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1 BIOMOLECULES All living organisms are made up of a large number of chemical substances.

es. While comparing the chemical constitution of living things with that of earths crust, we will obtain a similar list. The only difference between these two lists is that hydrogen and carbon is present in large amount in living organisms than earths crust.

Chemical Analysis to find The Organic Compounds of Living Organisms First take a living tissue like a vegetable or a piece of liver, etc. Grind the tissue in tri-chloroacetic acid (Cl3CCOOH) using a mortar a pestle. Strain the thick slurry obtained through a cheese cloth or cotton. Now we get a acid soluble filtrate portion known as acid pool and the acid insoluble precipitate portion known as acid insoluble pool. Chemical Analysis to find out The Inorganic Compounds of Living Organisms (Ash Analysis) First a small amount of living tissue like leaf, lever, etc is weighed and dried to get the dry weight. Dried tissue is then fully burned. During burning, carbon compounds are oxidized to CO2 and H2O. The remaining substance left is the ash. The ash contains the following inorganic constituents.

METABOLITES The biomolecules which occur in all living cells are called metabolites. They are classified into two. 1. Primary Metabolites Metabolites like carbohydrate, proteins, nucleic acids, lipids, etc. is present in all animal tissues and are called primary metabolites. 2. Secondary Metabolites In plants, fungus and microbial cells in addition to primary metabolites they posses the substances like alkaloids, flavonoids, rubber, essential oils, antibiotics, coloured pigments, scents, gums, spices, etc. These substances are called secondary metabolites.

Biomolecules are classified into biomicromolecules and biomacromolecules. BIOMICROMOLECULES Chemical compounds which have a molecular weight less than 1000 dalton are called biomicromolecules. They are seen in the acid soluble fraction obtained during chemical analysis. They include inorganic constituents. BIOMACROMOLECULES The biomolecules which are insoluble in acids and have very high molecular weight are called biomacromolecules. They have molecular weight above 10,000 dalton except lipids. Eg: Proteins, nucleic acids, polysaccharides, lipids. The Molecular Weight of Lipids are Below 800 Dalton but it is included in Biomacromolecules. Why? Lipids are smaller molecular weight compounds. It is present as such in cells and also the chief component of cell membranes and cell organelles. While we grind tissue, cell membranes and other membranes are broken into pieces and form vesicles which are insoluble in acid. These vesicles get separated along with the acid insoluble pool and hence included in the macromolecular fraction. Average composition of cells

PROTEINS Proteins are the polymers of amino acids and hence called polypeptides. Amino acids are linked together by peptide bonds.

3 Each peptide bond is formed by the reaction between the carboxyl group (COOH) of one amino acid with the amino group (NH2)of next amino acid with the elimination of water (dehydration reaction ) There are 20 amino acids present. They are classified into essential amino acids and non-essential amino acids. Essential Amino Acids(8 in number) These are amino acids that we get from food or diet Dietery proteins are the source of essential amino acids. Eg: Phenyl alanine, valine, threonine, triptophane, isoleucine, methionine, leucine and lysine. Non essential Amino Acids (12 in number) These are amino acids synthesized by the body. Eg: Arginine, histidine, alanine, cystine, glutamic acid, glycine, proline, serine, tyrosine, hydroxy proline, aspargine and aspartic acid. STRUCTURE OF AMINO ACIDS Each amino acid has a central carbon atom known as Alpha carbon atom. To the alpha carbon atom, one carboxyl group (COOH), one amino group (NH2), one hydrogen atom and a side chain denoted R is attached. The side chains are generally carbon chains or rings to which various functional groups may be attached. Based on the nature of R group there are many amino acids. Examples of Amino Acids 1. Glycine This is the simplest amino acid. In the position of the R group glycine has hydrogen atom.

2. Alanine This is the amino acid in which the side chain is methyl group (CH3).

3. Serine This is the amino acid in which R group is Hydroxy methyl (CH2-OH).

Based on the number of amino and carboxyl groups Amino acids are classified into the following groups.

4 1. Acidic Amino Acids:- Eg: Glutamic acid. 2. Basic Amino Acids:- Eg: Lysine. 3. Neutral Amino Acids:- Eg: Valine. The Examples of Amino Acids which posses an Aromatic Ring are Tyrosine, Phenyl Alanine, Tryptophan, etc. Ionisation Nature of Amino Acids The amino group (NH2) and carboxyl group (COOH) of amino acids shows ionisation properties. Hence in solution of different pH the structure of amino acids changes. The common nature of amino acids is in zwitter ion form (chemical compounds that carries a total net charge of Zero are zwitter ions). Thus they are electrically neutral but carry formal positive and negative charges on different atoms.

Functions of Some Proteins

Collagen is the most abundant protein in the animal world. RUBISCO (Ribulose Bi Phosphate Carboxylase Oxygenase) enzyme is the most abundant protein in the living world. Structural Levels of Proteins 1. Primary Structure: Primary structure refers to the linear sequence of amino acids in a protein molecule. A protein is imagined as a line, the left end represented by the first amino acid and the right end represented by the last amino acid. The first amino acid is called as N-terminal amino acid and the last amino acid is called is C-terminal amino acid.

2. Secondary Structure: A protein thread does not exist throughout as an extended rigid rod. The thread is folded in the form of a revolving staircase known as helix. In proteins, only right handed helices are observed.

3.Tertiary Structure: The polypeptide chains of protein molecules bend and fold to attain a three dimensional shape called Tertiary structure. The structure is helpful for many biological activities.

4. Quaternary Structure: More than one polypeptide chains unite together to form the complicated folded structure called Quaternary structure of protein.

6 Eg: Human haemoglobin has 4 polypeptide chains. Two are identical known as alpha chains and other two are also identical known as beta chains. The alpha and beta chains folded together to form a compact globular structure of haemoglobin. LIPIDS Lipids are biological molecules which are insoluble in water. Lipids include fattyacids, triglycerides, glycerol, phospholipids, cholesterol etc.

Fattyacids Fatty acids are composed of a long hydrocarbon chain called tail and a terminal carboxyl group called head. Most of the fatty acids have an even number of carbon atoms. Eg. Palmitic acid has 16 carbon atoms; arachidonic acid has 20 carbon atoms.

Based on the type of carbon carbon bonds, fatty acids are classified into saturated fatty acids and unsaturated fatty acids. Saturated Fatty Acids Fatty acids in which all carbon-carbon bonds are single bonds. No double bonds are present. Eg: Palmitic Acid Unsaturated Fatty Acids Fatty acids in which one or more carbon-carbon double bonds are present. Eg: Linoleic Acid. Unsaturated fatty acids are more common in nature especially in higher plants. Glycerols Glycerol is a simple lipid. It is chemically tri-hydroxy propane. Many lipids have both glycerol and fatty acids.

Triglycerides These are esters of fatty acids with glycerol.

7 Based on the number of fatty acids they may be monoglycerides (has one fatty acid chain), diglycerides (two fatty acid chain), tri-glycerides (three fatty acid chain). Fats that are generally liquid at room temperature are called oils. Oils are rich in unsaturated fatty acids and have low melting point. Phospholipids The lipids which contain a phosphate group along with fatty acids and glycerol are called phospholipids. Eg: Lecithin.

POLYSACCHARIDES (CARBOHYDRATES) These are long chains of sugars. It is formed of polymerization of monosaccharides. In a polysaccharide individual monosaccharide are linked by glycosidic bond formed between two carbon atoms of the adjacent monosaccharides Homopolysaccharides If the polysaccharide is formed of only one type of monosaccharide, it is known as homopolysacharide. Eg: Glycogen, Starch, and Cellulose. Starch is the store house of energy in plants. Glycogen is the stored polysaccharide in animals. Inulin is a polymer of fructose. Plant cells are made up of cellulose. Paper made from plant pulp is cellulose. Cotton fibre is cellulose. Heteropolysaccharides If the polysaccharide is formed of more than one type of monosaccharide it is known as heteropolysacchride Glucosamine and N-acetyl glucosamine are complex polysaccharides formed of amino sugars. Chitin is the polysaccharide seen in the exoskeleton of arthropods.

Diagrammatic representation of a portion of glycogen

o NUCLEIC ACIDS The building blocks of nucleic acids are called nucleotides. A nucleotide consists of nitrogenous base , pentose sugar and phosphate . Nitrogenous bases in nucleic acids are pyrimidines and purines Pyrimidines have a single heterocyclic ring and purines have two fused rings Pyrimidine bases are , cytosine , thymine (in DNA) and uracil (present in RNA in the place of thymine ) Adenine and guanine are called purine bases . The sugar present in DNA (Deoxy ribonucleic acid)is Deoxy ribose and that of RNA (Ribonucleic acid ) is ribose . Nitrogenous base and pentose sugar together called nucleoside. Adenosine , guanosine , thymidine , uridine ,and cytidine are nucleosides, Adenylic acid , thymidylic acid , guanylic acid , uridylic acid and cytidylic acid are nucleotides.

Nature of bond in nucleic acid In a nucleic acid phosphate moiety links the 3 carbon of one sugar of one nucleotide to the 5 carbon of the sugar of the next nucleotide. 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 known as phosphodiester bond Watson crick model of DNA This model says that DNA exists as a double helix. The two strands of polynucleotide are antiparallel i.e., run in the opposite direction. The back bone is formed by the sugar phosphate sugar chain.

9 The nitrogen bases interconnect the backbone. Adenine of one strand pairs with thymine of the other strand (A-T base pair). This is formed by two hydrogen bonds. Guanine pairs with Cytosine (G-C base pair). This is formed of three hydrogen bonds. One full turn of helical stair case has Ten base pairs. The total length of a turn is 34 A0 and the distance between two base pairs is 3.4A0 . This type of DNA is known as BDNA Diagram indicating secondary structure of DNA

Metabolism All the chemical reactions taking place inside the living organisms are collectively called metabolism . Metabolic reactions are divided into two categories anabolism and catabolism Anabolism In anabolism large , complex molecules are synthesized from smaller precursors .eg . Proteins synthesized from amino acids . Catabolism In catabolism large complex molecules are degraded into smaller simpler products. eg .in respiration glucose is oxidized to CO2 and water. Anabolism It includes constructive or building up processes Energy is used and stored as potential energy Eg . photosynthesis Catabolism It includes destructive or break down processes. Energy is released as kinetic energy. Eg . Cell respiration of glucose

ATP(Adenosine Triphosphate ) It is the most important form of energy currency in living system ENZYMES Enzymes are biological catalysts, which speeds up a chemical reaction without itself undergoing any permanent change. All enzymes are proteins. Ribozymes

10 These are nucleic acids that behave like enzymes. Active sites These are the regions of enzymes which react with the substrate molecule in chemical reaction. Carbonic anhydrase It is the enzyme which involved in the formation of carbonic acid in tissue respiration. Carbonic anhydrase catalyse the combination of CO2 and H2O to carbonic acid This is the fastest enzyme in the living world , with a speed of 6 lakhs molecule per second (in the absence of the enzyme the reaction rate is only 200 molecules per hour ) How enzyme bring about high rate of chemical conversions? In chemical reactions enzymes convert substrates (S) into products (P) S P During the action of enzymes, the active site of the enzyme combines with substrate and forms enzyme substrate complex (ES). After the expected chemical reaction, products are released. Mechanism of Enzyme Action The enzymes have active sites. These active sites combine with substrate forming enzyme-substrate complex. The formation of this complex needs some level of energy known as activation energy. Enzymes lower activation energy for the formation of enzyme substrate complex.

The substrate tightly bound with the active site of the enzyme. The active site of the enzyme breaks the chemical bonds of the substrate. Now the enzyme releases the products of the reaction and the free enzymes are ready to bind to another molecule of substrate. Factors Affecting Enzyme Activities (Properties of Enzymes) The important factors which affect the enzyme action are temperature, pH, change in the substrate concentration, etc. Temperature Enzymes show its highest activity at optimum temperature. i.e. 25 to 400C. Low temperature leads the enzyme in an inactive state, where as high temperature destroys enzyme activity because proteins are denatured by heat. pH Enzyme shows its highest activity at optimum pH. i.e. 6.5 to 7.

Concentration of Substrate

11 With the increase in substrate concentration, the velocity of enzymatic reaction rises at first and reaches a maximum velocity (Vmax). After this point, further rise in concentration of the substrate do not increase the reaction rate. Enzyme Inhibition Activity of the enzyme is inhibited by the presence of certain specific chemicals which bind with the enzyme. The process is called inhibition and chemicals are called inhibitors. When the inhibitor closely resembles the substrate in its molecular structure and inhibits the activity of the enzyme is known as competitive inhibition. Due to the similarity the inhibitor competes with the substrate for the substrate binding site of the enzyme. Eg: Inhibition of Succinic Dehydrogenase by Malonate, which closely resembles the substrate succinate in structure.

Classification and Nomenclature of Enzymes

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Apoenzyme The protein part of the enzyme is called apoenzyme. Co-Factors The non-protein parts associated with enzyme are called co-factors. The co-factors are of three types prosthetic group, co-enzymes and metal ions. Prosthetic Group The organic compounds which are tightly bind to the apoenzyme are called prosthetic group. Eg: the prosthetic group Haem is a part of the enzyme Peroxidase and Catalase, which catalyse the breakdown of hydrogen peroxide to water and oxygen. Co-Enzymes The organic compounds which are not firmly bound to the apoenzyme are called coenzymes. Many co-enzymes are vitamins. Eg: NAD (Nicotinamide Adenine Dinucleotide), NADP (Nicotinamide Adenine Dinucleotide Phosphate) contains the vitamin Niacin. Metal Ions A number of enzymes require metal ions for their activity. Eg: Zinc is a co-factor for the proteolytic enzyme carboxy peptidase.

Notes Prepared by BIJU T L HSST Zoology GHSS Mylachal, Tvpm