if differential reproduction continues in the same manner over many generations, the abundant reproducers will have a greater proportion of genes in the gene pool of the population. Therefore, a new trait that originates in one generation (black dots) spreads by differential reproduction, and becomes a standard feature of the whole population. This is the unit of evolutionary change. Many such units in a population accumulate and alter the organism, ultimately recognized as a new species. Suppose, in a population, a variation arises (11.5 A) in one individual (black dot) and that variant organism produces 3 offsprings. The non-variant organisms (white circles) each produce only one offspring. In the next generation there will be 3 variant types and 9 non-variant (11.5B) (i.e. 25% variants). In the third generation (11.5C) there will be 9 variants and 9 non-variants (i.e. 50% of variant types). In the fourth generation (11.5D) there will be 27 variants and 9 non-variants (i.e. 75% of the total forms). Figure 11.5 Black cells (dots) at are first less numerous and have higher reproductive rate; by fourth generation they outnumber white circle. Differential reproduction rates have changed the heredity of the population. In this manner the proportion of variant organisms goes on increasing and becomes a standard feature of the whole population. The individuals with suitable characters (favorable adaptations) are healthier and will produced more offspring. Thus, differential reproduction (described as ’selection’ by Darwin) plays an important role in evolution. (iv) Speciation. Speciation in simple terms means origin or evolution of new species. Before we study about speciation we must know what a species is. "A species may be defined as a group of physically, biochemically and behaviorally similar organisms that are capable of breeding with each other but not with members of another species." In other words a species is a group of fertile organisms that can interbreed and produce fertile offsprings only among themselves. A population is a group of interbreeding individuals (i.e., a species). A species may be subdivided into subspecies, races, varieties, demes, etc. A deme is an interbreeding subunit of species. If demes are isolated (geographically) they can give rise to new species. A variety is a subtype within a deme (e.g. different types of roses). A race is a genetically distinctive interbreeding group within the species. Several human races such as caucasians (European and other white races, Arabs, Egyptians and Indians), Negroid (Black Africans), Mongoloid (Chinese, Japanese, Koreans), etc. were applied term for once isolated geographical populations of interbreeding individuals which gave rise to common characteristics such as appearance, skin color, body build etc.due to deisolation of populations by migration via modern travel, these terms are becoming obsolete. Subspecies consists of races and includes several populations. Gene Pool (Figure 11.6). Population is a geographically localized group of individuals of the same species. A total collection of all genes in a population is called a gene pool. Thus, gene pool will have all genotypes, (i.e. genes of the organisms within that species). Figure 11.6 The Gene Pool A population in which the gene pool changes undergoes evolution. This change can take place due to recombination, mutations or by natural selection. If genes are exchanged between two different populations it is called gene flow. New genes are introduced in local populations by immigration of individuals of the same species by gene flow. PinkMonkey Online Study Guide-Biology Reproductive Isolation. When populations are isolated there is an interruption in interbreeding between them, and so gene flow takes place. The isolating mechanisms are of two types. (a) Prezygotic isolating mechanisms and (b) Postzygotic isolating mechanisms (a) Prezygotic isolating mechanisms include habitat isolation, seasonal isolation, ethological isolation and mechanical isolation. In all these types there is failure of zygote formation. Organisms may occur in different habitats; or their breeding periods differ; or their behavioral patterns are different or mating is not possible because of difference in size of reproductive organs. (b) Postzygotic isolating mechanisms include gametic mortality, zygotic mortality, hybrid inviability, development hybrid sterility or segregational hybrid sterility. It means either the gametes die, or if they meet, a zygote fails to develop, or if the embryo grows, the reproductive organs do not develop due to abnormal chromosomal combinations. Yes, I wish to receive information about Toyota Products & Promotional Offers. *conditions apply When species are geographically separated, they fail to interbreed and are called sympatric species. If they remain in the same habitat, but due to genetic changes through recombination or mutation fail to interbreed, they become allopatric species. Thus, due to isolation, an interruption in gene flow between sister populations takes place. If such sister species are separated for long periods, the differences become pronounced enough to prevent interbreeding. Thus, reproductive isolation develops and a new species is formed. Thus, the origin of species is a process regulated by natural selection and isolation. SUMMARY 1. Geological time scale explains that the deepest or oldest rocks show fossils of primitive forms and more recent rocks show fossils of higher animals. 2. There is basic common pattern of development of successive fossilized organisms. 3. Darwin suggested following facts: Fact (1)Without environmental pressures,organisms increase in number in geometric ratio. Fact (2) In spite of overproduction, the number of any particular organism remains more or less stable. Because of enormous growth in number there is struggle for existence. Fact (3) There are genetic variations. Fact (4) Environmental changes, and natural selection influence survival and new species are formed. 4. Study of comparative anatomy, homologous organs, vestigeal organs, study of fossils, physiology and biochemistry suggest common origins of living organisms. 5. Recombinations take place during sexual reproduction and result in variations. 6. Favorable variations are selected. 7. Favorable variations are described as adaptations. 8. Differential reproduction plays an important role in evolution. 9. Differential reproduction and isolation result in speciation. CHAPTER 12 : HUMAN EVOLUTION 12.0 Introduction All humans are members of the species Homo sapiens (Latin = "man who is wise"). Today, man may be considered a dominant species on the earth due to his: (1) Accumulation of achievements (e.g., language, tools and methods developed to feed and, shelter, organization in groups, achievements in arts, commerce and science); and (2) Cultural and biological evolution due to biological attributes or characters such as (a) excellent stereoscopic vision(b), a large brain with a unique capacity for learning and reasoning. (c) hands that can grasp and manipulate objects. (d) upright bipedal (two-footed) posture. (e) specialized teeth for an omnivorous diet. (f) presence of the foramen magnum below the cranium so that the head can be moved about freely. These biological characteristics appeared gradually over 70-80 million years of primate evolution. Homo sapiens belongs to the mammalian Order-Primates which also includes tree shrews, tarsiers, lemurs, lorries, monkeys and apes. The primate order is divided into : (1) Sub-order - Prosimi (Pro = almost, Simians-apes) e.g. lemurs, lorries, tarsiers, shrews. (2) Sub-order - Anthropoidea (Anthrop = man, oid = like) e.g. monkeys, apes, humans are closely related species are placed in super family - Hominoidea (man-like). Present and past Hominoids having man-like features are placed in family - hominidae. There were at least two species of the genus Homo (Homo habilis and Homo erectus), but the only living survivor is Homo Sapiens. We place ourselves in the order Primate because we resemble the Primates more than any other animal. Before we get to know our ancestors, the major groups of primates (Figure 12.1 A) related distinctly to human evolution are : Tree shrews - which resemble those mammals from which the primates arose. Tarsiers - with long tails, long hind limbs, stereoscopic vision, improved grip form, the most advanced prosimians because they are like the monkeys. Lorises and Lemurs - which colonized early in their evolutionary history, until humans arrived some two thousand years ago. Monkeys - can walk upright, they are relatively intelligent, live in groups, females care for the young, they have larger brains than prosimians, and have stereoscopic and color vision. Apes - are the closest kin to humans in size, form, physiology and behavior. They have bigger brains, and brachian style of locomotion (swing by their arms as shown in figure 12.1B) which is related to the evolution of an erect body posture and elongation of arms. Apes and humans constitute the hominoids. Besides humans, gibbons, orangutans, chimpanzees and gorillas are the only living forms of hominoids. Gibbons and orangutans are arboreal brachiators. Orangutans, chimpanzees and gorillas, when on ground walk on all fours, supporting their weight on their fists, (called - knuckle walkers). Chimpanzees and gorillas are more intelligent, can use simple tools and have the ability to learn sign language. Studies of DNA sequences have shown that humans are more closely related to chimpanzees than to any other primates. Human and chimp DNA are 99 percent identical; but that is not to say that the humans have descended from fossil chimps. Fossil records shows that humans and apes have both descended from a common ancestor, or such genera as Dryopithecus, Ramapithecus and Sivapithecus which lived in Africa and Asia. A brief account of various genera related with human evolution is adressed in section 12.3. 12.1 Palaeontological Evidences -Our Ancestors Fossil records of human evolution is quite incomplete and we have much to learn yet. In 1863, T.A. Huxley explained human evolution in his book Man’s Place in Nature. In 1871, Charles Darwin published his ideas of human evolution in the book The Descent of Man. Later on many attempts have been made to find the missing link between man and ape in the form of an original creature or its fossil. Eugene Dubo unearthed the first fossil record of an ancestor of man in the form of a small part of skull and jaw bone. Between 1920 to 1930 many human-like fossils were found in China called "Peking Man" or Sinanthropus. But these fossil evidences do not form a neat chain of links leading from ancient ape to the modern human. Yes, I wish to receive information about Toyota Products & Promotional Offers. *conditions apply It appears from the fossil evidence, that human and apes have both descended from a common ancestor, called Dryopithecus, that lived over 20 million years ago. At about the same time the first human-like fossils were found in India and Africa in the form of such primate genera as Ramapithecus and Sivapithecus. The arrangement of teeth was like our own, indicating that Ramapithecus was one of our ancestors. The next known genus Australopithecus africanus (1.5 to 3 millions years ago) appeared in Africa. It had a rounded skull with a brain capacity of 450 to 700 cm3 (compared to 1000 to 2000 cm3 for humans), apparently walked upright, and was about 5 feet tall. Some controversy still exists about these human ancestors and the gaps in evolutionary sequence, because the relevant fossils are rare, the remains did not survive until now, or have not yet been found. There is less controversy over the more recent stages of human evolution. The fossils are more abundant and there are fewer gaps. They show that Homo erectus, the first known member of our genus, followed Australpithecus. Some 2 to 3 million years ago Homo erectus emerged as an erect, bipedal creature, with a receding forehead and human-like skeleton. Remains of H. erectus have been found in Africa, South East Asia and China. The first fossil that belongs to our own species, Homo sapiens, appeared as recently as 100,000 to 40,000 years ago, and resembles us so closely that we call it human (Fig. 12.2). Homo sapiens survived as a result of erect bipedal posture, increased manual dexterity, feet suited for walking and running, and better developed creative brains. Archeological records of human evolution indicate that early humans started out as small bands of hunters who killed animals for food and supplemented this with foraged and gathered items. The hunt-gatherer cultures allowed humans to exploit agriculture, about 10,000 years ago. Humans began to farm seriously around 8,000 BC and there was full fledged agriculture in many places just after 4000 BC. The agriculture allowed establishment of stable populations, and the development of technology permitted the survival and growth of human population. 12.2 Ancestral forms of Homo sapiens As mentioned earlier, the palentological (fossil) record for human evolution is not continuous. Ever since the theory of evolution become scientifically acceptable, biologists and anthropologists have been trying to find the ‘missing link’, the species that would bridge the gap between humans and the great apes which are the closest living relatives of humans. The fossils collected from various regions indicate possible trends in human evolution. Some important ancestral forms of Homo sapiens are described below. (1) Dryopithecus It appears from fossil evidence, that humans and apes (Hominids) have both descended from a common ancestor, called Dryopithecus, that lived 20 million years ago (Miocene epoch). The first Dryopithecus fossils were found in 1930 on an island in Africa’s lake Victoria by Dr. Lewis Leakey. Later on they were also found in Africa, N. India, China and Europe. The Dryopithecus were first described as Sivapithecus, Proconsul and Ramapithecus. Dryopithecus were contemporary to another genus, Pliopithecus. These appear of be ancestors to apes and humans. Important anthropoid characters of Dryopithecus included a somewhat flattened face, a shortened jaw, enlarged incisors (typical of apes, but not human), arms and the legs of the same length and must have assumed a semi-erect posture on the ground and were more bipedal than the other apes. Figure 12.3 Human Evolution (2) Australopethicus Australopithecus africans represents the next known step in human evolution. The fossil remains from Africa belonged to early Pleistocene era (1.2 - 3 million years ago) and named by Raymond Dart in 1924. It weighed 40-60 pounds, bipedal form of primates, walked in an entirely erect posture, a distinct lumbar curve and had human-like teeth. The dental arch was a smoothly rounded parabola. However, Australopithecines had jaws and teeth larger than those of modern man. It had an ape-brain (capacity 450-700 cc.) rather than a human brain. They were living in groups assumed to be using tools (made by chipping pebbles) since the fossils are often found with piles of bones of hares, birds, baboons. This indicates that they were true hunter scavengers, who actually hunted animals they ate. Another form of hominid, Australopithecus robustus, appeared later, weighed 150-200 pounds, walked erect and had a brain size similar to that of the ape. Another type of hominid creature lived in the place and period as Australopithecus and was also bipedal, but had a larger brain and used tools. It was placed in genus Homo - its full name is Homo habilis (habilis = mentally skillful). PinkMonkey Online Study Guide-Biology (3) Homo erectus Remains of Homo erectus have been found in Africa, South East Asia and China and belonged to a later part of Pleistocene period. It lived from over 2 million years ago up to about 300,000 years ago. It contains specimens such as Java man (Pithecanthropus erectus), and Peking man (Sinathropus pekinensis), classified together as members of the species Homo erectus. Homo erectus had a receding forehead, heavy jaws and prominent bony brows. It was more than 5 feet tall, weighed 70 kg. had a human like skeleton and apparently walked upright as indicated by the position of the foramen magnum in their skulls - which is same as in modern humans. (Refer to figure 12.7). The cranial capacity was about 970 cm3 . Homo erectus lived in caves and had more-or-less permanent home bases, made a fire and brought it indoors to cook food or split stones. This stage of human evolution is correlated with colonization and migration to colder areas (Europe, China) and communal living in caves. The pre-human brain of Homo erectus could produce social and technological solutions - such as fire, clothing, stored food etc. to survive cold winters. 4) Homo neanderthalensis (Neanderthal Man) This first specimen of this kind was discovered in Neander valley of Germany in 1856. These early humans existed some 150,000 years ago and were widespread in Europe, Asia and North Africa. They closely resembled humans. This human species was short, stocky, with heavy jaws, a receding chin, with an erect stance and the hands used like man. The brain was as big as the modern man and with almost same cranial capacity (1450 cm3 ). They became extinct about 25,000 years ago probably in competition with Homo sapiens. Another theory is that they interbred with Homo sapiens and their distinctive characters disappeared into the common human gene pool. Culturally, Neanderthals were more advanced than the Homo erectus. They lived in caves, made simple tools, dug pits to trap large animals and were even cannibalistic sometimes. (5) The Cro-Magnons Fossils of men and women were discovered in France in 1868. They were very much like the modern man, therefore, Cro-Magnon man has been considered as a sub-species of Homo sapiens. The Cro-Magnons were about 150 cm tall, with a rounded forehead, distinct chin, narrow nose and broad face. They walked erect and were swift footed. The cranial capacity was 1650 cm3. They lived in caves, were experts at hunting, painting and became the farmers and metal workers of Egypt, philosophers of Greece, Indians of the America and Eskimos of the Arctic. They buried their dead according to their customs. The Cro-Magnons became extinct about 20,000 years ago and were more advanced than the Neanderthals. Figure 12.5 Cro-Magnon Man: Skull and restoration As the Cro-Magnons spread over the Earth; the environments exerted selective pressure. This resulted in different groups of people now called races, which differ in their skin color, predominant blood type, form, hair color, body features and size. Depending upon where one draws the lines we can count about 6 to 34 modern races. Further evolution of modern man after Cro-Magnon’s was more of culture than structure. (6) Homo sapiens They first appeared less than 1,00,000 years ago. During the evolution of Homo sapiens, we have seen that our ancestors changed from ape to apelike to human-like to human, and thus changed in several ways. For example (1) They changed from four-legged to two-legged posture, became erect and bipedal. (2) The feet lost their hand like features and became suited for upright walking and running. (3) The hands became more dexterous, free to manipulate, the thumb became opposable with precision and power grip. (Figure 12.6) (4) The brains grew larger, and a more creative intelligence developed. Figure 12.6 Hands and feet of tarsier, orangutan, gorilla and man The following evolutionary changes are seen in man: 1. Erect posture. 2. Balancing of head on neck. 3. Vertebral column showing four curvatures. (Figure 12.7 A) 4. Forelimbs shorter than hind limbs. 5. Small jaw and teeth. 6. The dental arches changed shape, all the teeth moved closer together and the canine teeth became shorter (Figure 12.7 B). 7. Man’s foot develop into a sturdy support with complete base. 8. The toes shortened and the big toe moved into line with others. The foot became arched. 9. Apes have long, slanting hip girdle. Man’s pelvis is short, wide and vertical. It permits erect posture and frees hands for manipulation. (Figure 12.7C) 10. Brain expansion (increased cranial cavity, complex cerebellum and cerebrum) and the use of tools are associated with the human evolution (12.D & E). Greater curvature of spine in human Figure 12.7A Figure 12.7B Change in shape of dental arches Figure 12.7C Pelvic girdle Figure 12.7D Figure 12.7E Changes in the proportion of the skull from ape to human. Note position of foramen magnum(arrows) Thus, we find that we are basically the same as our Cro-Magnon ancestors, who lived about 35,000 years ago. SUMMARY (1) Human beings, Homo sapiens, are primates whose ancestors were arboreal during the mesozoic era. (2) The arboreal characters were highly developed in anthropoid apes, which probably had a common ancestor with human in species like Dryopithecus during the Pliocene. (3) The two groups, apes and human ancestors diverged and the human ancestors gradually adapted for erect, bipedal locomotion on the open plants. (4) Further evolution of man revolved around the use of brain and hands to collect food, to make tools for hunting, collection and storing of food, colonization, agriculture and finally to make fires and clothes which permitted hominids to spread from their original home in Africa. (5) A common ancestry for a great apes and man is based on similarities in DNA content, chromosome number and banding patterns of chromosomes. CHAPTER 13 : THE UNITY AND DIVERSITY OF LIFE 13.0 Introduction The living world consists of millions of species of organisms. These present enormous diversity ranging from micro-organisms to the highest evolved plants and animals. The knowledge about all these organisms will be highly confusing, meaningless and useless if they are not properly identified and arranged systematically. The systematic arrangement of properly identified and named organisms is called classification, systematics or taxonomy. (taxis = arrangement, nomos = order or law) is a branch of biology which deals with collection of organisms, their identification, nomenclature and systematic grouping or classification into various categories. This is done on the basis of similarities and differences of their morphological, anatomical, cytological, genetical, physiological, biochemical, developmental and other characteristics. The similarities of characteristics between species or groups of species indicate their relationship. This is also gives us some idea about their phylogeny (i.e. their evolutionary history). The classification of plants into various groups is called plant taxonomy or systematic botany. Similarly, classification of animals is called animal taxonomy or systematic zoolog 13.1 Concept of Species The original concept of species has undergone a considerable change during the progress of taxonomy. John Ray (1627-1705) was the first to distinguish genus and species. However, the clear morphological concept of species was first given by Linnaeus (1707-1778). Later on, Darwin proposed the biological concept of species. The concept was further modified by Ernst Meyr. Carolus Linnaeus Morphological concept of species by Linnaeus. A species is the group of individual which resemble each other in most major morphological (vegetative and reproductive) characteristics. Biological concept of species by Darwin. In addition to morphology, the biological concept also takes into consideration ecology, geography, cytology, physiology, behavior, etc. According to the biological concept, a species is a group of individuals which resemble each other in morphological, physiological, biochemical, and behavioral characteristics. These individuals are capable of breeding with each other under natural conditions, but are unable to breed successfully with members of other species. Thus, species is a group of fertile organisms that can interbreed and produce fertile offspring only among themselves. The recent trend is to consider species as the groups of actually or potentially interbreeding natural populations of closely resembling individuals (Ernst Meyr). A species is considered to be the smallest, most basic unit of classification in most of the systems. It was thought to be an indivisible, stable and static unit (taxon). However, in modern taxonomy, sub-divisions of species, such as sub-species and populations, have been created which aid in our understanding through classification. 3.2 Taxa and Categories (1) Taxa (Singular: Taxon): A taxon is the taxonomic group of any rank in the system of classification (H.J.Lam, 1948). For example, in plant kingdom, each one of the following such as, angiosperms, dicotyledons, polypetalae, Malvaceae, Hibiscus esculentus, etc. represents a taxonomic group i.e. a taxon. A taxon may be a very large group such as a Division (e.g. angiosperms), or it can be a very small group such as a species (e.g. Hibiscus esculentus). (2) Categories (Singular: Category): In the system of classification, the various taxa are assigned definite ranks or positions according to their taxonomic status. Each such taxonomic rank is called the taxonomic category. The various major categories in the classification of plant kingdom are Kingdom, Division (Phylum), Class, Series, Order, Family, Genus and Species. The difference between the taxon and the category should be clearly understood. For example, when we say "Division- Angiosperms", 'Division' represents the taxonomic category while 'angiosperms' represents the taxon. Thus, a taxon is a group of organisms (living beings), whereas a category only indicates the rank or status of the taxon in the systematic hierarchy. 13.3 Systematic Hierarchy Arranging various taxonomic categories in their proper order on the basis of their taxonomic ranks is called taxonomic hierarchy (systematic hierarchy). In this hierarchy, the kingdom represents the category of highest rank while the species is the category of the basic rank. Following is an example of the taxonomic hierarchy representing the methodology of classifying a plant and an animal in a scientific manner. Categories Taxa (Plants) Tax (Animals) Kingdom Plantae Animalia Sub-kingdom Phanerogams ---------- Division/ Phylum Angiosperm Chordata Sub-phylum ----------- Vertebrata Class Dicotyledonous Reptilia Sub-Class Polypetalae Diapsida Series Thalamiflorae ----------- Order Malvales Squamata Family Malvaceae Elapidae Genus Gossypium Naja Species herbaceum (cotton) naja(Cobra) 13.4 Binomial Nomenclature The system of giving a scientific name to each properly identified plant or animal is called nomenclature. A system of nomenclature of plants and animals in which each scientific name consists of two parts or sub-names is called the system of binomial nomenclature. Thus according to this system the scientific name of sunflower is Helianthus annuus and that of man is Homo sapiens. In the above names, the first part of the name (i.e. Helianthus or Homo) represents the name of the genus (generic name). The second part of the name (i.e. annuus or sapiens) represents the name of the species (specific name). This system of binomial nomenclature was introduced by Carolus Linnaeus in 1753 in his book Species Plantarum. The system follows certain rules, such as : 1. The scientific name must be in Greek or Latin language. 2. Genetic name should come first and must begin with a capital letter. 3. The same name should not be used for two or more species under the same genus. 4. The scientific name must be either underlined or written in italics. 5. The name of the author who first described the species should be written after the specific name (e.g. Homo sapiens Linnaeus). Carolus Van Linnaeus : (1707-1778) Carolus Linnaeus is popularly known as the father of taxonomy, because of his remarkably outstanding contributions to the field of systematics. Linnaeus was a great Swedish naturalist. He studied at the University of Lund and later worked in the University of Uppsala. He described nearly 6000 plant species and 4000 animal species from different parts of the world. Linnaeus published a number of books on taxonomy. The most notable among these are Systema Naturae (1735) and Genera Plantarum (1737) which contain the artificial system of classification of angiosperms based on the sexual characters (e.g. characters of stamens). His book Species Plantarum (1753) is a landmark in the history of taxonomy. It contains the binomial system of nomenclature which has been practiced ever since. 13.5 Principles of Classification While developing a system of classification of organisms, certain basic principles are observed. Some of these are as follows: (i) Morphological criteria: Morphology forms the primary basis for classifying organisms into various taxonomic groups or taxa. In earlier artificial systems, only one or a few morphological characters were taken into consideration (e.g. plants were classified into herbs, shrubs, trees, climbers, etc. on the basis of their habit). The sexual system proposed by Linnaeus was based mainly on the characteristics of stamens and carpels. Later on, in the natural systems of classification (e.g. Bentham and Hooker's system of classification of plants), a large number of morphological characters were taken into consideration. As a result, classification of plant groups was more satisfactory and their arrangement was showing natural relationships with each other. The similarities in the morphological characters are used for grouping the plants together. Because, these similarities indicate their relationships. On the other hand, differences or dissimilarities of characters are used for separating the plant groups from each other. Plant groups with greater differences are considered to be unrelated or distantly related. fields marked (*) are mandatory For example, all flowering plants with ovules enclosed in an ovary cavity are grouped together as Division - Angiosperms whereas, the angiosperms are further classified into two classes: Dicotyledons and Monocotyledons, on the basis of differences of the characters of root system, leaf venation, flower symmetry and number of cotyledons in the embryo. (ii) Phylogenetic considerations : In the more recent systems of classification of plants, a greater emphasis is given on the phylogenetic arrangement of plant groups, an arrangement which is based on the evolutionary sequence of the plant groups. These systems also reflect on the genetic similarities of the plants. Some of the phylogenetic systems of classification of plants are the ones proposed by Engler and Prantle (1887-1899), Bessey (1915), Hutchinson (1926 and 1934), etc. However, none of these or any other systems is a perfect phylogenetic system. This is because, our present knowledge of the evolutionary history of plant groups is very fragmentary and incomplete. At best, the present day systems can be described as the judicious combination of both natural and phylogenetic systems. Modern taxonomy takes into consideration data available from all disciplines of botany for classification of plants. This helps immensely in establishing inter-relationships of various plant groups. As a result, taxonomic arrangement becomes more authentic and convincing. (iii) Chemical taxonomy or chemotaxonomy: is a comparatively recent discipline. Chemotaxonomy is the application of phyto-chemical data to the problems of systematic botany. The presence and distribution of various chemical compounds in plants serve as taxonomic evidences. Nearly 33 different groups of chemical compounds have been found to be of taxonomic significance. (iv) Numerical taxonomy : Application of numerical methods (data) in the classification of taxonomic units is called numerical taxonomy. Edgar Anderson (1949) was the first to make use of numerical taxonomy in the classification of flowering plants. It involves exhaustive quantitative estimation of taxonomic characters from all parts of the plant as well as from all stages in the life cycle. The numerical data thus collected for various plant groups is tabulated systematically. Computers are used for this purpose. The main objective of numerical taxonomy is to clarify and illustrate degrees of relationship or similarity in an objective manner. This branch is becoming an indispensable aid in modern systematics. SUMMARY - CLASSIFICATION (1) Classification is essential for the proper study and easy reference to the immense variety of life forms. (2) Systematics deals with identification, nomenclature and taxonomic classification of organisms. (3) Species has a great significance as a taxonomic unit. (4) Recent taxonomy gives more importance to sub-species and populations. (5) In the systematic classification of organisms, various taxa are arranged in the descending order of their taxonomic categories as per the taxonomic hierarchy. (6) Modern taxonomy makes use of the data from all branches of botany, including genetics, cytology, ecology, chemotaxonomy, numerical taxonomy, etc. in order to develop a phylogenetic system of classification of plants. CHAPTER 14 : VIRUSES 14.0 Introduction A five-kingdom classification system fails to classify viruses because they are not considered to be living. They neither reproduce independantly nor utilize energy. Viruses are now defined as ultramicroscopic disease-producing entities living in a host as obligatory intracellular parasites. Brief history Viruses were not known to biologists for a long time due to thier ultramicroscopic structure although its presence was apparent by infectious diseases which were not due to bacteria. They attracted the attention of investigators in the 19th century when mosaic disease (TMV) caused severe damage to commercially important tobacco crop. Figure 14.1 A few different shapes of viruses Mayer (1886) took the initiative and demonstrated that the disease could be transmitted just by applying the sap of infected leaves to the leaf of healthy plant. Mayer thought that the causative agent was a bacterium. A crucial experiment was performed by Russian biologist Iwanowsky (1892) who demonstrated that the sap of infected leaves, even after passing through the finest porcelain filter (which prevents bacteria to pass through), remained infective. He, therefore, ruled out the presence of bacterium but could not think of any other causative agent. Dutch microbiologist Beijerinck (1898) confirmed Iwanowsky’s findings and suggested that the causative agents were not any submicroscopic particles but the fluid itself which he called "contagium vivum fluidum" which means contagious living fluid. This was later on called viron (meaning poison) and the disease causing agent called virus. Twort (1915) and d’ Herelle (1917) independently discovered viruses attacking bacteria for the first time. After the discovery of the ultramicroscope, the controversy was finally laid down to rest when W. M. Stanley (1935), the American biochemist, isolated the virus in crystalline form and showed that even in this state it retains infectivity. These findings gave inspiration to other scientists all over the world to study more aspects of viruses. This marked the beginning of a new branch of science called virology. General characters: A large number of viruses are now known. They exhibit diversity of form and infect a number of organisms. Despite diversity of form and structure, they show the following important characteristics common to all viruses: 1) They are ultramicroscopic disease-producing entities. 2) They have no cellular organization and also no metabolic machinery of their own. 3) They are simple in structure, basically composed of nucleic acid wrapped up in a protein coat. 4) Nucleic acid is only of one type, either DNA or RNA, but never both. 5) They are obligatory intracellular parasites as they are completely inactive outside the host. 6) They multiply within the host by commandeering the metabolic machinery of the host cell. 7) They are specific in action, i.e. they always infect particular organ or organism. 8) They are incapable of growth and division. 9) They can be crystallized and even in crystalline form, they retain their infectivity. 10) They are unaffected by antimicrobial antibiotics. 11) They may undergo mutations. Size and shape : Viruses are minute entities, even smaller than the smallest bacterium. They can be seen only under electron microscope as small particles called virons. Being minute, they are measured in millimicrons (1m  = 1/1000  ). Generally they vary from 10 m to 300 mð in size. Viruses occur in three main shapes, viz. (I) Polyhedral or spherical, e.g. adeno virus, herpes virus etc. (II) Helical or rod-like, e.g. tobacco mosaic virus, (TMV), influenza virus, etc. (III) Complex or irregular, e.g. bacteriophage, vaccinia, etc. Structure: The virus is composed of two major parts: (I) Capsid and (ii) Nucleic acid. Figure 14.2 A generalized structure of a virus The capsid is the outer protective coat mostly made up of specific protein. It protects nucleic acid from inactivation by enzyme nuclease in the environment. It is often composed of many identical subunits called capsomeres. The shape and arrangement of capsomeres determine the shape of the virus. Some highly specialized viruses, for example. influenza virus, mumps virus etc. show an outer covering called an envelope which contains cell membrane obtained during exit of the virus from its host cell. The nucleic acid is in the central core. Unlike living organisms it contains a single molecule either of DNA or RNA, but never both. Nucleic acid is the only active part of a virus, hence viruses are sometimes called "wandering genes". The infectivity of virus is due to nucleic acid while host specificity is determined by the protein coat. The capsid in close contact with nucleic acid, is known as nucleocapsid. Viruses may be enveloped or non-enveloped (naked). Chemical composition: A virus is a nucleoprotein, i.e. mainly consisting of nucleic acid and proteins. Nucleic acid is-- either DNA or RNA, but never both. When only RNA is present, genetic information is solely carried by RNA, which is the unique property of virus. The envelope, if present, contains lipoproteins. The lipid is mostly derived from the host plasma membrane while the protein is virus coded. Viruses normally do not possess any biosynthetic enzymes. PinkMonkey Online Study Guide-Biology Figure 14.3 Tobacco mosaic virus (TMV) (plant virus) Classification of viruses : According to the type of hosts they infect, viruses may be classified as one of the following three types: (i) Plant viruses: These are pathogenic viruses which infect plants. They are usually rod-shaped, containing nucleic acid in the form of RNA, e.g. tobacco mosaic virus (TMV), beet yellow virus (BYV) etc. The capsomeres of TMV virus are elliptical and arranged helically around the central nucleic acid core (fig. 14.3). Common plant viral diseases are (a) mosaic disease of tobacco, papaya, apple etc., (b)black ring spot of cabbage, (c) leaf-roll of potato, and (d) spotted wilt of tomato. (ii) Animal viruses: These are pathogenic viruses infecting animals. They are generally polyhedral or spherical in shape. The capsid in some is surrounded by envelope, and the nucleic acid is either DNA or RNA. According to the type of tissue which they infect, they are as follows: (a) Dermatotropic: Viruses infecting the skin, e.g. measles, chicken pox. (b) Viscerotropic: Viruses infecting viscera, e.g. yellow fever, jaundice, mumps. (c) Neurotropic: Viruses infecting nervous system, i.e. polio, meningitis. (iii) Bacterial virus: These are pathogenic viruses infecting bacteria and are called bacteriophages or simply phages. their nucleic acid is DNA, e.g. T2, T4, T6 bacteriophages. Significance 1. Viruses are a kind of biological puzzle to biologists as they are at the threshold of living and non-living, showing the characteristics of both. 2. Viruses are used by humans in eradicating harmful pests like insects and in controlling the population of organisms such as rabbits by inducing viral infection. Thus they are used as a form of biological control. Figure 14.4. Adenovirus (animal virus) 3. Viruses have gained a prominent position in world because of their value as biological research tools. Due to simplicity of structure and rapid multiplication, they are widely used in research, in the fields of molecular biology, medicine and genetic engineering. Their role in fundamental research to unlock the intricate phenomena of life, can never be over- emphasized. Figure 14.5 Bacteriophage ( bacterial virus ) 4. Viruses have also concerned agriculturists. Apart from causing diseases in crops, bacteriophages attack the nitrogen fixing bacteria of the soil and are responsible for reducing fertility of the soil. 5. In industry, however, viruses are used in preparation of sera and vaccines to be used against diseases like rabies, polio, etc. The multiplication of viruses in bacterial cell is also utilized in the production of antibodies. Pathogenic nature of virus Viruses are causative agents of various dreadful diseases in plants, domesticated animals and man. A number of plants like tomato, tobacco, potato, sugarcane, etc. are affected and destroyed every year by viruses. Many domesticated animals are also destroyed. The common mammalian viral diseases are foot-and-mouth diseases of cattle, encephalomyeletis of horse, distemper of dog, rabies, etc. Common human diseases caused by viruses are mumps, measles, chicken pox, small pox, herpes, influenza, common cold, jaundice, polio, etc. Figure 14.6 Pathogenic human viruses Viruses and cancer Cancer is an uncontrollable and unorganized growth of cells causing malignant tumors, the cells of which have the capacity to spread indiscriminately anywhere in the body. Cancers grow by progressive infiltration, destruction and penetration of the surrounding tissues. It is curable in the initial stage but in the last stage called metastasia, the tumors break apart and the cells spread to other organs, the functions of which get disrupted, hence causing death of an individual. In the past it was thought that cancer was not caused by viruses, but in recent years, there have been increasing evidences to prove that the cancer is caused by the DNA virus called simian virus (SV-40) and a group of RNA viruses called retroviruses. The cancer causing-viruses are also called oncogenic viruses. Cancer can be cured in its initial stages by radiation, chemotherapy and surgery. Early diagnosis greatly decrease the hazards of cancer. It is believed that viruses are involved in leukemia, sarcomas and some kinds of breast cancer. Virus and Aids AIDS (Acquired Immune Deficiency Syndrome) is a recently discovered sexually transmitted viral disease. It is caused by Human Immuno Deficiency Virus (HIV), the target cell of which is T4 lymphocyte of the host, which usually forms the main line of defense. Due to failure of the human immune system, sufficient antibodies are not formed and the human body becomes susceptible to various infections. The disease is transmitted during blood transfusion, through sexual contact, from infected mother to the child during pregnancy or through breast feeding . There is currently no cure for AIDS. The treatment of AIDS, therefore, depends upon the efforts to check the secondary opportunistic infections attacking AIDS patients, as well as slowing or halting replication of the HIV virus. 14.1 KINGDOM : MONERA These are the oldest, simplest and most numerous microorganisms. They are distinguished by the following characters: I. They are prokaryotes. II. They are mostly unicellular, but may be in the form of colonies or filaments of independent cells. III. Their mode of nutrition is mainly absorptive, but some are photosynthetic or chemosynthetic. IV. They are usually nonmotile, but some may have flagella and gliding movements. Cilia are absent. V. Their reproduction is primarily asexual, by fission. Monera includes heterogenous microorganisms including archaebacteria, eubacteria, actinomycetes and cyanobacteria. (a) Archaebacteria : (Archaeos : old) Figure 14.7 Archaebacteria These are ancient bacteria which probably evolved 3 billion years ago. And are now known as "living fossils". They are biologically different from the present day bacteria in two respects, i.e. cell wall does not contain muramic acid, but it is composed of proteins and polysaccharides and the cell membrane consists of branched chain lipids. This enables them to tolerate the extremes of heat and pH. They are divided into two sub-groups: (i) Methanogens : These are strictly anaerobic bacteria which produce methane (CH4) from CO2 and formic acid, hence the name. They are present in salty, marshy places, in the stomach of cattle and in organic matter or sewage. Methane gas produced in biogas plants is due to these bacteria. They are also called halophiles as they have an affinity for salt. They can cause spoilage of salted fish. Examples: Halobacterium, Halococcus. PinkMonkey Online Study Guide-Biology (ii) Sulphur- dependent bacteria : These are aerobic bacteria which convert sulphur either into sulphuric acid (H2SO4) or into hydrogen sulphide (H2S). Hence, they are present in hot sulphur springs. They can tolerate highly acidic pH (pH=2) and high temperature (about 80o C). Hence, they are also called thermoacidophiles. Examples: Thermoplasma, Sulfolobus (b) Eubacteria (Eu: true): These are "true" bacteria ubiquitous in nature, i.e. they are found practically in all the environments, at all the attitudes and depths, in extremely low and high temperature, in fresh as well as in marine water and in bodies of plants and animals both living and dead. In fact, it is difficult to name any place where bacteria are not found. They show the following general characters: Figure 14.8 Forms of Eubacteria Shape and size : They are unicellular microorganisms of various shapes and accordingly, they are called cocci (spherical), bacilli (rod-shaped), spirilla (spiral) and vibrios (broken spirals or comma shaped). Their sizes vary from 0.1 to 20  in breadth and 0.2  to 80  in length. Locomotion : They are generally non-motile, but motile bacteria may have flagella at one end, at both ends, or all around the cell. Cell structure : Their cell wall contains peptidoglycan and muramic acid. Their cytoplasm is without streaming movements and without endoplasmic reticulum. However, free ribosomes are present. Mitochondria are absent but respiratory enzymes are located on the surface of mesosomes which are invaginations of plasma membrane. Golgi complex and true plastids are absent. However, photosynthetic bacteria show chromatophores containing bacteriochlorophyll (e.g. purple-S-bacteria) or chlorobium chlorophyll (e.g. green-S-bacteria). All three types of RNA are present. Cells are prokaryotic, i.e. without nuclear membrane, nucleoplasm and nucleolus. They contain a single molecule of circular double stranded DNA attached to the plasma membrane at one point. Respiration : They are aerobic or anaerobic. Nutrition : They show autotrophic or heterotrophic mode of nutrition. Autotrophic bacteria are of two types, viz., photosynthetic, which produce food material by using light energy (e.g. purple-S-bacteria and green-S-bacteria), and chemosynthetic which produce food material by using chemical energy which is derived by oxidizing certain inorganic compounds (e.g. Nitrosomonas, Nitrobacter). Heterotrophic bacteria are saprophytic, growing on dead and decaying organic matter, or parasitic, growing in living plants and animals, including humans. The parasitic bacteria may be pathogenic, causing diseases (e.g. Xanthomonas citri, Diplococcus pneumonae) or non-pathogenic, which usually form a symbiotic association with their hosts (e.g. Rhizobium, fixing nitrogen in leguminous plants, and cellulose-digesting bacteria in ruminant stomachs). Click here to enlarge Figure 14.9 Cell Structure of bacterium Staining : Those bacteria which retain Gram stain are called gram-positive bacteria, (e.g. Streptococcus) while those which do not retain the stain are called gram-negative bacteria, (e.g. Escherichia coli). 14.2 Kingdom : Protista (Eukaryotic unicellular organisms) Click here to enlarge Figure 14.13 Some Protista Protista includes all eukaryotic unicellular microorganisms, either plant-like or animal-like or showing overlapping characters of both plants and animals. Primarily they are aquatic and widely distributed all over the world, occurring in oceans, lakes, ponds and damp soils. They are autotrophic or heterotrophic. The latter are free-living or parasitic on or within multicellular organisms. Thus it reflects the lifestyles either of plants, animals or fungi. Phylogenetically they serve as the connecting link between prokaryotic Monera and complex multicellular kingdoms of plants fungi and animals. They are distinguished by the following characters: (i) They are first eukaryotes, having a well organized nucleus and complex membranous organelles. (ii) They are unicellular or colonial forms without distinct division of labor. (iii) They are autotrophic or heterotrophic showing varieties of metabolic systems. (iv) Locomotion is by pseudopodia, flagella or cilia. (v) They show mitosis, meiosis and simplest type of sexual reproduction for the first time. Common examples are Ameba, Paramecium, Euglena, diatoms and dinoflagellates. 1. Cilia and flagella Click here to enlarge Figure 14.14 Cilia and Flagella (A) Structure (B) Movement These are microscopic, contractile, motile hair-like locomotary organelles present in ciliated and flagellated protists like Paramecium and Euglena. Cilia and flagella are similar in structure. Each arises internally from the basal body and is made up of eleven microtubules, two single ones in the center connected to nine double ones arranged along the periphery (often referred to as 9 + 2 arrangement). The outer fibrils enter cytoplasm and converge to form the basal body. The central fibrils are connected to the peripheral ones by radial lamellae, like the spokes of a wheel. Cilia are short and numerous and beat in a coordinated manner simultaneously or one after the other, while flagella are long and whip-like, showing undulating movements. Their function is to propel the cell through the surrounding liquid medium or move the surrounding medium past the cells, gathering food particles. During movements cilia beat vigorously and rapidly (effective stroke) and they recover slowly (recovery stroke). Cilia and flagella are widely distributed in gametes, unicellular plants and animals and also on cells of more complex organisms forming the internal lining of ducts, such as trachea, oviduct, etc. All living organisms start their life with a single cell (zygote). In unicellular animals, cell division means reproduction which results in the formation of new organisms. In multicellular organisms, however, this cell further divides and thus forms the basis of growth. What initiates cell division is not exactly known but it is believed that when the ratio between the volume of cytoplasm and nucleus, (called nucleoplasmic index) exceeds its limit, the cell divides. Principally, there are two types of cell divisions: 1. Mitosis which is characteristic division of somatic or body cells. 2. Meiosis which is characteristic division in which germ cells are formed in the reproductive organs. Cell cycle and mitosis : The period from the beginning of one cell division to the beginning of the next cell division or the period between the end of one cell division to the end of next cell division, is known as cell cycle. It includes two main phases, that is, interphase and mitotic phase. The interphase is divided into following three phases as shown in (Figure 14.15). 1. First gap stage or G1 phase in which cell grows. 2. S phase or synthetic phase in which DNA replicates. 3. Second gap phase or G2 phase in which the protein synthesis increases. The completion of G2 phase is marked by the beginning of mitosis. The role of mitosis in cell cycle is to form two sets on identical chromosomes and to distribute one complete set at each end to form a daughter nucleus. Mitosis thus ensures that the new cell contains the identical number and types of chromosomes present in original mother cell, thus to continue the life-cycle. In unicellular animals, reproduction is by mitotic division but in higher organisms with evolution of sex, reproduction takes place by the union of two gametes -- male and female (sperm and egg). Hence, it is essential that at some stage (gamete formation) during life cycle the number of chromosomes should be reduced to half, so that their union will maintain the original number of chromosomes constant. This is done by meiosis. MEIOSIS Meiosis is the characteristic division of the germ cells. It is also called reduction division because in this the parent cell produces four daughter cells (tetrads) each having half the number of chromosomes present in the parent cell. In other words, meiosis is a process of cell division in which diploid (2n) number of chromosomes is reduced to haploid (n) number. Meiosis is completed in two distinct nuclear divisions which take place in quick succession, and are respectively called (1) First meiotic or reductional division in which the number of chromosomes is reduced to half and (2) Second meiotic division or equational division in which the number of chromosomes is the same as at the end of first division. Each division of meiosis like mitosis consists of four stages prophase, metaphase, anaphase and telophase. Cell division involves two stages, the nuclear division called karyokinesis and the division of cytoplasm known as cytokinesis. In any cell division the nucleus divides first followed immediately by the division of cytoplasm. It is the characteristic division of somatic or body cells resulting in the formation of daughter cells each receiving equal number of chromosomes like those of parent cells. Hence it is called equational division. It can be described into four orderly and consecutive phases such as prophase, metaphase, anaphase and telophase. Figure 14.15 Cell division: Mitosis Before the cell divides, it is said to be in the interphase which is sometimes inappropriately called ’resting phase’, though the cell is definitely not resting; in fact, all its metabolic or synthesizing activities are at its peak as the cell has to prepare itself for division. However, it is characterized by a large and distinct nucleus but indistinct chromosomes. Prophase : It literally means preparatory phase. It is initiated by the changes in the centrosphere. The centrosphere disappears and the two centrioles that are set free begin to move away from each other. Each of them radiates fibers, called an aster. The asters are absent in plant cells. The long chromatin threads of DNA undergo condensation to form a definite number of distinct chromosomes by dehydration and coiling. Each chromosome is double, consisting of two identical components called the chromatids connected by a common body called centromere. The nucleolus and nuclear membrane begin to disappear and the fibers radiating from pole to pole, called spindle fibers begin to appear. The spindle fibers, along with asters at opposite ends, are referred to as a mitotic figure. Metaphase : It literally means mid-way phase. The formation of spindle is complete. The chromosomes get still shorter and thicker and arrange themselves on the equatorial plane of the spindle. The spindle shows two types of fibers, those running from pole to pole (called interzonal fibers) and others connecting each pole to the centromere, (called tractile fibers). Anaphase : This is the separating phase. This begins with the division of the centromere of each chromosome. Thus the two sister chromatids of the same chromosome now completely separate and start repelling. These sister chromatids now known as daughter chromosomes take the form of a V or a U, and appear to be pulled towards the opposite poles along the tractile fibers. Gradually they reach the opposite poles, and that marks the end of anaphase. Telophase : This is the reconstruction phase. It includes the changes that are reversal of those in prophase. The chromosomes aggregate at the opposite poles and once again get elongated, uncoil and become indistinct. The spindle fibers simultaneously begin to disappear and the two daughter nuclei are formed at opposite poles, each containing an equal number of chromosomes as those of the parent nucleus. Cytokinesis, or division of cytoplasm, usually starts with the beginning of telophase. In animal cells it proceeds by a cleavage furrow around the cell at the equatorial region. This furrow increases and deepens until the cell is divided into two. Mitosis in animal cell and plant cells are basically similar except that in plant cells there are neither centrioles nor asters. Moreover, cytokinesis in plant cell is not accomplished by furrowing but by formation of a cell plate between the seperate sets of chromosomes. The cell plate is impregnated by pectin to form middle lamella. Later on cellulose is laid down on either side of the middle lamella to form the cell wall, thus dividing the mother cell into twodaughter cells. PinkMonkey Online Study Guide-Biology 1. Daughter cells receive same number of chromosomes as in parent cell. Thus it helps to maintain genetic integrity of the species. Click here to enlarge Figure 14.16 Cell cycle 1. Daughter cells receive same number of chromosomes as in parent cell. Thus it helps to maintain genetic integrity of the species. 2. Since equal number of chromosomes are distributed to the daughter cells, the daughter cells are similar to the parent cell quantitatively as well as qualitatively. 3. It is responsible for the replacement of old cells like those of the epidermis and blood corpuscles, having a short span of life. 4. It promotes growth development of the organism. In multicellular organisms, cell division either contributes to the cell replacement from wear and tear of the body (regeneration) or adds to the cell number, which results in the growth of the organism. First meiotic division Prior to meiosis some changes take place in the nucleus in which DNA begins to replicate. It is sometimes known as interphase. PinkMonkey Online Study Guide-Biology Prophase I. The prophase of meiosis 1 is much prolonged and can be divided further into five stages as follows: Figure 14.17 Stages in crossing over (i) Leptotene : The initial stage in which the replication of DNA started in interphase continues. The nucleus enlarges and the chromatin reticulum resolves into definite thread-like structures called chromosomes. The identical or homologous chromosomes received from the male and female parents become discernible. (ii) Zygotene : In this stage the homologous chromosomes begin to pair length to length and point to point in a zipper- like manner. This pairing is called synapsis, and pairs are referred to as bivalents formerly known as dyads (synapsis is absent in mitosis). (iii) Pachytene : The paired chromosomes at this stage become shorter and thicker. The chromosomes of each bivalent then split lengthwise to form four chromatids (tetrads). (iv) Diplotene : The force of attraction between the bivalents lapses; , however, they remain attached at certain points called chiasmata where mutual exchange of parts, called crossing over, can take place as shown in the figure 14. 17. (v) Diakinesis : The shortening of chromosomes reaches its maximum. They assume characteristic forms depending upon the position of chiasmata. The nucleolus and nuclear membrane begin to disappear and spindle begins to appear. Metaphase I : The spindle formation is complete. The bivalents move and arrange themselves on equatorial plane. Each chromosome of the bivalents gets attached to the spindle fiber at the centromere. MEIOSIS-I Figure 14.18 Cell Division: Meiosis I Anaphase I : The two chromosomes, or mates, of a bivalent (not the chromatids of the same chromosome) start moving towards the opposite poles. Thus the real reduction in the number of chromosomes takes place at this stage, each pole receiving half the number of original chromosomes. Telophase I : The chromosomes become long, thread-like and indistinct. The nucleolus and the nuclear membrane reappear thus forming two nuclei. The cytoplasm constricts in the middle to form two daughter cells, each containing single nucleus with half the number (haploid) of original number of chromosomes. Usually cytokinesis does not occur immediately but the nuclei undergo second meiotic division. The interval between the two division is called interkinesis. PinkMonkey Online Study Guide-Biology This division occurs simultaneously in both the nuclei formed as a result of first meiotic division. It is essentially similar to mitotic division and shows following four steps: Prophase II : The nuclear membrane begins to disappear and chromosomes get shortened. Each chromosome showing two sister chromatids attached at a single undivided centromere. Metaphase II : The spindle is formed usually at right angle to the plane of the spindle formed in Meiosis I. The chromosomes get arranged in an equatorial plane with centromeres attached to spindle fibers. Anaphase II : The centromere of each chromosome now divides for the first time separating sister chromatids which travel to the opposite poles. Telophase II : The set of chromatids at each pole organizes into a new daughter nucleus with the reappearance of nuclear membrane and nucleolus. Thus four daughter nuclei are formed each containing haploid number of chromosomes. Cytokinesis follows and four daughter cells are formed (tetrads) at the end of Meiosis-II, each with the nucleus containing haploid number of chromosomes. Meiosis, therefore, is a profound modification of mitosis in which the chromosomes first pair and then divide to form four haploid cells. Significance of Meiosis (i) It compensates for the doubling of chromosomes at gametic fusion and thus helps to keep the number of chromosomes constant, characteristic of each species. (ii) It is responsible for giving rise to large number of variations in the offsprings by crossing over and random distribution of maternal and paternal chromosomes. (iii) The variations coupled with heredity form the raw material for organic evolution. If it was not for meiosis, the evolution of species would be suspended. MEIOSIS - II Figure 14.19 Cell division : meiosis II. PinkMonkey Online Study Guide-Biology Comparison between mitosis and meiosis Mitosis 1. It takes place continuously in body cells or somatic cells. 2. The process is completed in one sequence or phase. 3. DNA replication takes place during interphase. 4. The duration of prophase is short usually of a few hours. 5. Homologous chromosomes do not show pairing or synapsis. 6. Chromosomes do not show crossing over a chiasmata. 7. Division of the centromeres or kinetochores takes place during anaphase. 8. Each of the cells formed contains the same number of chromosomes as in the parent cell. 9. Each diploid cell produces two diploid cells. 10. Shuffling of chromosomes does not take place. 11. Chromatids separate during anaphase. 12. The genetic constitution of the daughter cells is identified to that of the parent cells. Meiosis 1. It takes place during the process of gametogenesis to form germ cells. 2. It is completed in two succesive divisions which occur one after the other. 3. DNA replication takes place during interphase I but not in interphase II. 4. The duration of prophase is comparatively longer and may take days. 5. Homologous chromosomes show pairing or synapsis. 6. Chromosomes show crossing over at chiasmata. 7. There is no division of the centromeres during anaphase I. They divide only during anaphase II. 8. Each of the cells formed contains half the number of chromosomes. 9. Each diploid cell produces four haploid cells. 10. Shuffling of chromosomes takes place resulting in different combinations of chromosomes. 11. Homologous chromosomes (not chromatids) separate in anaphase I. 12. The genetic constitution of the daughter cells differs from that of parent cell due to crossing over and recombinations. Syngamy Syngamy is the fusion of two haploid nuclei or gametes. Click here to enlarge Figure 14.20 Syngamy place between the two identical gametes, it is called isogamy and when it takes place between the two dissimilar gametes, it is called anisogamy. As in higher organisms, when it takes place between a large, passive receptive gamete called an egg and a small active (motile) initiative gamete called sperm, it is called oogamy. Meiosis leads to the formation of haploid sex cells or gametes which are individually incapable of further development. Thus, the sex cells or gametes are arrested in their growth, but the syngamy removes the arrest and the diploid condition is restored. The diploid zygote formed by the union of haploid gametes is potentially capable of developing into a new individual. PinkMonkey Online Study Guide-Biology 3 Evolutionary precursors of complex life forms Protista is a diversified assembly of different groups of organisms which includes: (A) Unicellular algae-like protista, e.g. Diatoms, Dinoflagellates etc. (B) Fungi-like protista, e.g. slime molds (C) Animal-like protista, e.g. protozoa (A) Diatoms These are microscopic, usually single-celled or colonial forms. They are found both in fresh water and salt water. In ocean they occur in vast assembly as floating plankton. They show a variety of patterns showing extreme beauty and symmetry because of which they are sometimes called "jewels of the plant world." Figure 14.21 Diatoms General account : The cell is made up of two overlapping, ornamental halves fitting together like two petri dishes. The cell is composed of silica and manganese instead of cellulose. It is uninucleated with ribbon-like plastids, containing chlorphyll-a, chlorophyll-c, beta-carotene and oxanthophyll. They store food as oil and polysaccharides other than starch. The locomotion is of gliding type produced by the streaming of cytoplasm through raphae or grooves on the surface of the cell wall. There are two types of forms, viz. pinnate with bilateral symmetry, and centric with radial symmetry. Common life-cycle : Diatoms are diploid. They reproduce asexually as well as sexually. In asexual reproduction it divides by mitosis in which two valves are separated, each cell receiving one valve of the parent cell. Each of the two cells forms a new valve fitting into the old one. Thus, the size goes on reducing during repeated mitotic division. At a certain stage the protoplast escapes to form two haploid gametes by meiosis. These gametes fuse to form diploid zygotes called auxospores which increase in size to compensate for the reduction, before the new cell wall is laid down. Thus, the life-cycle shows the alternation of diploid and haploid generations. Common examples are Pinnularia and Navicula. Economic importance : (1) The diatoms play an extremely important role in the aquatic food web. They are the most abundant component of marine plankton forming the primary food source of marine animals. (2) The imperishable siliceous cells of diatoms are led down in various habitats. When dead, they form thick deposits of diatomaceous earth which is used as an ingredient in many commercial preparations such as detergents, polishes, paint removers, insulators, for decolorizing and deodorizing oils and also as fertilizers. (3) Being abundant, they help in releasing oxygen and maintaining the oxygen cycle. Diatomaceous earth The imperishable, siliceous dead cells of diatoms do not disintegrate but form thick deposits called diatomaceous earth or diatomite. It is procured from exposed deposits and lake bottoms. The largest deposits of diatomaceous earth are found in California. In Lampoc it is extending miles long and with average depth of 425 meters while in the oil fields of Santa Maria, it is 3000 feet thickness. Dinoflagellates : These are one celled, biflagellate organisms, mostly marine and are important photosynthesizers. Some species are bioluminiscent, often seen in ocean waters at nights. They are commonly called fire algae as they emit red light. General account : Their cell wall is made up of cellulose in the form of interlocking cellulose plate-forming theca. Most species have two unequal flagella hence called dinoflagellates. One flagellum runs lengthwise and extends behind like a tail and another encircles the body like a belt, in a transverse groove. The rotating or spinning movements of dinoflagellates are due to these flagella. The photosynthetic species have discoid plastids containing yellowish green carotenoids, chlorophyll and xanthophyll. They store food in the form of oil as well as polysaccharides. The nucleus is unique in that it has chromosomes permanently condensed and remain attached to nuclear membrane. Mitosis is intranuclear, i.e. it takes place within the nuclear membrane. They differ from diatoms in having flagella, absence of glossy skeleton of silicon and the cell wall is made up of cellulose plates. PinkMonkey Online Study Guide-Biology Figure 14.22 Dinoflagellates Common life-cycle: Asexual reproduction takes place by simple cell division (fission) or by zoospore formation. Recently sexual reproduction by isogamy has been reported in some. The examples are Ceratium, Noctiluca, Peridinium, Ganyaulux. Economic importance : They form an important constituent of marine plankton and thus play an extremely important role in the aquatic food web. A number of dinoflagellates like Ganyaulux are toxic, forming red tides killing a number of fish. Some species cause dermatitis in swimmers. They reproduce both sexually and asexually and the life history shows alternation of generations as shown by diatoms. (B) Slime molds General account: Slime mold is a mass of naked protoplasm without a rigid cell wall. It creeps along the substratum by ameboid movements and engulfs spores, bacteria and particulate debris of the substratum on which it grows. It commonly reproduces by structures called fruiting bodies which produce spores. Figure 14.23 Slime mold There are two types of slime molds, viz., acellular and cellular. Acellular slime molds have a vegetative body which is a multinucleated mass of protoplasm called plasmodium. It starts its life as a single diploid cell showing ameboid movements. Soon the nucleus divides repeatedly forming a large mass of naked protoplasm with number of nuclei. Every now and then it changes its shape and grows. Under unfavorable conditions, it develops little mounds on plasmodium, each of which gives a stalk bearing a sporangium at the tip. The spores are formed by meiosis, hence they are haploid. Each spore produces one to four flagellate spores which behave like undifferentiated gametes and fuse in pairs to form diploid zygotes. The zygote divides repeatedly by mitosis to form new plasmodium. Economic importance: In recent years slime molds have become important tools of research to study structure, streaming of movements and the physiology of protoplasm. (C) Protozoans Click here to enlarge Figure 14.24 Protozoans These are the protists which are more like animals. They are unicellular organisms found in fresh water, salt or any moist surroundings. They may be free living or parasitic, solitary or found in loose colonies. General account : They are distinguished by the following characteristics : (i) The body is covered by plasma membrane or labile pellicle and contains one or many nuclei. (ii) They are generally motile. Locomotion is carried out by flagella, cilia or pseudopodia. (iii) Most of them are holotrophic though some are saprophytic and others parasitic in nutrition. (iv) They show different organelles (cell organs) like food vacuoles, contractile vacuoles and, in some, cytostome and cytopharynx to perform various functions of life. (v) They are sensitive to various external stimuli like touch, temperature, light etc. inkMonkey Online Study Guide-Biology The protozoans fall into following four groups: 1. Sarcodina : They have no definite shape, move by pseudopodia and reproduce by binary fission. Example: Entamoeba : These are ameba-like animals with one or two pseudopodia, single nucleus but no contractile vacuole. It includes a number of species which are parasitic. The best known is Entamoeba histolytica, which causes amebic dysentery. 2. Mastigophora or flagellata : They move by one or two whip-like structures called flagella and reproduce by longitudinal binary fission. Example : Euglena : It is a fresh water protozoon with spindle-shaped body and a single flagellum. It shows cytostome and cytopharynx, but like plant, it also possesses chloroplasts. 3. Ciliophora : They have definite shape, move by cilia and mostly possess two nuclei. Example : Paramecium: A fresh water protozoon with definite shape like the sole of a slipper. Locomotion takes place by cilia. The animal has usually two nuclei and two contractile vacuoles. It reproduces by simple type of sexual reproduction called conjugation. 4. Sporozoa : These are parasitic forms. The locomotory organelles, food vacuoles and contractile vacuoles are absent. Example: Plasmodium: An intracellular blood parasite causing malaria. The life cycle is completed in two hosts, namely man and mosquito. Economic importance: Most of the protozoa are harmless but there are a few parasitic forms, such as Plasmodium, which causes malarial fever, Trypanosoma which develops sleeping sickness, and Entamoeba histolytica which causes dysentery. Protozoa are useful in sewage disposal. Symbiotic forms of Protista These are the organisms of different species which live in intimate relationship for mutual benefit. Some symbiotic forms are described below: Examples are lichen, and Trichonympha in the intestine of termites.. 1. Lichen : It is an obligatory association between, and plant, which together form a closely integrated unit called a lichen. The body of the lichen is composed of branching hyphae of the fungus which harbor algal cells. The fungus gets food synthesized by the alga while the alga in return gets shelter, moisture and minerals from the fungal partner. Figure 14.25 Diagram of a Lichen Economic importance : Lichens are used as food by human beings. They are also used in medicine, as dye stuffs for tanning hide into leather, etc. some like Usnea, are responsible for skin diseases, respiratory allergy etc. 2. Root tubercles : An obligatory association between plants and microbes, i.e. leguminous plant and the bacteria called Rhizobium. The latter are nitrogen fixing bacteria living in the root modules of leguminous plants like pea, bean, etc. Rhizobium fixes free nitrogen in the form of nitrates and makes it available to the plant and in return gets food and shelter from the latter. PinkMonkey Online Study Guide-Biology Figure 14.26 Root tubercles 3. Termites and flagellates : Several species of flagellates (protozoa) are found in the gut of termites where they participate in the digestion of wood. Termites feed on wood but are unable to digest it due to absence of proper enzymes. The flagellates present in the intestine digest wood with specific enzymes they secrete. The flagellates have no mouth or gullet; food particles are engulfed by pseudopodia at the posterior end. They convert the cellulose of wood into sugars. They use some of the sugars but much is left for the termites. The termites cannot survive without their intestinal flagellates. Newly hatched termites lick the anus of other termites to obtain flagellates. The flagellates in return get protection, food and lodging. Thus, the flagellate and termite live together for mutual benefit. Figure 14.27 Termites and Flagellates Ruminant stomach : Cud chewing animals like cow, sheep, goat, deer, giraffe etc. are called ruminants. They are herbivores. In these animals while grazing, food is cut into large pieces and swallowed without mastication. When at rest, the cud (i.e. the food once swallowed) is regurgitated into the mouth for thorough mastication, a process called rumination, or chewing the cud. fields marked (*) are mandatory In adaptation to this peculiar food eating habit the stomach of a ruminant is very modified. It consists of four interconnected chambers such as (i) rumen or pouch (ii) reticulum or honeycomb (iii) psalterium or manyplies or omasum and (iv) abomasum or runnet. Figure 14.28 Ruminant stomach The rumen is the first chamber in which food is received without mastication. The rumen is much enlarged and serves not only as a storehouse of food that is swallowed without mastication but also acts as a fermentation chamber due to its high contents of microbes. These symbiotic microbes digest cellulose which the ruminant cannot hydrolyze due to lack of cellulase. They also digest lipids into fatty acids and synthesize vitamin B. Absorption of these products by the rumen provides a significant amount of energy to the animal. PinkMonkey Online Study Guide-Biology 14.3 Kingdom : Plantae Kingdom Plantae includes all organisms which are truly multicellular and photosynthetic exept for algal protists. They are complex autotrophs preparing food material by photosynthesis for themselves as well as for rest of the other organisms. Hence, they are the chief producers of the world. They are found in all the types of environment: aquatic algae, amphibian mosses, and terrestrial ferns and seed-bearing plants. The plantae are distinguished by the following characters: (1) They are multicellular organisms, adapted to carry on photosynthesis, hence autotrophic. (2) Presence of cell wall of true cellulose, enclosing cytoplasm with large vacuole. (3) They perform photosynthesis due to chlorophyll present in chloroplasts. (4) They may show alternation of sexual and asexual generations in life-cycle. (5) They are non-motile, without definite size and shape. (6) Growth in these plants is intermittent. They are classified as follows: ALGAE Algae are chlorophyll-bearing unicellular or multicellular plants. When multicellular, they may be colonial or filamentous. Most of them are aquatic, either fresh water, (Volvox), or marine, (Spirogyra). Some are sheet-like (e.g., Ulva). Chlorophyll is present in chloroplasts, the number and shape of which are characteristic of each alga. Besides chlorophyll, they also show various carotenoid pigments which impart different colors to algae. According to the nature of photosynthetic pigments, they are further classified into three divisions such as Chlorophyta (green),. Phaeophyta (brown), and Rhodophyta (red). Life - cycles Algae show both a gametophytic (haploid) stage and a sporophytic (diploid) stage, which alternate. The life-cycle mainly shows two types, either haplontic or diplontic. Click here to enlarge Figure 14.29 Types of life - cycles (a) Haplontic life - cycle, when the plant body is a gametophyte i.e., haploid and is dominant or of long duration, and the zygote is diploid and of short duration. (b) Diplontic life-cycle, when the plant body is a sporophyte, i.e. diploid and is dominant or of long duration, and the gametophyte is haploid and of short duration. Green algae (Chlorophyta) These algae live in wide variety of habitats, marine to fresh water to damp soil. General Characteristics (i) These are unicellular (Chlamydomonas), colonial (Volvox) or filamentous. When filamentous they are unbranched (Spirogyra, Ulothrix) or branched (Chara). (ii) The cell wall consists of an inner layer of cellulose and outer layer of pectic compounds and may be covered by a gelatinous sheath. (iii) The protoplasm is divisible into cytoplasm and nucleus. Cytoplasm contains one or more vacuoles. Chlorophyll is present in chloroplasts, the shape and number of which are characteristic of each alga. (iv) Pigments chlorophyll-a and chlorophyll-b are predominant. However, carotene and xanthophyll are also present. (v) Food reserve is in the form of starch surrounding the proteinaceous refractile bodies called pyrenoids. (vi) Reproduction is vegetative by mitotic cell division in unicellular forms or by fragmentation in filamentous forms; asexual by formation of spores such as zoospores, aplanospores, hypnospore and akinates and sexual simply by conjugation or by gamete formation by isogamy or anisogamy or oogamy. (vii) The life-cycle is of haplontic type showing alternation of dominant haploid stage with short-lived diploid stage. Examples: Chlamydomonas, Volvox, Ulothrix, Spirogyra, Ulva etc. Click here to enlarge Figure 14.30 Types of Chlorophyta Economic importance : Algae are of certain economic importance to man. Chlorophyta serve as initial food producers and the first link in the aquatic food chain, both fresh water and marine. Some like Ulva and Chlorella are used as vitaminized food. Evolutionary significance : It is believed that chlorophyta has evolved from some flagellate unicellular ancestors like Chlamydomonas. These ancestors, during evolution, gave rise to complex filamentous forms which supposed to have given rise to land plants like bryophytes. Brown algae (Phaeophyta) These are multicellular, simple, filamentous or plant-like giant forms called kelps (sea weeds). These are mostly marine, found in cool shallow water. fields marked (*) are mandatory General Characters (i) The body is the multicellular thallus showing the highest degree of differentiation. The unicellular colonial forms are absent. Some brown algae called kelps or sea weeds exhibit giant forms extending over 50 meters in length and showing parenchymatous organization. (ii) The cell wall is made up of two layers. The inner firm layer is of cellulose while the outer layer is gelatinous containing compounds like algin, fucosin etc. (iii) The cytoplasm show one or many vacuoles and single large, distinct nucleus, with one or more nucleoli. Chloroplasts are either discoidal or band-shaped, without pyrenoids. (iv) Yellow-brown pigment fucoxanthin a type of xanthophyll is predominant which gives golden - brown color to algae, while other pigments such as chlorophyll-a and chlorophyll-b are also present. (v) The reserved food is in the form of soluble carbohydrates called laminarin and mannitol. Figure 14.31 Types of Phaeophyta (vi) Reproduction is vegetative by fragmentation, asexual by formation of haploid or diploid zoospores and sexual by gamete formation, by isogamy, anisogamy or oogamy. (vii) The life-cycle shows isomorphic alternation of generations where the gametophyte and sporophyte are morphologically similar (e.g., Ectocarpus), heteromorphic alternation or generations where the gametophyte and sporophyte are morphologically differentiated (e.g. Laminaric) while in there is no alternation of generations as gametophytic generation represented only by gametes. Examples: Fucus, Sargassum, Laminaria, Ectocarpus etc. Economic importance : "Komba", a product made from Laminaria, is widely used as food in Japan and oceanic islands. It is boiled with fish, meat or in soups or as a cooked vegetable. A gel called algin, obtained from Macrocystis, Laminaria, etc., is used in the preparation of toothpastes, ice-cream, etc. Sea weeds like Sargassum are used as a directory source of iodine and bromine. Evolutionary significance : The universal appearance of motile gametes probably suggests that Phaeophyta took its origin from unicellular brown, flagellated ancestors. These do not seem to be related to green algae because of the multicellular vegetative body and presence of fucoxanthin and laminarin which belong exclusively to this group. PinkMonkey Online Study Guide-Biology Red algae (Rhodophyta) These are exclusively marine, found in deep waters attached to rocks. General Characteristics (i) These are always multicellular, filamentous, radially symmetrical or compressed forms. There is no true parenchymatous construction. (ii) The cell wall is made up of two layers. The inner one is of cellulose while the outer one is of pectic compounds with mucilaginous envelope. (iii) The cytoplasm is uninucleate and shows a central vacuole. The chromatophores are with naked pyrenoids. (iv) The pigments are chlorophyll-a, chlorophyll-b, carotene and xanthophyll. However, the green color of chlorophyll-a is masked by red pigment, phycoerythrin and blue pigment phycocyanin. (v) Food is stored in the form of chemically distinctive starch called floridean starch. (vi) The reproduction is vegetative by fragmentation, asexual by non-flagellated, haploid carpospores, monospores or tetraspores, and sexual by formation of non-flagellate, non-motile male gametes and an egg, thus oogamous. (vii) The life-cycle shows either haploid forms or regular alternation of generations between similar haploid and diploid stages. Examples: Agardhiella, Palysiphonia, Batrachospermum, Gracilaria, etc. Figure 14.32 Types of Rhodophyta Economic importance : The gelatinous substance extracted from red algae (Gelidium, Gracilaria) is used to prepare agar as a medium for bacterial and fungal cultures, in preparation of ice-cream, jelly, cosmetics, medicines, etc. in Japan. Agar is also used in printing and dying processes in textile industry. Some species (Porphyra) are used as food. Evolutionary significance : It appears that this group has taken its origin from some unicellular, non-ciliate ancestor as it shows non-flagellated spores and gametes. Figure 14.33 Life cycle of a typical alga Economic importance of algae : Algae are of certain economic importance to mankind. They serve as initial food producers and the first link in the aquatic food chain, both fresh water and marine. Some of the fresh water algae and sea-weeds are used as vitamin-rich food. Brown algae contain iodine and algin. Some red algae are the source of agar jelly, used in the preparation of ice creams and culture media. However, algae sometimes cause contamination of water and some of them release many toxic substances killing millions of fish and other animals drinking this water. PinkMonkey Online Study Guide-Biology BRYOPHYTA These are terrestrial non-vascular plants which still require moist environment to complete their life-cycle, hence they are called amphibians of the plant kingdom. Bryophytes show advances over alga by developing special sex organs like antheridia (male) and archegonia (female) and show distinct alternation of generations. Bryophyta are the simplest of land plants, and include mosses, liverworts and hornworts. They are distinguished by the following characteristics: (1) They are small terrestrial plants. (2) They are without a distinct root system but attached to substratum by rhizoids. (3) They do not posses true vascular tissue. (4) Sex organs are multicellular with a protective jacket layer. (5) Gametophyte is dominant and independent. (6) Sporophyte is small and parasitic or semiparasitic on the gametophyte. (7) They show a distinct alternation of generations. Bryophytes are divided into three classes fields marked (*) are mandatory Class : Hepaticeae : These are lower forms with an undifferentiated thallus, Rhizoids are unicellular and unbranched, Protonema are absent. Sporophyte is short-lived and simple. However, in some forms it may be differentiated into foot, seta and capsule. Examples are Riccia, Marchantia. Class : Anthocerotae : Gametophyte is undifferentiated thallus, rhizoids are unicellular and unbranched. Protonema is absent. Sporophyte is differentiated into foot and capsule only. An example is Anthoceros. Class : Musci : These are higher forms in which the gametophyte is differentiated into stem-like and leaf-like parts showing radical symmetry. Rhizoids are multicellular and branched. Protonema present. Sporophyte is differentiated into foot, seta and capsule. An example is Funaria. External Morphology : Since bryophytes lack efficient conducting tissue, they do not become very large. They are small plants forming green velvety patches on moist substratum. They are green due to presence of chloroplasts. The plant body is either thallus or distinguished into stem-like and leaf-like structures. They are attached to the substratum by rhizoids. Liverworts Figure 14.34 Types of bryophytes The plant body is a thallus which is a gametophyte. It is dorsoventrally flat, showing dichotomous branching. The dorsal surface is marked by a groove throughout, while the ventral surface shows unicellular rhizoids. Reproduction takes place vegetatively, asexually as well as sexually. Vegetative reproduction takes place by production of vegetative reproductive bodies called gemmae. The gemmae eventually separate from the parent plant and grow into gametophytes. Sexual reproduction takes place by producing antheridia and archegonia which may be on erect branches called antheridiophores and archegoniophores. The antheridia produce biflagellate antherozoids. In presence of water they reach the archegonium, enter the neck and only one fertilizes the egg at the base, to form a diploid zygote developing into asporophyte. The sporophyte remains attached to the gametophyte. Asexual reproduction takes place by production of haploid spores which are produced by the sporophyte. The spore germinates to produce a gametophyte, thus showing alternation of generations. PinkMonkey Online Study Guide-Biology Mosses A moss plant begins as a filamentous, green, body called a protonema which produces buds giving rise to the mature moss plants. The moss plant is a gametophyte measuring about 2 to 3 cm in height. It is differentiated into stem-like (cauloid) and leaf-like (phylloid) appendages. There are no true roots. The plant is fixed to the substratum by multicellular rhizoids. The leaf-like appendages are sessile, spirally arranged on a short stem forming a cluster or rosette at the apex. Reproduction is mainly sexual, asexual and at times vegetative. At maturity antheridia (male) are borne at the tip of the main branch surrounded by a rosette of leaves, and archegonia (female) are borne at the tip of lateral branch surrounded by a rosette of leaves. The antheridia are club-shaped. At maturity they produce biflagellate, coiled antherozoids. The archegonia are flask-shaped, each containing one large female gamete called an egg at its broad base. Fertilization takes place in presence of water by the process of chemotaxis, i.e. under the influence of a chemical substance released by the archegonium. The resulting zygote is the beginning of a diploid sporophyte. Figure 14.35 A. Antheridium of moss B. Archegonium of moss The sporophyte is a leafless structure living as a semiparasite on the gametophyte. It consists of a foot which is embedded in the gametophyte and absorbs nourishment, the middle slender, long seta which is used for dispersal of spores, and the apical pear-shaped capsule provided with a lid. It produces haploid spores at maturity. In dry weather, the lid breaks open and the spores are dispersed by wind. Under suitable conditions, a spore germinates to form a protonema. The latter produces buds which give rise to gametophytes, thus completing the life-cycle. Life-cycle pattern : The life-cycle shows morphologically distinct alternation of generations in which gametophyte is the dominant, independent stage and the sporophyte is a semiparasite or parasite on the gametophyte. The plant is a gametophyte which at maturity produces haploid male and female gametes. The male and female gametes fuse to form a diploid zygote or oospore. The latter develops into a sporophyte. Sporophyte at maturity produces haploid spores which are released in dry weather. Spore germination produces a gametophyte. This successive appearance of two generations alternately one after the other (G-S-G-S) in the life-cycle is called alternation of generations. Figure 14.36 Life-cycle pattern (Bryophyta) Role of bryophytes in nature : (i) Bryophytes provide food for herbivores, birds and other animals. (ii) Bog mosses and peat mosses are used as water absorbing and water retaining material in seed beds and green houses. (iii) They are also used as shock absorbing (packing) material for shipment. (iv) Dead and decaying mosses form humus which increases fertility of soil. 14.4 Kingdom : Fungi The fungi are non-green plant-like organisms which are universal in their distribution. They grow in dark and moist habitat and the substratum containing dead organic matter. Mushrooms, molds and yeast are common examples of fungi. Fungi are distinguished by the following characters: (1) They have a definite cell wall made up of fungal cellulose. (2) They are without chlorophyll, hence they are heterotrophic. (3) They are usually non-motile. (4) They reproduce mostly by spore formation. However, sexual reproduction may also take place. Structure: The plant body is unicellular or multicellular. When multicellular, it is composed of profusely branched, interwoven, delicate, thread-like structures called hyphae, collectively called mycelium. Hyphae may be aseptate or septate. When aseptate they are coenocytic, containing many nuclei. Fungi are heterotrophic in nutrition i.e., they may be saprophytic, (living on dead organic matter) or parasitic (subsisting on other living organisms). The parasitic forms may be ectoparasite, living on the body of the host, or endoprasitic, living inside the body of the host. Some forms are symbiotic. The fungi are classified as follows: 1. Class : Zygomycetes (lower fungi) These are filamentous fungi which are terrestrial growing on moist, dead organic matter. They are mainly distinguished by the following characteristics : Figure 14.37 Mucor Figure 14.38 Rhizopus (i) The plant body is called a mycelium; it is made up of interwoven, thread-like structures called hyphae. (ii) The hyphae are aseptate and coenocytic. (iii) The sporangia are formed at the apex of aerial hyphae called sporangiophores. (iv) The spores are numerous and are formed endogenously (i.e. produced within the sporangium). (v) Sexual reproduction is isogamous (i.e. the pairing gametes are alike). (vi) The zygote is unicellular and simple. (vii) Motile zoospores are produced in some. Heterothallism In some fungi there is no morphological sex differentiation, but they show physiological sex differences and said to be having +ve and -ve strains. Such fungi are called heterothallic. (heteros= dissimilar). In these fungi sexual reproduction can occur only between thalli having +ve and -ve strains. Reproduction : Mucor reproduces asexually as well as sexually. Asexual reproduction takes place by formation of non-motile spores and sexual reproduction takes place by conjugation of similar gametes (isogametes). During asexual reproduction, mycelium gives out upright vertical hyphae called sporangiophores. As the growth proceeds, the tip develops a globular structure called sporangium. At maturity the sporangium breaks open and liberates the spores. On germination, each spore develops into a new mycelium. Sexual reproduction is isogamousas: it involves the conjugation of two similar gametes. During conjugation the two hyphae regarded as having positive and negative strains come closer (heterothallism). The conjugating hyphae give out club-shaped progametangia which release the terminal part (called gametangia). The gametangia fuse, the middle wall is dissolved and the nuclei fuse in pairs, thus forming a zygote. The latter develops a thick resisting wall to form a zygospore. Each zygospore, on germination, gives out promyucelium which develops sporangium at its tip. When the sporangium ruptures, the spores are liberated and germinate to produce new mycelia.


Sunday 8 January 2012

biology


Review Test
You got 15 out of 51 correct. (That's 29%.)
Scroll through the page to review your answers. The correct answer is highlighted in  green.  Your incorrect answers (if any) are highlighted in  red.  If you'd like to take the test over again, click the reset button at the end of the test.
The lipid bilayer is composed primarily of what two biological molecules?
(A) Sugars and fats
(B) Carbohydrates and proteins
(C) Proteins and fats
(D) Sugars and proteins
Which of the following eukaryotic intracellular components are not organelles?
(A) Golgi apparatus
(B) Cytoskeleton
(C) ER
(D) lysosomes
What is the typical width of the lipid bilayer?
(A) 3 nanometers
(B) 5 nanometers
(C) 7 nanometers
(D) 9 nanometers
Which of the following is the main component of the cytoplasm?
(A) Cytosol
(B) Cytosine
(C) Ectoderm
(D) Chlorophyll
Which of the following phrases best matches the definition of the term hydrophobic?
(A) "water-hating"
(B) "water-loving"
(C) "water-impartial"
(D) "water-storing"
The cytosol composes up to what percent of a cell's volume?
(A) 10%
(B) 30%
(C) 50%
(D) 90%
The term hydrophilic means which of the following?
(A) Repelled by water
(B) Insoluble in water
(C) Non-water containing
(D) Attracted to water
The function of the cytoskeleton is most similar to the function of what other cellular structure?
(A) Peroxisome
(B) Lipid bilayer
(C) Cytoplasm
(D) Mitochondria
A molecule that has both polar and nonpolar regions is called ___________.
(A) Hydrophobic
(B) Hydrophilic
(C) Amphipathic
(D) Hydrated
The cytoskeleton is primarily responsible for __________.
(A) Cell shape
(B) Cellular energy
(C) Cellular respiration
(D) Cell density
The most abundant class of lipids found in the lipid bilayer are the ___________.
(A) Phospholipids
(B) Glycolipids
(C) Sphingolipids
(D) Liposomes
Which of the following are not a cytoskeletal protein filament?
(A) Actin
(B) Intermediate filaments
(C) Primary filaments
(D) Microtubules
What is the name of the process by which plant cells convert light energy into biological energy?
(A) Photosynthesis
(B) Photorespiration
(C) Light-conversion
(D) Oxidative phosphorylation
Which of the following is not a property of the lipid bilayer?
(A) Fluidity
(B) Impermeability
(C) Polarity
(D) Permeability
What is the name of the structure around which microtubules grow?
(A) Centers
(B) Matrices
(C) Growth cones
(D) Centrosomes
Membrane proteins that cannot be easily removed from the cell membrane are called __________.
(A) Peripheral proteins
(B) Integral proteins
(C) Rigid proteins
(D) Locked proteins
What organelle is responsible for carrying out photosynthesis?
(A) Mitochondria
(B) Nucleus
(C) Vacuole
(D) Chloroplasts
Which of the cytoskeletal protein filaments has the largest diameter?
(A) Actin
(B) Intermediate filaments
(C) Primary filaments
(D) Microtubules
Membrane proteins that span the entire lipid bilayer are called __________.
(A) Membrane-spanners
(B) Integral proteins
(C) Peripheral proteins
(D) Transmembrane proteins
Which cytoskeletal filament is responsible for forming the nuclear lamina?
(A) Actin
(B) Intermediate filaments
(C) Primary filaments
(D) Microtubules
What configuration does a protein adopt when it crosses the lipid bilayer?
(A) Alpha-helical
(B) Beta-helical
(C) Gamma-helical
(D) Delta-helical
Molecules done being processed in the ER are often transported to which structure?
(A) Peroxisomes
(B) Mitochondria
(C) Golgi apparatus
(D) Vacuoles
The face through which molecules enter the golgi apparatus is called the __________ face.
(A) Cis
(B) Trans
(C) Medial
(D) Dorsal
Which cytoskeletal protein filaments line the cell membrane?
(A) Actin
(B) Intermediate filaments
(C) Primary filaments
(D) Microtubules
Which of the following is not a common destination of vesicles secreted from the golgi apparatus?
(A) Lysosome
(B) Cell membrane
(C) ER
(D) Mitochondria
Which of the following best describes the properties of a lipid-bound protein?
(A) Having its tail-end attached to the lipid bilayer
(B) Having its head-end attached to the lipid bilayer
(C) Being entirely located in the lipid bilayer
(D) Being loosely associated with the lipid bilayer
Which of the following eukaryotic organelles is primarily responsible for celluar digestion?
(A) Nucleus
(B) Lysosome
(C) Mitochondria
(D) Golgi apparatus
Which of the following is the largest organelle in eukaryotic cells?
(A) ER
(B) Golgi apparatus
(C) Lysosome
(D) Nucleus
Which of the following is not a specialized plant cellular structure?
(A) Lysosome
(B) Cell wall
(C) Chloroplast
(D) Vacuole
What is the name of the organelle that helps mediate endocytosis and exocytosis?
(A) Vacuole
(B) Peroxisome
(C) Lysosome
(D) Endosome
What is the name of the carbohydrate coat found on the outside of the lipid bilayer of higher- order cells cells?
(A) Glycosylation
(B) Glycocalyx
(C) Glycogen
(D) Glutamine
What structure in plants replaces the function that the mitochondria performs in animal cells?
(A) Vacuole
(B) Cytoskeleton
(C) Chloroplast
(D) Nucleus
In eukaryotes, the cell nucleus composes what fraction of the total cell volume?
(A) 10%
(B) 15%
(C) 20%
(D) 25%
What is the name of the process by which molecules naturally flow from an area of higher concentration to one of lower concentration?
(A) Respiration
(B) Transfusion
(C) Dialysis
(D) Diffusion
Which of the following organelles do not contain a double-membrane?
(A) Nucleus
(B) Lysosome
(C) Mitochondria
(D) Chloroplasts
Membrane transport that occurs without the input of extra energy can be classified as what type of transport?
(A) Passive
(B) Active
(C) Catalytic
(D) Inhibitory
The cell nucleus is not found in direct contact with which of the following cellular structures?
(A) Cytosol
(B) Cytoskeleton
(C) ER
(D) Mitochondria
Membrane transport that requires the input of additional enery is called _________.
(A) Passive
(B) Active
(C) Catalytic
(D) Inhibitory
What is the name of the inner-most space in a mitochondrial cell?
(A) Matrix
(B) Intermembrane space
(C) Cytosol
(D) Chlorophyll
Membrane proteins that mediate active transport are generally __________.
(A) Lipid-bound proteins
(B) Ionophores
(C) Channel proteins
(D) Carrier proteins
What is the main function of the mitochondria?
(A) Molecular digestion
(B) DNA storage
(C) Space-filler
(D) Enery-producer
The mitochondrial matrix is analogous to which structure in plant chloroplasts?
(A) Stoma
(B) Intermembrane space
(C) Cytosol
(D) Vacuole
Membrane proteins that mediate passive transport are generally _________.
(A) Lipid-bound proteins
(B) Ionophores
(C) Channel proteins
(D) Carrier proteins
Which eukaryotic organelle contains oxidizing enzymes?
(A) Lysosome
(B) Peroxisome
(C) Golgi apparatus
(D) ER
What is a typical thickness for a cell wall?
(A) 50 nanometers
(B) 50 micrometers
(C) 10 nanometers
(D) 10 micrometers
__________ are a class of membrane proteins that increase a cell's permeability to certain ions.
(A) Lipid-bound
(B) Ionophores
(C) Channel proteins
(D) Carrier proteins
__________ endoplasmic reticulum has ribosomes attached to its outer membrane.
(A) Smooth
(B) Spiked
(C) Rough
(D) Cytoskeletal
Vacuoles can occupy up to what percent of plant cells?
(A) 90%
(B) 75%
(C) 50%
(D) 25%
Membrane transport is important for which of the following biological processes?
(A) Protein synthesis
(B) Cell communication
(C) Maintenance of cellular pH
(D) All of the above
The ER plays a major role in the processing of which of the following biological molecules?
(A) Carbohydrates
(B) Proteins
(C) Adenosine triphosphate
(D) DNA
Which of the following is not a normal function of plant cell vacuoles?
(A) Cellular digestion
(B) Space-filling
(C) Energy production
(D) Storage

Terms
Active transport  -  The transport of molecules across a membrane and against their natural flow; mediated by carrier proteins and requiring outside energy.
Carrier protein  -  A protein responsible for mediating the active transport of molecules from one side of the lipid bilayer to the other. Transport is carried out by a conformational change that occurs within the protein that forms an opening for specific molecules to pass through.
Channel protein  -  A protein responsible for mediating the passive transport of molecules from one side of the lipid bilayer to the other. Transport is carried out by its membrane-spanning hydrophilic structure which, when open, allows molecules to pass through.
Diffusion  -  The transport process in which molecules naturally travel from an area of higher concentration to an area of lower concentration.
Glycocalyx  -  A layer of carbohydrates that coats the exterior of higher-ordered cells. Functions in protecting the cell from damage.
Hydrophilic  -  A polar molecule that selectively associates itself with water through hydrogen bonds.
Hydrophobic  -  A nonpolar molecule that does not readily associate with water through hydrogen bonds.
Integral protein  -  A membrane protein that cannot be easily removed from the lipid bilayer.
Ionophore  -  A class of membrane transport proteins. Small, hydrophobic molecules that increase membrane permeability to certain ions.
Lipid bilayer  -  A thin double layer of phospholipid molecules. Provides the structure of a cell membrane. Structure is a result of hydrophobic and hydrophilic forces.
Lipid-bound protein  -  Membrane proteins that are located entirely within the lipid bilayer, having no part touching either the inside or outside of the cell.
Multi-pass protein  -  Transmembrane proteins that cross the lipid bilayer more than one time.
Osmosis  -  The process by which water naturally travels from an area of high concentration to one of lower concentration.
Passive transport  -  Transport mediated by channel proteins. The movement of molecules across a membrane according to the natural flow.
Peripheral protein  -  A membrane protein that can be easily removed from the lipid bilayer.
Single-pass protein  -  A transmembrane protein that only crosses the lipid bilayer one time.
Transmembrane protein  -  A membrane protein that spans the lipid bilayer having portions in contact with both the inside and outside of the cell. Area within the lipid bilayer forms an alpha-helix.

The Lipid Bilayer

Lipid Bilayer Structure

The lipid bilayer is a universal component of all cell membranes. Its role is critical because its structural components provide the barrier that marks the boundaries of a cell. The structure is called a "lipid bilayer" because it is composed of two layers of fat cells organized in two sheets. The lipid bilayer is typically about five nanometers thick and surrounds all cells providing the cell membrane structure.

Lipids and Phospholipids


The structure of the lipid bilayer explains its function as a barrier. Lipids are fats, like oil, that are insoluble in water. There are two important regions of a lipid that provide the structure of the lipid bilayer. Each lipid molecule contains a hydrophilic region, also called a polar head region, and a hydrophobic, or nonpolar tail region.
http://img.sparknotes.com/figures/A/a981208a1abd542364d5a13c08702881/lipid.gif
Figure %: Basic Lipid Structure
The hydrophilic region is attracted to aqueous water conditions while the hydrophobic region is repelled from such conditions. Since a lipid molecule contains regions that are both polar and nonpolar, they are called amphipathic molecules.
The most abundant class of lipid molecule found in cell membranes is the phospholipid. The phospholipid molecule's polar head group contains a phosphate group. It also sports two nonpolar fatty acid chain groups as its tail.
http://img.sparknotes.com/figures/A/a981208a1abd542364d5a13c08702881/phospholipid.gif
Figure %: Phospholipid Structure
The fatty acid tail is composed of a string of carbons and hydrogens. It has a kink in one of the chains because of its double-bond structure.

The Bilayer

The phospholipids organize themselves in a bilayer to hide their hydrophobic tail regions and expose the hydrophilic regions to water. This organization is spontaneous, meaning it is a natural process and does not require energy. This structure forms the layer that is the wall between the inside and outside of the cell.
http://img.sparknotes.com/figures/A/a981208a1abd542364d5a13c08702881/lipidbilayer.gif
Figure %: Lipid Bilayer

Properties of the Lipid Bilayer

As we have already mentioned, the most important property of the lipid bilayer is that it is a highly impermeable structure. Impermeable simply means that it does not allow molecules to freely pass across it. Only water and gases can easily pass through the bilayer. This property means that large molecules and small polar molecules cannot cross the bilayer, and thus the cell membrane, without the assistance of other structures.
Another important property of the lipid bilayer is its fluidity. The lipid bilayer contains lipid molecules, and, as we will discuss later, it also contains proteins. The bilayer's fluidity allows these structures mobility within the lipid bilayer. This fluidity is biologically important, influencing membrane transport. Fluidity is dependent on both the specific structure of the fatty acid chains and temperature (fluidity increases at lower temperatures).
Structurally, the lipid bilayer is asymmetrical: the lipid and protein composition in each of the two layers is different.


Cell Membranes


Problems

Problem : Identify the lipid bilayer in the following diagram of a cell.

http://img.sparknotes.com/figures/A/a981208a1abd542364d5a13c08702881/prob1.gif

Cell

Solution for Problem 1 >>

http://img.sparknotes.com/figures/A/a981208a1abd542364d5a13c08702881/solution1.gif

Solution

The lipid bilayer is the outer-most layer surrounding the cell.

Close


Problem : What is the main function of the lipid bilayer?

Solution for Problem 2 >>

The lipid bilayer acts as a barrier between the inside and outside of the cell. It is highly impermeable and does not allow most molecules to freely pass through it into or out of the cell.

Close


Problem : Why is the structure called a lipid bilayer?

Solution for Problem 3 >>


Problem : Fill in the blanks.
A phospholipid molecule contains two distinct regions. The __________ region is attracted to water and the ___________ region is repelled from water. As a result of its both polar and nonpolar regions, it is classified as a(n) __________ molecule.

Solution for Problem 4 >>

Hydrophilic. Hydrophobic. Amphipathic.

Close


Problem : Are the two layers of the lipid bilayer identical in composition?

Solution for Problem 5 >>

No. As a result of the bilayer's fluidity, structures such as lipids and proteins can freely move around within the lipid bilayer.

Membrane Proteins

In addition to the lipid bilayer, the cell membrane also contains a number of proteins. We have already mentioned the presence of certain proteins in the cell membrane. In this section we will discuss the different classes of proteins found there. While the lipid bilayer provides the structure for the cell membrane, membrane proteins allow for many of the interactions that occur between cells. As we discussed in the previous section, membrane proteins are free to move within the lipid bilayer as a result of its fluidity. Although this is true for most proteins, they can also be confined to certain areas of the bilayer with enzymes. Membrane proteins perform various functions, and this diversity is reflected in the significantly different types of proteins associated with the lipid bilayer.

Classifications of Membrane Proteins


Proteins are generally broken down into the smaller classifications of integral proteins, peripheral proteins, and lipid-bound proteins.

Integral Proteins

Integral proteins are embedded within the lipid bilayer. They cannot easily be removed from the cell membrane without the use of harsh detergents that destroy the lipid bilayer. Integral proteins float rather freely within the bilayer, much like oceans in the sea. In addition, integral proteins are usually transmembrane proteins, extending through the lipid bilayer so that one end contacts the interior of the cell and the other touches the exterior. The stretch of the integral protein within the hydrophobic interior of the bilayer is also hydrophobic, made up of non-polar amino acids. Like the lipid bilayer, the exposed ends of the integral protein are hydrophilic.
http://img.sparknotes.com/figures/A/a981208a1abd542364d5a13c08702881/transmembrane.gif
Figure %: Membrane Proteins
When a protein crosses the lipid bilayer it adopts an alpha-helical configuration. Transmembrane proteins can either cross the lipid bilayer one or multiple times. The former are referred to as single-pass proteins and the later as multi-pass proteins. As a result of their structure, transmembrane proteins are the only class of proteins that can perform functions both inside and outside of the cell.

Peripheral Proteins

Peripheral proteins are attached to the exterior of the lipid bilayer. They are easily separable from the lipid bilayer, able to be removed without harming the bilayer in any way. Peripheral proteins are less mobile within the lipid bilayer.

Lipid-Bound Proteins

Lipid-bound proteins are located entirely within the boundaries of the lipid bilayer.

The Cell Surface

The protein and lipid cell membrane is covered with a layer of carbohydrate chains on its outer surface. This layer is called a cell coat or glycocalyx. The exact composition and distribution of these chains is very diverse. The chains are thought to provide the cell with protection against damage. Glycocalyx are only found on the surface of the cells of higher organism's.
http://img.sparknotes.com/figures/A/a981208a1abd542364d5a13c08702881/cellmembrane.gif
Figure %: A detailed view of a Cell Membrane (phospholipid bilayer and associated proteins)
Problems
Problem : Will you find the same set of membrane proteins in each cell membrane?
No. Membrane proteins perform a number of functions within cells, as a result, different proteins are necessary in different regions of cells depending on the function of the cell and the interactions it may take part in.

Problem : What are the names of the two main classes of membrane proteins and how could you tell one from the other?
The two main classes of membrane proteins are integral versus peripheral proteins. Since peripheral proteins are easily dissociated from the lipid bilayer, one could treat a cell with a mild detergent that does not disrupt the cell membrane and then see if the specific protein remains associated with the lipid bilayer or is removed.

Problem : What is the name of the configuration that membrane proteins adopt in regions that span the lipid bilayer?
This configuration is called an alpha-helix. It is the same structure that DNA adopts naturally.

Problem : Which class of proteins, integral or peripheral, are freer to move around within the lipid bilayer?
Integral proteins can be thought of as icebergs that float in a lipid bilayer sea. They are relatively mobile in the cell membrane.

Problem : The cell surface is covered with an additional set of molecules. What name is given to these structures and what is their function in the cell?
The cell surface is covered with a cell coat or glycocalyx which consists of carbohydrate chains. They help protect the cell from damage.


Structures Responsible for Membrane Transport

We have discussed how the lipid bilayer acts as an efficient barrier by only allowing a very small number of non-polar molecules to freely enter or exit a cell. While for the most part this selectivity is a valuable function and allows the cell to maintain its integrity, cells do need to move certain large, polar molecules such as amino acids, sugars, and nucleotides across their membranes. As a result, cell membranes require specific structures that allow for the transport of certain molecules.

Membrane Transport

There are a number of different ways that molecules can pass from one side of a cell membrane to the other. Some such means, like diffusion and osmosis, are natural processes that require no expenditure of energy from the cell and are called passive transport. Other methods of transport do require cellular energy and are called active transport. In addition to these two forms of transport, there exist other forms of transport such as endocytosis and exocytosis, which will be discuss later and do not require the same set of membrane proteins for their function.

Passive Transport

Diffusion is the natural phenomenon in which nonpolar molecules naturally flow from an area of higher concentration to an area of lower concentration. Osmosis is a similar process, but refers specifically to water molecules. Both of these classes of molecules we have already discussed as capable of crossing the lipid bilayer. As seen in , neither diffusion nor osmosis require the expenditure of energy.

Active Transport

Active transport occurs when a cell actively pumps a molecule across its membrane, against the natural direction dictated by diffusion, osmosis, or polarity. As seen in , such transport requires energy.

Figure %: Active and Passive Transport Proteins

Transport Proteins

Both of passive and active transport are mediated with the help of transmembrane proteins that act as transporters. shows the two main classes of transport proteins: carrier proteins and channel proteins. For the most part, carrier proteins mediate active transport while channel proteins mediate passive transport. Carrier proteins create an opening in the lipid bilayer by undergoing a conformational change upon the binding of the molecule. Channel proteins form hydrophilic pores across the lipid bilayer. When open, these pores allow specific molecules to pass through. There is one other class of transport proteins called ionophores. These are small, hydrophobic proteins that increase bilayer permeability for specific ions.
Transport proteins are critical to cell life and cell interactions. They allow for the proper distribution of ions and molecules in multicellular organisms. Additionally, they can help to maintain proper intra- and extra-cellular pH levels, facilitate communication between cells, and are involved numerous other essential functions including protein sythesis.


Cell Membranes


Problems
Problem : Why is it necessary for cell membranes to have proteins that help transport molecules?
The cell membrane is composed of a lipid bilayer that is highly impermeable to most molecules. As a result, outside structures are required to help transport essential large, polar molecules across the cell membrane.

Problem : What is the name of the natural process by which molecules flow from an area of higher concentration to one of lower concentration?
Diffusion.

Problem : What is the difference between the behavior of carrier and channel proteins?

Problem : What is the function of an ionophore?
Ionophores function to increase a membrane's permeability to a specific ion thereby facilitating its movement across that cell's membrane.

Problem : Name two specific functions of membrane transport.
Membrane transport helps maintain the proper distribution of ions across a cell membrane; helps maintain proper cellular pH, and helps mediate communication between cells in multi-cellular organisms.




Cell Differences


Terms
Cell wall  -  The thick and rigid layer that covers the plasma membrane in plant cells. Composed of fat and sugar molecules in a matrix.
Chlorophyll  -  A pigment located within a chloroplast that absorbs light in plant cells, helping to convert light energy into biological energy in the process of photosynthesis.
Chloroplast  -  A double membrane-bound organelle found in plant cells that contains chlorophyll and is responsible for mediating photosynthesis.
Photosynthesis  -  A process in which plants convert sunlight into energy sources that can be used inside the cell to sustain life.
Vacuole  -  Membrane-bound, fluid-filled organelle found only in plant cells. Can compose up to 90% of a cell's volume and performs diverse functions in plant cells, including digestion of intracellular molecules.


Plant Cells

http://img.sparknotes.com/figures/9/93c5cab1f150fcaaa9f2533d0a0b45c2/plantcell.gif
Figure %: Generalized Plant Cell
Structurally, plant and animal cells are very similar because they are both eukaryotic cells. They both contain membrane-bound organelles such as the nucleus, mitochondria, endoplasmic reticulum, golgi apparatus, lysosomes, and peroxisomes. Both also contain similar membranes, cytosol, and cytoskeletal elements. The functions of these organelles are extremely similar between the two classes of cells (peroxisomes perform additional complex functions in plant cells having to do with cellular respiration). However, the few differences that exist between plant and animals are very significant and reflect a difference in the functions of each cell.
Plant cells can be larger than animal cells. The normal range for an animal cell varies from 10 to 30 micrometers while that for a plant cell stretches from 10 to 100 micrometers. Beyond size, the main structural differences between plant and animal cells lie in a few additional structures found in animal cells. These structures include: chloroplasts, the cell wall, and vacuoles.
http://img.sparknotes.com/figures/9/93c5cab1f150fcaaa9f2533d0a0b45c2/plantanimal.gif
Figure %: Plant Cell v. Animal Cell

Chloroplasts

In animal cells, the mitochondria produces the majority of the cells energy from food. It does not have the same function in plant cells. Plant cells use sunlight as their energy source; the sunlight must be converted into energy inside the cell in a process called photosynthesis. Chloroplasts are the structures that perform this function. They are rather large, double membrane-bound structures (about 5 micrometers across) that contain the substance chlorophyll, which absorbs sunlight. Additional membranes within the chloroplast contain the structures that actually carry out photosynthesis.
Chloroplasts carry out energy conversion through a complex set of reactions similar to those performed by mitochondria in animals. The double membrane structure of chloroplasts is also reminiscent of mitochondria. The inner membrane encloses an area called the stoma, which is analogous to the matrix in mitochondria and houses DNA, RNA, ribosomes, and different enzymes. Chloroplasts, however, contain a third membrane and are generally larger than mitochondria.

The Cell Wall

Another structural difference between in plant cells is the presence of a rigid cell wall surrounding the cell membrane. This wall can range from 0.1 to 10 micrometers thick and is composed of fats and sugars. The tough wall gives added stability and protection to the plant cell.

Vacuoles

Vacuoles are large, liquid-filled organelles found only in plant cells. Vacuoles can occupy up to 90% of a cell's volume and have a single membrane. Their main function is as a space-filler in the cell, but they can also fill digestive functions similar to lysosomes (which are also present in plant cells). Vacuoles contain a number of enzymes that perform diverse functions, and their interiors can be used as storage for nutrients or, as mentioned, provide a place to degrade unwanted substances.

Cell Differences


Problems
Problem : Which of the following cellular components are not shared between plant and animal cells?
  • Mitochondria
  • Nucleus
  • Chloroplasts
  • Vacuoles
  • Cell membrane
  • Endoplasmic Reticulum
  • Golgi apparatus
  • Lysosomes
  • Peroxisomes
  • Cell wall
In the list all structures are shared between plant and animal cells except cholorplasts, vacuoles, and cell wall.

Problem : Why are chloroplasts found in plant cells and not in animal cells?
Plant cells use sunlight for energy. In order to effectively use the light, it must be converted within the cell. Chloroplasts are structures that perform this function. Animal cells do not use this special mechanism for energy and therefore do not need the additional structure.

Problem : What is the name of the process by which plant cells convert sunlight into energy a cell can use for biological functions?
Photosynthesis

Problem : Which is generally larger, an animal or plant cell?
Plant cells are generally larger than animal cells. They can be as large as 100 micrometers in diameter.

Problem : Vacuoles are most similar to what other organelle found in both plant and animal cells? Why?
Vacuoles are most similar to lysosomes because both have digestive functions in cells. Vacuoles and lysosomes both contain enzymes that can break down unwanted molecules in a cell.



Cell Differences


Prokaryotic Cells
Unlike eukaryotic cells, prokaryote cells lack membrane-bound organelles. However, whereas prokaryote cells are less structurally complex than eukaryotes, they are more chemically complex, since all of the prokaryote cell's biomolecules are floating around together. These biomolecules must interact only with other appropriate molecules to perform biological function.
Prokaryotic cells contain a single compartment enclosed within the cell membrane. In this space reside DNA, RNA, ribosomes and other molecules. Prokaryotes lack a defined nucleus (which is where DNA and RNA are stored in eukaryotic cells), mitochondria, ER, golgi apparatus, and so on. In addition to the lack of organelles, prokaryotic cells also lack a cytoskeleton. Recall that in addition to its role as structural support for the interior of the cell, the cytoskeleton is also involved in intracellular organelle transport. Since there are no organelles to be transported in prokaryotic cells, such a function is unnecessary.
Like the eukaryote cell, the prokaryote cell is filled with cytosol. The prokaryote cytosol is filled with enzymes, which carry out respiratory processes reserved in eukaryotes for the mitochondria. Prokaryote and eukaryote ribosomes also differ slightly, reflect minor differences in prokaryotic versus eukaryotic processing of DNA.
Cell Differences


Problems
Problem : Fill in the blank. Prokaryotic cells differ structurally from eukaryotic cells because they lack membrane-bound __________.
Organelles.

Problem : Fill in the blank. Eukaryotic cells are more complex __________, but prokaryotic cells are more complex ____________.
Structurally. Chemically.

Problem : What structures of a cell that we have discussed are conserved between prokaryotic and eukaryotic cells?
The cell membrane in both prokaryotic and eukaryotic cells have the same structure. Additionally, prokaryotic cells also contain cytosol in its cytoplasm.

Problem : Are multi-cellular organisms more likely to be prokaryotic or eukaryotic?
Eukaryotic.

Problem : What is a reason for the lack of a cytoskeleton in prokaryotic cells?
The cytoskeleton functions in eukaryotic cells in intracellular organelle transport. Since prokaryotic cells do not have organelles, this function is unnecessary.


Terms
Actin  -  A very abundant protein in eukaryotic cells that is the main component of actin filaments.
Actin Filaments  -  Approximately 5-9 nanometers in diameter. Provide structural support to the plasma membrane. As a cytoskeletal protein provides for movement of organelles within cells.
Centromere  -  A round structure that holds together sister chromatids.
Centrosome  -  A region of the cell near the nucleus from which microtubules sprout. Centrosomes are not found in all cells. Centrosomes are comprised of two centrioles.
Chromosome  -  A structure composed of DNA and proteins containing all the genetic material of a cell. Found in the cell nucleus.
Cytoplasm  -  A fluid found in the main compartment of eukaryotic cells. Includes everything outside the cell nucleus but the organelles and the cytoskeleton. The main component is cytosol.
Cytoskeleton  -  A system of protein filaments found throughout the cytoplasm of eukaryotic cells that help provide for cell structure. Composed of actin, intermediate filaments, and microtubules.
Cytosol  -  The main component of the cytoplasm that fills the main compartment of eukaryotic cells.
Endoplasmic reticulum  -  A membrane-bound organelle found in eukaryotic cells. Makes direct contact with the cell nucleus and, since it is dotted with ribosomes, is the site of lipid and protein synthesis. Comes in two forms, smooth and rough.
Endosome  -  A membrane-bound organelle found in eukaryotic cells. Responsible for delivering molecules to the lysosome for digestion.
Eukaryote  -  An organism composed of one or more cells with defined intracellular components including a nucleus and cytosol. Includes all organisms except bacteria and viruses.
Golgi apparatus  -  A membrane-bound organelle found near the cell nucleus in eukaryotic cells. Responsible for sorting and packaging proteins for secretion to various destinations in the cell.
Intermediate filament  -  One of three protein components of the cytoskeleton. A fibrous protein filament approximately 10 nanometers in diameter. Forms the nuclear lamina that helps protect the cell nucleus.
Intermembrane space  -  The space between the outer and inner membrane in a mitochondria.
Lysosome  -  A membrane-bound organelle found in eukaryotic cells. Contain acids and enzymes that degrade unwanted molecules.
Matrix  -  The space inside the inner membrane of mitochondria.
Microtubule  -  One of three protein components of the cytoskeleton. Long, cylindrical structures approximately 25 nanometers in diameter. Extend from the centrosome to all parts of the cell, forming tracks on which organelles can travel within the cell. Microtubules can be either kinetocore microtubules or non-kinetocore microtubules. Kinetocore microtubules bind to sister chromatids during mitosis; non-kinetocore microtubules do not.
Mitochondria  -  An organelle within the cell. Much of cell respiration is carried out within its bounds.
Nucleus  -  A large, double membrane-bound organelle found in eukaryotic cells. Contains DNA and RNA.
Organelle  -  A membrane-bound sub-cellular structure found in eukaryotic cells. The Cell nucleus, mitochondria, ER, and golgi apparatus are all examples.
Peroxisome  -  A small, membrane-bound organelle found in eukaryotic cells. Contains oxidizing enzymes that oxidize organic molecules and process hydrogen peroxide in the cell.
Prokaryote  -  An organism composed of usually one, but occasionally more, cells that lack defined sub-cellular compartments. All essential material is enclosed within the cell membrane. Includes all bacteria and close relatives.
Ribosome  -  A molecule composed of ribosomal RNA* {biology/molecularbiology/translation}* and proteins, and located on the endoplasmic reticulum**. Responsible for mediating protein synthesis.
Rough endoplasmic reticulum  -  Endoplasmic reticulum that is coated with ribosomes and involved in protein synthesis.
Smooth endoplasmic reticulum  -  Naked endoplasmic reticulum that lacks ribosomes and is more involved in lipid synthesis.

Intracellular Components


The Cytoskeleton and Cytosol

In this section we will discuss the intracellular components that are not organelles. The cytoskeleton and cytosol are structural elements that help provide the cell with its structure. The cytoskeleton is composed of protein filaments and is found throughout the inside of a eukaryotic cell. The cytosol is the main component of the cytoplasm, the fluid that fills the inside of the cell. The cytoplasm is everything in the cell except for the cytoskeleton and membrane-bound organelles. Both structures, the cytoskeleton and cytosol, are "filler" structures that do not contain essential biological molecules but perform structural functions within a cell.

The Cytosol


The interior of a cell is composed of organelles, the cytoskeleton, and the cytosol. The cytosol often comprises more than 50% of a cell's volume. Beyond providing structural support, the cytosol is the site wherein protein synthesis takes place, and the provides a home for the centrosomes and centrioles. These organelles will be discussed more with the cytoskeleton.
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/cytosol.gif
Figure %: Location of the cytosol within a cell.

The Cytoskeleton

The cytoskeleton is similar to the lipid bilayer in that it helps provide the interior structure of the cell the way the lipid bilayer provides the structure of the cell membrane. The cytoskeleton also allows the cell to adapt. Often, a cell will reorganize its intracellular components, leading to a change in its shape. The cytoskeleton is responsible for mediating these changes. By providing "tracks" with its protein filaments, the cytoskeleton allows organelles to move around within the cell. In addition to facilitating intracellular organelle movement, by moving itself the cytoskeleton can move the entire cells in multi-cellular organisms. In this way, the cytoskeleton is involved in intercellular communication.
The cytoskeleton is composed of three different types of protein filaments: actin, microtubules, and intermediate filaments.

Actin

Actin is the main component of actin filaments, which are double-stranded, thin, and flexible structures. They have a diameter of about 5 to 9 nanometers. Actin is the most abundant protein in most eukaryotic cells. Most actin molecules work together to give support and structure to the plasma membrane and are therefore found near the cell membrane.

Microtubules

Microtubules are long, cylindrical structures composed of the protein tubulin and organized around a centrosome, an organelle usually found in the center of the cell near the cell nucleus. Unlike actin molecules, microtubules work separately to provide tracks on which organelles can travel from the center of the cell outward.

Microtubules are much more rigid than actin molecules and have a larger diameter: 25 nanometers. One end of each microtubule is embedded in the centrosome; the microtubule grows outward from there. Microtubules are relatively unstable and go through a process of continuous growth and decay. Centrioles are small arrays of microtubules that are found in the center of a centrosome. Certain proteins will use microtubules as tracks for laying out organelles in a cell.

Intermediate filaments

Intermediate filaments are the final class of proteins that compose the cytoskeleton. These structures are rope-like and fibrous, with a diameter of approximately 10 nanometers. They are not found in all animal cells, but in those in which they are present they form a network surrounding the nucleus often called the nuclear lamina. Other types of intermediate filaments extend through the cytosol. The filaments help to resist stress and increase cellular stability.
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/cytoskeleton.gif
Figure %: Organization of actin, microtubules, and intermediate filaments within a cell.
These three types of protein are distinct in their structure and specific function, but all work together to help provide intra-cellular structure. Because they are so diverse, it is very difficult to study the specific functions of the cytoskeletal components.

Intracellular Components



Problem : What are the main functions of the cytosol and cytoskeleton?
The cytosol is the site of protein synthesis and the cytoskeleton helps provide intracellular structure and helps with organelle movement in cells.

Problem : Label the locations of the cytoskeleton and cytosol in the following diagram.
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/problem1.gif
Figure %: Cell
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/solution1.gif
Figure %: Solution
The cytosol is a liquid that fills the interior of a cell. The cytoskeleton is composed of protein filaments found in the cytosol.

Problem : In what way is the function of the cytoskeleton similar to the function of the lipid bilayer?
The lipid bilayer provides the structure of the cell membrane. Similarly, the cytoskeleton helps provide the structure of the interior of the cell.

Problem : The cytosol makes up most of what intracellular component?
The cytoplasm.

Problem : Name the three proteins that compose the cytoskeleton. Which of these is responsible for forming the nuclear lamina?
The three types of protein filaments are actin molecules, microtubules, and intermediate filaments. Intermediate filaments form the nuclear lamina.

Intracellular Components


Eukaryotic Organelles: The Cell Nucleus, Mitochondria, and Peroxisomes

We will now begin our discussion of intracellular organelles. As we have mentioned, only eukaryotic cells have intracellular sub-divisions, so our discussion will exclude prokaryotic cells. We will also focus on animal cells, since plant cells have a number of further specialized structures. In this section we will discuss the importance of the cell nucleus, mitochondria, peroxisomes, endoplasmic reticulum, golgi apparatus, and lysosome.

The Cell Nucleus

The cell nucleus is one of the largest organelles found in cells and also plays an important biological role. It composes about 10% of the total volume of the cell and is found near the center of eukaryotic cells. Its importance lies in its function as a storage site for DNA, our genetic material. The cell nucleus is composed of two membranes that form a porous nuclear envelope, which allows only select molecules in and out of the cell.
The DNA that is found in the cell nucleus is packaged into structures called chromosomes. Chromosomes contain DNA and proteins and carry all the genetic information of an organism. The nucleus gains support from intermediate filaments that both form the surrounding nuclear lamina and makes direct contact with the endoplasmic reticulum. The nucleus is also the site of DNA and RNA synthesis.
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/section2.gif
Figure %: Location of the cell nucleus, mitochondria, and peroxisomes in a cell.

Mitochondria

The mitochondria, with its specialized double-membrane structure, generate adenosine triphosphate (ATP), a molecule that provides organisms with energy.
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/mitochondria.gif
Figure %: Mitochondrial structure
The outer and inner membranes of the mitochondria form two sub-compartments: the internal matrix space and the intermembrane space. Those few proteins found withn the mitochondria are located within the inner membrane. Mitochondria synthesize ATP with energy supplied by the electron transport chain and a process called oxidative phosphorylation.

Peroxisomes

Peroxisomes are single-membrane structures found in all eukaryotic cells. They are small, membrane-bound structures that use molecular oxygen to oxidize organic molecules. The structure is one of the major oxygen utilizing organelles, the other being the mitochondria. Peroxisomes contain oxidative enzymes and other enzymes that help produce and degrade hydrogen peroxide.
Because of their varying enzymatic compositions, peroxisomes are diverse structures. Their main function is to help breakdown fatty acids. They perform specific functions in plant cells, which we will discuss later.

The Endoplasmic Reticulum

The endoplasmic reticulum, or ER, is a very important cellular structure because of its function in protein synthesis and lipid synthesis. For example, the ER is the site of production of all transmembrane proteins. Since nearly all proteins that are secreted from a cell pass through it, the ER is also important in cellular trafficking. In addition to these major roles, the ER plays a role in a number of other biological processes. There are two different types of ER: smooth ER and rough ER (RER).
The rough ER has its name because it is coated with ribosomes, the structures most directly responsible for carrying out protein synthesis. Smooth ER lacks these ribosomes and is more abundant in cells that are specific for lipid synthesis and metabolism.
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/endoplasmic.gif
Figure %: The Endoplasmic Reticulum
In addtion to protein and lipid synthesis, the ER also conducts post-synthesis modifications. One such modification involves the addition of carbohydrate chains to the proteins, though the function of this addition is unknown. Another major modification is called protein folding, whose name is rather self- explanatory. Another role of the ER is to capture calcium for the cell from the cytosol. Finally, the ER can secrete proteins into the cell that are usually destined for the golgi apparatus.
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/er.gif
Figure %: The location of the Endoplasmi Reticulum, golgi apparatus, and lysosome in a eukaryotic cell.

The Golgi Apparatus

The golgi apparatus is usually located near the cell nucleus. It is composed of a series of layers called golgi stacks. Proteins from the ER always enter and exit the golgi apparatus from the same location. The cis face of the golgi is where proteins enter. A protein will make its way through the golgi stacks to the other end called the trans face where it is secreted to other parts of the cell.
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/golgi.gif
Figure %: Structure of the Golgi Apparatus
In the golgi apparatus, more carbohydrate chains are added to the protein while other chains are removed. The golgi stacks also sort proteins for secretion. After sorting, the membrane of the golgi buds off, forming secretory vesicles that transport proteins to their specific destination in the cell. A protein's destination is often signaled with a specific amino acid sequence at its end. A protein secretion most often travels back to the ER, to the plasma membrane where it can become a transmembrane protein, or to the next structure we will discuss, the lysosomes.

Lysosomes

Lysosomes are sites of molecular degradation found in all eukaryotic cells. They are small, single-membrane packages of acidic enzymes that digest molecules and are found throughout eukaryotic cells. As such, Lysosomes are a sort of cellular "garbage can," getting rid of cellular debris. Proteins that are not correctly folded or have significant mutations can be secreted to the lysosomes and be degraded instead of taking up space in the cell. Detritus proteins and other molecules can find their way to the lysosome in a variey of ways.
Molecules from outside a cell can be taken in through a process called endocytosis. In this process, the cell membrane invaginates, forming a vesicle containing the transported molecule that will eventually reach a lysosome. The reverse of endocytosis is exocytosis. In this process, molecules within a cell are secreted into an endosome, a membrane-bound structure that delivers the molecule to the lysosome. After reaching the lysosomes, the molecules are secreted from a cell in membrane vesicles. Proteins secreted by the golgi apparatus into the plasma membrane can also be taken back to the lysosome by endosomes.

Intracellular Components


Problems
Problem : Identify the cell nucleus, mitochondria, and peroxisomes in the following diagram.
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/problem2.gif
Figure %: Eukaryotic cell
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/section2.gif
Figure %: Solution

Problem : What is the name of the structures into which DNA is packaged inside the cell nucleus?
DNA is packaged into chromosomes with proteins in the cell nucleus.

Problem : Does the nucleus allow molecules to pass across its double membrane?
Yes. The nuclear membrane contains pores that allow only certain molecules to pass across its membrane either in or out of the cell.

Problem : Why does the mitochondria have two distinct sub-compartments?
Mitochondrial membranes have two layers—an inner and outer membrane. As a result, there are two distinct spaces in the organelle. One between the inner and outer membranes, called the intermembrane space, and one within the inner membrane, called the matrix space.

Problem : What is the chemical process that occurs in the peroxisomes?
Oxidation. The peroxisomes contain enzymes that oxidize intracellular molecules like fatty acids.

Problem : Identify the endoplasmic reticulum, golgi apparatus, and lysosome in the following diagram.
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/problem1.gif
Figure %: Eukaryotic cell
http://img.sparknotes.com/figures/D/d479f5da672c08a54f986ae699069d7a/solution2.gif
Figure %: Solution

Problem : Why is it called "rough" endoplasmic reticulum?
It is called rough endoplasmic reticulum because it is coated with small ribosomal particles that for a bumpy coat on the cytosolic side of the ER membrane. It is contrasted with smooth ER which lacks these ribosomes.

Problem : How are proteins segregated in the golgi apparatus for secretion?
Most proteins contain a signal sequence at its end that tell the golgi to where in the cell it should be secreted.

Problem : Into which face of the golgi apparatus do proteins from the ER enter? Which face do they exit from?
Proteins enter the golgi apparatus through the cis face and exit through the trans face.

Problem : What is the function of the lysosome?
The lysosome functions to remove intracellular debris by digesting it with the acidic enzymes found inside it.


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Review of Cell Structure

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Review Test
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Scroll through the page to review your answers. The correct answer is highlighted in  green.  Your incorrect answers (if any) are highlighted in  red.  If you'd like to take the test over again, click the reset button at the end of the test.
The lipid bilayer is composed primarily of what two biological molecules?
(A) Sugars and fats
(B) Carbohydrates and proteins
(C) Proteins and fats
(D) Sugars and proteins
Which of the following eukaryotic intracellular components are not organelles?
(A) Golgi apparatus
(B) Cytoskeleton
(C) ER
(D) lysosomes
What is the typical width of the lipid bilayer?
(A) 3 nanometers
(B) 5 nanometers
(C) 7 nanometers
(D) 9 nanometers
Which of the following is the main component of the cytoplasm?
(A) Cytosol
(B) Cytosine
(C) Ectoderm
(D) Chlorophyll
Which of the following phrases best matches the definition of the term hydrophobic?
(A) "water-hating"
(B) "water-loving"
(C) "water-impartial"
(D) "water-storing"
The cytosol composes up to what percent of a cell's volume?
(A) 10%
(B) 30%
(C) 50%
(D) 90%
The term hydrophilic means which of the following?
(A) Repelled by water
(B) Insoluble in water
(C) Non-water containing
(D) Attracted to water
The function of the cytoskeleton is most similar to the function of what other cellular structure?
(A) Peroxisome
(B) Lipid bilayer
(C) Cytoplasm
(D) Mitochondria
A molecule that has both polar and nonpolar regions is called ___________.
(A) Hydrophobic
(B) Hydrophilic
(C) Amphipathic
(D) Hydrated
The cytoskeleton is primarily responsible for __________.
(A) Cell shape
(B) Cellular energy
(C) Cellular respiration
(D) Cell density
The most abundant class of lipids found in the lipid bilayer are the ___________.
(A) Phospholipids
(B) Glycolipids
(C) Sphingolipids
(D) Liposomes
Which of the following are not a cytoskeletal protein filament?
(A) Actin
(B) Intermediate filaments
(C) Primary filaments
(D) Microtubules
What is the name of the process by which plant cells convert light energy into biological energy?
(A) Photosynthesis
(B) Photorespiration
(C) Light-conversion
(D) Oxidative phosphorylation
Which of the following is not a property of the lipid bilayer?
(A) Fluidity
(B) Impermeability
(C) Polarity
(D) Permeability
What is the name of the structure around which microtubules grow?
(A) Centers
(B) Matrices
(C) Growth cones
(D) Centrosomes
Membrane proteins that cannot be easily removed from the cell membrane are called __________.
(A) Peripheral proteins
(B) Integral proteins
(C) Rigid proteins
(D) Locked proteins
What organelle is responsible for carrying out photosynthesis?
(A) Mitochondria
(B) Nucleus
(C) Vacuole
(D) Chloroplasts
Which of the cytoskeletal protein filaments has the largest diameter?
(A) Actin
(B) Intermediate filaments
(C) Primary filaments
(D) Microtubules
Membrane proteins that span the entire lipid bilayer are called __________.
(A) Membrane-spanners
(B) Integral proteins
(C) Peripheral proteins
(D) Transmembrane proteins
Which cytoskeletal filament is responsible for forming the nuclear lamina?
(A) Actin
(B) Intermediate filaments
(C) Primary filaments
(D) Microtubules
What configuration does a protein adopt when it crosses the lipid bilayer?
(A) Alpha-helical
(B) Beta-helical
(C) Gamma-helical
(D) Delta-helical
Molecules done being processed in the ER are often transported to which structure?
(A) Peroxisomes
(B) Mitochondria
(C) Golgi apparatus
(D) Vacuoles
The face through which molecules enter the golgi apparatus is called the __________ face.
(A) Cis
(B) Trans
(C) Medial
(D) Dorsal
Which cytoskeletal protein filaments line the cell membrane?
(A) Actin
(B) Intermediate filaments
(C) Primary filaments
(D) Microtubules
Which of the following is not a common destination of vesicles secreted from the golgi apparatus?
(A) Lysosome
(B) Cell membrane
(C) ER
(D) Mitochondria
Which of the following best describes the properties of a lipid-bound protein?
(A) Having its tail-end attached to the lipid bilayer
(B) Having its head-end attached to the lipid bilayer
(C) Being entirely located in the lipid bilayer
(D) Being loosely associated with the lipid bilayer
Which of the following eukaryotic organelles is primarily responsible for celluar digestion?
(A) Nucleus
(B) Lysosome
(C) Mitochondria
(D) Golgi apparatus
Which of the following is the largest organelle in eukaryotic cells?
(A) ER
(B) Golgi apparatus
(C) Lysosome
(D) Nucleus
Which of the following is not a specialized plant cellular structure?
(A) Lysosome
(B) Cell wall
(C) Chloroplast
(D) Vacuole
What is the name of the organelle that helps mediate endocytosis and exocytosis?
(A) Vacuole
(B) Peroxisome
(C) Lysosome
(D) Endosome
What is the name of the carbohydrate coat found on the outside of the lipid bilayer of higher- order cells cells?
(A) Glycosylation
(B) Glycocalyx
(C) Glycogen
(D) Glutamine
What structure in plants replaces the function that the mitochondria performs in animal cells?
(A) Vacuole
(B) Cytoskeleton
(C) Chloroplast
(D) Nucleus
In eukaryotes, the cell nucleus composes what fraction of the total cell volume?
(A) 10%
(B) 15%
(C) 20%
(D) 25%
What is the name of the process by which molecules naturally flow from an area of higher concentration to one of lower concentration?
(A) Respiration
(B) Transfusion
(C) Dialysis
(D) Diffusion
Which of the following organelles do not contain a double-membrane?
(A) Nucleus
(B) Lysosome
(C) Mitochondria
(D) Chloroplasts
Membrane transport that occurs without the input of extra energy can be classified as what type of transport?
(A) Passive
(B) Active
(C) Catalytic
(D) Inhibitory
The cell nucleus is not found in direct contact with which of the following cellular structures?
(A) Cytosol
(B) Cytoskeleton
(C) ER
(D) Mitochondria
Membrane transport that requires the input of additional enery is called _________.
(A) Passive
(B) Active
(C) Catalytic
(D) Inhibitory
What is the name of the inner-most space in a mitochondrial cell?
(A) Matrix
(B) Intermembrane space
(C) Cytosol
(D) Chlorophyll
Membrane proteins that mediate active transport are generally __________.
(A) Lipid-bound proteins
(B) Ionophores
(C) Channel proteins
(D) Carrier proteins
What is the main function of the mitochondria?
(A) Molecular digestion
(B) DNA storage
(C) Space-filler
(D) Enery-producer
The mitochondrial matrix is analogous to which structure in plant chloroplasts?
(A) Stoma
(B) Intermembrane space
(C) Cytosol
(D) Vacuole
Membrane proteins that mediate passive transport are generally _________.
(A) Lipid-bound proteins
(B) Ionophores
(C) Channel proteins
(D) Carrier proteins
Which eukaryotic organelle contains oxidizing enzymes?
(A) Lysosome
(B) Peroxisome
(C) Golgi apparatus
(D) ER
What is a typical thickness for a cell wall?
(A) 50 nanometers
(B) 50 micrometers
(C) 10 nanometers
(D) 10 micrometers
__________ are a class of membrane proteins that increase a cell's permeability to certain ions.
(A) Lipid-bound
(B) Ionophores
(C) Channel proteins
(D) Carrier proteins
__________ endoplasmic reticulum has ribosomes attached to its outer membrane.
(A) Smooth
(B) Spiked
(C) Rough
(D) Cytoskeletal
Vacuoles can occupy up to what percent of plant cells?
(A) 90%
(B) 75%
(C) 50%
(D) 25%
Membrane transport is important for which of the following biological processes?
(A) Protein synthesis
(B) Cell communication
(C) Maintenance of cellular pH
(D) All of the above
The ER plays a major role in the processing of which of the following biological molecules?
(A) Carbohydrates
(B) Proteins
(C) Adenosine triphosphate
(D) DNA
Which of the following is not a normal function of plant cell vacuoles?
(A) Cellular digestion
(B) Space-filling
(C) Energy production
(D) Storage

Cell Respiration: Introduction



Terms

Acetyl Coenzyme A  -  A small molecule that carries acetyl functional groups in cells. Composed of an acetyl group attached to a coenzyme A molecule. The starting product of the citric acid cycle.
Adenosine Triphosphate (ATP)  -  The molecule from which cells derive energy. Comprised of an adenosine molecule bonded to three phosphates, each phosphate bond contains energy, especially the third bond. By breaking that one bond and reducing ATP to adenosine diphosphate (ADP), the cell can get the energy to carry out its various processes.
Aerobic respiration  -  A metabolic process involving oxygen in the breakdown of glucose.
Anabolic  -  Term describing enzyme-catalyzed reactions in a cell that involves the synthesis of complex molecules out of simpler subunits and which uses energy.
Anaerobic respiration  -  A metabolic process that does not involve oxygen in the breakdown of glucose.
Carbohydrate  -  A molecular compound containing carbon, hydrogen, and oxygen. Subunits are sugars.
Catabolic  -  Term describing enzyme-catalyzed reactions in a cell that involve the degradation of molecules into more simple subunits with the release of energy.
Chemotroph  -  An organism that derives its energy from the ingestion of food molecules.
Citric acid cycle  -  Also known as the Krebs Cycle; a metabolic pathway found in aerobic organisms that oxidizes acetyl coA groups to carbon dioxide and water.
Coenzyme  -  A molecule that participates in an enzyme-catalyzed reaction and functions to transfer atoms or electrons between itself and various molecules.
Elimination reaction  -  A reaction that involves the ejection of a specific group from a molecule, often resulting in the formation of a carbon-carbon double bond.
Glycolysis  -  A metabolic pathway occurring in the cell *cytosol that during a series of reactions converts glucose to pyruvate and synthesizes ATP**.
Isomerization  -  A reaction that does not change the atomic make-up of a molecule, but rather changes its geometric conformation, yielding a slightly different molecule.
Lipid  -  An organic molecule that is insoluble in water. A main component of cell membranes.
Metabolism  -  All the reactions occurring in an organism that participate in the acquisition or conversion of energy for use in the organism.
Nicotinamide adenine dinucleotide  -  A coenzyme that participates in oxidation and reduction reactions. An important electron carrier in oxidative phosphorylation.
Oxidation  -  A reaction that involves the overall loss of electrons from a specific molecule or atom. Can occur with the addition of an oxygen or by the removal of a hydrogen.
Oxidative phosphorylation  -  A process occurring in the mitochondria that results in the formation of ATP from the flow of electrons to oxygen.
Photosynthesis  -  A process in which plants convert sunlight into energy sources that can be used inside the cell to sustain life.
Phototroph  -  Organisms that obtain energy from sun light through photosynthesis.
Protein  -  An essential molecule found in all cells. Composed of amino acid subunits.
Reduction  -  A reaction that results in the overall gain of electrons to a specific molecule or atom. Can occur with the addition of a hydrogen atom or by the removal of an oxygen atom.
Respiration  -  A process that occurs in cells in which cells breakdown food molecules to yield ATP. Can be either aerobic or anaerobic.
Cellular Energy Sources
The goal of cellular respiration and metabolism in animals and plants is, ultimately, the conversion of one type of energy source to another. Presumably, the original energy source comes in a form that cannot be immediately used to support cellular activities. For humans, our external energy sources are the foods we eat. Once we ingest and digest the food, our cells metabolic processes convert the energy contained within the food into a form of energy that can function in our cells. These constant conversions are what allow us to perform our day-to-day activities.

Since energy is the ultimate goal of metabolism, it will be helpful to understand what these various external and internal energy sources really are. As we have mentioned, food is the external energy source for humans. Different foods are composed primarily of one of the following three macromolecules: carbohydrates (breads and pastas), lipids (fats and oils), or proteins (meats and beans). During digestion of food, when the food is first broken down internally, these large molecules are broken into subunits. Depending on their type, subunits can be metabolized in different ways and then used as internal energy sources.
The distinct means of metabolizing specific subunits all have the same goal, the production of the primary cellular energy source: adenosine triphosphate.
http://img.sparknotes.com/figures/B/ba1857792caee2733c4d6806ac495bc2/atp.gif
Figure %: Chemical structure of ATP
As you can see in the figure above, ATP contains three phosphate groups. These groups are primarily responsible for ATP's role as an energy source. During metabolic reactions, these phosphate groups can be transferred from ATP to yield either adenosine diphosphate (ADP) or adenosine monophosphate (AMP).
ATP -> ADP + P + energy, or
ATP -> AMP + 2P + energy
The release of one or more phosphate groups is energetically favorable: the reaction produces energy. ATP can also undergo a reaction with water to yield ADP or AMP to release energy. The cell can use the energy produced from the breakdown of ATP for whatever purpose is necessary. Often, the energetically favorable breakdown of ATP is often coupled with another, energetically unfavorable reaction that is designed to drive the first reaction forward through the synthesis of additional ATP.
ATP synthesis is almost exactly opposite to the process by which ATP is broken down to produce energy: phosphate groups are brought in contact with either ADP or AMP. While this process is not as favorable, it is able to occur with the energy derived from metabolizing foods. In addition to ATP, there are a number of other reactive molecules that are involved in the production of cellular energy. These are called coenzymes and their role is to help transfer other chemical groups like hydrogens. Coenzymes work in conjunction with metabolic enzymes to drive metabolic reactions. Among these are nicotinamide adenine dinucleotide (NADH) and acetyl coenzyme A. We will discuss the specific roles of both these molecules more in following sections.

Metabolism

Basics of Metabolism

Metabolism is a process of energy acquisition and conversion. It is necessary because organisms are constantly undergoing cellular changes--they are not in a state of equilibrium. Metabolism is an attempt to regulate cellular conditions by making internal changes to maintain a steady cellular state. As a general rule, nature's tendency is towards conditions of disorder. This means that disorderly conditions are energetically favorable--they release energy. Highly ordered and organized conditions are not energetically favorable and require energy to occur. As a result, the thousands of reactions that constantly occur inside us to maintain cellular organization need energy. The body produces this needed energy by breaking down ATP, and then using this energy to promote energetically unfavorable, but biologically necessary reactions.

In order to begin any of these processes, cells need an external energy source. The breakdown of the external source can provide the energy that can couple to drive other reactions. Cells acquire this external energy in one of two ways. Phototrophs get their energy from the sun through photosynthesis. Plants are phototrophs. Plants use light energy to convert carbon dioxide and water into carbohydrates and oxygen. Chemotrophs, such as humans, derive energy from the breakdown of organic compounds such as carbohydrates, lipids, and proteins. Our focus in discussing cell respiration and metabolism will be on this second, chemical type of energy acquisition. The relationship between phototrophs and chemotrophs is complimetary: chemotrophs require oxygen and expire carbon dioxide while phototrophs require carbon dioxide and expire oxygen. Additionally, many of the carbohydrates ingested by chemotrophs derive from the metabolic carbohydrate products of phototrophs.
Among chemotrophs, there are two major categories of metabolic pathways. The distinction between the two is that one involves degradation reactions while the other involves synthesis reactions. Catabolic pathways involve the breakdown of ingested food molecules. Anabolic pathways involve the synthesis of essential biomolecules. Along each of these pathways, a number of enzymes work in combination to help drive the reactions. The catabolic pathways are involved in breaking down carbohydrates and proteins into their polysaccharide, or sugar, and amino acid subunits. These reactions release energy needed by the cell (this is why food, the source of carbohydrates and proteins, is essential for survival). Anabolic pathways take the simple products of catabolic degradation--ATP, for example--and use energy from their degradation to synthesize complex biomolecules.
As we have mentioned, the breakdown of ATP is an energetically favorable reaction. This is true because it involves splitting one larger, more organized molecule into two smaller ones. The energy that is released in this process can be used to drive other, less favorable reactions forward. In this way, ATP acts as a major energy source for cells.
As one can imagine, there are many different anabolic and catabolic reactions going on at any second in our bodies. As a result, metabolic pathways must be highly regulated as to ensure that the proper enzymes for synthesis and degradation are active at the appropriate times. Some of this regulation is made possible by different metabolic processes occurring in distinct parts of the cell.

Types of Metabolic Reactions

Oxidation and Reduction Reactions

There are a number of different types of metabolic reactions that typically take place. One class of reactions that will be mentioned a lot in this guide are oxidation and reduction reactions. These reactions involve the gain and loss of electrons and often also involve the cleavage of carbon-hydrogen bonds. When they are favorable, such reactions yield a large amount of free energy. In order to understand the specifics of what occurs in these reactions, a strong chemistry background is necessary. Here, it will suffice to understand that an oxidation reaction involves the loss of electrons (which corresponds to the breaking of bonds) and that a reduction reaction involves a gain of electrons (corresponding to a making of bonds).

Elimination Reactions and Isomerization Reactions


Another class of reactions are elimination reactions. These involve the elimination of atoms from a molecule and result in the formation of carbon- carbon double bonds. Molecules that can be eliminated include, among others, water, ammonia, and hydroxyls. Isomerization reactions involve intramolecular shifting of hydrogen atoms. The products of an isomerization reaction have the same atomic components but are found in a different conformation.

Again, these descriptions of metabolic reactions are just simple introductions so that we can use them in our discussion of glycolysis and the citric acid cycle. The specifics of these reactions use organic chemistry that is not covered here.