Page 1 : NAVAS CHEEMADAN, , Biomolecule, Introduction, The living organisms are made of different, types of compound, The chemical analysis reveals that it is, composed of elements like C,H,O,, A piece of non living matter also contains, same type of elements, In fact the living things and non living, things are made up of same elements, However the relative abundance of, Carbon, hydrogen is higher in the living, organism than in non living matter, , How to analyze chemical composition ?, Take any living tissue (a vegetable or a piece, of liver, etc.) and grind it in trichloroacetic, acid (Cl3CCOOH) using a mortar and a pestle., We obtain a thick slurry. If we were to strain, this through a cheesecloth or cotton we, would obtain two fractions., a)the filtrate or, the acid-soluble pool, (micromolecule/biomolecule ),, b) the retentate or the acid-insoluble fraction, (Biomacromolecule )., a)Acid soluble pool, Scientists have found thousands of, organic compounds in the acid-soluble pool., There is one feature common to all those, compounds found in the acid soluble pool. They, have molecular weights ranging from 18 to, around 800 daltons (Da) approximately., Micromolecules have molecular weight less than, 1000 Da., SOHSS-AREEKODE, , SOHSS-Areekode, , b)Acid insoluble pool, The acid insoluble fraction,, has only four types of organic compounds i.e.,, proteins, nucleic acids, polysaccharides and, lipids. But the molecular weights of lipids do not, exceed 800 Da, come under acid insoluble, fraction. Because Cell membrane and other, membranes are broken into pieces during the, experiment , and form vesicles which are not, water soluble. Therefore, these membrane, fragments in the form of vesicles get separated, along with the acid insoluble pool and hence in, the macromolecular fraction. Therefore lipids are, not strictly macromolecule., The acid insoluble fraction has molecular, weight greater than 10000 Da., Analysis of inorganic elements and compounds, in the living tissue, All the carbon compounds that we, get from living tissues can be called, ‘biomolecules’. However, living organisms have, also got inorganic elements and compounds in, them. A slightly different but destructive, experiment has to be done. One weighs a small, amount of a living tissue (say a leaf or liver and, this is called wet weight) and dry it. All the water,, evaporates. The remaining material gives dry, weight. Now if the tissue is fully burnt, all the, carbon compounds are oxidised to gaseous form, (CO2, water vapour) and are removed. What is, remaining is called ‘ash’. This ash contains, inorganic elements (like calcium, magnesium, etc). Inorganic compounds like sulphate,, phosphate, etc., are also seen in the acidsoluble fraction., , 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 organism.,
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Page 2 : NAVAS CHEEMADAN, , SOHSS-Areekode, , 1. AMINO ACIDS, Amino acids are building blocks of, proteins. Amino acids are organic compounds, containing an amino group an acidic group as, substituents on the same carbon i.e., the α, carbon. Hence, they are called α-amino acids., They are substituted methanes. There are four, substituent groups occupying the four valency, positions. These are hydrogen, carboxyl group,, amino group and a variable group designated, as R group., , Primary and secondary metabolites, Metabolites are organic compounds, constantly utilzed in various metaolic activities, in the cells. There are two types of metabolites, Primary metabolites: It is essential to the, growth of the cell. They are produced, continuously during the growth phase and are, involved in primary metabolic processes such, as respiration and photosynthesis, Eg:, proteins,, nucleic, acids,, and, polysaccharides, Secondary metabolites : They are the, compounds which are derived by pathways, from primary metabolic routs, and are not, essential to sustain the life of cells. These, compounds do not have a continuous, production Secondary metabolites are the end, products of primary metabolites such as, alkaloids, toxins, steroids, essential oils, lectins,, drugs etc, , Based on the nature of R group there, are many amino acids. However, those which, occur in proteins are only of twenty types., , Classification of amino acids, a)Based on number of amino and carboxyl, groups, amino acids are classified into, a)acidic amino acids, Eg: Glutamic acid, Aspartic acid, , b)Basic amino acids, , Eg: Lysine, c)Neutral aminoacids: Eg: Valine, , There are aromatic amino acids, Eg: tyrosine, phenylalanine, tryptophan, , SOHSS-AREEKODE, ,
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Page 3 : NAVAS CHEEMADAN, , , , Sulphur containing amino acid, Eg:Cyteine, , b)Based on the need to the human body ,, Amino acids are also classified into, a)Essential amino acids, b)Non essential amino acids, a)Essential amino acids, The amino acids that cannot be, synthesized in our body and it should be, provided through food is called essential amino, acids, b)Non essential amino acids, The amino acids that can be synthesized, in our body and no need to be supplied, through food is called non essential amino, acids, ZWITTER ION, A particular property of amino acids, is the ionizable nature of –NH2 and –COOH, groups. Hence in solutions of different pHs,, the structure of amino acids changes. At a, particular pH (Isoelctric point) of solution,, amino acids occur as a dipolar ions with +ve, and –ve charge in the same molecule. They are, called Zwitter ions, , 2. PROTEINS, Proteins are polypeptides formed of, number of amino acids linked together by, means of Peptide bond. Peptide bond is, formed 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 (the, process is called dehydration) Proteins are, formed of number of different amino acids and, hence proteins are heteropolymers. Based on, structure proteins can be classified into, a)Primary structure of proteins, Here the amino acids are arranged in a, line .If a protein is imagined as a line, the left end, represented by the first amino acid and the right, SOHSS-AREEKODE, , SOHSS-Areekode, , end represented by the last amino acid. The first, amino acid is also called as N-terminal amino, acid. The last amino acid is called the C-terminal, amino acid. The primary structure of protein, gives the positional information of amino acids in, a protein., , b)Secondary structure of protein, If the polypeptide is coiled to form of a, helix (similar to a revolving staircase) the, structure is called secondary structure of, protein. In proteins, only right handed helices, are observed., c)Tertiary structure of protein, If protein chain is also folded upon itself, like a hollow woolen ball, giving rise to the, tertiary structure. 3-dimensional view of a, protein., Tertiary, structure, is, absolutely, necessary for the many biological, activities of proteins., d)Quaternary structure, If proteins are formed of more than one, polypeptide chain or subunits The manner in, which these individual folded polypeptides or, subunits are arranged with respect to each, other (e.g. linear string of spheres, spheres, arranged one upon each other in the form of a, cube or plate etc.) is the architecture of a, protein otherwise called the quaternary, structure of a protein., Eg: adult Haemoglobin consist of 4 subunits., It consist of 2α and 2β chain., , Functions of proteins, 1. some proteins acts as intercellular ground, substance, eg: collagen, 2. Some of the hormones are proteins,
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Page 4 : NAVAS CHEEMADAN, , 3. Some proteins helps in the transport of, substance, eg: GLUT- 4 (it helps in the transport of glucose, into the cell), 4. Some proteins fight against infectious agents, Eg: antibodies, 5. Some proteins helps in blood coagulation, Eg:Fibrinogen, 6. Most of the proteins are enzymes, Eg:Trypsin, 7. Proteins acts as a receptor in the the sensory, receptions like taste, smell, hormones etc., Collagen is the most abundant protein in, animal world, Ribulose bisphosphate CarboxylaseOxygenase (RuBisCO) is the most, abundant protein in the whole of the, biosphere, , SOHSS-Areekode, , The R group could be a methyl (–CH3), or, ethyl (–C2H5) or higher number of –CH2 groups, (1 carbon to 19 carbons)., For example, (1)palmitic acid : It has 16 carbons including, carboxyl carbon., , (2)Arachidonic acid : It has 20 carbon atoms, including the carboxyl carbon., Fatty acids could be, i), saturated-it is without double bond, ii), unsaturated-It is with one or more, C=C double bonds)., Another simple lipid is glycerol which is, trihydroxy propane, , Many lipids have both glycerol and fatty, acids. Here the fatty acids are found esterified, with glycerol. They can be, i)monoglycerides= 1 Fatty acids+ 1 Glycerol, ii)diglycerides= 2 fatty acids+ 1glycerol, iii) triglecerides=3 fatty acids+1 glcyerol, , 3. LIPIDS, Lipids are water Insoluble, Contains, a)fatty acids., A fatty acid has a carboxyl group attached, to an R group., , SOHSS-AREEKODE, , , , , , These are also called fats and oils based on, melting point. Oils have lower melting point, (e.g., gingely oil) and hence remain as oil in, winters.Fats have high melting point and, occur in solid form in room temperature., Some lipids have phosphorous and a, phosphorylated organic compound in them., These are phospholipids. They are found in, cell membrane.,
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Page 5 : NAVAS CHEEMADAN, , SOHSS-Areekode, , Eg: Lecithin, , , , , , 4. Polysaccharide, Polysaccharides are long chains of, sugars. They are threads containing different, monosaccharides, as, building, blocks., , , , , , , For example,, 1)cellulose is a polymeric polysaccharide, consisting of only one type of monosaccharide, i.e., glucose. Cellulose is a homopolymer. Plant, cell walls are made of cellulose, 2)Starch is a variant of this but present as a store, house of energy in plant tissues. It is also a, homopolymer of glucose., 3.Glycogen : Animals have another variant called, glycogen. It is also a homopolymer of glucose., 4.Inulin is a polymer of fructose., In a polysaccharide chain (say glycogen),, the right end is called the reducing end, and the left end is called the non-reducing, end., Starch forms helical secondary structures. starch, can hold I2 molecules in the helical portion. The, starch-I2 is blue in colour. Cellulose does not, contain complex helices and hence cannot hold, I2., 6)Exoskeletons of arthropods have a complex, polysaccharide called chitin. It is a homopolymer, Amino sugars : Glucosamine, N-acetyl, galactosamine, , SOHSS-AREEKODE, , , , , , , , , , 5. Nucleic acids, Nucleic acids are macro molecule and found, in the acid insoluble part .Nucleic acids act as, the genetic material in all organisms. Nucleic, acids are of two types DNA and RNA, DNA (Deoxy ribonucleic acid ), DNA is formed of two polynucleotides. Each, poly nucleotides are formed of number of, nucleotides., A Single nucleotide is formed of nucleoside, and phosphate . Adenylic acid, thymidylic, acid, guanylic acid, uridylic acid and cytidylic, acid are nucleotides, A nucleoside formed of sugar and nitrogen, base, Adenosine, guanosine, thymidine,, uridine and cytidine are nucleosides., Sugar in DNA is deoxyribose and sugar in RNA, is ribose, Nitrogen bases are heterocyclic compounds.It, is of two types, purines (Double rings ) and, Pyramidine (Single ring)., Purines include adenine, guanine,, Pyramidine include uracil, cytosine and, thymine, Nitrogen bases in DNA are Adenine, guanine,, thymine, Cytosine, Nitrogen bases in RNA is Adenine, guanine,, uracil ,Cytosine, There are two hydrogen bonds between A, and T and three hydrogen bonds between G, and C., At each step of ascent, the strand turns 36°., One full turn of the helical strand would, involve ten steps or ten base pairs.The pitch, would be 34Å. The rise per base pair would be, 3.4Å. This form of DNA with the above, mentioned salient features is called B-DNA., ,
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Page 6 : NAVAS CHEEMADAN, , SOHSS-Areekode, , , , Turnover, One of the greatest discoveries, ever made was the observation that all these, biomolecules, have, a, turn, over., Biomoleculues are constantly being changed, into some other biomolecules and also made, from some other biomolecules. This is called, turn over. This breaking and making is, through chemical reactions constantly, occurring in living organisms. Together all, these chemical reactions are called, metabolism., Majority of these metabolic reactions are, always linked to some other reactions. This, series of linked reactions is called metabolic, pathways. This metabolic pathways are, similar to automobile traffic in a city., Another feature of these metabolic reactions, is that every chemical reaction is a catalysed, reactions and it is catalysed by enzymes. So a, multistep chemical reactions, when each of, the step is catalysed by the same enzyme, complex or different enzyme is called a, metabolic pathway., Eg: 1. In Glycolysis, glucose becomes Pyruvic, acid through ten different enzymes catalysed, metabolic reactions. But under normal, aerobic condtions pyruvic acid is formed., Eg :2 .In yeast, during fermentation, the same, pathway leads to the production of ethanol., Eg: 3. In our skeletal muscle, under anaerobic, condtions, lactic acid is formed, Metabolism, SOHSS-AREEKODE, , The chemical reactions taking place in a, living organism is called metabolism., Metabolic pathways include 2 processes., a)Catabolism : It is the breakdown process., This process lead to the release of energy, Eg: When glucose is degraded to lactic acid in, our skeletal muscle , energy is liberated, which stored in the form of chemical bonds., When needed this bond energy is utilized, b)Anabolism :It is a synthetic phase. It, requires energy, The energy currency in living systems is the, bond energy in a chemical called ATP, (Adenosine triphosphate ), , The living state, The system at equilibrium cannot, perform a work. As living organisms work, continuously, they cannot afford to reach, equilibrium. Hence the living state is a non, equilibrium steady state to be able to perform, a work., 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., The blood concentration of glucose in, a normal healthy individual is, 4.2 mmol/L–6.1 mmol/L,, , 6. Enzymes, Enzymes are biological catalyst, capable of promoting a biochemical reactions, within a living system. Almost all enzymes are, proteins. But some nucleic acids behave like, enzymes are called ribozymes., Substrate : Substance upon which the enzyme, act., Active site : it is the substrate binding site of an, enzyme, End product : the substance obtained at the end, of enzymatic reactions, Enzymes are damaged at high temperature, (Above 40 c), Some enzymes isolated from organism who, normally, live, under, extreme, high, temperature (like hot vents ) are stable and,
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Page 7 : NAVAS CHEEMADAN, , , , retain their catalytic power even at high, temperature (80-90 c)., Thermal stability is thus an important quality, of such enzymes isolated from thermophilic, organisms ., , Nature of Enzyme action, Each enzyme (E) has a substrate (S), binding site in its molecule so that a highly, reactive enzyme-substrate complex (ES) is, produced. This complex is short-lived and, dissociates into its product(s) P., The catalytic cycle of an enzyme, action can be described in the following, steps:, 1. First, the substrate binds to the active site of, the enzyme, fitting into the active site., 2. The binding of the substrate induces the, enzyme to alter its shape, fitting more tightly, around the substrate., 3. The active site of the enzyme, now in close, proximity of the substrate breaks the, chemical bonds of the substrate and the new, enzyme- product complex is formed., 4. 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, , Factors affecting enzyme activity, The activity of an enzyme can be affected, by a change in the conditions which can alter, the tertiary structure of the protein. These, include temperature, pH, change in substrate, concentration or binding of specific chemicals, that regulate its activity, a)Temperature and pH, , SOHSS-AREEKODE, , SOHSS-Areekode, , Enzymes generally function in a, narrow range of temperature and pH. Each, enzyme shows its highest activity at a, particular temperature and pH called the, optimum temperature and optimum pH., Activity declines both below and above the, optimum value. Low temperature preserves, the enzyme in a temporarily inactive state, whereas, high, temperature, destroys, enzymatic activity because proteins are, denatured by heat., b) Concentration of Substrate, , With the increase in, substrate, concentration, the velocity of the enzymatic, reaction rises at first. The reaction ultimately, reaches a maximum velocity (Vmax) which is not, exceeded by any further rise in concentration of, the substrate. This is because the enzyme, molecules are fewer than the substrate, molecules and after saturation of these, molecules, there are no free enzyme molecules, to bind with the additional substrate molecules, , c) Enzyme Inhibition, The substance that shutoff the enzyme, activities are called inhibitors and the process is, called enzyme inhibition. When the inhibitor, closely resembles the substrate in its molecular, structure and inhibits the activity of the enzyme,, it is known as competitive inhibitor. Due to its, close structural similarity with the substrate, the, inhibitor competes with the substrate for the, substrate binding site of the enzyme (Active site)., Consequently, the substrate cannot bind and as a, result, the enzyme action declines,, e.g., inhibition of succinic dehydrogenase by, malonate which closely resembles the, substrate succinate in structure., Such competitive inhibitors are often used, in the control of bacterial pathogens.,
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Page 8 : NAVAS CHEEMADAN, , 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 type of reactions they, catalyse. Enzymes are divided into 6 classes each, with 4-13 subclasses and named accordingly by a, four-digit number., 1.Oxidoreductases/dehydrogenases:, Enzymes, which catalyse oxidoreduction between two, substrates S and S’ e.g.,, S reduced + S’ oxidised → S oxidised + S’ reduced., 2.Transferases: Enzymes catalysing a transfer of a, group, G (other than hydrogen) between a pair of, substrate S and S’ e.g.,, S - G + S’ → S + S’ - G, 3.Hydrolases: Enzymes catalysing hydrolysis of, ester, ether, peptide, glycosidic, C-C, C-halide or, P-N bonds., , SOHSS-Areekode, , transient, usually occurring during the course of, catalysis., The essential chemical components of many, coenzymes are vitamins, e.g., coenzyme, nicotinamide adenine dinucleotide (NAD) and, NADP contain the vitamin niacin., c)Metal ions :A number of enzymes require metal, ions for their activity which form coordination, bonds with side chains at the active site and at, the same time form one or more cordination, bonds with the substrate,, e.g., zinc is a cofactor for the proteolytic enzyme, carboxypeptidase., Catalytic activity is lost when the co-factor, is removed from the enzyme, , 4.Lyases: Enzymes that catalyse removal of, groups from substrates by mechanisms other, than hydrolysis leaving double bonds., , 5.Isomerases: Includes all enzymes catalysing, inter-conversion of optical, geometric or, positional isomers., 6.Ligases: Enzymes catalysing the linking together, of 2 compounds, e.g., enzymes which catalyse, joining of C-O, C-S, C-N, P-O etc. bonds., , Co-factors, The protein art of an enzyme is called, apoenzyme. The non protein part of en enzyme is, called cofactor.Three kinds of cofactors may be, identified: prosthetic groups, co-enzymes and, metal ions., a)Prosthetic groups:, they are organic, compounds and are distinguished from other, cofactors in that they are tightly bound to the, apoenzyme., Example: in peroxidase and catalase, which, catalyze 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., b)Co-enzymes : they are also organic compounds, but their association with the apoenzyme is only, SOHSS-AREEKODE, ,
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Page 9 : NAVAS CHEEMADAN, , SOHSS-Areekode, , Previous years question, 1. Match the following, , (HSE-July-2019)(3), , 2. ........... is the most abundant protein in the animal, world., (HSE March 2019)(1), 3. Observe the diagram A and B given below, , (iv) The protein part of the enzyme, 5. Observe the graph given below, (HSE-Aug-2018)(3), , a) Identify the graph., b) Mention the role of Enzyme in this, process., 6. The molecular structure of 2 amino acids are, given below Name them.(HSE-March-2018)(2), , 7. a)Complete the diagrammatic representation, showing the nature of enzyme action :, (HSE-March-2018)(3), a)What is A and B’, b)Mention the other two levels of protein, structure ?, (HSE March 2019)(2), 4. General formula of amino acid is given below, (HSE-Model-2019)(3), , (a) Prepare the amino acide serine using this, formula, (b) Proteins carry out many functionsin living, organisms, Iist any four., (c) Give one word, (i) The nucleic acid that behave like, enzymes, (ii) The organic compound tightly, bound to the apoenzyme., (iii) The, non-protein, organic, compound that are not tightly, bound to the apoenzyme, SOHSS-AREEKODE, , b) List out any two factors affecting enzyme, activity., c)Based on the reaction formulae given, below, identify the classes of the enzymes., , 8. a) Effect of change in concentration of, substrate on enzyme activity is graphically, represented' After reaching a maximum, velocity (Vmax)" the reaction is not exceeded, by any further rise in concentration of, substrate' Explain", b) Mention any 2 other factors that affect, enzyme activity ?, (HSE-Model-2018)(3), ,
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Page 10 : NAVAS CHEEMADAN, , SOHSS-Areekode, , 9. Fill in the blanks suitably (HSE-Model-2018)(2), In a proteins aminoacids are linked by, ….(a)…In, a, polysacharides, individual, monosacharides are linked by…….(b)….., 10. Identify the wrong statement from the, following and correct it, (HSE-July-2017)(1), a)Lipds are not strictly macromolecule, b)Cellulose is not a polysaccharide, 11. Examples of 2 enzymatic reactions A and B, are given. Identify the class of enzyme in A, , (HSE-July-2017)(2), , and B, , A) S reduced + S’ oxidised → S oxidised + S’ reduced., , (S,S’- Substrate ), B) S - G + S’ → S + S’ – G, (S,S’- substrate,G-Group), , OR, 12. “ Proteins is a heteropolymer not a, homopolymer “ . Substantiate the statement, ?, (HSE-July-2017)(2), 13. Identify the given biomolecule that comes, under fat, (HSE-sept-2016)(1), , SOHSS-AREEKODE, , 14. a)Name the biomacromolecule (Polymer) in, which peptide bond is present ?, b)Name the bond present between, phosphate and hydroxy group of sugar in, nucleic acid ?, , (HSE-sept-2016)(2), , 15. Metabolites are organic compunds constantly, utilzed in various metaolic activities in the, cells (HSE-March-2016)(2), a)What are the two types of metabolites in, the cells?, , b)Give an example for each type of, metabolites?, 16. Enzymes are biocatalyst which regulate, various biochemical reaction, Illustrate the following reaction, (HSE-March-2016)(2), , 17. Compelete, , the following sequence, with approprite words, (HSE September-2015)(1), Amino acids:………(a)…….bond:protein, ………(b)………: glycosidic bond :, polysacharide, 18. Based on the graph given below,, explain the effect of concentration of, substrate on enzyme activity., (HSE September-2015)(2), ,
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Page 11 : NAVAS CHEEMADAN, , SOHSS-Areekode, , c.Identify the type of protein structure, of a and b, (HSE August-2014)(3), , 19. Identify the protein structures, (a) and, , (B) from the following figure, (HSE March-2015)(1), , 20. Analyze the graph showing the activity, , of an enzyme, influenced by, temperature, (HSE march-2015)(2), , a)What is meant by optimum, temperature?, b)why does enzyme activity declines at, too low and at too high temperature?, 5. a. Why are proteins heteropolymers?, b.Identify the proteins from the given, list of iomacromolecule and write its, functions, (Cellulose,starch,antibody, inulin), SOHSS-AREEKODE, , 6. Symbolic presntation of a functional, enzyme is given below, (HSE August-2014)(3), , a.Write one difference between, cofactor and apoenzyme?, b.name the different types of cofactor, c.what is the cofactor for the enzyme ,, carboxypeptidase, 7. Name the chemical bond formed, between the following, (HSE March-2014)(1), a. Amino acids in a protein moleucle, b. Sugar and phosphate in a nucleic, acid, 8. Distinguish between cofactor and, coenzyme with an example for each?, (HSE March-2014)(2), 9. Oserve the graph and answer the, following (HSE-SEPTEMBER-2013)(3), ,
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Page 12 : NAVAS CHEEMADAN, , a.Find out the role of enzyme?, b.Mention any two factors that, influence the activity of an enzyme and, state their influences?, 10., , (HSE MARCH-2013)(1.5), a. Identify this compound?, b. Name the bond produced when, another compound of the same, category combine with this?, c. If a number of such molecule, bonded together , what will e the, resultant molecule ?, 11.Oserve the graph shoing the activity of, an enzyme influenced y pH, (HSE march-2013)(2), , SOHSS-AREEKODE, , SOHSS-Areekode, , a. Name the possible enzyme involved, in this reaction?, b. Where is its site of action, c. Mention any other factor which, affects this enzyme, d. Name another, similar enzyme, acting on the same sustrate, 12.Fill in the blanks, (HSE September-2012)(1), Carbohydrate : sugar, Proteins:………….., 13.Analyse the graph showing the activity, of salivary amylase, (HSE September-2012)(1), , a.Which, is, the, optimum, temperature for salivary amylase, from the graph?, b.Why the activity declines below, the optimum value ?, 14.Non protein constituent called cofactor, are bound to the enzyme to make the, enzyme catalytically activity, (HSE March-2011)(3), a.Name the protein portion of the, enzyme, b.What happens to the catalytic, activity when the cofactor is removed, from the enzyme?, ,
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