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CONTENTS, Chemistry, , Classification, Mechanism, , of Enzyme Action, Enzyme Kinetics, Inhibition, Activation, Specificity
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CHEMISTRY
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Introduction, , , Enzymes are biological catalysts that speed, up the rate of the biochemical reaction., , , , Most enzymes are three dimensional globular, proteins (tertiary and quaternary structure)., , , , Some special RNA species also act as, enzymes and are called Ribozymes e.g., hammerhead ribozyme., , Hammerhead enzyme
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STRUCTURE OF ENZYMES, , , The active site of an enzyme is the region that binds, substrates, co-factors and prosthetic groups and contains, residue that helps to hold the substrate., , , , Active sites generally occupy less than 5% of the total surface, area of enzyme., , , , Active site has a specific shape due to tertiary structure of, protein., , , , A change in the shape of protein affects the shape of active, site and function of the enzyme.
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ACTIVE SITE, o, , Active site can be further divided into:, Active Site, , Binding Site, , Catalytic Site, , It chooses the substrate, , It performs the catalytic, , and binds it to active site., , action of enzyme.
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CO-FACTORS, o, , Co-factor is the non protein molecule which carries out, chemical reactions that can not be performed by standard 20, amino acids., , o, , Co-factors are of two types:, Organic co-factors, Inorganic cofactors
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INORGANIC CO-FACTORS, These are the inorganic molecules required for the proper, activity of enzymes., Examples:, ++, Enzyme carbonic anhydrase requires Zn for it‟s activity., Hexokinase has co-factor Mg, , o, , , , , ++, , ORGANIC CO-FACTORS, o, , , , These are the organic molecules required for the proper, activity of enzymes., Example:, Glycogen phosphorylase requires the small organic, molecule pyridoxal phosphate.
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TYPES OF ORGANIC CO-FACTORS, Prosthetic Group, o, , A prosthetic group is a, tightly bound organic cofactor e.g. Flavins, heme, groups and biotin., , Coenzyme, o, , A coenzyme is loosely, +, bound organic co-factor., E.g. NAD +
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Types of co-factors, , Continued…, , , , An enzyme with it‟s co-factor removed is designated as, apoenzyme., , , , The complete complex of a protein with all necessary small, organic molecules, metal ions and other components is, termed as holoenzyme of holoprotein.
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SUBSTRATE, , , The reactant in biochemical reaction is termed as substrate., , , , When a substrate binds to an enzyme it forms an enzymesubstrate complex., , Substrate, , Joins, , Enzyme
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SITES OF ENZYME SYNTHESIS, o, , Enzymes are synthesized by ribosomes which are attached to, the rough endoplasmic reticulum., , o, , Information for the synthesis of enzyme is carried by DNA., , o, , Amino acids are bonded together to form specific enzyme, according to the DNA‟s codes.
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INTRACELLULAR AND, EXTRACELLULAR ENZYMES, o, , o, , , , , o, , , , Intracellular enzymes are synthesized and retained in the cell, for the use of cell itself., They are found in the cytoplasm, nucleus, mitochondria and, chloroplast., Example :, Oxydoreductase catalyses biological oxidation., Enzymes involved in reduction in the mitochondria., Extracellular enzymes are synthesized in the cell but, secreted from the cell to work externally., Example :, Digestive enzyme produced by the pancreas, are not used, by the cells in the pancreas but are transported to the, duodenum.
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CHARACTERISTICS, , , , , , , , , , , , Enzymes speed up the reaction by lowering the activation, energy of the reaction., Their presence does not effect the nature and properties of, end product., They are highly specific in their action that is each enzyme, can catalyze one kind of substrate., Small amount of enzymes can accelerate chemical reactions., Enzymes are sensitive to change in pH, temperature and, substrate concentration., Turnover number is defined as the number of substrate, molecules transformed per minute by one enzyme molecule., , Catalase turnover number = 6 x106/min
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NOMENCLATURE OF ENZYMES, o, , o, , o, , o, , An enzyme is named according to the name of the substrate it, catalyses., Some enzymes were named before a systematic way of, naming enzyme was formed., Example: pepsin, trypsin and rennin, By adding suffix -ase at the end of the name of the, substrate, enzymes are named., Enzyme for catalyzing the hydrolysis is termed as hydrolase., Example :, , maltose + water, , maltase, , glucose + glucose
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CLASSIFICATION
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CLASSIFICATION OF ENZYMES, , , A systematic classification of enzymes has been developed by, International Enzyme Commission., , , , This classification is based on the type of reactions catalyzed, by enzymes., , , , There are six major classes., , , , Each class is further divided into sub classes, sub sub-classes, and so on, to describe the huge number of different enzymecatalyzed reactions.
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MECHANISM OF ENZYME, ACTION
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MECHANISM OF ENZYME ACTION, , , The catalytic efficiency of enzymes is explained by two, perspectives:, , Thermodynamic, changes, , Processes at the, active site
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THERMODYNAMIC CHANGES, , , All chemical reactions have energy barriers between reactants, and products., , , , The difference in transitional state and substrate is called, activational barrier.
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THERMODYNAMIC CHANGES, , , , , , , , , , , , Only a few substances cross the activation barrier and change, into products., That is why rate of uncatalyzed reactions is much slow., Enzymes provide an alternate pathway for conversion of, substrate into products., Enzymes accelerate reaction rates by forming transitional, state having low activational energy., Hence, the reaction rate is increased many folds in the, presence of enzymes., The total energy of the system remains the same and, equilibrium state is not disturbed.
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PROCESSES AT THE ACTIVE SITE, Covalent, catalysis, Acid base, catalysis, , Catalysis, by strain, Catalysis, by, proximity
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COVALENT CATALYSIS, o, , Enzymes form covalent linkages with substrate forming, transient enzyme-substrate complex with very low activation, energy., , o, , Enzyme is released unaltered after completion of reaction.
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ACID-BASE CATALYSIS, , , Mostly undertaken by oxido- reductases enzyme., , , , Mostly at the active site, histdine is present which act as both, proton donor and proton acceptor.
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CATALYSIS BY PROXIMITY, , , In this catalysis molecules must come in bond forming, distance., , , , When enzyme binds:, A region of high substrate concentration is produced at active, site., This will orient substrate molecules especially in a position, ideal for them., , , ,
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CATALYSIS BY BOND STRAIN, , , , , , , , Mostly undertaken by lyases., The enzyme-substrate binding causes reorientation of the, structure of site due to in a strain condition., Thus transitional state is required and here bond is unstable, and eventually broken., In this way bond between substrate is broken and converted, into products.
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LOCK AND KEY MODEL, , , , , , Proposed by EMIL FISCHER in 1894., Lock and key hypothesis assumes the active site of an, enzymes are rigid in its shape., There is no change in the active site before and after a, chemical reaction.
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INDUCED FIT MODEL, , , , , More recent studies have revealed that the process is much, more likely to involve an induced fit model(proposed by, DANIAL KOSH LAND in 1958)., According to this exposure of an enzyme to substrate cause a, change in enzyme, which causes the active site to change it‟s, shape to allow enzyme and substrate to bind.
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INDUCED FIT MODEL, , 32
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ENZYMES KINETICS
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INTRODUCTION, “It is a branch of biochemistry in which we study the rate of, enzyme catalyzed reactions.”, , , Kinetic analysis reveals the number and order of the individual, steps by which enzymes transform substrate into products, , , , Studying an enzyme's kinetics in this way can reveal the, catalytic, mechanism, of, that, enzyme,, its, role, in metabolism, how its activity is controlled, and how a drug or, an agonist might inhibit the enzyme
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RATES OF REACTION AND THEIR, DEPENDENCE ON ACTIVATION ENERGY, Activation Energy (Ea):, “The least amount of energy needed for a chemical reaction to, take place.”, Enzyme (as a catalyst) acts on substrate in such a way that, they lower the activation energy by changing the route of the, reaction., The reduction of activation energy (Ea) increases the amount, of reactant molecules that achieve a sufficient level of, energy, so that they reach the activation energy and form the, product., Example:, Carbonic anhydrase catalyses the hydration of, 10⁶ CO₂, molecules per second which is 10⁷x faster than spontaneous, hydration.,
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ENZYMES LOWER THE ACTIVATION ENERGY OF A, , Energy levels of molecules, , REACTION, , Initial energy state, of substrates, , Activation energy, of enzyme catalysed, reaction, , Activation energy, of uncatalysed, reactions, , Final energy state of, products, , Progress of reaction (time)
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KINETICS OF ENZYMES CATALYSIS, , , Enzymes catalysis:, , “ It is an increase in the rate of reaction with the help of, enzyme(as catalyst).”, , , , , Catalysis by enzymes that proceed via unique reaction, mechanism, typically occurs when the transition state, intermediate forms a covalent bond with the enzyme(covalent, catalysis)., During the process of catalysis enzymes always emerge, unchanged at the completion of the reaction.
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FACTORS AFFECTING RATE OF, ENZYME CATALYZED REACTIONS, Temperature, Hydrogen ion concentration(pH), Substrate concentration,
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EFFECT OF TEMPERATURE, , , , , , , , , , Raising the temperature increases the rate of enzyme, catalyzed reaction by increasing kinetic energy of reacting, molecules., Enzymes work maximum over a particular temperature known, as optimum temperature. Enzymes for humans generally, exhibit stability temperature up to 35-45 ᵒC., The temperature coefficient is a factor Q₁₀ by which the rate of, biological processes increases for a 10 ᵒC increase in, temperature., For most biological processes Q₁₀ = 2., However some times heat energy can also increase kinetic, energy to a point that exceed the energy barrier which results, in denaturing of enzymes.
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Temperature, , 5- 40oC, Increase in Activity, , Rate of Reaction, , 40oC - denatures, , 0, <5oC - inactive, , 10, , 20, , 30, , 40, , 50, , 60
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EFFECT OF PH, , , , , , , Rate of almost all enzymes catalyzed reactions depends on, pH, Most enzymes exhibit optimal activity at pH value between 5, and 9, High or low pH value than optimum value will cause ionization, of enzyme which result in denaturation of enzyme
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PH AFFECTS THE FORMATION OF HYDROGEN BONDS, AND SULPHUR BRIDGES IN PROTEINS AND SO AFFECTS, SHAPE., trypsin, , arginase, , Rate of Reaction (M), , pepsin, , Acidic, , 2, , 4, , 6, , pH, , 8, , 10, , Basic
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MICHAELIS-MENTEN MODEL & EFFECTS OF, SUBSTRATE CONCENTRATION, , , Michaelis-Menten Model:, “According to this model the enzyme reversibly combines with, substrate to form an ES complex that subsequently yields, product, regenerating the free enzyme.”, , E + S, , , , , , , , k₁, k₋₁, , ES, , k₂, , where:, S is the substrate, E is the enzyme, ES-is the enzyme substrate complex, P is the product, K1,K-1 and K2 are rate constants, , E + P
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MICHAELIS-MENTEN EQUATION, , , Michaelis-Menten Equation:, , “It is an equation which describes how reaction velocity varies, with substrate concentration.”, , Vmax [S], Vo=, , Km+[S], , , , , , , Where, Vo is the initial reaction velocity., Vmax is the maximum velocity., Km is the Michaelis constant = (k₋₁+k₂)/k₁., [S] is the substrate concentration.
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ASSUMPTIONS FOR MICHAELIS-MENTEN, EQUATION, , , , , , , Following assumptions are made in deriving the MichaelisMenten equation:, Relative concentrations of E and S., Steady-State assumptions, Initial Velocity
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SUBSTRATE CONCENTRATION
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SUBSTRATE CONCENTRATION
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PHARMACEUTICAL IMPORTANCE, , , Enzymes are virtually involved in all physiological processes, which makes them the targets of choice for drugs that cure or, ameliorate human disease., , , , Applied enzyme kinetics represents the principal tool by which, scientist identify and characterize therapeutic agents that, selectively inhibit the rates of specific enzymes catalyzed, processes., , , , Enzymes kinetics thus play a critical role in drug discovery as, well as elaborating the mode of action of drugs.
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INHIBITION
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INHIBITION, o, , The prevention of an enzyme process as a result of interaction of, inhibitors with the enzyme., , , , INHIBITORS:, Any substance that can diminish the velocity of an, enzyme catalyzed reaction is called an inhibitor.
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TYPES OF INHIBITION, Inhibition, , Reversible, , Competitive, , Uncompetitive, , Irreversible, , Mixed, , Noncompetitive
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REVERSIBLE INHIBITION, o, , It is an inhibition of enzyme activity in which the inhibiting, molecular entity can associate and dissociate from the, protein„s binding site., , TYPES OF REVERSIBLE INHIBITION, o, , There are four types:, , , , Competitive inhibition., , , , Uncompetitive inhibition., , , , Mixed inhibition., , , , Non-competitive inhibition.
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COMPETITIVE INHIBITION, , , In this type of inhibition, the inhibitors compete with the, substrate for the active site. Formation of E.S complex is, reduced while a new E.I complex is formed.
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EXAMPLES OF COMPETITIVE INHIBITION, , , Statin Drug As Example Of Competitive Inhibition:, , , , Statin drugs such as lipitor compete with HMG-CoA(substrate), and inhibit the active site of HMG CoA-REDUCTASE (that, bring about the catalysis of cholesterol synthesis).
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UNCOMPETITIVE INHIBITION, , , In this type of inhibition, inhibitor does not compete with the, substrate for the active site of enzyme instead it binds to, another site known as allosteric site.
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MIXED INHIBITION, o, , o, , In this type of inhibition both E.I and E.S.I complexes are, formed., Both complexes are catalytically inactive., , NON COMPETITIVE INHIBITION, o, o, , It is a special case of inhibition., In this inhibitor has the same affinity for either enzyme E or, the E.S complex.
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IRREVERSIBLE INHIBITION, , , , , , This type of inhibition involves the covalent attachment of the inhibitor, to the enzyme., The catalytic activity of enzyme is completely lost., It can only be restored only by synthesizing molecules.
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EXAMPLES OF IRREVERSIBLE, INHIBITION, , , Aspirin which targets and covalently modifies a key enzyme, involved in inflammation is an irreversible inhibitor., , , , SUICIDE INHIBITION :, It is an unusual type of irreversible inhibition where the, enzyme converts the inhibitor into a reactive form in its active, site., ,
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ACTIVATION
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ACTIVATION, , , Activation is defined as the conversion of an inactive form of, an enzyme to active form which processes the metabolic, activity., , TYPES OF ACTIVATION, , , , Activation by co-factors., Conversion of an enzyme precursor.
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ACTIVATION BY CO FACTORS, , , Many enzymes are activated by co-factors., , Examples:, , , , , DNA polymerase is a holoenzyme that catalyzes the, polymerization of de -oxyribonucleotide into a DNA strand. It, uses Mg- ion for catalytic activity., Horse liver dehydrogenase uses Zn- ion for it‟s activation.
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CONVERSION OF AN ENZYME, PRECURSOR, , , Specific proteolysis is a common method of activating, enzymes and other proteins in biological system., Example:, , , , The generation of trypsin from trypsinogen leads to the, activation of other zymogens.
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ENZYME SPECIFICITY
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ENZYME SPECIFICITY, , , , , , , Enzymes are highly specific in nature, interacting with one or, few substrates and catalyzing only one type of chemical, reaction., Substrate specificity is due to complete fitting of active site, and substrate ., Example:, Oxydoreductase do not catalyze hydrolase reactions and, hydrolase do not catalyze reaction involving oxidation and, reduction.
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TYPES OF ENZYME SPECIFICITY, , , Enzymes show different degrees of specificity:, , , , Bond specificity., Group specificity., Absolute specificity., Optical or stereo-specificity., Dual specificity., , , , ,
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BOND SPECIFICITY, , , , , In this type, enzyme acts on substrates that are similar in, structure and contain the same type of bond., Example :, Amylase which acts on α-1-4 glycosidic ,bond, dextrin and glycogen, shows bond specificity., , in starch
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GROUP SPECIFICITY, , , , , In this type of specificity, the enzyme is specific not only to the, type of bond but also to the structure surrounding it., Example:, Pepsin is an endopeptidase enzyme, that hydrolyzes central, peptide bonds in which the amino group belongs to aromatic, amino acids e. g phenyl alanine, tyrosine and tryptophan.
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SUBSTRATE SPECIFICITY, , , , , , , In this type of specificity ,the enzymes acts only on one, substrate, Example :, Uricase ,which acts only on uric acid, shows substrate, specificity., , Maltase , which acts only on maltose, shows substrate, specificity.
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OPTICAL / STEREO-SPECIFICITY, , , , , , , In this type of specificity , the enzyme is not specific to, substrate but also to its optical configuration, Example:, D amino acid oxidase acts only on D amino acids., , L amino acid oxidase acts only on L amino acids.
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DUAL SPECIFICITY, , , , , , There are two types of dual specificity., The enzyme may act on one substrate by two different, reaction types., Example:, Isocitrate dehydrogenase enzyme acts on isocitrate (one, substrate) by oxidation followed by decarboxylation(two, different reaction types) .
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DUAL SPECIFICITY, , , The enzyme may act on two substrates by one reaction type, , •, , Example:, Xanthine oxidase enzyme acts on xanthine, and, hypoxanthine(two substrates) by oxidation (one reaction type)
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REFERENCES, Woodbury.: Biochemistry for the Pharmaceutical, Sciences, Lehninger.: Principles of biochemistry, Lippincott.: Biochemistry, Harper's Illustrated Biochemistry, Mushtaq Ahmed.: Essentials of Medical, Biochemistry, Pfeiffer, J.: Enzymes, the Physics and Chemistry of, Life, Martinek, R.: Practical Clinical Enzymology,
