Biomolecules Notes

Biomolecules INTRODUCTION   Living matter of cell is called protoplasm.  Protoplasm (Gr. Protos - first + Plasma -  organization) is a living organized substance which is the place for all physical and chemical  transformations, as a characteristics of life.  Protoplasm also includes membranes, cytoplasmic contents and nucleus.  Protoplasm is “physical basis of life”.  Protoplasm is the medium & source of all biological activities.  Max Schultze (1863) stated that protoplasm is the physical basis of life. Hanstein (1880) proposed the term protoplast for such organized mass of protoplasm, without cell wall in plants. O. Hertwig (1892) propound the protoplasmic theory according to which all living matter, out of which animals and plants are formed, is protoplasm. Fisher, Hardy and Wilson (1916) proposed colloidal theory of protoplasm. Protoplasm basically differentiates a nonliving PHYSICAL NATURE OF PROTOPLASM  Protoplasm is a greyish, translucent, from living. jelly-like, odourless and viscous substance. HISTORY  Protoplasm is heavier than water.  Corti (1772) observed protoplasm first time.  Protoplasm behaves as a moderate conductor of electricity.  Felix Dujardin (1835) studied the jelly-like substance in protozoa and called it sarcode. i.e.  Size of colloidal particles is 0.001 to 0.1 m. flesh of cell.  Mineral ions and smaller inorganic and organic  J.E. Purkinje (1840) coined the term Molecules (sugar, salts, simple acids, bases etc.) protoplasm for the living substance. occurs as crystalloid solutes in the protoplasm, while larger, organic molecules (proteins, polysac  Hugo von Mohl (1846) applied this name charides and nucleic acid) occur as colloidal (protoplasm) for the contents of the embryonic solutes. Thus protoplasm is crystallo-colloidal cells of the plants. mixture.  43 Biomolecules      Scientists call it a “mixture of mixtures”, or MODERN COLLOIDAL THEORY “supermixture”.  This was first suggested by R.A. Fisher (1894) Protoplasm is a reversible colloidal system i.e. and latter by Hardy (1899) and Wilson (1916). it can change from a thicker, highly viscous “gel”  It consists of a fluid matrix or ground substance state to a comparatively more fluid and less (liquid phase) dispersion phase and dispersed viscous “sol” state and vice-versa. phase of granules and globules. Being a liquid mixture, the protoplasm has a  The solid and semisolid particles range in surface tension. diameter from 0.001 to 0.1 (1 or micron = Viscosity = 2 – 20 centipoises. 1/1000 mm.) Refractive index = 1.4  The particle are too big to form a suspension and are too small to form a true solution, they thus remain in the matrix forming a colloidal system. Physical appearance of Protoplasm :  Old theories : Protoplasm appears differently in different phases.  Alveolar theory-Butschli (1892) : Protoplasm consists of bubbles or alveoli of a fluid of lesser density distributed in a fluid of greater density.  The liquid phase or dispersion phase of protoplasmic colloids consists mainly of water having dissolved inorganic ions, salts and small molecules.  Granular theory : Altmann(1893) : The  protoplasm consists of numerous fine granules dispersed uniformly in homogeneous fluid  medium. The dispersed phase comprises mainly of large molecules of proteins, lipids and carbohydrate.   Fibriller theory-Fisher (1894) and Flemming (1897) This theory maintains that protoplasm consists of numerous minute fibrils or thread-   like structures dispersed in a fluid medium. Phase reversal in protoplasm is due to its colloidal nature. Non living colloid are irreversible in phase change. (Gel Sol) Protoplasm shows elasticity. Elasticity, viscosity, contractility, rigidity are physical properties due to colloidal nature.  Protoplasm shows viscosity.  Colloidal particles show scattering of light, when a beam of light is passed through colloid it be comes visible. It is called Tyndall effect.  Colloidal particles show zig-zag or irregular movement. The movements are called as Brownian movement. It occurs during sol state.  Protoplasm responds to the stimulus of chemicals, light and heat or mechanical and thus it shows irritability.  Protoplasm shows conductivity of impulse produced by stimulus. Reticular theory-Hanstein, Klein and Carnoy : According to this theory protoplasm  consists of numerous minute fibrils which forms a network or reticulum in a fluid medium. All colloidal solution shows ageing. After some time (age) various activities stops. 44 Biomolecules MOVEMENTS OF PROTOPLASM  It can show following types of movement: Amoeboid movement :  Naked mass of protoplasm shows creeping movement to form pseudopodia. e.g. Amoeba, Slime moulds, Neutrophils. Cyclosis :  Streaming movement of cytoplasm is called cyclosis. It is of two types. (a) circulation (b) Rotation CHEMICAL NATURE OF PROTOPLASM Elements :   COMPOUNDS OF PROTOPLASM Although some elements occur in protoplasm as About 36 elements are known to occur in free ions but mostly they are found in the form protoplasm. of different kinds of compounds. About 13 elements are found in more quantity. Average composition of cells These universal elements are C, H, O, N, Cl, Ca, P, Na, K, S, Mg, I, Fe.  Carbon, hydrogen, nitrogen and oxygen are found greatly in the protoplasm and make up 95% of all living material. Thus they are called major element.  Remaining 23 elements are called trace element. They are in very small amount (about 0.376%). they are copper, Cobalt, magnese, zinc, chromium molybdenum, boron, silicon, vanadium, nickle, INORGANIC COMPOUNDS 1. Water : florine, selenium etc  Most abundant substance of all living organism.  It forms about 70-90% of the cell.  Water is transparent, colourless and odourless.  It has high surface tension, high specific heat, high heat of vaporization.  pH value of water is 7.  The density of water is maximum at 40C.  It freezes at 00C and boils at 1000C.  The molecule of water is composed of 2 atoms of hydrogen and one atom of oxygen linked by covalent bonds. Bond angle 1040.  Water exists in two forms(i) Free water-about 95% (ii) Bound water -5% 45 Biomolecules FUNCTION OF WATER  Water is an important structural component.  Water gives an ideal medium for chemical reactions. It is a universal solvent.  A number of waste products are eliminated in solution form mainly as urine with the help of water.  Water keeps the surface of tissues and organs moist.  In living organism, water gives a medium for distribution or transportation of living matter. 2. Water, works as a dispersion phase in the  colloidal system of protoplasm.    Its high specific heat prevents temperature hazards due to sudden change.  Mineral salts : Salts in protoplasm occur in ionised form Salt responsible for conducitivity & irritibility Some important minerals and their functions given in below table 46  3. Acids and Bases :  They form buffer system & maintain pH of protoplasm (carbonic acid -bicarbonate buffer)  Phosphoric acid (H3PO4) - found in nucleic acids.  Hydrochloric acid (HCl) - found in gastric juice.  4. Gases :  There are four major gases in protoplasm, which remains dissolved in its free water.  These four gases are CO2 > O2 > N2 > H2 (Solubility order)  CO2 is used in synthesis of urea and dissociation of oxyhaemoglobin.  O2 is used in the oxidation of the substance.  H2 is used for ETS.  Biomolecules Biomolecules which have molecular weight less than one thousand dalton are called microbiomolecule or biomolecule, while those which are found in acid insoluble fraction called macromolecule or macrobiomolecule. Lipid which is insoluble in water. These lipids, because of their association with plasma membranes separate in the macromolecular fraction. Hence, lipids are not strictly macromolecules. The acid soluble pool represents roughly the cytoplasmic composition. The macromolecules from cytoplasm and organelles become the acid insoluble fraction. Together they represent the entire chemical composition of living tissues or organisms. ORGANIC COMPOUND According to NCERT Biomolecules   All the carbon compounds that we get from living tissues can be called biomolecules. Four organic compound are found in acidinsoluble pool protein, nucleic acid, carbohydrate, lipid.  Those compounds which have molecular weights  less than one thousand dalton usually referred as biomicromolecules or simply biomolecules.  Acid soluble pool contain those compounds which have molecular weights ranging from 18  to around 800 daltons (Da) approximately. There are three main organic compounds in the protoplasm.     In organic compounds, the main bonds exist between C–C and C–H. Normally, the organic compounds remain suspended or dissolved in the water of the protoplasm. Those molecules which are found in the acid insoluble fraction is called macromolecules or TYPES OF ORGANIC COMPOUNDS biomacromolecules. There are following types of organic compounds The acid insoluble fraction, has only four types in protoplasm. of organic compounds i.e., proteins, nucleic acids, polysaccharides and lipids. These classes  Carbohydrates of compounds with the exception of lipids, have  Amino acids & Proteins molecular weights in the range of ten thousand  Lipids daltons and above  Nucleic acid The molecules in the insoluble fraction with the Enzyme exception of lipids are polymeric substance but  Vitamins lipid is not a polymer. Lipids are small molecular  weight compounds, whose weight do not exceed Do You know 800 Dalton. 1. Hardest material in animal kingdom is enamel. 2. Hardest material in plant kingdom is sporopollenin. 47 Biomolecules CARBOHYDRATE  These compounds are made up of carbon,  hydrogen and oxygen. Ratio of H & O is 2 : 1. These are colourless or white, mostly sweet and crystalline solids which are freely soluble in water.  Carbohydrate are aldehyde or ketone derivatives  of polyhydroxy alcohol. Monosaccharide molecules have the general formula, C nH2nOn or Cn (H2O)n.  A carbohydrate may contain aldehyde or ketone  group and is called aldose or ketose, respectively. They do not undergo hydrolysis but oxidises to CO2 & H2O.  Certain carbohydrates contain some nitrogen,  phosphorous, or sulphur.  Carbohydrate are produced by green plants  during photosynthesis. About 80 percent of the dry weight of the plant is made up of (a) carohydrates. (b) Carbohydrate are also called saccharides or  sugar. They contain 3 to 7 carbons.    Carbohydrate provides 55-65% of total energy (i) required.  Caloric value - 4.1 Kcal/gm  Storage site - mostly liver and muscles  Daily requirement - 500gm approx. Suffix - Ose is used in their nomenclature. On the basis of nature of functional group they are classified in two groups. Aldoses : They have aldehyde group (–CHO). Ketoses : They have ketone group (–C=O). Classification based on number of Carbon atoms. Trioses :They have 3 carbon atoms, C3H6O3 e.g., dihydroxyacetone and glyceraldehyde. (ii) Tetroses : Tetroses contain 4 carbon atoms, C4H8O4 e.g. erythrose, erythrulose. (iii) Pentoses : They contain 5 Carbon atoms, C5H10O5 e.g. ribose, deoxyribose, xylose, ribulose, arabinose (Gum arabic).  Furanose - Types of carbohydrate : Carbohydrates are of three types. (A) Monosaccharides (B) Oligosaccharides (C) Polysaccharides (A) Monosaccharides :  These are simple sugars.  Monosaccharides are the simplest and smallest carbohydrates. Five member ring sugar e.g. Ribose (C5H10O5). 48 Biomolecules (iv)  (v) Hexoses : They have 6 carbon atoms, C6H12O6 e.g. glucose, fructose, galactose and mannose. 4. Mannose :  Mannose is not found in free state. In aqueous solutions glucose occur in cyclic structure.  Mannose occurs in albumin of egg and in wood as component of hemicellulose. 5. Ribose and Deoxyribose :  They are found in nucleic acid, ATP, NAD, NADP, FAD, FMN, Vitamin B2. e.g. Glucose (C6H12O6). (B) Oligosaccharide : Heptoses : They have 7 carbon atoms C7H14O7 e.g. sedoheptulose.  Oligosaccharides are formed by condensation of 2 to 10 molecules of monosaccharide.  Oligosaccharides on hydrolysis yields 2 to 10 monosaccharide units (monomers). Pyranose - Six member ring sugar Few Important Monosaccharide : 1. Glucose :  Glucose is dextrorotatory so it is called “dextrose”.  In oligosaccharides, monosaccharides are linked together by glycosidic bonds.  Glucose is aldose sugar having –CHO group.   Glucose is found in grapes in abundant quantity so it is also known as “Grape sugar”. Aldehyde or ketone group of one monosaccharide reacts with alcoholic group of another monosaccharide to from glycosidic bond.   2.     Glucose is the main - respiratory substrate in the body. One molecule of H 2 O eliminates during glycosidic bond formation. Types of Oligosaccharides : Other types of hexose are converted into glucose Disaccharide : in liver.  They are formed by condensation of two Fructose : molecules of monosaccharides e.g. sucrose, Fructose is Levorotatory so it is called maltose, lactose. “Levulose”. Fructose is a ketose sugar having C=O group. Trisaccharides :  They are formed by 3 monosaccharide molecules e.g. raffinose, rhaminose and gentianose. Fructose is found in honey (32-40%) and sweet fruits so it is called as “Fruit Sugar”. Tetrasaccharides :  Fructose is the sweetest natural sugar.   Fructose is source of energy for sperms and semen. They are formed by condensation of four molecules of monosaccharides e.g., scorodose and stachyose. 3. Galactose :   Galactose is not found in free state- In mammalian body galactose is found in milk sugar lactose. Pentasaccharide e.g. verbinose, barbacose (Galactose + Galactose + Glucose + Glucose + Fructose)  Galactose is also found as a component of galactolipids. i.e. In cerebroside & ganglioside. 49 Biomolecules Important Disaccharides : (3) Maltose (Malt sugar) : (1) Sucrose (cane sugar) :   Sucrose is obtained from sugar cane and sugar beet, called cane sugar.  Sucrose is a commercial sugar.  It is the storage product of photosynthesis in these plants. Maltose or malt sugar is found in germinating starchy seeds.Maltose is formed by condensation of two molecules of -D glucose and -D glucose by a 1, 4 glycosidic bond is formed between two molecules of glucose. It is reducing sugar.  Sucrose is formed by the condensation of one molecule each of glucose and fructose with the removal of one molecule of water. (-D-Glucose + -D fructose)  1, 2 glycosidic bond is formed between glucose and fructose. C6H12O6 + C6H12O6  C12H22O11 + H2O Functions of Simple Carbohydrate : Glucose  Glucose acts as most common respiratory substrate.  Glucose is the blood sugar of many animals.  Mammary glands synthesis lactose of milk from glucose and galactose.  Glucose is utilised in the synthesising fats and amino acids.  Trioses, tetroses, pentoses and heptoses are intermediates in the path way of photosynthesis. Fructose Sucrose (2) Lactose (Milk Sugar) :  Lactose or Milk sugar is found naturally in mammalian milk. (C) Polysaccharides :  Lactose is a reducing sugar.  These are complex carbohydrates.  Lactose is formed inside mammary glands by  condensation of one molecules of each of glucose and galactose (-D glucose + -D-galactose)  Lactose have -1- 4 glycosidic linkage between glucose and galactose.   They are formed by polymerisation of 11 to thousands of monosaccharide monomers. n(C6H12O6) ––– (C6H12O6)n + nH2O Monosaccharide Polysaccharide General formula (C6H10O5)n  They are tasteless and soluble in water.  Suffix-ans is used in nomenclature. Normally they are called as glycans. (Polymers of glucose)  In a polysaccharide chain (like glycogen), the right end is called the reducing end and the left end is called non-reducing end. 50  (a)  (b)   (i)   (1)    Depending upon the composition, polysaccharides are of two types. Homopolysaccharides or Homoglycans Made up of only one type of monosaccharide monomers. For example - starch, cellulose and glycogen, inulin Heteropolysaccharides or Heteroglycans These are formed by condensation of either monosaccharide derivatives or more than one type of monosacharide monomers. e.g., chitin, agar, hemicellulose, arabagalactans, arabaxylans, pectin etc.  Biomolecules Starch consists of two components: amylose and amylopectin (both glucose polymers).  Amylose is more soluble in water but amylopectin is insoluble.  Amylose have 250-300 glucose units are arranged in an unbranched chain by  1-4 linkage.  Amylopectin is a branched chain molecule. Approximately 30 glucose units are linked in one branchby -1,4 and -1,6 linkage.  Based on function, polysaccharide are grouped into three categories: Storage and  structural. Food storage polysaccharides : They are those polysaccharides, which act as (2) reverve food in the living organisms.  The main storage polysaccharides are starch, glycogen and inulin.  Starch :  Starch is the reserve food in plants. It is also called amylum.  It is found in abundance in cereal grains (wheat, rice, maize), legumes (pea, gram, beans), potato, banana etc.  Starch can hold I2 molecules in the helical portion and starch-I2 is blue in colour. Starch present in potato contains 20% amylose and 80% amylopectin. Glycogen It is a main reserve food in animals, bacteria and fungi. It is also known as animal starch. Glycogen is stored in muscle cells and liver cells. Liver of an adult human may store upto 0.91 kg of glycogen. Glycogen gives red colour with iodine. Figure: Diagrammatic representation of a portion of glycogen 51 Biomolecules (3)    (ii) (1)               Inulin Linear polymer of fructose units linked with -1,4 bonds, Inulin is found in roots of Dahalia and Artichoke. It is water soluble polysaccharide. It is not metabolised in human body and filtered through kidney. It is therefore, used in testing of kidney function, (glomerular filtration). Structural polysaccharides : Cellulose : It is a homopolysaccharide of -D glucose, having  1, 4 glycosidic bonds. The chains are unbranched. It is the main structural component of cell wall of plants, some fungi and protists. Tuncin of tunicate (marine chordate) is related to cellulose (also called as animal cellulose) Cellulose is the most abundant organic substance of the plants & also on earth. Cotton fibres have about 90% of cellulose & Wood contain 25-50% of cellulose. Cellulose is fibrous polysaccharide with a high tensile strength. A cellulose molecule consists of an unbrached and linear chain of 6000 or more glucose residues with molecular weight between 0.5 to 2.5 millions. Cellulose form the bulk of human food and most of the herbivorous. It can not digested by the human beings, because they lack the enzyme cellulase, required to digest cellulose. Cellulose is an important constituent of diet of ruminats such as cows and buffaloes. Cellulose rich wood is used in production of paper and as fuel. Cellulose containing fibres of cotton, linen and jute are used for textile and ropes. Cellulose nitrate is used in propellant explosives. Cellulose does not contain complex helices and hence cannot hold 2. (2) Chitin :  Chitin is the second most abundant organic compound in nature.  It is present in the exoskeleton of arthropods and in the cell walls of fungi.  In fungal walls, the chitin is often known as fungus cellulose.  The monomer of chitin is not glucose but nitrogen containing glucose derivative known as N-acetyl glucosamine. (3) Pectin :  It is a heteropolysaccharide composed of sugars arabinose and galactose.  Pectin found in cell wall where it binds with cellulose fibrils in bundles.  Salts of pectin i.e. Ca and Mg-pectates form middle lamella in plants. (4) Hemicellulose :  It is mixture of polysaccharides xylans, galactans, arabagalactans and glucomannans.  It is found in the cell wall. It is hardest known carbohydrate. (5) Hyaluronic acid (Animal cement) :  It is found in skin, vitreous humour of the eye, the umbilical cord, synovial fluid.  It is a linear polymer of disaccharide repeat units linked with the help of -1,4 glycosidic bonds.  Disaccharides repeat units are D-glucoronic acid and N-acetyl -D- glucosamine. (6) Chondriotin sulphates :  They are found in cornea, cartilage, tendons, skin, heart, saliva etc.  The repeating unit is a disaccharides consisting of glucoronic acid and sulphate ester of N-acetyl galactosomines, linked through a -1,3 bond. The disaccharides are linked with each other by -1, 4 bonds. 52 Biomolecules (7) Heparin :  It is secreted by mast cells in the intestinal mucosa, liver, lung, spleen and kindey.  It is an anticoagulant. (8) Agar-Agar :  It is a polysaccharide found in few red algae such as gracillaria, gelidium etc. It is made up of sulfated galactose. It is important as tissue culture medium. (9) Tunicin :  It is cellulose like glycan. It costitutes exoskeleton like covering on Urochordata. (iii) Mucopolysaccharides :  They contain acidic or aminated polysaccharide formed from galactose, mannose, sugar derivatives and uronic acids.  These are jelly like compounds important in packing and connection. PROTEIN  Protein name is derived from a greek word proteioses which means “holding first place” (Berzelius and Mulder).  Essential elements in protein are C, H, O, N, (sulphur is also present in less amount)  After water, proteins are most abundant compounds in protoplasm. (10-15%) Amount of proteins is different in different sources -20% in muscle, 7% in blood plasma, 3.5% in cow milk, 12% in cereal grain, 20% in nuts and pulses, 11-13% in white part of egg. 15-17 % in yellow part of egg.  Different elements in simple proteins have following proportion Carbon- 50-55%, Hydrogen- 7%, Oxygen- 2024%, Nitrogen-14-18%, Sulphur- 0.3-0.5%.  Caloric value - 5.6 kcal/gm  Daily requirement - 70 - 100gm  Proteins are polymer of amino acid (Fisher and Hofmeister).  Mucopolysaccharides are found in the cell walls Do You know of bacteria and in the connective tissues of 1. Protein is a heteropolymer and not a homopolymer. animals as well as in body fluids. 2. Collagen is the most abundant protein in anima  Hyaluronic acid, chondriotin sulphate and world. heparin are comon mucopolysaccharides. 3. Ribulose bisphosphate carboxylase - Oxygenase (RUBISCC) is the most aboundant protein in the Function of Carbohydrate : whole of the biosphere.  They are the primary source of energy.  Normally body obtains 58 to 65% of its required Amino Acid : energy from the carbohydrate.  Amino acids are organic acids.  Ribose & Deoxyribose are used in the  All amino acids contain carboxylic acid group and amino acid group, both linked to a single fromation of RNA, DNA, ATP, NAD, FAD etc. carbon atom called  carbon.  Starch in plants & glycogen in animals are the stored form of food.  Cellulose is used in the formation of cell wall.  Chitin forms exoskeleton in arthropods and few fungal cell wall.  Heparin (in human blood), Mosquitin & herudin (in herudinaria) act as anti-coagulants.  Chondriotin sulphate is a component of  cartilage, tendons & bones, heart valves.  Number of known amino acids are more than 100. Only 20 amino acids are commonly found in proteins of organism. (Magic 20) 53 Biomolecules  These 20 amino acids can be classified into two types.  Semi essential amino acids- Are those amino acids which are synthesized in animal cells but not in sufficient quantity, thus there presence in food is essential. They are - Arginine and Histidine.  Amino acids are amphoteric compound which exhibits both the acidic (due to –COOH group) and basic (due to –NH2 group) properties. It is also called as dipolar or zwitter ions. Neutral amino acids :  When R group of such proteinaceous amino acids could be a hydrogen, then amino acid is called glycine, if methyl group then alanine amino acid and if hydroxy methyl in place of R group then amino acid is serine and their structures are This comprises the largest group and can be further subdivided into aliphatic, aromatic, heterocyclic and sulphur containing amino acids. They have all of them one amino and one carboxylic group, each. A. Aliphatic amino acids :  Glycine (Gly) G (Aminoacetic acid) H | H – C – COOH | NH2 Classification of Amino acids : Amino acids can be classified into three groups  depending on their NH2 or –COOH group number. (1) Neutral (2) Acidic and Valine (Val) V (-aminoisovaleric acid) (3) Basic 54 Biomolecules B. Aromatic Amino acids II. Acidic amino acids :  Phenylalanine (Phe) F  Glutamic acid (Glu) E  (-amino, (-aminoglutaric -phenyl propionic acid) acid) Tyrosine (Tyr) Y (p-hydroxyphenylalanine) III. Basic Amino Acids :  Lysine (Lys) K (, -diaminocaproic acid)  Tryptophan (Trp) W (-amino, -indole Structure of proteins : propionic acid) (1) Primary structure :  A straight chain of amino acids linked by peptide bond form primary structure of proteins. C. Heterocyclic amino acid  Cysteine (Cys) C  This structure of proteins is most unstable. (a-amino, b-mercapto  Newly formed proteins on ribosomes have primary structure. propionic acid) 55 Biomolecules (3)  (2) Secondary structure :  Protein molecules are spirally coiled.  In addition to peptide bond, amino acid are linked by hydrogen bond formed between  oxygen of carboxylic group and hydrogen of amide group. This structure is of two types- (i) -Helix :  Right handed rotation of spirally coiled chain with approximately 3½ amino acid in each trun.  This structure have intramolecular hydrogen bonding i.e. between two amino acid of same chain e.g. Keratin, Myosin, Tropomyosin (ii) -Helix or -pleated structure :  Protein molecule have zig-zag structure.  Two or more protein molecules are held together by intermolecular hydrogen bonding, e.g. fibroin (silk).    Proteins of secondary structure are insoluble in water and fibrous in appearance. Keratin is a fibrous, tough resistant to digestion, sclero (4) protein. Hardness of keratin is due to abundance  of cystein amino acid in its structure.    Tertiary structureProteins of tertiary structure are highly folded to give a globular appearance. Mostly are water soluble. This structure of protein have following bonds(i) Peptide bonds (ii) Hydrogen bonds (iii) Disulphide bond (iv) Hydrophobic bond (v) Ionic bond The tertiary structure of the protein molecules are so arranged as to hide non-polar sides inside and expose the polar side chains. Majority of proteins and enzymes in protoplasm exhibit tertiary structure. Quaternary structure: Two or more poly peptide chains of tertiary structure unit by different types of bond to form quaternary structure of protein. Different polypeptide chains may be similar (lacticdehydrogenase) and disimilar types (Haemoglobin, insulin). Quaternary structure is most stable structure of protein. Adult human haemoglobin consists of 4 subunits two of these are identical to each other. Hence, two subunits of  type and two subunits of  type. 56 Biomolecules Properties of proteins : 2. Globular proteins :  Proteins are large sized molecules.   Many protein form colloidal solutions. They are spherical non-contractile proteins which may be enzymatic or non-enzymatic.  A protein may bind as well as react with a variety  of chemicals.   Proteins can not pass through cell membranes.  The distruption of bond of tertiary proteins structure is called denaturation. Smaller globular proteins are usually soluble in water and are not coagulated by heat e.g., histones.  Egg albumin, serum globulins and glutelins are examples of large globular proteins, which get coagulated by heat. Protein are of three types- (a) Albumins : (i) Simple proteins  They are water soluble and occur as serum albumin in blood plasma and loctoalbumin in milk. (b) Globulins :  They are soluble in weak acids and alkaline solution but insoluble in water e.g. lactoglobulin in milk. (c) Histones :  They are water soluble and are rich in lysine and arginine (amino acids) they occur in eukaryotic DNA. (d) Protamines :  These water soluble arginine rich proteins occur in DNA of spermatozoa of some fishes e.g. salmine in Salmon. (e) Gluteins : Types of Proteins :  They have tertiary or quaternary structure. (ii) Conjugated proteins (iii) Derived proteins (i) Simple Proteins :  They occur only in plants like wheat e.g., glutenin.  They are made up of only amino acids. (f) Prolamines :  They are of two types - Fibrous and globular  proteins. They occur only in plants e.g., zein in corn and gliadin in wheat. 1. Fibrous proteins : (ii) Conjugated proteins :  They are thread like structural proteins.   Fibrous protein generally contain secondary structure and are insoluble in water e.g., collagen of connective tissue, actin and myosin of  muscles, keratin of scales, feathers, hairs, (a) claws, nails, horns and hoofs, silk of spider  web. These are formed by the binding of a simple protein with a non-protein called the prosthetic group. These are of following typesChromoproteins : These proteins contain pigment (coloured) as prosthetic group e.g., haemoglobin, haemocyanin, cytochrome, flavoprotien and rhodopsin. 57 Biomolecules (b)  (c) (d)  (e)  (f)  (g)  (iii)   Glycoproteins : Contain protein + carbohydrate less than 4% eg., plasma glycoprotein secreted from liver and immunoglobulin produced by lymphocyetes. Mucoprotein :They have carbohydrate more than 4% e.g., Muerins of bacteria cell wall ossomucoid in bones, tendenomucoid in tendons, chondromucoid in cartilage. Various mucoproteins are found in vitrous humor synovial fluid. Nucleoproteins : Contain protein + nucleic acid. e.g., histone and non-histone protein join with DNA to make chromosomes. Metalloproteins : Contain protein + metal ions e.g., Arginase (Mn & Mg), Carbonic anhydrase (Zn), Tyrosinase (Cu), Xanthine oxidase (Mo) etc. Phosphoproteins : Contain protein + phosphate e.g., casein in milk and ovo-vitellin in eggs. Lipoproteins : Contain protein + lipids e.g., high density lipoprotein (HDL), low density lipoprotein (LDL) and very low density lipoprotein (VLDL). Mostly important in membranes. Derived proteins : These are denatured or hydrolysed protein. Primary derived protein : Denatured product e.g. Fibrin, Myosan Secondary derived protein : Digestion product of proteins eg. Peptones, Proteose di & tripeptide. Function of proteins : 1. Structural proteins :  Many proteins serve as building material of cells and tissues.  Some proteins form supporting structures e.g., elastin of ligaments, collagen of tendons, cartilages, cartilage bone and connective tissue. 2.  Protective structure : Fibrous protein keratin is the major constituent of external protective structure of animals like hair, feather, horny layer of skin, nails, claws, hoofs etc. 3.  Enzymes : Many proteins function as enzymes to catalyse biochemical reactions. Carrier proteins : Some proteins act as carriers which bind and transport specific molecules across a membrane or in a body fluid. Haemoglobin transports oxygen in the body. -globulin of blood carries thyroxine, bilirubin and -globulin transport vitamin A, D and K. Receptor proteins : A number of proteins present on the external surface of cell membrane act as receptor molecules. Hormones : Some hormones are proteinaceous e.g., insulin Contractile proteins : Myosin and actin make the muscle fibres contractile to bring about movements and locomotion. Defence : Some proteins act as antibodies that participate in the defence mechanism of the body. Storage proteins : These occur in milk, eggs and seeds to nourish the young ones. Iron storing protein commonly found in animal tissue is ferritin. 4.    5.  6.  7.  8.  9.   58 Biomolecules 10. Protein Buffers : 13. Blood clotting proteins :  Proteins also help in maintaining a balance of acidity and alkalinity by combining with excess acids and bases.  The proteins fibrinogen and thrombin help in blood clotting to check bleeding from injuries. 14. Sweetest substance : 11. Visual pigments :   Rhodopsin and iodopsin are protein pigments. Monellin, a protein derived from an African berry in 2000 times sweeter than sucrose. 12. Toxins : 15. Repressor :  Many toxins of microbes, plants and animals are proteins.  Most of the repressor that regulate gene (operon concept) are protein in nature. LIPIDS  They are made of carbon, hydrogen and oxygen. hydrogen and Oxygen ratio is never same as H2O.  The number of oxygen atoms in a lipid molecule is always less than number of hydrogen and carbon atoms.  Sometimes small amount of phosphorus, nitrogen  and sulphur are also present. They include substance like cooking oil, butter, ghee, natural rubber, cholesterol etc.  Lipids are esters of fatty acids and related substances. Lipids exhibit a variety of structures but have certain common characteristics.  59 Biomolecules  Lipids are insoluble in water. But soluble in  organic solvents like chloroform, benzene and acetone.  The basic components of all lipids are fatty acids (i) and many lipids have both glycerol (tri hydroxy  propane) and fatty acids.  Structure of Glycerol     Calorific value -  9 Kcal/gm  Storage site – subcutaneous fat, adipose cells  Daily requirement – 50gm  Lipids in protoplasm are about 2%. These are present as small globules in protoplasm. (ii) They do not undergo further polymerisation.   Fatty acids :    Fatty acids are organic acids with a hydrocarbon chain ending in carboxylic group (–COOH). The hydrocarbon chains of fatty acid may possess straight or ring structure. Most fatty acids have an even number of carbon atoms between 14 and 22, mostly 16 or 18.  Plants and few animals can synthesis all types of fatty acids.  Some animals including man cannot synthesis few fatty acids eg. linoleic acid, linolenic acid and arachidonic acids. These fatty acid are called essential fatty acids (EFA). They obtain these fatty acids through edible oils eg. sunflower, groundnut cotton seed, coconut oils etc.      Fatty acids are of two types: (i) Saturated fatty acids (ii) Unsaturated fatty acids Saturated Fatty acids : They do not have double bonds in their carbon chains. They have higher melting points and are solid at normal temperature. Saturated fatty acids have general formula CnH2nO2. The most common fatty acids are e.g., palmitic acid (C 16 H32 O 2 ) or CH 3(CH 2) 14 COOH or C15H31–COOH and stearic acid (C18H36O2) or CH3(CH2)16COOH or C17H35–COOH Animals that living in warm climate have large quantity of saturated fatty acids. Unsaturated fatty acids : They have one or more double or triple bonds in their carbon chains. Most common unsaturated fatty acids are e.g., Oleic acid (C18H34O2), linoleic acid (C18H32O2) and arachidonic acid (C20H32O2). (most essential fatty acids) The unsaturated fatty acids have lower melting points and are liquid at normal temperature. More unsaturated fatty acids are found in higher plants and in animals that live at low temperature. In hydrogenation unsaturated fatty acids are changed to saturated and the oil becomes a solid fat. Do You Know 1. Oils have lower melting (e.g., gingely oil) and hence remain as oil in winters. 2. The fatty acids are found esterified with glycerol. They can be then monoglycerides, diglycerides and triglycerides. 3. 60 Biomolecules Classification of lipids : 2. Waxes :  Bloor (1943) classified lipids into three types-  simple, compound and derived. Waxes are highly insoluble esters of long-chain. Monohydroxy alcohol. (i) Simple lipids :   Simple lipids are formed of fatty acids and trihydric alcohol (glycerol) only. Waxes are esters of fatty acids of high molecular weight with alcohol except glycerol.  Simple lipids are of following types-  Waxes have a higher melting point than neutral fats. 1. Neutral or true fats- (Glycerides and triglycerides) :   Fats are esters of fatty acid and glycerol. Sebaceous glands of mammalian skin secrete waxy sebum which acts as a lubricant to keep the hair and skin soft.  Each molecule of glycerol can react with three  molecules of fatty acids.  Fatty acid (3 molecules) + glycerol (one molecule)  Lipid (one molecule) + water (three molecule) The sebum secreted by skin glands of wooly mammals is commonly called lanolin or “wool oil”.     Triglycerides are the most common fats in cells.  Ceruminous and sebaceous glands of the skin that covers the external ear passage in mammals secrete ear wax.  Spermaceti, a wax found in skull of whale, dolphin. Mono-and di-glycerides occur as intermediates in certain biosynthetic reaction.  The three fatty acids are similar only in few fats. They are called pure fats. Honey bees constructed their beehives with bees wax (myricyl palmitate) secreted by their abdominal glands. Most fats have dissimilar or two of the three fatty  acids are similar. They are called mixed fats, (e.g., butter) Paraffin wax is obtained from petroleum. Candles are made of paraffin wax and stearic acid.  Carnauba wax (myricyl cerotate) obtained from leaves of carnauba palm.  Depending on the physical nature, fats are differentiated into oils and hard fats. (A)  Oils are generally liquid at room temperature. (ii) Oils are rich in unsaturated fatty acids and short  chain fatty acids. e.g., groundnut oil, rape seed oil, mustard oil.  The oils have a tendency to solidify, are called  drying oils. (B) Hard fats are solid at room temperature.  Hard fats contain long chain saturated fatty acids  and have high melting point e.g., animal fat. 1. Compound lipids : The compound lipids contain fatty acid, alcohols and other compound as phosphorus, aminonitrogen, carbohydrates. Compound lipids are of following typesPhospholipids (Fatty acids + Glycerol + H3PO4 + Other compound) : These are triglyceride lipids in which one fatty acid is replaced by a phosphate group. 61 Biomolecules 2. Glycolipids :  Glycolipids contain fatty acids, and amino alcohol and one or more simple sugars. Phospholipids are amphipathic carrying both  hydrophillic (water attracting) polar and hydrophobic (water repellant) non-polar groups because of this property they form bilayers.  The glycolipids are components of cell membranes, myelin sheath of nerve fibres and membrane of chloroplasts.  In aqueous medium, phospholipid molecules arrange (a) in a double layered membrane or lipid bilayer.  Few examples of phospholipids are- Cerebrosides : are important lipids of white matter of cells of brain and myelin sheath of the nerve fibres.   (a) Some phospholipids also have a nitrogenous compound such as choline (in lecithin), ethanolamine (in cephalin). (b) Lecithin : It is formed by one molecule of glycerol, two molecules of fatty acids and one molecule of phosphoric acid. Choline is attached with phosphoric acid. Lecithin is found in yolk, 3. brain, soyabean membrane. It also acts as lipid  carrier in blood. Lipoprotein are composed of lipids (mainly phospholipids) and proteins. They are present in the blood, milk and egg yolk.  Cutin is a complex lipid found in plant cell walls and cuticle. It binds epidermal cells and reduces transpiration.  Suberin is a mixture of fatty substances. It is present in the wall of cork cells and endodermal cells. It makes cell wall strong and impermeable to water.  Cephalin is found in yolk, blood platelets and Nerve tissues. (iii) Plasmalogens : Occur in vertebrate cardiac  muscles, ciliate protists and certain cells of invertebrates.  (d) Lipoproteins : Cutin and suberin : Cephalin : It is like lecithine but choline is replaced by amino ethyl alcohol(Ethanol amine)  Gangliosides : are found in grey matter of the brain, membraneof RBCs, spleen. They also have neuraminic acid. 4. (b) (c) Animal cells contain cerebrosides and gangliosides. The plasmalogens is platelet-activating factor (PAF) which is released from basophils (WBC, in Vertebrates) to stimulate the blood platelets.  Sphingolipid : It is similar to lecithin but have 1. sphingosin in place of glycerol. Sphingomylins are  important as myelin sheath. Derived lipids : These lipids are obtained by the hydrolysis of simple or compound lipids. Although these are the products of hydrolysis of lipids, but even then they have some properties of lipids. Derived lipids are following types. Steroids (sterols) : Important steroids which have ketone group are called as sterone eg. Testosterone, sterols have – OH group eg. cholesterol. 62  Sterols are lipids of high molecular weight e.g.,  cholesterol, ergosterol, stigmasterol, campesterol etc.  Cholesterol (C27H45OH) is the common sterol  found in many animals, human beings and some plants e.g, Potato.  Cholesterol and its esters are insoluble in water.     Biomolecules They are present in human seminal fluid, testis, kidney, placenta, uterus, stomach, lung, brain and heart. The main function of prostaglandins is binding of hormones to membranes of target cells. Regulation of B.P. gonadial peristalsis and osmoregulation. Function of lipids : Some steroides are hormones like progesterone, 1. Food material : estrogen, testosterone and carticosterone.  Lipids provide food, highly rich in calorific value. Cholesterol forms vitamin D on exposure to One gram lipid produces  9 kilocalories of heat. ultraviolet rays. 2. Food reserve : Cholesterol in an essential component of animal Lipids are insoluble in aqueous solutions, and cell membrane and the cell membrane of  therefore can be stored readily in the body as a mycoplasmas. food reserve. Ergosterol and stigmasterol are found in 3. Structural components : plants, fungi.  They make an impotant constituent of the cell membrane. 4. Heat insulation :  The fats are characterised for their high insulating capacity. Great quantities of fat are deposited in the sub-cutaneous layers in aquatic mammals such as whale and in animals living in cold climates. 3. Terpenes :  Terpenes are lipid like hydrocarbons formed of 5. isoprene (C5H8) units.  They are major components of ‘essential oils’ produced by certain plants. Fatty acid absorption : The terpenes include certain fat soluble vitamins 6. like A, E, K, carotenoids and certain coenzymes  like coenzyme Q. Hormone synthesis :   4.  Prostaglandins : 7. Prostaglandins are hormone like compound  derived from 20 carbon polysaturated fatty acids such as arachidonic acid. Phospholipids play important role in the absorption and transportation of fatty acids & fat soluble vitamins. The sex hormones, adrenocorticoids, cholic acids and also vitamin D are all synthesised from cholesterol, a steroidal lipid. Vitamin carriers : Lipids act as carriers of natural fat-soluble vitamin such as vitamin A, D and E. 63 Biomolecules 1. NUCLEIC ACID  "The other type of macromolecule that one would find in the acid insoluble fraction of any living tissue is the nucleic acid. (i)  These are polynucleotides. Together with polysaccharides and polypeptides these comprise the true macromolecular fraction of any living tissue or cell.  For nucleic acids, the building block is a (ii) nucleotide. A nucleotide has three chemically distinct components. One is a heterocyclic (iii) compound, the second is a monosaccharide and the third a phosphoric acid or phosphate.  It is of two types (A) DNA (B) RNA (A) DNA (Deoxyribonucleic Acid)  Term was given by Zacharis, which is found in (a) the cells of all living organisms except plant viruses,where RNA forms the genetic material (b) and DNA is absent.    In bacteriophages and viruses there is a single molecule of DNA, which remains coiled and is enclosed in the protein coat. In bacteria, mitochondria, plastids and other prokaryotes, DNA is circular and lies naked in the cytoplasm In eukaryotes it is found in nucleus and known as carrier of genetic information and capable of self replication. Nitrogenous base Nucleoside Chemical Composition The chemical analysis has shown that DNA is composed of three different types of compound. Sugar molecule : Levene identified a five carbon sugar, ribose in nucleic acid in 1910. It is represented by a pentose sugar the deoxyribose or 2-deoxyribose which derived from ribose due to the deletion of oxygen from the second carbon. Phosphoric acid : H3PO4 that makes DNA acidic in nature. Nitrogeneous base : Kossel demonstrated the presence of two pyrimidines (cytosine and thymine) and two purines (adenine and guanine) in DNA and he was awarded Nobel Prize in 1910. These are nitrogen containing ring compound. Which classified into two groups: Purines : Two ring compound namely as Adenine and Guanine. Pyrimidine : One ring compound included Cytosine and Thymine. In RNA Uracil is present instead of Thymine. Nucleosides : Nucleosides are formed by a purine or pyrimidine nitrogenous base and pentose sugar. DNA nucleosides are known as deoxyribosenucleosides. Nucleotides : In a nucleotide, purine or pyrimidine nitrogenous base is joined by deoxyribose pentose sugar (D), which is further linked with phosphate (P) group to form nucleotides. Nucleotide 64 Biomolecules Fig. : Some structures related to biomolecules 65 2. Biomolecules The hydrogen bonds are the only attractive forces between the two polynucleotides of double helix. These serve to hold the structure together. Watson and Crick’s model of DNA In 1953 James Watson and Francis Crick suggested that in a DNA molecule there are two such polynucleotide chains arranged antiparallal  The two polynucleotides in a double helix are or in opposite directions i.e., one polynucleotide complementary. The sequence of nitrogenous chain runs in 5’ to 3’ direction, the other in 3’to 5’ bases in one determines the sequence of the direction. It means the 3’ end of one chain lies nitrogenous bases in the other. Complementary beside the 5’ end of other in right handed manner. base pairing is of fundamental importance in Important features molecular genetics.  Nucleic acids exhibit a wide variety of secondary 20 A° structures. For example, one of the secondary structures exhibited by DNA is the famous Watson-Crick model. This model says that DNAexists as a double helix. Shallow groove  The double helix comprises of two polynucleotide chains. 3.4 A°  The two strands (polynucleotide chains) of double helix are anti-parallel due to phosphodiester bond. Deep groove 10 A°  Each polynucleotide chain has a sugar-phosphate ‘backbone’ with nitrogeneous bases directed inside the helix.  The nitrogenous bases of two antiparallel Major axis Shallow polynucleotide strands are linked through groove hydrogen bonds. There are two hydrogen bonds between A and T, and three between G and C. Diagram indicating secondary structure of DNA 66  Erwin Chargaff (1950) made quantitative analysis of DNA and proposed “base equivalence rule”. Starting molar concentration 1. of A = T & G  C or AG AT =1 and CT GC which  is constant for a species. Sugar deoxyribose and  phosphate occur in equimolar proportion. Ten base pairs occur per turn of helix  (abbreviated 10bp). The spacing between adjacent base pairs is 3.4Å. The helix is 20Å (19.8Å) in diameter and DNA molecule found  360o in a clockwise. Biomolecules In general, three types of RNAs have been distinguished : Messenger RNA (mRNA) : Name mRNA was given by Jacob and Monod (1961) on the basis of his informative work. It forms 5% of total RNA. It is complementary strand to DNA and carries genetic information in cytoplasm for the synthesis of proteins. It acts as a template for protein synthesis and has a short life span. (B) RNA (Ribonucleic Acid) 2. Ribosomal RNA (rRNA) : 1. Structure of RNA  rRNA constitutes redundant nature upto 80% of total RNA of the cell. More commonly RNA is a single stranded structure consisting of an unbranched  polynucleotide chain, but it is often folded back on itself forming helices. DNA is a double  stranded structure and its two polynucleotide chains are bounded spirally around a main axis. It is made up by : (1) Sugar : Ribose (2) Phosphate : In the form of H3PO4. (3) Nitrogenous base : Two types: (a) Purine,  (b) Pyrimidine (a) Purine is further divided into Adenine and Guanine. 3. (b) Pyrimidine divided into Cytosine and Uracil.   2. Types of RNA (a) Genetic RNA : Which established by Conrat. In most of the plant viruses, some animal viruses and in many bacteriophages DNA is not found  and RNA acts as hereditary material. This RNA may be single stranded or double stranded.  Nongenetic RNA : In the all other organisms where DNA is the hereditary material, different types of RNA are nongenetic. The nongenetic RNA is synthesized from DNA template. (b) It occurs in ribosomes, which are nucleoprotein molecules. Inside the ribosomes of eukaryotic cells rRNA occurs in the form of the particles of four different dimensions. These are designated 28S, 18S, 5.8S and 5S. The 28S, 5.85S and 5S molecules occur in large subunit (60S subunit) of ribosome, whereas 18S molecules is present in the small subunit (40S subunit) of ribosome. In prokaryotic cells there are only 23S, 16S and 5S rRNA are found. Which are synthesized in Nucleolus / SAT region. Transfer RNA (tRNA) : It is about 10-15% of RNA of the cell. tRNA molecules have been variously termed as soluble RNA or supernatant RNA or adapter RNA. tRNA molecules are smallest, containing 75 to 80 nucleotides. The transfer RNA is a family of about 60 small sized ribonucleic acids which can recognize the codons of mRNA and exhibit high affinity for 20 activated amino acids, 67 METABOLISM  1. DYNAMIC STATE OF BODY CONSTITUENTS - CONCEPT OF METABOLISM  Basically livingorganisms, like a simple bacterial cell, a protozoan, a plant or an animal, contain  thousands of organic compounds.    These compounds or biomolecules are present in certain concentrations (expressed as mole/cell or mole/Iitre etc.). 2. All these biomolecules have a turn over. This  means that they are constantly being changed into some other biomolecules and also made from some other biomolecules. This breaking and making is through chemical reactions constantly occuring in living organisms. Together all these chemical reactions are called metabolism.  Each of the metabolic reactions results in the transformation of biomolecules. A few examples for such metabolic transformations are: removal of CO2 from amino acids making an amino acid  into an amine, removal of amino group in a nucleotide base; hydrolysis of a glycosidic bond in a disaccharide, etc. In other words, metabolites  are converted into each other in a series of linked reactions called metabolic pathways. These metabolic pathways are similar to the automobile traffic in a city.These pathways are either linear or circular.  These pathways criss- cross each other, i.e.,  there are traffic junctions. Flow of metabolites through metabolic pathway has a definite rate and direction like automobile traffic.  This metabolite flow is called the dynamic state of body constituents. Most important is that this  interlinked metabolic traffic is very smooth and without a single reported mishap for healthy conditions. Biomolecules Another feature of these metabolic reactions is that every chemical reaction is a catalysed reaction. There is no uncatalysed metabolic conversion in living systems. Even CO2 dissolving in water, a physical process, is a catalysed reaction in living systems. The catalysts which hasten the rate of a given metabolic conversation are also proteins. These proteins with catalytic power are named enzymes. METABOLIC BASIS FOR LIVING : Metabolic pathways can lead to a more complex structure from a simpler structure (forexample, acetic acid becomes cholesterol) or lead to a simpler structure from a complex structure (for example, glucose becomes lactic acid in our skeletal muscle). The former cases are called biosynthetic pathways or anabolic pathways The latter constitute degradation and hence are called catabolic pathways. Anabolic pathways, as expected, consume energy. Assembly of a protein from amino acids requires energy input. On the other hand, catabolic pathways lead to the release of energy. Forexample,when glucose is degraded to lactic acid in our skeletal muscle, energy is liberated.This metabolic pathway from glucose to lactic acid which occurs in 10 metabolic steps is called glycolysis. Living organisms have learnt to trap this energy liberated during degradation and store it in the form of chemical bonds. As and when needed, this bond energy is utilised for biosynthetic, osmotic and mechanical work that we perform. The most important form of energy currency in living systems is the bond energy in a chemical called adenosine triphosphate (ATP). 68 3. THE LIVING STATE :  Basically tens and thousands of chemical compounds in a living organism, otherwise called metabolites, or biomolecules, are present at concentrations characteristic of each of them. For example, the blood concentration of glucose in a normal healthy individual is 4.5-5.0 mM, while that of hormones would be nanograms/ mL. In animal tissue carbohydrate, protein, lipid, amino acid etc. are called primary metabolite and rubber, antibiotic, flavinoid, pigments etc. are called secondary metabolite.    1. GROWTH :  All living organisms grow.  Increase in mass and increase in number of individuals are twin characteristics of growth.  A multicellular organism grows by cell division.  In plants, this growth by cell division occurs continuously throughout their life span. In animals, this growth is seen only up to a certain age. The most important fact of biological systems is that all living organisms exist in a steady-state  characterised by concentrations of each. of these biomolecules. These biomolecules are in a metabolic flux.  Any chemical of physical process moves spontaneously to equilibrium.   The steady state is a non-equilibirium state.  One should remember from physics that systems  at equilibrium cannot perform work. As living organisms work continuously, they cannot afford  to reach equilibrium.  Hence the living state is a non-equilibrium steadystate to be able to perform work.  Living process is a constant effort to prevent falling  into equilibrium. This is achieved by energy input.  Metabolism provides a mechanism for the production of energy. Hence the living state and  metabolism are synonymous. Without metabolism there cannot be a living state. WHAT IS “LIVING”?   Biomolecules One can add a few more features like metabolism, ability to self-replicate, self-organise, interact and emergence to this list. Let us try to understand each of these.  However, cell division occurs in certain tissues to replace lost cells. Unicellular organisms also grow by cell division. In majority of higher animals and plants, growth and reproduction are mutually exclusive events. One must remember that increase in body mass is considered as growth. Non-living objects also grow if we take increase in body mass as a criterion for growth. Mountains, boulders and sand mounds do grow. However, this kind of growth exhibited by nonliving objects is by accumulation of material on the surface. In living organisms, growth is from inside. Growth, therefore, cannot be taken as a defining property of living organisms. Conditions under which it can be observed in all living organisms have to be explained and then we understand that it is a characteristic of living systems. A dead organism does not grow. When we try to define ‘living’, we conventionally look for distinctive characteristics exhibited by REPRODUCTION  Reproduction, likewise, is a characteristic of living organisms. living organisms. Growth, reproduction, ability to sense environment and mount a suitable response come  to our mind immediately as unique features of living organisms. In multicellular organisms, reproduction refers to the production of progeny possessing features more or less similar to those of parents. Invariably and implicitly we refer to sexual reproduction. 69  Organisms reproduce by asexual means also.  Fungi multiply and spread easily due to the millions of asexual spores they produce.  In lower organisms like yeast and hydra, we observe budding. In Planaria (flat worms), we  observe true regeneration, i.e., a fragmented organism regenerates the lost part of its body and 4. becomes, a new organism. The fungi, the filamentous algae, the protonema    of mosses, all easily multiply by fragmentation.  When it comes to unicellular organisms like bacteria, unicellular algae or Amoeba, reproduction is synonymous with growth, i.e.,  increase in number of cells. 3. METABOLISM  Another characteristic of life is metabolism.  All living organisms are made of chemicals. These chemicals, small and big, belonging to various classes, sizes, functions, etc., are constantly being made and changed into some other biomolecules.  These conversions are chemical reactions or metabolic reactions.  There are thousands of metabolic reactions occurring simultaneously inside all living  organisms, be they unicellular or multicellular.   Biomolecules Hence, while metabolism is a defining feature of all living organisms without exception, isolated metabolic reactions in vitro are not living things but surely living reactions. Hence, cellular organisation of the body is the defining feature of ife forms. SENSES Perhaps, the most obvious and technically complicated feature of all iving organisms is this ability to sense their surroundings or environment and respond to these environmental stimuli which could be physical Chemical or biological. We sense our environment through our sense Organs. Plants respond to external factors like light, water, temperature, other organisms, pollutants, etc. All organisms, from the prokaryotes to the most complex eukaryotes can sense and respond to environmental use. Photoperiod affects reproduction in seasonal breeders, both plants and animals. All organisms handle chemicals entering their bodies.  All plants, animals, fungi and microbes exhibit metabolism. All organisms therefore, are ‘aware’ of their surroundings. Human being is he only organism who is aware of himself, i.e., has selfconsciousness.  The sum total of all the chemical reactions  occurring in our body is metabolism. Consciousness therefore, becomes the defining property of living organisms.  No non-living object exhibits metabolism.   Metabolic reactions can be demonstrated outside the body in cell-free systems. An isolated  metabolic reaction(s) outside the body of an organism, performed in a test tube is neither living nor non-living. When it comes to human beings, it is all the more difficult to define the living state. We observe patients lying in coma in hospitals virtually supported by machines which replace heart and lungs. The patient is otherwise braindead. The patient has no self-consciousness. Are such patients who never come back to normal life, living or non-living? 70 Biomolecules ENZYME 1. History of cellular enzymes :  Enzymes (Gk. en = in; zyme = yeast) are proteinaceous substances which are capable of catalysing chemical reactions of biological origins without themselves undergoing any change.  Enzymes are biocatalysts. An enzyme may be defined as “a protein that enhances the rate of biochemical reactions but does not affect the nature of final product”.  They are produced by living cells only.  Enzymes are also called ‘biological middle man’.  The study of the composition and function of the enzyme is known as enzymology.  The term enzyme (meaning in yeast) was used by Willy Kuhne (1878), while working on fermentation. At that time living cells of yeast were thought to be essential for fermentation of sugar.  Edward Buchner (1897), a German chemist proved that extract zymase, obtained from yeast cells, has the power of fermenting sugar (alcoholic fermentation).  There are some nucleic acids that behave like enzymes. These are called ribozymes. Ex : RNA enzymes (RNase)  Northrop and Kunitz prepared crystals of pepsin, trypsin and chymotrypsin  Arber and Nathans got noble prize in 1978 for the discovery of restriction endonucleases which break both strands of DNA at specific sites and produce sticky ends. These enzymes are used as microscissors in genetic engineering. Do You Know ? Zymogen :- These are precursor of enzymes are known as zymogens Examples pH2 (1) Pepsinogen   Pepsin Pep sin (2) Prorennin    Rennin 2. Types of enzymes Two types of enzymes are - (i) Simple enzyme-Made up of only protein. Ex.Urease, Amylase, Trypsin, Pepsin (ii) Conjugated enzyme- Made up of protein and nonprotein part. Non protein part is called cofactor Protein part is called Apoenzyme. Both Combinely called Holoenzyme. Holo enzyme = Apoenzyme + co-factor  Activity of enzyme is due to co-factor, which can be separated by dialysis. co-factor is small, heat stable and may be organic or inorganic in nature.  Three types of cofactors may be identified. Prosthetic group, coenzyme and metal ions. (i) Prosthetic group : Prosthetic groups are organic compounds distinguished from other cofactors in that they are permanently bound to the apoenzyme, e.g., in peroxisomal enzymes peroxidase and catalase which catalyzes breakdown of hydrogen peroxide to water and oxygen. haem is the prosthetic group and it is a part of the active site of the enzyme. (ii) Coenzymes : Lipmann discovered coenzymes. Coenzymes are also organic compounds but their association with the apoenzyme is transient, usually occurring only during the course of catalysis. In general coenzymes not only assist enzymes in the cleavage of the substrate but also serve as temporary acceptor for one of the product of the reaction. The essential chemical component of many coenzymes are vitamins, e.g., coenzyme nicotinamide adenine dinucleotide (NAD), nicotinamide adenine dinucleotide phosphate (NADP) contains the vitamin niacin. Enterokina se (3) Trypsinogen    Trypsin Tryp sin (4)Chymotrypsinogen   Chymotrypsin 71 (iii) Metal ions : A number of enzymes require metal (i) ions for their activity. The metal ions form coordination bonds with specific side chains at the active site and at the same time form one or more coordination bonds with the substrate. The latter assist in the polarization of substrate bonds to be cleaved by the enzyme. The common metal (ii) ions are Zn++, Cu++, Mg++. Inorganic part of enzyme acts as prosthetic group in few enzymes they are called activators. These activators are generally metals. Hence these enzymes are called Metalloenzyme such as : Biomolecules Oxidoreductases/dehydrogenases : These enzymes catalyse oxidation reduction reactions, usually involving the transfer of hydrogen atoms or ions from one molecule to another. S reduced + S’ oxidised  S oxidised + S’ reduced. Transferases : These enzyme catalyse the transfer of a specific group (e.g., amino, methyl, acyl, phosphate) from one kind of molecule to another. G (other than hydrogen) between a pair of substrate S and S’. e.g. :- S - G + S’  S + S’ - G Ex. Phosphotransferase, Peptidyl transferase etc. (iii) Hydrolases : These enzyme catalyse the hydrolysis of organic foods i.e., the breakdown of large molecules by addition of water. Most of the hydrolysing (digestive) enzymes are located in lysosomes. e.g., all digestive enzymes such as lipases (digest the stored food material of castor seeds). (iv) Lyases : These enzymes catalyse the breakage of specific covalent bonds and removal of groups without hydrolysis e.g., fumerases, carboxylases, aminases, histidine decarboxylase that splits C– C-bond of histidine, forming CO2 and histamine. 3. Classification and Nomenclature of enzymes:  Thousands of enzymes have been discovered, isolated and studied. Most of these enzymes have been classified into different groups based on the (v) type of reactions they catalyse.  Enzymes are divided into 6 classes each with 413 subclasses and named accordingly by a fourdigit number.  The first digit denotes the class, the second subclass, the third sub-sub-class and the fourth one is for the particular enzyme name. Thus, E.C. (vi) 2.7.1.1 denotes class 2 (Transferases)-subclass 7 (transfer of phosphate) sub-sub-class 1 (an alcohol functions as phosphate acceptor). The 4th digit indicates hexokinase. X Y | | C – C  X  Y  C  C Isomerases : These enzymes catalyse the rearrangement molecular structure to form isomers. e.g., phosphohexose isomerase (phosphoglucomutase) act on glucose 6phosphate to form fructose 6-phosphate (both C6 compounds) Ligases or Synthetases : These enzymes form bonds and join two molecules together, using energy supplied from the breakdown of ATP, e.g., DNA ligase is used to repair breaks in DNA molecules. 72 4. Mechanism of enzyme action : Energy is required to bring the inert molecules into the activated state. The amount of energy required to raise the energy of molecules at which chemical reaction can occur is called activation energy. Enzymes act by decreasing the activation energy so that the number of activated molecules is increased at lower energy levels. If the 1. activation energy required for the formation of the enzyme-substrate complex is low, many more 2. molecules can participate in the reaction than would be the case if the enzyme were absent. 3. 4. Biomolecules intermediate formation of the enzyme-product complex (EP). - The formation of the ES complex is essential for catalysis. The catalytic cycle of an enzyme action can be described in the following steps: First, the substrate binds to the active site of the enzyme, fitting into the active site. The binding of the substrate induces the enzyme to alter its shape, fitting more tightly around the substrate. The active site of the enzyme, now in close proximity of the substrate breaks the chemical bonds of the substrate and the new enzymeproduct complex is formed. The enzyme releases the products of the reaction and the free enzyme is ready to bind to another molecule of the substrate and run through the catalytic cycle once again. There are two theories to explain the mode of action of enzymes. Lock and Key hypothesis : The hypothesis was put forward by Emil Fisher (1894). According to this hypothesis the enzyme and its substrate have a complementary shape. The specific substrate molecules are bound to a specific site of the enzyme molecule. The theory can be explained easily by the fact that a particular lock can be opened by a particular key specially designed to open it. Similarly enzymes have specific sites where a particular substrate can only be attached. The lock and key model accounts for enzyme specificity. 5. Nature of Enzyme Action Each enzyme (E)has a substrate (S)binding site in its molecule so that a highly reactive enzymesubstrate complex (ES) is produced. This complex is short-lived and dissociates into its product (P) and the unchanged enzyme with an 73 Induced fit hypothesis : This hypothesis was proposed by Daniel, E. Koshland (1959). According to this view, active site is not rigid but static and it has two groups – buttressing group and catalytic group. Initially substrate bind to the buttressing group which induces the catalytic group to fit the substrate and catalytic group weakes the bonds of reactant or substrate by electrophilic and nucleophilic forces. Biomolecules other factors, A general rule of thumb is that rate doubles or decreases by half for every 10ºC change in either direction. Catalysed reactions proceed at rates vastly higher than that of uncatalysed ones. When enzyme catalysed reactions are observed, the rate would be vastly higher than the same but uncatalysed reaction. For example. anhydrase CO2 + H2O Carbonic     H2CO3  — Carbon dioxide water 6. Properties of enzymes : (1) Chemical reactions In the absence of any enzyme th is reaction is very slow, with about 200 molecules of H2CO3 being formed in an hour. However, by using the enzyme present within the cytoplasm called carbonic anhydrase, the reaction speeds dramatically with about 600,000 molecules being formed every second. The enzyme has accelerated the reaction rate by about 10 million times. The power of enzymes is incredible indeed Chemical compounds undergo two types of changes. A physical change simply refers to a change in shape without breaking of bonds. This is a physical process. Another physical process is a change in state of matter when ice melts into water, or when water becomes a vapour. These are physical processes. However, when bonds are broken and new bonds are formed during transformation, this will be called a chemical (2) reaction. For example Ba(OH)2 + H2 SO4  BaSO4 + 2H2O is an inorganic chemical reaction. Similarly, hydrolysis of starch into glucose is an organic chemical reaction. Rate of a physical or chemical process refers to the amount of product formed (3) per unit time. It can be expressed as rate = carbonic acid P t Rate can also be called velocity if the direction is specified. Rates of physical and chemical processes are influenced by temperature among There are thousands of types of enzymes each catalysing a unique chemical of metabolic reaction. A multistep chemical reaction, when each of the steps is catalysed by the same enzyme complex or different enzymes, is called a metabolic pathway. For example. Glucose  2 Pyruvic acid C6H12O6 + O2  2C3H4O3 + 2H2O Colloidal nature : All enzymes are colloidal in nature and thus provide large surface area for reaction to take place. They posses extremely low rates of diffusion and form colloidal system in water. Catalytic properties : Enzymes are active in extremely small amounts, e.g., one molecule of invertase can effectively hydrolyze 1,000,000 times its own weight of sucrose. One molecule of catalase is able to catalyze conversion of 5,000,000 molecules of hydrogen peroxide. 74 Biomolecules (4) High efficiency : The effectiveness of an enzymatic reaction is expressed in terms of its turn over number or catalytic centre activity means number of substrate molecules on which one enzymes molecules acts in one minute. (5) Molecular weight : Enzymatic proteins are substances of high molecular weight. Bacterial ferredoxin one of the smaller enzymes has  molecular weight of 6,000, where as pyruvic dehydrogenase one of the largest-has a molecular weight of 4600000. (6) Specificity of enzyme : Most of the enzymes are highly specific in their action. A single enzyme will generally catalyze only a single substrate or a group of closely related substrates. The active site possess a particular binding site which complexes only with specific substrate. Thus, only a suitable substrate fulfils the requirements of active site and closely fixes with it. (7) Reversibility of reaction : The enzymecontrolled reactions are reversible. The enzymes affect only the rate of biochemical reactions, not the direction. e.g., Lipase can catalyse splitting of fat into fatty acids and glycerol as well as  synthesis of fatty acids and glycerol into fats. Do You Know ? Highest turn over number is of carbonic anhydrase (36 million/min or 600000 per second) and lowest is of lysozymes (30/min or 0.5 per second). So carbonic anhydrase is fastest enzyme and lysozymes is slowest enzyme. 7. Factors affecting the enzyme activity :  Hydrogen ion concentration (pH) : Some enzyme act best in an acid medium, other in an alkaline medium, for every enzyme there is an optimum pH where its action is maximum e.g., 2 for pepsin, 6.8 for salivary amylase, 8.5 for trypsin. Most enzyme show maximum activity in a pH range of about 6.0 to 7.5 i.e., near neutral pH (endoenzymes). Temperature : Within certain limits (5-40°C) the rate of an enzyme catalyzed reaction increases as the temperature increases. The Q10 of most enzymatic reactions is 2, i.e., every 10°C rise in temperature doubles the rate of reaction. Most enzymes show maximum activity in a temperature range of 25 to 40°C. Beyond this temperature, enzymes becomes denatured but The enzymes are not destroyed by freezing, and regain their lost activity if the temperature is raised to normal. Substrate concentration : If there are more enzyme molecules than substrate molecules, a progressive increase in the substrate molecules increases the velocity of their conversion to products. However, eventually the rate of reaction reaches the maximum. At this stage the active sites of all the available enzyme molecules are occupied by the substrate molecules. Therefore, the substrate molecules occupy the active sites vacated by the products and cannot increase the rate of reaction further. 75 Michaelis constant : Michaelis and Menten  (1913) introduced a constant Km (Michaelis constant). It is a mathematical derivative or constant which indicates the substrate concentration at which the chemical reaction  catalysed by an enzyme attains half its maximum velocity (Vmax). Km indicates affinity of the enzyme for its substrate. Km = 1 V K value differs 2 max m from substrate to substrate because different enzymes differ in their affinity towards different substrates. A high Km indicates low affinity while  a low Km shows strong affinity. Protease acts on different proteins. So it’s Km value will differ from protein to protein. Biomolecules The effect of a competitive inhibitor on activity is reversed by increasing the concentration of substrate. In it Vmax remain constant and Km increases. A classic example of competitive inhibition is succinic acid dehydrogenase which oxidises succinic acid to fumaric acid. If concentration of malonic acid, is added, the activity of succinic dehydrogenase decreases rapidly. Hence malonic acid acts as a competitive inhibitor since it has structural resemblance to succinic acid. The competitive inhibition can be reversed by increasing the concentration of the substrate. Competitive inhibitors are used in control of bacterial pathogens. 8 Enzyme inhibition : (ii) Non-competitive inhibition : (i) Competitive inhibition :   Substances (inhibitors) which are structuraly similar to the substrates and competes for the active site of the enzyme are known as  competitive inhibitors.  Usually such inhibitors show a close structural resemblance to the substrates to the enzyme they inhibit. In such a case, inspite of enzyme substrate complex, enzyme inhibitor complex is formed and  enzyme activity is inhibited. These substances (poisons) do not combine with active sites but attach somewhere else and destroy the activity of enzyme.  E (Enzyme) + I (Inhibitor)  EI (Enzyme Inhibitor complex EI)  The concentration of EI complex depends on the concentration of free inhibitor. Because EI complex readily dissociates, the empty active sites are then available for substrate binding. Both EI and ES complexes are formed. Inhibitor binding alters the three dimensional configuration of the enzyme and thus blocks the reaction. Non competitive inhibitor do not competes directly with the substrate for binding to the enzyme. In it Vmax in lowered and Km is changed.  The non-competitive inhibition can not be reversed by increasing the concentration of the substrate i.e., irreversible. e.g., cyanide inhibits the mitochondrial enzyme cytochrome oxidase which is essential for cellular respiration. This kills the animals.  AMP is a non competitive inhibitor of fructose biphosphate phosphatase, the enzyme that catalyzes the conversion of fructose 1, 6 biphosphate to fructose 6 phosphate. 76  (a) Feedback inhibition :  In number of cases, accumulation of the final product of the reaction is capable of inhibiting the first step of reaction. The product P checks the activity of enzyme which converts A into B. It  is quite useful mechanism because it checks the accumulation of products.  Biomolecules Change of active site form prevent the binding of substrate to the enzyme and stops the reaction. The process is called allostery or allosteric inhibition, The enzyme with allosteric sites are called allosteric enzymes. Jacob and Monod have termed this phenomenon as allosteric transition. An example of allosteric enzyme inhibition is hexokinase that converts glucose to glucose 6phosphate. Glucose 6-phosphate causes allosteric inhibition of hexokinase. This is called feedback allosteric inhibition.  The phenomenon in which the end product of a metabolic pathway can regulate its own production by inhibition of the sort is called feed back inhibition or negative feed back inhibition.  This type of inhibition can be shown in Escherichia coli bacterium which synthesises the amino acid isoleucine from a substrate threonine PRIMARY AND SECONDARY by a series of intermediate reactions (i.e.,  METABOLITES ketobutyrate threonine deaminase,  Aceto Primary metabolites : Substances that is hydroxy butyrate,  keto  methyl valerate etc). required for growth of living organisms When isoleucine accumulates in amounts more Secondary metabolites : Substances that is not than required, it stops its own production by required (waste material) for growth of living inhibiting the activity of the enzyme. organisms Threonine deaminase which catalyzes the first However, many of them are useful to 'human reaction of the series. welfare' (e.g., rubber, drugs, spices, scents and This type of metabolic control in which the first pigments). Some secondary metabolites have enzyme of a series is inhibited by the end ecological importance. product, is known as end product inhibition.    (b) Allosteric inhibition (Modulation) :  Allosteric literally means ‘another place’. Still other inhibitors join an enzyme at a specific site and change the form of the active site meant for the substrate.  These inhibitors are known as modifiers or modulators and the sites where they fit in are called allosteric sites. Modulators are of two types-positive (activators) and negative (inhibitors). 77 POINTS TO BE REMEMBER   Most of the vitamins of B complex group act as coenzyme.  Myosin a structural component of muscle. It has  ATPase activity also.  Smallest enzyme oxydase and largest enzyme  catalase, which are found in peroxysome.  Synthesis of enzymes occur in polysome (aggregation of ribosomes).  Competitive inhibitor increase Michaelis constant (Km) but it has no effect on Vmax.  Regulators of metabolism are enzymes, vitamins and hormones.  RNA polymerase enzyme form RNA from DNA and DNA polymerase is responsible for synthesis  of DNA from DNA   Enzyme that catalyses the conversion of soluble proteins into insoluble ones, process is called  enzyme coagulation. Biomolecules The bond between the phosphate and hydroxyl group of sugar is an ester bond. As there is one such ester bond on either side, it is called phosphodiester bond. Nucleic acids exhibit a wide variety of secondary structures. For example, one of the secondary structures exhibited by DNA is the famous Watson-Crick model. This model says that DNA exists as a double helix. The two strands of polynucleotides are antiparallel i.e., run in the opposite direction. The backbone is formed by the sugarphosphate-sugar chain. The nitrogen bases are projected more or less perpendicular to this backbone but face inside. A and G of one strand compulsorily base pairs T and C, respectively, on the other strand. There are two hydrogen bonds between Aand T. There are three hydrogen bonds between G and C. Albinism is caused by the deficiency of tyrosinase.  Each strand appears like a helical staircase.  Nitrogenase enzyme is inactivated by oxygen.   Some enzyme are active at very high temperature (70–80°C) called extermozyme e.g., Taq polymerase.  In a polypeptide or a protein, amino acids are linked by a peptide bond which is formed when  the carboxyl (-COOH)group of one amino acid reacts with the amino (–NH2) group of the next amino acid with the elimination of a water moiety (the process is called dehydration).  In a polysaccharide the individual monosaccharides are linked by a glycosidic bond. This bond is also formed by dehydration.  This bond is formed between two carbon atoms of two adjacent monosaccharides. In a nucleic acid a phosphate moiety links the 3'-carbon of one sugar of one nucleotide to the 5' -carbon of the sugar of the succeeding nucleotide. Each step of ascent is represented by a pair of bases. At each step of ascent, the strand turns 36°. One full turn of the helical strand would involve ten steps or ten base pairs. Attempt drawing a line diagram.  The pitch would be 34Å. The rise per base pair would be 3.4A. This form of DNA with the above mentioned salient features is called BDNA. RNA is found in the cytoplasm and nucleolus. Inside the cytoplasm it occurs freely as well as in the ribosomes. RNA can also be detected from mitochondria, chloroplasts and associated with the eukaryotic chromosomes. In some plant viruses RNA acts as hereditary material. 78