Biomolecules PDF

C HA P TE R 9 Biomolecules | 129 BÏØMØLËÇÜLËS 130 | BIOMOLECULES Biomolecules are chemical compounds found in living organisms. They include organic and inorganic compounds...

C HA P TE R 9 Biomolecules | 129 BÏØMØLËÇÜLËS 130 | BIOMOLECULES Biomolecules are chemical compounds found in living organisms. They include organic and inorganic compounds Grind a living tissue (vegetable or piece of 1 liver etc.) in trichloroacetic acid (Cl3CCOOH) to get a thick slurry. Strain this through a cheesecloth or cotton cloth to get two fractions such as filtrate ÅÑÅLÝSÏS ØF 2 (acid-soluble pool) and the retentate ÇHËMÏÇÅL (acid-insoluble fraction). ÇØMPØSÏTÏØÑ The filtrate contains micromolecules ÏÑ Å TÏSSÜË 3 (biomolecules having molecular weight less than 1000 Dalton). The retentate contains biomacromolecules 4 (biomolecules having molecular weight higher than 1000 Dalton). ÅÑÅLÝSÏS ØF ÏÑØRGÅÑÏÇ ÇØMPØÜÑDS It is fully burnt to The ash contains oxidize all carbon inorganic elements compounds to (Ca, Mg, Na, K Weigh a living gaseous form (CO2 tissue and dry it to etc.) & inorganic & water vapour) evaporate water. compounds and are removed. The remaining is (SO42-, PO42-, NaCl, called 'ash'. CaCO3 etc.). Biomolecules | 131 Comparison of Elements in Non-living & Living Matter Element % Weight Earth’s crust Human body Hydrogen (H) O.14 0.5 Carbon (C) 0.03 18.5 Oxygen (O) 46.6 65.0 Nitrogen (N) Very little 3.3 Sulphur (S) 0.03 0.3 Sodium (Na) 2.8 0.2 Calcium (Ca) 3.6 1.5 Magnesium (Mg) 2.1 0.1 Silicon (Si) 27.7 Negligible KNOWLEDGE CORNER Molecular weight of micromolecules found in the acid soluble pool ranges from 18 to 800 Dalton (Da). The acid soluble pool represents the cytoplasmic composition. They include amino acids, sugars, nitrogen bases etc. 1. ÅMÏÑØ ÅÇÏDS  A typical amino acid is formed of an amino group (-NH2), an acid group (-COOH), hydrogen & a variable group (R). The groups – NH2 & –COOH are attached to the same carbon atom (α-carbon). Hence they are called α-amino acids.  They are substituted methanes.  Based on the nature of R group, there are many amino acids. However, those which occur in proteins are only of 20 types. 132 | COOH COOH COOH    H2N ¾ C ¾ H H2N ¾ C ¾ H H2N ¾ C ¾ H    H CH3 CH2OH Glycine Alanine Serine (Hydrogen as R group) (Methyl as R group) (Hydroxy methyl as R group) BÅSËD ØÑ THË ÑÜMBËR ØF ÅMÏÑØ ÅÑD ÇÅRBØXÝL GRØÜPS, THËÝ ÅRË ØF 3 TÝPËS: Acidic amino acids: e.g. Glutamic acid, Aspartic acid. Basic amino acids: e.g. Lysine, Arginine Neutral amino acids: e.g. Valine  Some amino acids are aromatic. E.g. tyrosine, phenylalanine and tryptophan.  Amino acids have ionizable nature. So, structure of amino acids changes in solutions of different pH.  Amino acids can behave as zwitter ion (neutral but contains both positive and negative charges. R R R    NH3+ ¾ CH ¾ COOH  NH3+ ¾ CH ¾ COO-  H2N ¾ CH ¾ COO- B is zwitterionic form (A ) (B) (C) AMAZING FACT Amino acids can be essential or non-essential. Essential amino acids: They cannot be synthesized by the body and should be supplied through diet. E.g. Lysine, leucine, isoleucine, tryptophan etc. (AIPMT 2010) Non-essential amino acids: They can be synthesized by the body. E.g. Glycine, alanine, serine, arginine etc. Biomolecules | 133 2. LÏPÏDS  Water insoluble and simple fatty acids. (AIPMT 2012)  A fatty acid has a carboxyl group attached to an R group. The R group could be a methyl or ethyl or higher number of -CH2 groups.  E.g. Palmitic acid has 16 carbon atoms (CH3–(CH2)14–COOH or C15H31– COOH) and Arachidonic acid has 20 carbon atoms. FÅTTÝ ÅÇÏDS ÅRË ØF 2 TÝPËS 01 Saturated fatty acids: They have no double or triple bonds between carbon atoms. E.g. Palmitic acid, Stearic acid (C17H35COOH) etc. 02 Unsaturated Fatty acids: They have one or more C = C or C ≡ C E.g. Oleic acid (C17H33COOH), Arachidonic acid (C19H31COOH) etc. TÝPËS ØF LÏPÏDS: a. Simple Lipids: These are formed of fatty acids and alcohol such as glycerol.  Structure of glycerol (trihydroxy propane): CH2-OH CH-OH CH2-OH  Fatty acids are esterified with glycerol through ester bond forming monoglycerides, diglycerides & triglycerides. 1 glycerol + 1 fatty acid = Monoglyceride 1 glycerol + 2 fatty acid = Diglyceride 1 glycerol + 3 fatty acid = Triglyceride (NEET 2016) Based on melting point, lipids are of 2 types:  Fats: Higher melting point.  Oils: Lower melting point. (Eg. Gingelly oil) b. Compound lipids: These are the esters of fatty acids and alcohol with additional groups. E.g. Phospholipids (fatty acids + glycerol + phosphate). They are found in cell membranes. E.g. Lecithin. (AIPMT 2012) 134 | O  O CH2 ¾ O ¾ C ¾ R1   R2 ¾ C ¾ O ¾ C ¾ H O   CH2 ¾ O ¾ P ¾ O ¾ CH2 ¾ CH2   OH N H3C  CH3 Phospholipid (Lecithin) CH3 c. Derived lipids: These are the products of hydrolysis of simple lipids and compound lipids. E.g. Cholesterol. HO Cholesterol 3. SÜGÅRS (ÇÅRBØHÝDRÅTËS) Sugars are sweet and water-soluble carbohydrates. They are formed of C, H and O in the ratio of 1:2:1. 4. ÑÏTRØGËÑ BÅSËS These are the nitrogen containing heterocyclic rings found in nucleic acids. They are of 2 types: a. Purines: Includes Adenine(A) & Guanine(G) b. Pyrimidines: Includes Cytosine(C), Thymine(T) & Uracil (U). (NEET 2016) Biomolecules | 135 NH 2 O N N HN N Purine H 2N N N N H H Adenine Guanine NH 2 O O N HN HN CH3 Pyrimidine O O O N N N H H H Cytosine Uracil Thymine ÑÜÇLËØSÏDË Nitrogenous base attached to a sugar Nitrogen base + Sugar = Nucleoside Adenine + Sugar = Adenosine Guanine + Sugar = Guanosine Cytosine + Sugar = Cytidine Thymine + Sugar = Thymidine Uracil + Sugar = Uridine HOCH2 O Adenine O Uracil HOCH2 OH OH OH OH Adenosine Uridin e ÑÜÇLËØTÏDË Nitrogenous base attached to a sugar which is esterified to a phosphate group. 136 | Nitrogen + Sugar + Phosphate = Nucleotide base Adenine + Sugar + Phosphate = Adenylic acid Guanine + Sugar + Phosphate = Guanylic acid Cytosine + Sugar + Phosphate = Cytidylic acid Thymine + Sugar + Phosphate = Thymidylic acid Uracil + Sugar + Phosphate = Uridylic acid Nucleic acids (DNA & RNA) are made up of nucleotides and function as genetic material. O O Adenine HO P OCH2 OH OH OH Adenylic a cid Biomolecules having molecular weight greater than 1000 Da include Proteins Molecular weight is in the range of 10,000 Da Polysaccharides and above. Nucleic acids Acid insoluble fraction (macromolecular fraction) includes macromolecules from cytoplasm and organelles. Lipid is not strictly a macromolecule as its molecular weight does not exceed 800 Da. But it comes under acid insoluble fraction because many lipids are arranged into structures like cell membranes. When a tissue is grinded, cell membranes are broken and form water insoluble vesicles. They cannot be filtered along acid soluble fraction. Biomolecules | 137 Water 70-90 % Protein 10-15 % Average composition Carbohydrates 3% of cells Lipids 2% Nucleic acids 5-7 % Ions 1% 1. PRØTËÏÑS Peptide bond is formed They are when –COOH group of one Proteins are polypeptides. i.e., linear chains amino acid reacts with –NH2 heteropolymer group of next amino acid of amino acids of amino acids. linked by peptide by releasing a molecule of bonds. water (dehydration). Peptide bond H H H OH H OH N C C N C C H O H O Carboxyl Amino Side group group Chain H O H H OH N C C N C C H O H Peptide bond O H H 138 | 1 For growth and tissue repair. Transport nutrients across cell membranes 2 (e.g. GLUT-4 enables glucose transport into cell). FÜÑÇTÏØÑS ØF PRØTËÏÑS Acts as intercellular ground substance (e.g. 3 collagen). Acts as antibodies to fight infectious 4 organisms. Acts as receptors (e.g.receptors of smell, 5 taste, hormones). Some are hormones (e.g. Insulin), enzymes (e.g. trypsin), pigments (e.g. hemoglobin) etc. KNOWLEDGE CORNER Most abundant protein in animal world: Collagen. Most abundant protein in the biosphere: Ribulose bisphosphate carboxylase - oxygenase (RuBisCO) (NEET 2020) STRÜÇTÜRÅL LËVËLS ØF PRØTËÏÑ  Primary structure: It describes the sequence of amino acids, i.e. the positional information in a protein. Left end of the chain has first amino acid (N-terminal amino acid). Right end has last amino acid (C-terminal amino acid).  Secondary structure: Here, a polypeptide chain is folded in the form of α-helix or β- pleated sheets. Proteins have only right- handed helices. E.g. Keratin, Fibroin (silk fibre). Biomolecules | 139 Secondary structure H H O H N C C OH amino acid R Alpha-helix Beta-pleated sheet Primary structure Tertiary Quaternary structure structure  Tertiary structure: Here, helical polypeptide chain is further folded like a hollow woolen ball. It gives 3D view. Tertiary structure is necessary for many biological activities of proteins. E.g. Myoglobin, enzymes.  Quaternary structure: Here, more than one polypeptide chains from tertiary structure where each chain functions as subunits of protein. E.g. Haemoglobin has 4 sub units. 2. PØLÝSÅÇÇHÅRÏDËS (ÇØMPLËX ÇÅRBØHÝDRÅTËS)  These are polymers of sugars (monosaccharides). E.g. Starch (polymer of glucose) Cellulose (polymer of glucose) Homopolymers Glycogen (polymer of glucose) (AIPMT 1993) Insulin (polymer of fructose)  In a polysaccharide chain (glycogen), the right end is called the reducing end and the left end is called non-reducing end.  There are complex polysaccharides formed of amino-sugars and chemically modified sugars (e.g., glucosamine, N-acetyl galactosamine etc.).  Chitin is the homopolymer of N-acetyl glucosamine. Seen in exoskeleton of arthropods and fungal cell wall. (NEET 2013)  Glycosidic bond in polysaccharides: It is the bond formed when individual monosaccharides are linked between 2 carbon atoms followed by dehydration. 140 |  Cellulose has no complex helices and so cannot hold I2. (AIPMT 2002) Plant cell walls are made of cellulose. Paper made from plant pulp and cotton fibre is cellulosic. CH2 OH CH2OH O O O O OH OH O O OH O O OH OH CH 2 O O O O O  Starch forms helical secondary structure. Starch holds I2 molecules in the helical portion giving blue colour.  Nucleic acids are of 2 types: DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid) having deoxyribose and ribose sugar, respectively. SËÇØÑDÅRÝ STRÜÇTÜRË ØF DÑÅ (WÅTSØÑ - ÇRÏÇK DØÜBLË HËLÏX MØDËL)  DNA is different types such as A, B, C, Z etc. DNA consists of 2 polynucleotide strands arranged antiparallely as a double helix.  In DNA, a nucleotide consists of nitrogen base, deoxyribose sugar and phosphate group  Backbone of DNA is formed by the sugar- phosphate-sugar chain.  Steps are formed of Nitrogen base pairs.  Nitrogen bases include Adenine (A), Guanine (G), Thymine (T) and Cytosine (C). Uracil absent.  A pairs with T (A=T) by 2 hydrogen bonds.  G pairs with C (G ≡ C) by 3 hydrogen bonds.  A phosphate molecule links the 3'-carbon atom of the sugar of one nucleotide to the 5'-carbon of the sugar of the succeeding nucleotide Biomolecules | 141 5'end 3'end Hydrogen bond Sugar Purines Pyrimidines G-Guanine T-Thymine Phosphate A-Adenine C-Cytosine 3'end 5'end One full turn of helical strand has 10 steps (10 base pairs). (AIPMT 2003) ÏÑ Length of one full turn (pitch) = 34 Å B-DÑÅ: (i.e. 3.4 Å for each step). At each step, the strand turns 36°. (AIPMT 2007) MËTÅBØLÏSM  All the biochemical reactions taking place inside a living system together constitute metabolism. Some of the examples are:  Removal of CO2 from amino acids to form amine.  Removal of amino group in a nucleotide base.  Hydrolysis of a glycosidic bond etc.  In metabolism, there is a series of linked multistep chemical reaction called metabolic pathways. It is of 2 types: 142 | Anabolic (biosynthetic) pathways Catabolic pathways Simpler molecules form complex Complex molecules form simple structures (Constructive process) structures (destructive process) It consumes energy. It releases energy E.g. Formation of acetic acid from E.g. Formation of lactic acid from cholesterol, assembly of amino glucose (glycolysis), respiration acids to protein, photosynthesis etc. etc.  Metabolites are organic compounds taking part in metabolism. THËÝ ÅRË ØF 2 TÝPËS: 1 2 Primary metabolites: They Secondary metabolites: They have identifiable functions in are not directly involved in physiological processes and normal growth, development necessary for life. E.g. amino or reproduction. Many of these acids, sugars, nucleic acids, are useful for the human lipids, vitamins etc. welfare and some have ecological importance. Pigments: Carotenoids, Anthocyanins etc. 1 Alkaloids: Morphine, Codeine etc. 2 Terpenoids: Monoterpenes, Diterpenes etc. 3 Essential oils: Lemon grass oil etc. MËTÅBØLÏTËS SËÇØÑDÅRÝ 4 Toxins: Abrin, Ricin etc. 5 Lectins: Concanavalin A 6 Drugs: Vinblastin, curcumin etc Polymeric substances: Rubber, 7 gums, cellulose etc. Biomolecules | 143  Flow of metabolites through the metabolic pathways has a definite rate & direction like automobile traffic in a city. This metabolic flow is called dynamic state of body constituents.  The energy released through catabolism is stored in the form of chemical bonds. When needed, this bond energy is utilized for biosynthetic, osmotic and mechanical works.  The most important energy currency in living system is the bond energy in adenosine triphosphate (ATP). (AIPMT 2000) Enzymes are biological Ribozymes: Nucleic acids catalysts which (RNA) that behave like influence the speed of enzymes. (NEET-II 2016) biochemical reactions. Almost all enzymes Enzymes form tertiary structure (3D) with are proteins but some crevices (pockets) all proteins are not ËÑZÝMËS called ‘active site’ into enzymes. which the substrate fits. Carbonic anhydrase is Enzymes are specific. the fastest enzyme. It i.e. each enzyme has its accelerates the following own substrate. reaction 10 million times. Carbonic anhydrase CO2 + H2O   H2CO3   In the absence of enzyme, only 200 molecules of H2CO3 are formed in an hour. In the presence of carbonic anhydrase about 600,000 molecules are formed per second. In a metabolic pathway, each step is catalysed by different enzymes. E.g. In glycolysis [Glucose (C6H12O6)®2 Pyruvic acid (C3H4O3)] ten different enzymes take part. ÑÅTÜRË ØF ËÑZÝMË ÅÇTÏØÑ (ÇÅTÅLÝTÏÇ ÇÝÇLË) It includes the following steps: 144 | 01 The substrate binds to the active site of enzyme (E+S). This induces some changes in enzyme so that the substrate is tightly bound with active site of enzyme to form enzyme-substrate complex (ES)-transition state. 02 03 The active site breaks chemical bonds of substrate to form enzyme- product complex (EP). 04 The enzyme releases the products and the free enzyme is ready to bind to other molecules of the substrate (E+P). This pathway goes through some unstable transition state structures. (NEET 2013) E+S ES EP E+P HØW DØ ËÑZÝMËS SPËËD ÜP Å ÇHËMÏÇÅL RËÅÇTÏØÑ? (ÇØÑÇËPT ØF ÅÇTÏVÅTÏØÑ ËÑËRGÝ)  Activation energy is the Transition state additional energy required Activation energy to start a chemical reaction. without enzyme Potential Energy (NEET-II 2016) Activation  In an exothermic or energy with enzyme endothermic reaction, the Substrate (s) substrate must go through a much higher energy state. Product (P) It is called transition state. Therefore, activation energy Progress of reaction Biomolecules | 145 is the difference between average energy of substrate from that of transition state.  If the product (P) is at a lower energy level than the substrate (S), the reaction is an exothermic reaction (spontaneous reaction). It requires no energy (by heating) to form the product.  In a biochemical reaction, enzymes lower the activation energy. As a result, speed of the reaction increases.  Rate of reaction can be doubled or decreased by half for every 10°C change in either direction. FÅÇTØRS ÅFFËÇTÏÑG ËÑZÝMË ÅÇTÏVÏTÝ Å) TËMPËRÅTÜRË ÅÑD PH  Enzymes show highest Optimum Temp. Optimum pH Rate of Reaction activity at optimum Rate of Reaction temperature & pH. Activity declines below and above optimum value. (AIPMT 2010, 2011) Temperature pH  At low temperature, enzyme temporarily becomes inactive.  At high temperature, enzymes destroy because proteins are denatured by heat.  Inorganic catalysts work at high temperature & pressure. But enzymes get damaged at high temperature (> 40°C).  Thermophilic organisms have enzymes which are stable at high temperature (up to 80-90°C). B) ÇØÑÇËÑTRÅTÏØÑ ØF SÜBSTRÅTË With the increase in substrate V max concentration, the velocity of enzyme (c) Vel oc i t y of reac t i on (V ) action rises at first and reaches a maximum velocity (Vmax). This is not exceeded by further rise in V max concentration because enzyme 2 molecules are fewer than the substrate molecules i.e. No free enzyme molecules present to bind with additional substrate molecules. Km [S] 146 | Ç) PRËSËÑÇË ØF ÏÑHÏBÏTØR  The binding of specific chemicals (inhibitor) shuts off the enzyme activity. This is called inhibition.  The inhibitor is closely similar to the substrate in its molecular structure and is called as competitive inhibitor. It competes with the substrate for the binding site of the enzyme. As a result, the substrate cannot bind and the enzyme action declines. (AIPMT 2005)  E.g. Malonate is similar to the substrate succinate. So, it inhibits succinic dehydrogenase in the following reaction. (NEET 2020) Succinic dehydrogenase Succinate Fumarate  Competitive inhibitors are used to control bacterial pathogens. ÇLÅSSÏFÏÇÅTÏØÑ ÅÑD ÑØMËÑÇLÅTÜRË ØF ËÑZÝMËS Oxido-reductases / Transferases: Catalyze Dehydrogenases: Catalyze transfer of a group, G (other oxido- reduction b/w two than hydrogen) between a substrates. pair of substrate S and S'. S reduced + S’ oxidized ® S-G + S’ ® S’-G +S S oxidized + S’ reduced Hydrolases: Catalyze hydrolysis Lyases: Catalyze removal of ester, ether, peptide, of groups from substrate glycosidic, C-C, C-halide or P-N by mechanisms other than bonds. hydrolysis leaving double bonds. C–C®X–Y+C=C | | X Y Isomerases: Catalyze Ligases: Catalyze the linking inter-conversion of optical, of 2 compounds together. E.g. geometric or positional enzymes catalyzing joining of isomers. bonds like C-O, C-S, C- N, P-O etc. Biomolecules | 147 ÇØ-FÅÇTØRS  These are non-protein constituents bound to the enzyme to make the enzyme catalytically active.  Apo-enzyme: Protein portion of the enzyme.  Co-factor + Apoenzyme = Holoenzyme  When the co-factor is removed from the enzyme, its catalytic activity is lost. Co-factors are of 3 types:  Prosthetic group: Organic compounds. Tightly bound to apoenzyme. E.g. Haem in peroxidase and catalase which catalyse the breakdown of hydrogen peroxide to water and oxygen. (NEET 2019)  Co-enzymes: Organic compounds. Loosely bound to apoenzyme. Many co-enzymes contain vitamins. E.g. NAD and NADP contain niacin.  Metal ions: They form co-ordination bonds with side chains at active site and one or more co-ordination bonds with the substrate. E.g. Zn is a cofactor for carboxypeptidase. Notes 148 | Notes