Biomolecules PDF

Biomolecules © © 2022, 2022, Aakash Aakash BYJU'S. BYJU'S. All All rights rights reserved reserved Key Takeaways 1 Metabolites 2 3 Lipids 8 Summary © 2022, Aakash BYJU'S. All rights reserved Nucleic Acids 6 7 Enzymes Carbohydrates 4 5 Amino Acids and Protein Biomolecules Metabolism Components of Lif...

Biomolecules © © 2022, 2022, Aakash Aakash BYJU'S. BYJU'S. All All rights rights reserved reserved Key Takeaways 1 Metabolites 2 3 Lipids 8 Summary © 2022, Aakash BYJU'S. All rights reserved Nucleic Acids 6 7 Enzymes Carbohydrates 4 5 Amino Acids and Protein Biomolecules Metabolism Components of Life Components of life Organic components Biomicromolecules © 2022, Aakash BYJU'S. All rights reserved Biomacromolecules Inorganic components Elements (Ca, Mg, etc) Biomolecules Biomolecules: Carbon containing compounds which form the basic chemical structure of all life forms Biomolecules Micromolecules Small size Low mol wt. 18 - 800 Daltons Found in the acid soluble pool E.g., Simple sugars, amino acids, nucleotides © 2022, Aakash BYJU'S. All rights reserved Macromolecules      Large size High mol wt. >1000 Daltons Found in the acid insoluble pool E.g., Complex carbohydrate, lipid, protein, nucleic acids Metabolites  Carbon content of a cell - Metabolite content  Metabolites - Molecules that take part in metabolic reaction  Metabolism : Sum total of all the chemical reactions occurring in the body Metabolites Primary metabolites Involved directly in growth Secondary metabolites Produced for defence purposes and stress responses Carbohydrates Coloured pigments - Carotenoids Lipids Alkaloids - Morphine Proteins Nucleic acids Polymeric substances - Rubber, Gums Essential oils - Lemongrass oil Antibiotics, toxin, scents, spices etc © 2022, Aakash BYJU'S. All rights reserved Carbohydrates  Carbohydrates are the hydrates of carbon  Have carbon, hydrogen and oxygen in the ratio 1:2:1 Aldehyde group CHO H C OH OH C H Keto CH2OH group C O OH C H  Contain at least 3 carbon atoms  Have multiple –OH groups  General formula- Cn(H2O)n H C OH H C OH  Can be aldehydes or ketones H C OH H C OH  Can be classified based on the number of monomeric units  Saccharide = Sugar © 2022, Aakash BYJU'S. All rights reserved CH2OH Glucose (C6H12O6) : Aldose CH2OH Fructose (C6H12O6) Ketose Carbohydrates Types of carbohydrates Monosaccharides Polysaccharides E.g., glucose, fructose, mannose, galactose, etc E.g., glycogen, starch, hyaluronic acid, cellulose, etc Derived monosaccharides E.g., deoxyribose, glucosamine, mannitol, etc Disaccharides Oligosaccharides E.g., sucrose E.g., raffinose, stachyose, etc Monosaccharides  Simplest carbohydrates  Form the building blocks of larger carbohydrates  Cannot be hydrolysed into smaller units  Glucose (universal sugar) , fructose (fruit sugar), mannose, galactose are hexoses Monosaccharides Trioses Tetroses Pentoses Hexoses Have 3 carbon atoms Have 4 carbon atoms Have 5 carbon atoms Have 6 carbon atoms H O C H C OH CH2OH O H O H H OH H OH H OH H OH H OH CH2OH CH2OH Glyceraldehyde © 2022, Aakash BYJU'S. All rights reserved Erythrose Ribose CH2OH O C OH H H C C H OH H OH C Glucose C H OH Derived monosaccharides  Modified monosaccharides  Deoxy sugar : e.g., deoxyribose  Amino sugar : e.g., glucosamine  Sugar acid : e.g., glucuronic acid, ascorbic acid  Sugar alcohol : e.g., mannitol (present in brown algae) 5 HOCH2 OH on Carbon 2 4 C H O H H C C 3 C H OH OH 2 Ribose (C5) © 2022, Aakash BYJU'S. All rights reserved 5 HOCH2 OH 1 Deoxygenation 4 C H OH O H H C 3 C OH H C 2 H Deoxyribose (C5) Constituent of DNA 1 No OH on Carbon 2 Disaccharides Examples: Polymers of monosaccharides with 2 monomeric units Di = Two; Saccharide = Sugar unit Two monosaccharide units join with a glycosidic bond Sucrose = Glucose + Fructose Lactose = Glucose + Galactose H20 + Monosaccharide (Glucose) Monosaccharide (Glucose) Disaccharide (Maltose) Oligosaccharides  Oligosaccharides are the polymers of monosaccharides with 3 - 9 monomeric units.  Monosaccharides unit are bound together by glycosidic bond.  Depending on the number of monosaccharide molecules, there are different types of oligosaccharides.  E.g. - Raffinose with 3 monomeric units is referred to as a trisaccharide.  Similarly, stachyose with 4 monomeric units is referred to as a tetrasaccharide. © 2022, Aakash BYJU'S. All rights reserved Polysaccharides  Polysaccharides are the polymers of monosaccharides with 10 or more monomeric units.  They have a reducing end and a non-reducing end in their chemical structure. Homopolysaccharides Structural polysaccharides Cellulose Made up of different monomeric units Polysaccharides Made up of same monomeric units Storage polysaccharides Chitin © 2022, Aakash BYJU'S. All rights reserved Starch Heteropolysaccharides Peptidoglycan Glycogen Agar Inulin Hyaluronic acid Homopolysaccharides Storage polysaccharides Starch  Polymer of glucose  Gives blue colour with iodine  Major reserve food in plants  Consists of amylopectin and amylose Glycogen  Polymer of glucose  Food reserve in animals  Highly branched  Stored in liver and muscles Inulin  Polymer of fructose  Not metabolised in human body  Stored in Dahlia, dandelion and artichoke © 2022, Aakash BYJU'S. All rights reserved Structural polysaccharides Cellulose  Polymer of glucose  Forms structural part of plants (cell wall)  Straight chain and unbranched  Cotton fibres contain 90% of cellulose Chitin  Polymer of N-acetyl-Dglucosamine  Form structural part of living organisms (exoskeleton of arthropods)  Complex polysaccharide Homopolysaccharides Agar Peptidoglycan  Component of bacterial cell wall, which is degraded by lysozyme  Obtained from the red algae - Gelidium and Gracilaria  Made of two different repeating units o N-Acetyl glucosamine (NAG) o N-Acetyl muramic acid (NAM)  Agar is a mixture of agarose and agaropectin  Used as medium in labs Oligopeptide​ Hyaluronic acid NAM © 2022, Aakash BYJU'S. All rights reserved NAG  Responsible for the toughness and flexibility of cartilage and tendon  Made of two different units o D-glucuronic acid o N-acetyl-D-glucosamine Reducing Sugars  Reducing sugars: Free aldehyde (CHO) /ketone group (C=O) present  Benedict and Fehling’s test: reducing sugars reduce the Cu2+ ions to Cu+ which gives brick red colour  All monosaccharides are reducing sugars Add an equal amount of Benedict’s solution About 2ml of test solution (glucose) © 2022, Aakash BYJU'S. All rights reserved Heat in water bath H O H HO C C H H C C H CH2OH C C O HO C H H C OH H C OH OH H OH OH H C OH HO C H HO C H H C OH CH2OH CH2OH Glucose Fructose CH2OH Galactose Monosaccharide Brick red precipitate O C Non-Reducing Sugars  Non-reducing sugars: No free aldehyde/ketone group  All polysaccharides and sucrose are non-reducing  Among disaccharides, only sucrose is non-reducing sugars Reducing end Non-reducing end CH2OH O H H OH H O H H HO CH2OH CH2OH OH O OH H H OH O OH H Polysaccharide © 2022, Aakash BYJU'S. All rights reserved O O H H H H H O H H CH2OH CH2OH H H H H OH O n OH H H OH OH HO CH2OH O H CH2OH H OH H H OH H HO O OH Disaccharide: Sucrose H H Lipids  Water insoluble organic compounds  They are insoluble in water  Consists of carbon, hydrogen and oxygen  They are not polymeric like polysaccharides (carbohydrates)  Molecular weight is less than 800 daltons Classification of lipids Simple Neutral/ True fats Waxes © 2022, Aakash BYJU'S. All rights reserved Compound Phospholipids Glycolipids Lipoprotein Derived Chromolipids Simple Lipids  Simple lipids are esters (organic acid and alcohol react to form esters) of fatty acids with various alcohol.  Neutral or true fats are esters of fatty acids with glycerol, called glycerides o Glycerol is an alcohol with three carbons, five hydrogens, and three hydroxyl (OH) groups (Trihydroxypropane) o Fatty acids: Carboxylic acid with an R group attached. R groups can be Methyl (-CH3) Ethyl (-C2H5) 1- 19 (-CH2) groups CH2 OH CH OH OHHO Fatty acid structure O ester bonds C R H2C O C OHHO C R O R HC O C R O H2C OHHO C R H2C 3H2O © 2022, Aakash BYJU'S. All rights reserved O O HC OH O OH CH2 Glycerol H2C C R O C triglyceride Esterification reaction R Simple Lipids Glycerides Monoglycerides Condensation of one fatty acid and glycerol Triglycerides Condensation of two fatty acid and glycerol Condensation of three fatty acid and glycerol C FA C FA C C FA C FA C C C FA C FA Diglycerides Monoglyceride © 2022, Aakash BYJU'S. All rights reserved Diglyceride Triglyceride Simple Lipids Fatty acids (Based on structure) Saturated Essential fatty acids: Cannot be synthesised by the body, so they must be obtained from diet E.g., Linoleate Unsaturated  Without a double bond  With a double bond  Mostly solid at room temperature  Mostly liquid at room temperature  Higher melting point  Lower melting point OH Arachidonic acid (20 Carbon atoms) Palmitic acid (16 Carbon atoms) © 2022, Aakash BYJU'S. All rights reserved O Non-essential fatty acids: Can be synthesised by the body Simple Lipids Simple lipids Fats Similarities Fats and oils Waxes Esters of fatty acids and glycerol E.g.,- Butter, ghee, oils Esters of long chain fatty acids and fatty alcohol E.g.,- Bee wax © 2022, Aakash BYJU'S. All rights reserved Differences Oils Triglycerides Triglycerides Solid at room temperature Liquid at room temperature Mainly from animal sources Mainly from plant sources Relatively more saturated Relatively more unsaturated High melting point E.g., Ghee Low melting point E.g., Oil Compound Lipids  Esters of fatty acids and alcohol with additional groups  Additional groups could be phosphorus, proteins or sugar  Usually found in cell membrane Compound lipids Phospholipids Glycolipids Lipoproteins Chromolipids  Phosphate group + nitrogen choline + fatty acid  Glycolipid = fatty acid + alcohol + carbohydrate group  Contain lipids (phospholipids) and proteins  Contains pigment such as carotenoids  Major component of cell membranes  Found on the cell membrane surface  Membranes are composed of proteins  E.g., Carotene and vitamin A  E.g., Lecithin  Help in cell recognition © 2022, Aakash BYJU'S. All rights reserved Derived Lipids  Lipids derived from simple or conjugated lipids CH3 CH3  Steroids do not contain fatty acids yet have fat like properties CH3 CH3  Most common steroids are sterols  Complex in structure  E.g., Cholesterol o Most common sterols o Tetracyclic in nature o CH3 HO Essential component of animal plasma membrane, also synthesised in live  E.g., Prostaglandins o Derived from arachidonic acid o Group of hormone which function as messenger substance between the cell © 2022, Aakash BYJU'S. All rights reserved Cholesterol Lipids Functions of lipids Long term energy storage Protection against heat loss (insulation) Protection against physical shock Protection against water loss Chemical messengers (hormones) Major component of membranes (phospholipids) © 2022, Aakash BYJU'S. All rights reserved Nucleic Acids Nucleic acids are polymers of macromolecules Polymers of repeating units of nucleotides (building blocks) Nucleic acids DNA RNA Deoxyribonucleic acid Ribonucleic acid Monomers of nucleic acid Nucleotide Pentose sugar Nitrogenous base Nucleoside Phosphoric acid Phosphate Nitrogenous base Pentose sugar Nucleotide © 2022, Aakash BYJU'S. All rights reserved Nucleic Acids Pentose sugar  5-Carbon monosaccharide  Central molecule in a nucleotide © 2022, Aakash BYJU'S. All rights reserved RNA has ribose sugar DNA has deoxyribose sugar Ribose Deoxyribose Nucleic Acids Heterocyclic Nitrogencontaining compounds Nitrogenous bases Purines Pyrimidines Have double ringed structure Have single ringed structure H O H N N H C C N C N H C N C C N H H Adenine (A) H H N H C N C C N H N H Guanine (G)  In both DNA and RNA O H N C H C H C C N C C N O H Cytosine (C) H H N N H C C C H N H C C O H C O H Uracil (U) H C C N H Thymine (T)  In DNA, cytosine and thymine are found  In RNA, cytosine and uracil are found © 2022, Aakash BYJU'S. All rights reserved O Nucleic Acids Phosphodiester Bond - Phosphodiester bond © 2022, Aakash BYJU'S. All rights reserved  Ester bond formed between the phosphate group of one nucleotide and hydroxyl group of the sugar of the next nucleotide -  Connecting link between two consecutive nucleotides Double Helix Model  Made up of two polynucleotide chains, existing as a double helix  Two polynucleotide strands are joined together by hydrogen bonds between purines and pyrimidines Backbone of DNA Antiparallel strands 5’ end - 5th carbon of pentose sugar is free Sugar – phosphate backbone 3’ end - 3rd carbon of pentose sugar is free Right-handed coiling Each base pair strand turns 36 degree Helix diameter 2 nm Full turn involves 10 base pairs Helical pitch 3.4 nm Nitrogen bases facing inside Complementary base pairing Helical rise 0.34 nm A © 2022, Aakash BYJU'S. All rights reserved Pyrimidines Purines T C G Hydrogen bonds Double Helix Model 5’ 3’ 0.34 nm Minor groove 3’ 5’ Major groove 3.4 nm 3’ 5’ Phosphodiester H- Bonds bond 3’ T A Forms two hydrogen bonds 5’ C G Forms three hydrogen bonds 2 nm © 2022, Aakash BYJU'S. All rights reserved DNA Forms of DNA (with right handed coiling) B - form A - form C - form D - form Usual DNA 11 base pairs per turn Like B-form Like B-form 10 base pairs per turn Not perpendicular to the axis but slightly tilted 9 base pairs per turn 8 base pairs per turn DNA with left-handed coiling is called Z - DNA with 12 base pairs Chargaff’s rule Concluded by Erwin Chargaff for DNA molecule (A+T)/ (G+C) constant for a given species only (A + G) Purines = Pyrimidine (T + C) A = T and G = C Equal proportion of deoxyribose sugar and pentose sugar RNA  Usually single stranded but sometimes double stranded (Reovirus and Rice dwarf virus)  Does not follow Chargaff’s rule Forms of RNA Messenger (m- RNA)  5% of total cellular RNA © 2022, Aakash BYJU'S. All rights reserved Ribosomal (r- RNA)  80% of total cellular RNA Transfer/ soluble (s- RNA, t- RNA)  10-15% of total cellular RNA Amino Acids Amino acids Amino acids are substituted methanes General structure: Four substituent groups occupying the four valency positions Based on nature of R group there are many amino acids. For e.g., COOH COOH H C NH2 H H Glycine C CH3 Alanine NH2 Carboxyl group Amine group COOH H C H NH2 CH2 OH Serine N R=H © 2022, Aakash BYJU'S. All rights reserved R = CH3 R = CH2-OH O H H C H R C O Classification of Amino Acids Based on number of amine and carboxyl groups Acidic Basic Neutral 2 carboxyl and 1 amine group E.g., glutamic acid, aspartate 1 carboxyl and 2 amine group E.g., lysine, arginine and histidine 1 carboxyl and 1 amine group E.g., valine, alanine and glycine H H COOH H2N CH2 C COOH CH2 CH2 H2N C CH2 H CH2 COOH CH2 H2N C COOH H Based on the presence of aromatic ring H2N Non-aromatic Aromatic Have straight chains and no aromatic rings Have aromatic (benzene) rings E.g., tyrosine, phenylalanine, tryptophan H C O C OH H2N H C O C OH CH2 CH2 H2N H C O C CH2 Glycine HN NH2 Aspartic acid Lysine Phenylalanine Tryptophan OH Tyrosine OH Amino Acids Amino acids Essential Obtained through diet; body does not synthesise Non-essential Synthesised by the body Semi-essential amino acid: Synthesised very slowly by human beings. E.g., arginine and histidine © 2022, Aakash BYJU'S. All rights reserved Essential Non essential Phenylalanine Proline Valine Alanine Threonine Glycine Tryptophan Glutamate Isoleucine Cysteine Methionine Serine Lysine Amino Acids Zwitterions:  Molecule with one functional group having positive charge and the other having negative charge  Positive charge = Negative charge  Net charge = Zero  -NH2 is a strong base and can pick up protons (H+) from -COOH group ○ Due to this, NH2 acquires positive charge (NH3+ ) and COOH acquires negative charge (COO-) Amino acids Cation + R Zwitterion + NH3 C COOH H Low pH Zwitterions R NH3 C Anion NH2 - COO H pH Scale R C H High pH Different pH = Different states of amino acids © 2022, Aakash BYJU'S. All rights reserved - COO Proteins Polypeptides are linear chains of amino acids linked by peptide bonds. Polypeptides undergo modification to form proteins. Proteins are heteropolymers made by different amino acids. There are 20 types amino acids, a protein is a heteropolymer and not a homopolymer. Amino acids © 2022, Aakash BYJU'S. All rights reserved Polypeptide Protein Proteins Formation of peptide bond Amino acid 1 H O N C H H O C H Amino acid 2 R C-terminal H O N C H H R H O H C N C H Amino acid 2 O C C R H N-terminal Water molecule elimination © 2022, Aakash BYJU'S. All rights reserved N H O C Amino acid 1 H Peptide bond H O R Proteins Structure of proteins Primary structure Complexity Secondary structure Tertiary structure Quaternary structure © 2022, Aakash BYJU'S. All rights reserved Proteins Primary structure  Linear chain of amino acids  Positional information  N- Terminal : Free Amine group with alpha carbon  C-Terminal : Free Carboxyl group with alpha carbon C-terminal amino acid H O H O H O H O N C N C N C N C H C H C R H C R N-terminal amino acid © 2022, Aakash BYJU'S. All rights reserved H O C R H H R Amino acids Proteins Secondary structure  Folding of the polypeptide chain due to interactions between amino acids Secondary structure α-helices © 2022, Aakash BYJU'S. All rights reserved Alpha-helix Beta- pleated sheet Polypeptide chain folds in the form of righthanded helices resembling a spring. E.g., Keratin Segments of polypeptide chain line up next to each other resembling pleated paper. E.g.,Fibroin β-sheets Proteins Tertiary structure Quaternary structure  Three-dimensional structure  Two or more polypeptide chains  Protein is folded upon itself like a hollow woollen ball  Each chain = Subunit  Biologically active  E.g., Globular protein, Myoglobin  Arrangement of each folded polypeptide chains with respect to each other determines the structure  Adult human haemoglobin consists of 4 subunits o two subunits of α type o two subunits of β type E.g., Haemoglobin Polypeptide 1 Polypeptide 2 Tertiary structure © 2022, Aakash BYJU'S. All rights reserved Quaternary structure Types of Proteins Based on composition Simple Composed of long chains of amino acids © 2022, Aakash BYJU'S. All rights reserved Conjugated Protein part + Non-protein part (Prosthetic group) Simple proteins Conjugated proteins Collagen found in the skin Nucleoproteins (prosthetic groupnucleic acid) e.g., Protamines. Myosin found in the muscles Metalloproteins (prosthetic groupmetals) e.g., Ferritin. Insulin produced by the pancreas Chromoproteins (prosthetic group-pigment) e.g. Cytochromes. Keratin found in the hair Phosphoproteins (prosthetic group-phosphoric acid) e.g., Casein of milk. Egg albumin Lipoproteins (prosthetic grouplipids) e.g., Chylomicron. Serum globulins Glycoproteins (prosthetic groupcarbohydrates) e.g., Mucin. Types of Proteins Based on shape and structure Fibrous Elastin found in the skin © 2022, Aakash BYJU'S. All rights reserved Globular  Form long and narrow fibers  Round or spherical in shape  Provide structural support  Have multifunctional role  Examples: Keratin, collagen, fibroin, elastin  Examples: Haemoglobin, insulin, ovalbumin Ovalbumin found in egg whites Types of Proteins Based on function Structural Nutrient Defence Catalytic Examples: Elastin, keratin, collagen Examples: Casein, and whey Examples: Antibodies Examples: Enzymes such as trypsin Contractile Regulatory Transport Examples: Actin and myosin Examples: Hormones (like insulin, glucagon) and their receptors Examples: Haemoglobin and hemocyanin Note: Most abundant animal protein: Collagen Most abundant protein in the biosphere: RuBisCO © 2022, Aakash BYJU'S. All rights reserved Metabolism Metabolism: All the chemical reactions occurring in a living organism Metabolism Anabolism Catabolism  Biosynthetic pathways Breakdown or degradation pathway  Endothermic Exothermic Energy Energy © 2022, Aakash BYJU'S. All rights reserved ATP - Energy Currency ATP Triphosphate Adenine Ribose Absorb energy Release energy ADP Diphosphate Adenine © 2022, Aakash BYJU'S. All rights reserved Ribose Catabolic reactions release energy to be used in an anabolic reaction Metabolic Pathways High energy bond ATP Adenine CH2 Anabolic reactions store energy released from a catabolic reaction Ribose Adenine CH2 Energy released © 2022, Aakash BYJU'S. All rights reserved Energy required Metabolic reactions are linked to other reactions and are not isolated Ribose ADP Metabolic Pathways Pyruvic acid NAD+ NADH CO2 Acetyl - CoA CoA Citric Acid (6C) Metabolic pathways can be cyclic (E.g., Krebs cycle) CAA (4C) CO2 NADH NAD+ FADH2 CO2 FAD ATP © 2022, Aakash BYJU'S. All rights reserved ADP +1P NAD+ NADH NAD+ NADH Metabolic Pathways Glucose ATP ADP Unstable Metabolic pathways can be linear (E.g., Glycolysis) ATP ADP P P Fructose-1, 6-bisphosphate P DHAP All the DHAP will be converted into glyceraldehyde-3phosphate P Glyceraldehyde - 3 -phosphate NAD+D NADH ADP ATP ADP ATP Pyruvate © 2022, Aakash BYJU'S. All rights reserved Living State  Living organisms exists in steady state  Living organisms = non-equilibrium steady state to be able to perform work  Biomolecules in steady state = Metabolic flux  Metabolic flux : rate of turnover of molecules through a metabolic pathway © 2022, Aakash BYJU'S. All rights reserved Enzymes  Enzymes are usually proteins and act as catalysts (speed up a process or reaction without getting consumed) also known as biocatalysts.  Exceptions of enzyme (non-proteinaceous in nature) o Ribozymes (RNA enzyme) o Ribonuclease P (RNA enzyme) Organic catalysts (Enzymes) Inorganic catalysts Proteins Metal ions or complex molecules  There are two types of catalysts: organic and inorganic.  They are unused in reaction.  They are highly specific in action due to the presence of active site (Crevice or pocket for binding the substrate).  Enzymes isolated from thermophilic organisms shows thermal stability even at 80-900C. © 2022, Aakash BYJU'S. All rights reserved Most of them are damaged at high temperatures (>40 degree celsius) Example: Lipases, chymosin, etc. Work efficiently at high temperatures and pressures Example: Platinum, palladium, etc. Enzymes Made up entirely of amino acids. For e.g., “pepsin” Apoenzyme (Protein part) Biologically inactive Enzymes Conjugated Simple + Cofactor (Non-protein part) Activates catalytic activity Holoenzyme = Apoenzyme + Cofactor The complete, biologically active conjugated enzyme where both apoenzyme and cofactor are present is known as holoenzyme. © 2022, Aakash BYJU'S. All rights reserved Made up of amino acids and a prosthetic group  A coenzyme or metal ion that is very tightly (covalently or noncovalently) bound to the enzyme protein is called a prosthetic group.  It is a type of the cofactor.  For example, in peroxidase and catalase, which catalyse the 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. Enzymes Types of Cofactor (Non-protein part) Prosthetic group Organic compound, tightly bound with apoenzyme For e.g., Haem ( present in peroxidase, it catalyses hydrogen peroxide) Metal ion Coenzymes (Organic) Organic compound, associated with apoenzyme for a short period of time For e.g., NAD and NADP, contain vitamin niacin For e.g.; enzyme named carboxypeptidase is associated with zinc Form coordination bonds ○ with side chains at the active site ○ one or more coordination bonds with the substrate Zn tightly bound carboxypeptidase Niacin NAD+ Coordination bond Chemical Reaction Chemical reaction: Process of formation or breaking of bonds Reactant 1 (Substrate 1) Reactant 2 (Substrate 2) Product (P)  Rate of reaction: The amount of product formed per unit time  Catalysed reactions proceed at rates vastly higher than that of uncatalysed one Without catalyst: CO2 H2CO3- H2O 200 molecules With catalyst: carbonic anhydrase CO2 © 2022, Aakash BYJU'S. All rights reserved H2O H2CO3- 2,160,000,000 molecules Chemical Reaction Chemical Reaction E n e r g y Endothermic Exothermic Energy (heat) needed Energy (heat) released Products Reactants Progress of reaction © 2022, Aakash BYJU'S. All rights reserved E n e r g y Reactants Heat of reaction Products Progress of reaction Enzymes Mechanism of action Substrate (S) + Enzyme (E) E-S Complex Activation energy: The difference in free energy between the transition state and that of reactant E-P Complex Enzyme (E) + Product (P) Enzymes increase the rate of reaction by:  Decreasing the activation energy  Forming weak bonds with the substrate © 2022, Aakash BYJU'S. All rights reserved Enzymes Enzyme-Substrate complex: Two important model have been proposed to describe the enzyme and substrate binding. 1. Lock and key model:  Proposed by Fischer Substrates Product  Enzymes have an active site at which the substrate Active Site binds.  The binding of substrate and active site can be compared to a lock and key mechanism. Enzymes  Every active site has a specific substrate which can bind to it. Enzyme - Substrate complex 2. Induced fit model:  Proposed by Koshland  The enzyme changes shape on substrate binding.  Enzymes have two groups ○ Buttressing (for support) ○ Catalytic ( for catalysis) © 2022, Aakash BYJU'S. All rights reserved Enzymes Active Site S E + S E Factors Affecting Enzyme Activity Temperature pH  High temperature : Denaturation Enzymes are sensitive to pH  Low temperature : Temporary inactive state Rise or fall in pH : reduces enzyme activity Optimum pH : maximum action Temperature increases activity 2 Denaturation decreases activity 0 10 © 2022, Aakash BYJU'S. All rights reserved 20 30 40 o Temperature / C 1 2 Optimum rate Rate of reaction 20 1 Percentage active enzyme 100% 30 50 60 0% Factors Affecting Enzyme Activity Substrate concentration Low substrate concentration: Low enzyme activity  Optimum substrate concentration: Maximum enzyme activity  Higher substrate concentration: No change in maximum activity  KM (Michaelis constant) : Indicates the substrate concentration at which the chemical reaction catalysed by an enzyme attains half its maximum velocity (Vmax) © 2022, Aakash BYJU'S. All rights reserved VMax ½ VMax Rate of reaction  KM Substrate concentration Factors Affecting Enzyme Activity Inhibitors : Chemicals that shut off enzyme activity Inhibitors Non-competitive Changes the shape of active site such that substrate is not able to bind © 2022, Aakash BYJU'S. All rights reserved Competitive Allosteric modulation Resembles the substrate Binds to the enzyme at sites other than active site Competes with substrate for active site Low molecular weight substance Inhibitors Competitive inhibitors  Effect on Vmax: Decreases  Effect on Km: Increases for a given substrate  In the presence of competitive inhibitor more substrate is needed to achieve 1/2 Vmax  Examples: o Max inhibition of alcohol dehydrogenase by ethanol in methanol poisoning o Sulpha drugs for folic acid synthesis in bacteria o Inhibition of succinic dehydrogenase by malonate and oxaloacetate. © 2022, Aakash BYJU'S. All rights reserved Enzyme Enzyme Succinate Malonate Fumarate + Enzyme Succinateenzyme complex Malonateenzyme complex No product is formed Inhibitors Non-competitive inhibitors  Effect on Vmax: Decreases  Effect on Km: Remain same  Increased substrate levels will not be able to reverse the inhibitor’s action since the inhibitor is not in direct competition with the substrate  Examples: Cyanide kills an animal by inhibiting cytochrome oxidase Normal Substrate © 2022, Aakash BYJU'S. All rights reserved Non competitive Inhibitor Inhibitors Allosteric modulation  Also known as feedback inhibition  After binding, they can increase or decrease the enzyme action  Examples: o Allosteric inhibition of hexokinase by glucose 6- phosphate o Phosphofructokinase activated by ADP and inhibited by ATP o Inhibition of threonine deaminase by isoleucine Normal Substrate © 2022, Aakash BYJU'S. All rights reserved Classification and Nomenclature of Enzymes Enzyme Oxidoreductase Transferases Hydrolases Lyases Isomerases Example Function Catalyses oxidation-reduction reactions Ared Box Aox Dehydrogenase Bred Catalyses transfer of groups between molecules A-B C A B-C Catalyses breaking of bonds by adding water A-B A-H H2O Proteases B-OH Catalyses breaking of bonds without using water A=B A-X HX B-H Catalyses the switch between isomers AB Transaminase Aldolase Isomerase BA Catalyses joining of molecules by forming bonds Ligases © 2022, Aakash BYJU'S. All rights reserved A B ATP A-B ADP Ligase Summary Metabolites Secondary metabolites Primary metabolites NH2 R OH O OH H2N H3C n N N HO OH OH Amino acids O Fatty acids OH Mono saccharides OH N N Nucleobases Nucleotides Proteins Lipids © 2022, Aakash BYJU'S. All rights reserved Complex carbohydrate Nucleic acids Pigments Carotenoids, Anthocyanins, etc. Alkaloids Morphine, Codeine, etc Terpenoids Monoterpenes, Diterpenes, etc. Essential oils Lemongrass oil, etc, Toxins Abrin, Ricin Lectins Concanavalin A Drugs Vinblastine, Curcumin, etc Polymeric substances Rubber, gums, cellulose Summary Types of carbohydrates Monosaccharides Polysaccharides Derived monosaccharides Derived monosaccharides Oligosaccharides Classification of lipids Simple Neutral/ True fats Compound Waxes Phospholipids Glycolipids Lipoprotein Derived Chromolipids Summary Amino acids Amino acids Essential Non-essential Obtained through diet; body does not synthesise Synthesised by the body Semi-essential amino acid: Synthesised very slowly by human beings. E.g., arginine and histidine © 2022, Aakash BYJU'S. All rights reserved Essential Non essential Phenylalanine Proline Valine Alanine Threonine Glycine Tryptophan Glutamate Isoleucine Cysteine Methionine Serine Lysine Summary Nucleic acids Nucleic acids DNA RNA Deoxyribonucleic acid Ribonucleic acid Monomers of nucleic acid Nucleotide Pentose sugar Nitrogenous base Nucleoside Phosphoric acid Phosphate Nitrogenous base Pentose sugar Nucleotide © 2022, Aakash BYJU'S. All rights reserved Summary Double helix model Backbone of DNA Antiparallel strands 5’ end - 5th carbon of pentose sugar is free Sugar – phosphate backbone 3’ end - 3rd carbon of pentose sugar is free Right-handed coiling Each base pair strand turns 36 degree Helix diameter 2 nm Full turn involves 10 base pairs Helical pitch 3.4 nm Nitrogen bases facing inside Complementary base pairing Helical rise 0.34 nm A © 2022, Aakash BYJU'S. All rights reserved Pyrimidines Purines T C G Hydrogen bonds Summary Forms of DNA (with right handed coiling) B - form A - form C - form D - form Usual DNA 11 base pairs per turn Like B-form Like B-form 10 base pairs per turn Not perpendicular to the axis but slightly tilted 9 base pairs per turn 8 base pairs per turn Forms of RNA Messenger (m- RNA) Ribosomal (r- RNA) Transfer/ soluble (s- RNA, t- RNA) Summary Types of proteins Based on shape and structure Fibrous Globular Based on function Structural Contractile Nutrient Regulatory Defence Transport Catalytic Summary Inhibitors Non-competitive Changes the shape of active site such that substrate is not able to bind © 2022, Aakash BYJU'S. All rights reserved Competitive Allosteric modulation Resembles the substrate Binds to the enzyme at sites other than active site Competes with substrate for active site Low molecular weight substance