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2
CHAPTER
BIOLOGICAL MOLECULES Major Concepts: 2.1
Biological Molecules in Protoplasm (2 Periods)
2.2
Importance of Water (1 Period)
2.3
Carbohydrates (4 Periods)
Number of allotted teaching periods: 21
2.3.1 Classification and Role of Carbohydrates 2.4
Proteins (4 Periods) 2.4.1 Structure of Proteins 2.4.2 Classification of Proteins 2.4.3 Role of Proteins
2.5
Lipids (4 Periods) 2.5.1 Classification and Role of Lipids
2.6
Nucleic Acids (5 periods) 2.6.1 Structure of Nucleic Acids 2.6.2 Classification and Role of Nucleic Acids
2.7
Conjugated Molecules (1 Period)
About 4 billion years ago the EarthÂ’s surface was covered with newly formed oceans, but they were devoid of life. The atmosphere consisted of water vapour and mixture of gases, some containing carbon. Bombarding the planet were ultraviolet, volcanic heat, radioactive decay, and lightening that caused the first carbon based molecules to form. Life as we know it is dependent on carbon based i.e. organic molecules.
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2.1
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BIOLOGICAL MOLECULES IN PROTOPLASM
Biochemistry is the science concerned with the various molecules that occur in living cells and organisms and with their chemical reactions. Biochemistry can be defined more formally as the science concerned with the chemical basis of life. Because life depends on biochemical reactions, biochemistry has become the basic language of all biological sciences. Biochemistry is concerned with the entire spectrum of life, from relatively simple viruses and bacteria to complete human beings. Biochemistry and medicine are intimately related. Advances in biochemical knowledge have illuminated many areas of medicine, agriculture, fermentation industries e.g. baked products, dietaries, food production and preservation. A sound knowledge of biochemistry and other related basic disciplines is essential for medical science, agriculture, fermentation industry, botany, zoology, genetics, molecular biology, molecular genetics, genetic engineering, biotechnology, pharmacology, pathology, toxicology, oncogenesis, laboratory tests in relation to diseases etc. Thus biochemistry is one of the unifying theme of biology. Chemical Composition of Protoplasm Early biologists thought that the cell consists of a homogeneous jelly, which they called protoplasm. Today the word protoplasm if used at all is applied in a very general way. Specifically, the portion of protoplasm outside the nucleus is called cytoplasm, and the corresponding material within the nucleus is termed nucleoplasm. The cytoplasm is composed of several types of organelles and a fluid matrix, the cytosol (literally cell solution) in which the organelles resides. The cytosol is a watery solution of salts, sugars, amino acids, proteins fatty acids, nucleotides etc. Therefore the term cytoplasm includes both the cytosol and all the organelles other than the nucleus.
Trace elements (less than 0.01%): Boron, chromium, cobalt, copper, fluorine, iodine, iron, manganese, molybdenum, selenium, silicone, tin, vanadium and zinc.
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The Elements found in living organisms are H, C, N, O, P, S, Na + Mg +2 Cl –, K +, Ca +2, Mn, Fe, Co, Cu, Zn, B, Al, Si, V, Mo and I. The six commonest bioelements account for 99% of biomass are oxygen 65%, carbon 18.5%, hydrogen 9.5%, nitrogen 3.3% calcium 1.5%, phosphorus 1%. Today chemists recognize 92 elements occurring in nature. About 25 of the 92 natural elements are essential to life. As you can see in the table 2.1 four of these oxygen, carbon, hydrogen and nitrogen make up about 96.3% of the human body, which is typical of living matter. Calcium, phosphorus, potassium, sulphur and a few other elements account for most of the remaining 3.5%. The trace elements are essential to at least some organisms but only in minute quantities. Some trace elements such as iron, are needed by all forms of life. Others are required only by certain species. The structure and function of cells depend on the various biochemicals, which form the cells. 70% of a typical mammalian cell consists of water. Water and electrolytes are present throughout the cell. The function of the electrolyte is to establish osmotic gradients, pH and membrane potential. The protoplasm has proteins, carbohydrates, lipids, nucleic acid, enzymes, hormones and metabolites. Table: 2.2 Total Cell Weight as per components
Four Fundamental Kinds of Biological Molecules The four fundamental kinds of biological molecules are carbohydrates, proteins, lipids and nucleic acids. Carbohydrates are present in the inclusions of the cells and provide fuel for the metabolic activities of the cell. Proteins are present in the membranes, ribosomes, cytoskeleton and enzymes of the cell. Lipids are present on the membranes of Golgi complex and inclusion of the cell. Lipids provide a reserved energy source, shape, protect and insulate the cells. The nucleic acid DNA is present in the nucleus, chromosome and gene. It controls the cell activity. The nucleic acid RNA is present in the nucleoplasm and cytoplasm. It transmits genetic information and takes part in protein synthesis.
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Condensation and Hydrolysis A macromolecule is a giant molecule made from many repeating units. Molecules built like this are known as polymers. The individual units are known as monomers. During condensation, when two monomers join, a hydroxyl (–OH) group is removed from one monomer and a hydrogen (–H) is removed from the other. Water is given off during a condensation reaction.
Fig: 2.1 Monomer and Polymer
Condensation involves a dehydration synthesis because water is removed (dehydration) and bond is made (synthesis). Condensation does not take place unless the proper enzyme is present and the monomers are in an activated energy- rich form. Polymers are broken down by hydrolysis, which is essentially the reverse of condensation. During hydration, an OH group from water is attached to the other monomer. Hydration involves a hydrolysis reaction because water is used to break a bond. Again, the proper enzyme is required. (a) In cells, synthesis often occurs when monomers are joined by condensation (removal of H2O). (b) Hydrolysis occurs when the monomers in a polymer separate after the addition of H2O.
Fig: 2.2 (a) Condensation (b) Hydrolysis of Polymers
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2.2 IMPORTANCE OF WATER As we know life originated in water, so no life can exist without water. Water provides an environment for the organism that live in it. Of the smallest molecule water is most abundant. All living things are composed of 60-95% of water. Water is an inorganic substance as carbon is absent in H-O-H. The properties of water are: High polarity, hydrogen bonding, high specific heat, high heat of vapourization, cohesion, hydrophobic interaction, ionization, lower density of ice. High Polarity: Normally the sharing of electrons between two atoms is fairly equal and the covalent bond is nonpolar. In the case of water, however the sharing of electrons between oxygen and hydrogen is not completely equal. A polar covalent bond is a chemical bond in which shared electrons are pulled closer to the more electronegative atom, making it partially negative and the other atom partially positive. Thus, in H2O, the O atom actually has a slight negative charge and each H atom a slight positive charge, even though H2O as a whole is neutral. Because of its polar covalent bonds, water is a polar molecule i.e. it has a slightly negative pole and two slightly positive ones. Q. When hydrogen gas combines with oxygen gas to form water, is the hydrogen reduced or oxidized? Hydrogen Bonding: The polarity of water molecules makes them interact with each other. The charged regions on each molecule are attracted to oppositely charged regions on neighbouring molecules, forming weak bonds. Since the positively charged region in this special type of bond is always an H atom, the bond is called a hydrogen bond. This bond is often represented by a dotted line because a hydrogen bond is easily broken. Because of hydrogen bonding, water is a liquid at temperatures suitable for life. It boils at 1000C and freezes at 0 0C. High Specific Heat: The heat capacity of water is the amount of heat required to raise the temperature of 01 kg of water by 010C. Water has a high heat capacity. This means that a large increase in heat energy results in a relatively small rise in temperature. This is because much of the energy is used in breaking the hydrogen bonds, which restrict the movement of molecules. The many hydrogen bonds that link water molecules help water absorb heat without a great change in temperature. When water cools down
BIOLOGY XI: Chapter 2, BIOLOGICAL MOLECULES
Fig: 2.3 Hydrogen Bonds Between Water Molecules
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Fig: 2.4 Water shell
heat is released. Water holds heat and its temperature falls more slowly than other liquids. This property of water is important not only for aquatic organisms, but also for all living organisms. Water protects organisms from rapid temperature changes and helps them to maintain their normal internal temperature. High Heat of Vapourization: The high heat of vapourization means that water has a high boiling point. Because water boils at 1000C, it is in a liquid state at a temperature suitable to living things. This property of water helps to moderate the Earth s temperature. It also gives animals, in a hot environment an efficient way to release excess body heat. When an animal sweats, body heat is used to vapourise the sweat thus cooling the animal. The high heat of vapourization means that a large amount of heat can be lost with minimal loss of water from the body. Cohesion: Cohesion is the force whereby individual molecules stick together. Water flows freely owing to cohesion. They adhere to surfaces, particularly polar surfaces therefore water exhibits adhesion. Hydrophobic Interactions: Nonionized and nonpolar molecules that cannot attract water are said to be hydrophobic (Gk: hydrias of water and phobos, fear). Such hydrophobic (water hating) interactions are important in the formation of membranes. Ionization: When water ionizes, it releases an equal number of hydrogen and hydroxide ion: H O H H+ + OH
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This– reaction is reversible but equilibrium is maintained at 250C. The H and OH ions affect and take part in many of the reactions that occur in cells, e.g. it helps to maintain or change the pH of the medium. +
Lower Density of Ice: Most substances contract when they solidify, but water expands; because water molecules in ice form a lattice in which the hydrogen bonds are farther apart than in liquid water. As water cools, the molecules come closer together. They are densest at 4 0C but they are still moving about. At temperatures below 4 0C, there is only vibrational movement and hydrogen bonding becomes more rigid but also more open. This means that water expands as it freezes. It also means that ice is less dense than liquid water and therefore ice floats on liquid water. Q. Why ice covers more area than the same amount of water? Skills: Analyzing, Interpreting and Communication Draw model diagrams to describe the hydrogen bonding. Develop a table to align the properties of water with the benefits of life.
2.3 CARBOHYDRATES The word carbohydrate means hydrated carbon. They are composed of C, H, O in the ratio of 1:2:1. Their general formula is Cx (H2O)y where x is the whole number from three to many thousand. Chemically carbohydrates are defined as polyhydroxy aldehydes or ketones or complex substances, which on hydrolysis yield polyhydroxy aldehyde or ketone subunits.
2.3.1 CLASSIFICATION AND ROLE OF CARBOHYDRATES Carbohydrates are classified into three major classes: monosaccharides, oligosaccharides and polysaccharides. Monosaccharides (Greek: mono, singly, saccharide, sweet). These are simple sugars. They cannot be hydrolyzed into further simple units. They are sweet in taste and are easily soluble in water. All monosacchrides are reducing sugar. The sugars are crystalline. Chemically they are either polyhydroxy aldehyde or ketones. All carbon atoms in a monosaccharide except one have a hydroxyl
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group. The remaining carbon atom is either a part of an aldehyde group or a keto group. The sugar with aldehyde group is called aldo sugar and with the keto group as keto sugar e.g. the aldehyde form is glyceraldehyde whereas ketonic form is dihydroxyacetone. The two trioses are intermediate in respiration and phototsynthesis. are:
Role of Monosaccharides: The chief functions of monosaccharides
1) Trioses: C3H6O3 e.g. glyceraldehydes, dihydroxyacetone. Intermediates in respiration (see glycolysis), photosynthesis (see dark reactions) and other branches of carbohydrate metaboism. 2) Pentoses: C5H10O5 e.g. ribose, deoxyribose, ribulose. (a) Synthesis of nucleic acids; e.g. ribose is a constituent of RNA deoxyribose of DNA. (b) Synthesis of some coenzymes, e.g. ribose is used in the synthesis of NAD and NADP. (c) Synthesis of ATP requires ribose. (d) Ribulose bisphosphate is the CO2 acceptor in photosynthesis and is made from the 5C sugar ribulose. 3) Hexoses: C6H12O6 e.g. glucose, fructose, galactose. (a) Source of energy when oxidised in respiration; glucose is the most common respiratory substrate and the most common monosaccharide. (b) Synthesis of disaccharides; two monosaccharide units can link together to form a disaccharide. (c) Synthesis of polysaccharides; glucose is particularly important in this role. Classification of Monosaccharides They have general formula Cn(H2O)n. They are classified depending upon the number of carbon. In nature monosaccharides with3 7 carbon atoms are found. Their name always ends in ose. On the basis of number of carbon atoms these are named as:
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or Glycerose
Comparison of Isomers and Stereoisomerisms of Glucose Open Chain and Ring Form: The figure No. 2.5 shows glucose as having either an ‘open chain’ or ring structure. In the ring structure, the carbon atoms are numbered clockwise from one to six e.g. glucose and one to five in ribose.
G Fig: 2.5 Structure of the open chain and Ribulose is also shown.
and
ring forms of glucose. A five Carbon
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Alpha ( ) and beta ( ) isomers Isomers (GK: iso equal and meros, part) are molecules that have identical molecular formulas, but they are different molecules because the atoms in each are arranged differently. For example glucose can exist in two possible ring forms, known as the alpha ( ) and beta ( ) forms. The hydroxyl group on carbon atom 1 can project below the ring (glucose) or above the ring (glucose). In solution a glucose molecules can switch spontaneously from the open chain to either of the two rings form and back again. Glucose and fructose are structural isomers. In fructose (a ketone) the double bonded oxygen is linked to a carbon within the chain rather than to a terminal carbon as in glucose (which is a aldehyde). Because of these differences, the two sugars have different properties. For example, fructose tastes sweeter than glucose. D and L Isomerism An important feature of monosaccharide structure can be seen by examining the formula of glucose or glyceraldehyde. The second carbon atom is a chiral (like the carbon in most aminoacids). It carries four
Fig: 2.6 D and L Isomerism of Glycerose and Glucose
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different substances therefore there are two enantiomers of the monosacchride which are mirror image of one another and are designed as the D (dextro or right handed) and L (Laevo or Levo or left handed) forms (fig. 2.6). The molecules which exists in right handed or left handed forms are called enantiomers. Stereoisomers are isomeric compounds that have identical structures but differ in the arrangement of atoms in three dimensional space. Disaccharides Two monosaccharides combine to form a disaccharide. It is a kind of oligosaccharides. Disaccharides are less sweet in taste and less soluble in water. These can be hydrolyzed to give monosaccharides. Hydrolysis can be brought about either by strong acids or enzyme. Examples: Maltose
=
Glucose
+
Glucose
Lactose
=
Glucose
+
Galactose
Sucrose
=
Glucose
+
Fructose
The monosaccharide units are called residues once they have been linked. The general formula of disaccharide is : C 12 H 22 O 11 (two hexoses). Role of Disaccharides: Maltose occurs mainly as a breakdown product during digestion of starch by enzymes called amylases. This commonly occurs in animals and in germinating seeds. Maltose is fermented by yeast to alcohol. This involves conversion of maltose to glucose by the action of the enzyme maltase, a process that also occurs in animals during digestion. Lactose or milksugar is found exclusively in milk. Sucrose or canesugar is the most abundant disaccharides in nature. It makes a good transport sugar because it is very soluble and can therefore be moved efficiently in high concentrations in plants. It is also relatively unreactive chemically. This means it tends not to enter into general metabolism on the way from one place to another. It is sometimes stored for the same reason. Reducing Disaccharides: Some disaccharides including maltose and lactose are reducing sugars, meaning that they can carry out a type of chemical reaction known as reduction. Sucrose is the only common nonreducing sugar because aldehyde group of glucose and ketonic group of
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fructose are combined to make the bond between these two molecules and there is no reducing group present in sucrose. Glucoside Linkage: The bond formed between two monosaccharides is called glucoside linkage. Water is removed during formation of this linkage. (a)
Maltose
=
1,4, glucoside linkage
(b)
Sucrose
=
1,2 glucoside linkage
Fig: 2.7 - A Disaccharide
Polysaccharides Polysaccharides consist of many monosaccharides monomers linked by glycoside bonds. They are usually branched and are sparingly soluble or insoluble in water. Polysaccharides are quite abundant in nature and their molecular weight range from several thousand to millions. Their general formula is Cx(H2O)y. They are non-reducing, and are non-crystalline, white solids. They are neither sweet nor chemically very reactive. One aspect of fundamental biological importance are the manner in which the links in a polysaccharide are established. Role of Polysaccharides : Polysaccharides function chiefly as food and energy stores e.g. starch, glycogen, and structural material e.g. cellulose. They are convenient storage molecule for several reasons. Their large size makes them more or less insoluble in water, so they exert no osmotic or chemical influence in the cell; they fold into compact shapes and they are easily converted to sugars by hydrolysis when required. Examples of polysaccharides are starch, glycogen, cellulose, chitin and murein.
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Starch Starch is a polymer of (alpha) glucose formed by glucosidic chain. Such a compound yielding only glucose is a photopolymer called glucosan or glucan. It is the most important food source of carbohydrate and is found in cereals, potatoes, legumes and other vegetables. It is a major fuel store in plants, but is absent in animals. It can be easily converted back to glucose. Glucose is used by plants in respirations and by germinating seeds to make cellulose and other material needed for growth. Starch has two components: amylose and amylopectin. Amylose has a straight chain structure consisting of several thousand glucose residues (joined by 1, 4 bonds). Amylopectin forms 80-85% of the starch, and consists of branched chain composed of 24-30 glucose residues. Starch molecules accumulate to form starch grains. These are visible in many plant cells. Glycogen It is the strange polysaccharide of the animal body. It is often called animal starch. It is made from glucose. Many fungi also store it. In vertebrates glycogen is stored chiefly in the liver and muscles. Its conversion back to glucose is controlled by hormones particularly insulin. It is very similar in structure to amylopectin but shows more branching. It forms tiny granules inside cells, which are usually associated with smooth endoplasmic reticulum.
Fig: 2.8 Polysaccharide (A) Starch (B) Glycogen
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Cellulose About 50% carbon found in plants is in cellulose and it is the most abundant organic molecule on Earth. It is found in some non-vertebrate animals and ancestral fungi. Cellulose consists of long chains of glucose residues with about 10,000 residues per chain. The (beta) 1,4 linkages make the chains straight in contrast to starch where (alpha) 1,4 linkages cause the chains to be curved. Cellulose is an important food source for some animals, bacteria and fungi. Commercially cellulose is important. It is used to make cotton goods and is a constituent of paper sellotape.
Fig: 2.9 Cellulose
Chitin Chitin is an important polysaccharide found in the exoskeleton of crustaceans and insects. It also occurs in some fungi, where its fibrous nature contributes to the cell wall structure. It forms bundles of long parallel chains like cellulose. Laboratory manufacturing sweeteners are the left handed sugar and cannot be metabolized by the right handed enzymes. Laboratory manufactured sugars such as tagatose, sucralose etc. are left-handed. The two enantiomers of a molecule will respond identically in a chemical reaction, but not so in biological systems. Proteins and cell receptors are designed to react only with particular enantiomers. For example the enzymes in your stomach can digest only right-handed sugars. Likewise left-handed sugars cannot be metabolised by right-handed enzymes. Just as the glove fits only on the proper hand, a right-handed enzyme cannot fit on or react with a left-handed substrate. The substrate must fit on the proper active site of the enzyme. So for the left handed substrate (sweetener) the enzyme must be left-handed.
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BIOLOGY XI: Chapter 2, BIOLOGICAL MOLECULES Skills: Analyzing, Interpreting and Communication Draw the ring forms of alpha and beta glucose. Illustrate the formation and breakage of maltose, sucrose and lactose.
maltose
lactose
2.4. PROTEINS Proteins are the main structural components of the cell. All proteins contain C, H, O and N. Some contains P, S. Few proteins have Fe, I and Mg incorporated into the molecule.
2.4.1 STRUCTURE OF PROTEINS Amino acids are the building blocks of proteins. Some other types of molecules may be attached to proteins e.g. nucleic acids, lipids and carbohydrates. There are many amino acids known to occur, but only 20 are commonly found in proteins. Plants are able to make all amino acids from simpler substances. The amino acids are built on a common plan. Each contains a carbon atom. It is called (alpha) carbon to this a hydrogen atom, an amino group - NH2, a carboxyl group –COOH and a variable Fig: 2.10 General Structure of an Amino Acid
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group known as –R group are attached. The R group has a different structure in each of the 20 biologically important amino acids and determines their individual chemical properties. How Amino Acids Fit Together? The bond formed to unite two amino acids is called peptide bond. It is between amino group of one amino acid and carboxyl group of another amino acid. Thus the bond is between C—N. The linkage of C=O and NH 2 is called amide or peptide linkage. Water is removed in this process. The chain of amino acids joined by peptide bonds is called a polypeptide chain.
Fig: 2.11 Amino Acids Joined Together by Peptide Bond
Protein consists of chain of amino acids arranged in definite order. The primary structure of a protein is the sequence of amino acids joined by polypeptide bonds. Insulin is a small protein. The protein is constructed by two polypeptide chains of 21 and 30 amino acids. There is also a disulphide bridge between two cysteine of the smaller chain.
Fig: 2.12 Primary Structure of Protein (Insulin)
Significance of Amino Acid Sequence A protein molecule may have 51 to 3000 amino acids. All the amino acids must be in proper position in the polypeptide chain. If the proper site of even a single amino acid is changed the normal structure and function of the protein is changed. Protein consists of chain of amino acids arranged in definite order. In 1956 Vernon Ingram was able to determine the structural difference between normal haemoglobin (HbA) and sickle cell haemoglobin (HbS). (beta)
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Fig: 2.13 Sickle Cells. Glutamic Acid Has Been Replaced By Valine
chain of normal haemoglobin contains negatively charged glutamate at 6th position. In sickle cell hemoglobin the glutamate is replaced by nonpolar valine. Haemoglobin contains two types of polypeptide chain designed as and . Only the (beta) chain is affected in persons with sickle cell trait and sickle cell disease. In persons with sickle cell disease the red blood cells are not biconcave discs Fig: 2.14 Haemoglobin molecule like normal red blood cells, they are sickle shaped, due to crystallization of haemoglobin. Just one replacement of a single amino acid can change the entire structure and function of the polypeptide.
Science Titbits Because of their angular shape, sickle cells do not flow smoothly in the blood vessels. Blood flow to body parts is reduced, resulting in periodic fever, severe pain and damage to various organs including heart, brain, kidneys and spleen. It occurs more in African people. The person may die before the age of forty.
Fig: 2.15 Normal and Sickle Shaped Red Blood Cells
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2.4.2 CLASSIFICATION OF PROTEINS The shapes of protein molecules are in accordance with their function. Thus shape of protein molecules has a significant role. On the basis of shapes and structure proteins may be fibrous, globular and intermediate. Fibrous: These proteins have long parallel polypeptide chains cross— linked at intervals forming long fibres or sheets. These have secondary structures physically tough and insoluble in water. Globular: Polypeptide chains are tightly folded to form spherical shape, having tertiary structure. These are the most important ones and are easily soluble. Intermediate: These proteins are intermediate in shape between globular and fibrous protein and are soluble. Skills: Analyzing, Interpreting and Communication Draw table to illustrate different structural and functional proteins with roles of each. Illustrate the synthesis and breakage of peptide linkages.
2.4.3 ROLE OF PROTEINS Proteins play important functions in the living organisms. Brief accounts of roles of structural and functional proteins with their functions are given in the table 2.3 and table 2.4.
2.5 LIPIDS The term lipids is simply a convenient name for organic compounds that are hydrophobic (water hating) and insoluble in water but soluble in organic solvent such as acetone, alcohol, chloroform, benzene, ether etc. Lipids have a greasy or oily consistency. Lipids are composed of carbon, hydrogen and oxygen. However they have relatively less oxygen in proportion to carbon and hydrogen than do carbohydrates. Oxygen atoms are characteristic of hydrophilic (water loving) functional group, so lipids with little oxygen are much less soluble in water than most carbohydrates.
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2.4
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57
2.5.1 CLASSIFICATION AND ROLE OF LIPIDS Lipids constitute many, heterogeneous substances and are not made up of one building block. Lipids are therefore classified on the basis of solubility and on the products obtained upon hydrolysis. Lipids have been classified as: (a) acylglycerol (b) phospholipids (c) terpenes (d) waxes. Acylglycerol The most abundant lipids in living things are the neutral fats or acylglycerol. Chemically, acylglycerols can be defined as esters of fatty acids and alcohol. An ester is the compound produced as the result of a chemical reaction of an alcohol with acid and a water molecule is released. C2H5OH + HOOCCH3 Functional group of Ester
Alcohol + acetic acid
C2H5OOCCH3 + H2O an ester + water
A neutral fat consists of glycerol joined to one, two or three fatty acids. Glycerol is three carbon alcohols that contain three OH groups. A fatty acid is long, straight chain of carbon atoms, with a carboxyl group (COOH) at one end. When a glycerol molecule combines chemically with one fatty acid, a monoglycerol (or monoglyceride) is formed. When two fatty acids combine with a glycerol a diglycerol (or diglyceride) is formed and when three fatty acids combine with one glycerol molecule a triglycerol (or triglyceride) is formed.
Fig: 2.16 A Triglyceride
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About 30 different fatty acids are found. Fatty acids vary in length. They have an even number of carbon atoms. For example butyric acid has four carbon atoms and oleic acid has 18 carbon atoms. Fatty acids are either saturated or unsaturated. Saturated Fatty Acids: Fatty acids in which all of the internal carbon atoms possess hydrogen side groups are said to be saturated because they contain the maximum number of hydrogen atoms that are possible e.g. butyric acid. Saturated fatty acids tend to be solid at room temperature.
Fig: 2.17 Saturated And Unsaturated Fatty Acids
Unsaturated Fatty Acids: These have one or more pairs of carbon atoms joined by a double bond. They therefore are not fully saturated with hydrogen. Unsaturated fatty acids may further divided as: (a) Monounsaturated (b) Ployunsaturated (c) Eicosanoids. Fatty acids with one double bond are called monounsaturated fatty acids, while those with more than one double bond are polyunsaturated fatty acids. Unsaturated fatty acids are liquid at room temperature, e.g. oleic acid.
Critical Thinking
The atoms and bonds within a molecule determine its chemical and physical properties. Compare fats that contain mostly saturated fatty acids with oils that contain mostly unsaturated fatty acids to demonstrate this concept.
Role of Unsaturated Fatty Acids: Triglycerides containing hydrocarbons chains melt at a low temperature. This is useful for living things. For example feet of rein deer and penguins contain unsaturated triglycerides and this help to protect these exposed parts from freezing. Prostaglandins Prostaglandins were originally discovered in seminal plasma but now known to exist in virtually every mammalian tissue, acting as local hormones,
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they have important physiologic and pharmacologic activities. There are sixteen types of prostaglandins. Role of Prostaglandins in Living Organisms: Prostaglandins produced endogenously in tissues act as local signals that finetune the response of a specific cell type. Their Science, Technology and functions vary widely depending on the tissue. Society Connections Some reduce blood pressure, whereas other raise it. Relate the role of Prostag Those synthesized in the temperature-regulating landin in inflammation centre of the hypothalamus cause fever. Infact, the with the inhibition of pros ability of aspirin and acetaminophen to reduce t a g l a n d i n s y n t h e s i s fever and decrease pain depends on the inhibition through aspirin. of prostaglandin synthesis.
Science Titbits The cyclo-oxygenase pathway is responsible for prostanoid synthesis. Prostanoid synthesis involves the consumption of two molecules of O2 catalyzed by prostaglandin H synthase (PGHS), which possesses two enzymatic activities, cyclo-oxygenase and peroxidase. PGHS is present in two isoenzymes, PGS-1 and PGHS-2, each having cyclo-oxygenase and peroxidase activities. The product of the cyclo-oxygenase pathway is endoperoxidase (PGH), which is converted to prostaglandins D, E, F etc. Aspirin a nonsteroidal anti inflammatory drug, inhibits cyclo-oxygenase of both PGHS-1 and PGHS-2 by acetylation. Phospholipids (GK: phos light, lipos fat) as implied by the name, contains a phosphate group. Phospholipids are phosphorylated derivatives of phosphatidic acid. A phospholipid molecule consists of two fatty acids linked to a glycerol molecule and a phosphate group linked to the glycerol s third carbon. One end of the molecule, containing the phosphate group is hydrophilic. In other words, it is polar and readily soluble in water. The other end, containing the fatty acid side chains, is hydrophobic, that is non-polar and insoluble in water.
Fig: 2.18 Phospholipid Molecule
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Fig: 2.19 Phosphatidylcholine (Lecithin)
Phospholipids in Biological Membrane In water, every phospholipid molecule orients so that its polar head faces water and its non-polar tails face away. By forming two layers with the tails facing each other, no tails are ever in contact with water. The structure resulted is called lipid bilayer, which are formed spontaneously. Lipid bilayer sheet of this sort is the foundation of all biological membranes. The bilayer itself is a fluid and viscous. Hydrogen bonding of water holds the membrane together. The lipid bilayers form a barrier to the passage of watersoluble molecules, which is the key biological property of the lipid bilayer.
Fig: 2.20 Phospholipid Bilayer
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Terpenes All the terpenes are synthesized from a five-carbon building block known as isoprene unit. This unit condenses in different ways to form many compounds. Two isoprene units form a monoterpene e.g. menthol, four form a diterpene e.g. vitamin A and six a triterpene e.g. ambrein. Natural rubber is a polyterpene. Terpenoids are made from repeating units of isoprene. This unit condenes in different ways to form many compounds e.g. vitamin A and chlorophyll contain terpenoid alcohol called phytol.
Isoprene Unit
Steroids Steroids are crystallizable lipids of high molecular weight. A steroid consists of 17 carbon atoms arranged in four attached rings, three of the rings contain six carbon atoms, and the fourth contains five. The length and structure of the side chains that extend from these rings distinguish one steroid from another steroids. These structures are synthesized from isoprene units. Among the steroids of biological importance are sterols, ergosterol, vitamin D, cholesterol, bile salts, hormones secreted by the adrenal cortex and reproductive hormone estrogens, androgens.
Progesterone
Fig. 2.21 Steroids
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Physiological Role of Steroids Cholesterol is probably the best known steroid because of its association with atherosclerosis. However biochemically it is also of significance because it is the precursor of a large number of equally important steroids which include the bile acids male sex hormone testosterone, female sex hormone progesterone and estrogen, adrenal cortex hormone aldosterone cortisone, and insect molting hormone ecdysone, sitosterols of the plant, kingdom and some alkaloids. Cholesterol is a structural component of animal cell membrane, plant cell membrane contains molecules similar to cholesterol. Bile salts emulsify fats. Vitamin D, which help to regulate calcium metabolism is a steroid. Waxes Waxes are lipids having odd number of carbon atoms varying from C 25 to C 35. Waxes are mixture of long chain alkanes (C nH 2n+2) with alcohols (R OH), Ketones (R-O-R), esters (R-CO-R) and long chain fatty acids. These are chemically inert and resistant to atmospheric oxidation. Waxes have protective functions in plants and animals. It forms protective coating on fruits and leaves. Protects plants from water loss, abrasive damage and reduce the rate of transpiration. Provides water barrier for insects, birds, and sheep. Examples of waxes are bee wax and lanolin (obtained from sheep wool).
2.6 NUCLEIC ACID Friederic Miescher was a German biochemist. He isolated a substance in 1869 and named the substance as nuclein, because it was located in the nucleus of the fish sperm cells. Nuclein was later on called nucleic acid, as it acidic. Nucleic acid is a linear unbranched polymer. The monomer of the nucleic acid is called nucleotide.
2.6.1 STRUCTURE AND ROLE OF NUCLEIC ACIDS In 1920 the basic structure of nucleic acids was determined by the biochemist P. A. Levene. He found that nucleic acids are made of repeating units called nucleotides. Each nucleotide consists of pentose sugar, a phosphate and nitrogen containing ring structure called bases. The ring structures are called bases because of unshared pair of electron on nitrogen atoms, which can thus acquire a proton.
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Phosphoric acid (H 3PO 4), which gives nucleic acid their acid characteristics, forms ester linkage with –OH group of a pentose sugar. In a typical structure the nitrogen base is attached to pentose sugar. Base plus sugar is called nucleoside, and when a phosphate is added to a nucleoside it becomes a nucleotide. Nitrogen base is attached to carbon number 1 of a pentose sugar and a phosphate group is attached to carbon number 5 of the sugar. In addition a free hydroxyl (OH) group is attached to 3-carbon atom.
Nucleoside
Nucleotide
Nitrogen Bases Found in Nucleic Acids Bases may be grouped as purine and pyrimidine. Purine includes Adenine and Guanine, which are double ring structures. Pyrimidine includes Thymine, Cytosine and Uracil, which are single ring structures. The nucleotides are named after the name of base attached to it e.g. adenine nucleotide. Bases are represented by their initial letter: Adenine = A, Guanine = G, Thymine = T, Cytosine = C, Uracil = U
Fig: 2.22 Nitrogen Bases of DNA
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Mononucleotide Adenosine triphosphate (ATP) is a nucleotide. As shown in fig. 2.23 ATP has three parts, connected by covalent bonds: (a) adenine, a nitrogen base, (b) ribose, a five carbon sugar, (c) three phosphates. The two covalent bonds linking the three phosphates together are usually indicated by a squiggle (~) and are called high-energy bonds. ATP can be converted to ADP and inorganic phosphate (P) by hydrolysis. This reaction releases energy. The third phosphate group splits from the ATP and this phosphate remains in the cell in inorganic form. ADP and phosphate can be converted back to ATP, by condensation. Addition of inorganic phosphate to an organic molecule is called phosphorylation e.g. ADP + Pi = ATP
Fig: 2.23 ATP Consists of a Nucleotide Joined to two Terminal Phosphate Groups of Unstable High-energy Bonds (Indicated by wavy lines)
ATP is known as the energy currency of cells. ATP is made from the oxidation of organic molecules during respiration. Since the energy to add the phosphate to ADP comes from oxidation, the process is known as oxidative
Science Titbits What does phosphate have to do with energy? Phosphate (PO4) is a func足 tional group. The phosphate group itself has nothing directly to do with en足 ergy, however its bonding characteristics as a part of certain molecules re足 sults in high energy bonds that release a large amount of free energy. When the bonds are broken this energy can be used to drive other chemical reac足 tions.
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phosphorylation. Most of the ATP in the cell is made in mitochondria. The actual amount of ATP in the cell at any time is small. Dinucleotide Nicotinamide adenine dinucleotide (NAD) consists of two nucleotides. One nucleotide consists of base-nicotinamide, sugar and phosphate. Other nucleotide consists of base-adenine-sugar and phosphate. The two bases are joined by their phosphate group forming a dinucleotide. NAD is a coenzyme. FAD (Flavin adenine dinucleotide) is another coenzyme for oxidation-reduction.
Fig: 2.24 NAD-A Dinucleotide
Polynucleotide Phosphate groups link each nucleoside in the polymer of DNA to neighbouring nucleosides. These phosphates connect the 3 carbon of one sugar with the 5 carbon of the adjacent nucleoside sugar. The reaction between 5-phosphate group of one nucleotide and 3 hydroxy group of another form a covalent bond with the elimination of a water molecule. The linkage is called a phosphodiester bond because the phosphate group is now linked to the two sugars by means of a pair of ester (P-O-C) bonds. Nucleotides can join together forming a long polynucleotide chain.
Fig. 2.25 A Dinucleotide Showing Phosphodiester Bond
2.6.2 CLASSIFICATION OF NUCLEIC ACID There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The structure of RNA is similar to DNA except the ribose replaces the deoxyribose. Linear strands of DNA or RNA no matter how long, will almost have a free 5/ phosphate group at one end and a free 3/ hydroxyl group at the other end. The 3/ and 5/ carbons of the sugars are used in describing the direction of the polynucleotide strand runs in a molecule.
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Watson and Crick Model of DNA A model is a visual image of an object or idea, which simplifies the object, or idea. James Watson and Francis Crick assembled the molecular model and published their two-page article on their molecular model of DNA in the journal “Nature” in April 1953. Few milestones in the history of biology have as broad an impact as their double helix. Watson and Crick were awarded Nobel Prize in 1962 for their model of DNA. Here we will see the important
Twist Fig: 2.26 A Rope Ladder Model for the Double Helix
Fig: 2.27 DNA Model
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Fig: 2.28 DNA Structure
points of ladder model of DNA: There are two polynucleotide strands running in opposite directions and winding out each other in a form of double helix. The double helix looks like a ladder. The sugar and phosphate part of the nucleotide makes the upright part of ladder. The nitrogen bases of nucleotide make up the rungs of the ladder. A double ring base purine must always be paired with single ringed base pyrimidines on the opposite strand. Individual structures of bases form the pairing more specifically. Each base has chemical side groups that can best form hydrogen bonds with one appropriate partner. The matching of the bases are specific. Adenine makes the pair with Thymine and Guanine with Cytosine. The base pairs are held together by the hydrogen bond. There are three hydrogen bonds between Guanine and Cytosine and two hydrogen bonds between Adenine and Thymine. The ratio of A: T and C: G is equal but the ratio of AT : CG is different. The helix is 2nm in diameter and makes a full spiral turn every 3.4nm i.e. after every ten base pair. The distance between two base pairs is 0.34nm. There are two grooves a major groove and a minor groove. The helix rotates about its
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Science Titbits Scanning tunnelling microscopy (STM) is one of the predominant methods for examining the nano-world. The Scanning tunneling microscope was invented in 1980. It can allow scientists to view atoms on the surface of a solid. The electrons surrounding the surface atoms tunnels i.e. project out from the surface boundry a very short distance. The STM has a needlelike probe with a point so sharp that often there is only one atom at its tip. If a small voltage is applied between the tip and specimen, electrons flow through a narrow channel in the electron clouds. This tunnelling current is extraordinary sensitive to distance. It is a very powerful tool that can be used to resolve features less than a nanometer. As the tip moves up and down its motion is recorded and analyzed by a computer to create an accurate three-dimentional image of the surface atoms, which is displayed on a computer screen. The microscopeÂ’s inventors, Gerd Binnig and Heinrich Rohrer were awared Nobel Prize in Physics in 1986.
The Golden STM
DNA Nanotechnology Seeman's group worked on the DNA nanotechnology. They constructed molecular building blocks from unusual DNA motifs. They used the stable branched DNA molecules to construct a covalently closed A Scanning Tunnelling Micrograph DNA molecule whose helix axes have the of the DNA Double Helix connectivity of a cube or a truncated octahedron. In the DNA constructions, the lack of a rigid molecule was a key feature. However recently they have used the antiparallel DNA double crossover molecules to incorporate in DNA assembles that make use of this rigidity to achieve control on the geometrical level as well as on the topological level.
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axis 3.60 longitudinally with each base pair or rung, the spiral winds through a full circle i.e. 360 in the length of helix occupies by ten base pairs. There is no restriction of the sequence of nucleotides along the length of a DNA strand. The sequence can vary in countless ways. The sequence is specific for different species, organisms and even individuals. Science, Technology and Society Connections Correlate the scanning tunnelling microscope as the latest advancement for seeing the atoms of DNA. What is a gene? A unit of Inheritance: Gregor Mendel proposed in 1866 that the characteristics of organisms were determined by hereditary units, which he called elements. These were later termed genes and shown to be located on chromosomes, which transmitted them from generation to generation. Thus a gene may be defined as unit of biological inheritance. This is perfectly acceptable definition but it does not tell us anything about the physical nature of the gene. A Unit of Function: A gene can be defined as a piece of DNA which codes for protein or more precisely, a gene is the DNA code for a polypeptide, since some proteins are made up of more than one polypeptide chain and therefore coded for more than one gene. Ribonucleic Acid (RNA) RNA is a polymer of nucleotide. It consists of sugar ribose and the base adenine, cytosine, guanine and uracil. RNA is singly stranded and does not form a double helix in the same manner as DNA. There are three major classes of RNA each with a special function in protein synthesis. These RNA are transcribed from DNA template. Messenger RNA (mRNA) A mRNA consists of a singly strand of variable length. Its length depends upon the size of the gene, as well as the protein for which it is taking message. For example, for a protein molecule consisting of 1,000 amino acids, the mRNA will have the length of 3,000 nucleotides. mRNA is about 3 to 4% of the total RNA in the cell. mRNA takes the genetic message from the nucleus to the ribosome in the cytoplasm to form particular protein. It is transcribed from DNA template i.e. the base of sequence of mRNA is according to the base sequence of DNA. It becomes attached to the ribosome.
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Fig: 2.29 RNA
Fig: 2.30 mRNA
At ribosome, amino acids are attached one by one to form a polypeptide chain as per base sequence of mRNA. This process is known as translation. Ribosomal RNA (rRNA) Ribosome consists of rRNA and protein, rRNA is transcribed by the genes present on the DNA of the several chromosomes found within the region of the nucleolus known as nuclear organizer. It is called rRNA because it eventually becomes part of ribosome. The rRNA is packaged with a variety of proteins into ribosomal subunits, one of which is larger than the other. The base sequence of rRNA is similar from bacteria to higher plants and animals. rRNA is a part of ribosome where protein synthesis takes place. Transfer RNA: It is the smallest of the RNA molecule. A tRNA is a single stranded nucleic acid and folds double on itself to create regions where complementary bases are bonded to one another. The structure of a tRNA molecule is generally known as a flat cloverleaf. The whole molecule consists of 80 nucleotides but only 20 show the complementary base pairing. There are at least one tRNA molecule for each
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Fig: 2.31 Cloverleaf Model of tRNA
of the 20 amino acids found in proteins. Sixty tRNA have been identified. Human cells contain about 45 different kinds of tRNA molecules. The 5/ end, ends in Guanine base while the 3/ end always is the base sequence of ACC. The nucleotide sequence of the rest of the molecule is variable. tRNA has three loops. The middle loop in all the tRNA is composed of 7 bases, the middle three of which form the anticodon, it is complementary to specific codon of mRNA. For example, a tRNA that has anticodon GAA binds to the codon CUU and carries amino acid Leucine. The D loop recognizes the activation enzyme. Theta ( ) loop recognizes the specific place on the ribosome for binding during protein synthesis.
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BIOLOGY XI: Chapter 2, BIOLOGICAL MOLECULES Skills: Analyzing, Interpreting, and Communication Draw the Watson—Crick model of DNA Illustrate the formation of phosphodiester linkage Skills: Initiating and Planning Hypothesize, which came first DNA or RNA
2.7 CONJUGATED MOLECUELS Molecules when joined by other kinds of molecules are called conjugated molecules. The examples are glyocolipids, glycoproteins, lipoproteins and nucleoproteins. Glycolipids: These are complex lipids containing one or more simple sugars in connection with long fatty acids or alcohol. The carbohydrates form the polar head to the molecule. Glycolipids are present in white matter of brain and myelin sheath of nerve fibres and chloroplast membrane. Glycoproteins: Glycoproteins are formed when proteins are covalently bound to carbohydrates. Glycoproteins are widely distributed in the cells. They function as enzymes, hormones, transport proteins, structured 0 proteins and receptors. In Antarctica at 2 C temperature the blood would freeze. The fish contains antifreeze glycoproteins, which lower the freezing point of water. The blood group antigens contain glycoproteins, which also play a determined role in blood grouping. Lipoproteins: The lipoproteins are formed by the combination of protein with phospholipids. Phospholipid protein complexes are widely distributed in plant and animal material. They occur in milk, blood, cell nucleus, egg yolk membrane and chloroplasts of plants. They are also found in bacterial antigens and viruses. Cutin found in cuticle of plant cell walls and ruberin in the wall of cork cells are lipoproteins. Nucleoproteins: The nucleoprotein consists of simple basic protein and nucleic acid. They are most abundant in tissues, both plants and animals having a large proportion of nuclear material, such as yeast, asparagus (a plant of genus liliaceae), thymus and sperm.
BIOLOGY XI: Chapter 2, BIOLOGICAL MOLECULES
SECTION I : MULTIPLE CHOICE QUESTIONS Select the correct answer 1. An amino acid molecule has the following structure:
Which two of the groups combine to form a peptide link? A) 1 and 2
B)
1 and 3
C) 2 and 3 D) 2 and 4
2. Which class of molecule is the major component of cell membrane A)
phospholipid
B)
cellulose
C)
wax
D)
triglyceride
3. Glycerol is the back bone molecule for A)
ATP
B)
glucose
C)
triglyceride
D)
enzyme
4. A fatty acid is unsaturated if it A)
contains hydrogen
B)
contains double bonds
C)
contains an acid group
D) bonds to glycogen
5. In RNA the nitrogen base that takes the place of thymine is A)
adenine
B)
cytosine
C)
guanine
D)
uracil
6. The ending—ose means a substance is a A)
sugar
B)
lipid
C)
protein
D)
nucleic acid
7. Glycolipids and lipoprotein are important components of
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BIOLOGY XI: Chapter 2, BIOLOGICAL MOLECULES A)
proteins
B)
nucleic acids
C)
bone structure
D)
cellular membranes
8. When two amino acids are linked to form peptide linkage .......... is removed A)
hydroxyl
B)
water
C)
carbon
D)
nitrogen
9.What is the theoretical number of chemically different dipeptides that may be assembeled from 10 different aminoacids. A)
400
B)
300
C)
200
D)
100
10. A polar molecule is .. in water A)
soluble
B)
insoluble
C)
reactive
D)
a functional group
11. Estrogen, androgen and cholesterol are all examples of A)
glycolipids
B)
lipoproteins
C)
terpenes
D)
steroids
SECTION II : SHORT QUESTIONS 1. What role do lipids play in living organisms? 2. Why phospholipids form a thin layer on the surface of an aqueous solution? 3. What is the role of water as a solvent in the life of an organism? 4. What is the function of ATP in cell metabolism? 5. Why sucrose is a non-reducing sugar? 6. What are the functions of waxes in organisms? 7. Why do water molecules form a lattice structure? 8. How is peptide bond formed? 9. What are carbohydrates? Give their general formula. 10. How might an error in the DNA of an organism effect protein function? 11. All major chemical blocks found in living organisms form polymers. Why are polymers specially useful in organization of living systems?
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SECTION III : EXTENSIVE QUESTIONS 1. Write the importance of biochemistry. 2. Why does water form hydrogen bonds? Enumerate some of the properties of water that result from hydrogen bonding. How do these properties contribute to the role of water as essential component organisms? 3. Give a detailed account of monosaccharides. 4. Describe the role of disaccharides. 5. Write an essay on polysaccharides. 6. Describe the structure,and significance of sequence of amino acid. What are the functions of proteins? 7. Describe structure and functions of acylglycerol. 8. Write notes on: nucleotides, steroids, prostaglandins, terpenes, conjugated molecules. 9. Describe the structure of DNA. 10. Explain the structure and role of three types of RNA. 11. Structurally and functionally compare and contrast RNA and DNA.
ANSWER MCQS 1. B 2. A 3. C 4. B
5. D 6. A 7. D
8. B 9. D 10. A 11. D
SUPPLEMENTARY READING MATERIAL 2. Campbell N.A. Mhchell, L.G. & Reece J.B., Biology Concepts and connections, 2nd edition Benjamin/Cummings Company California, 2003 3. Mader, S.S. Human Biology, McGraw Hill, New York, 1998.
USEFUL WEBSITES 1. en.wikipedia.org/wiki/Carbohydrate 2. www.hsph.harvard.edu/nutritionsource/carbohydrates.html 3. www.cem.msu.edu/~reusch/VirtualText/carbhyd.html