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BIOC12Fall2012 Lecture Week 10 Notes

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University of Toronto Scarborough
Biological Sciences
Rongmin Zhao

1 BIOC12Fall2012 Lecture Week 10 Notes: Enzymes – classification and kinetics (Chapter 13) The general notion of enzyme o Biological catalysts  all catalyst properties can be applied o Notation of thermodynamics and kinetics aA  bB  cC  dD G  RT ln K eq o o the Keq refers to thermodynamics of reaction  tells you which way reaction is more favoured to go towards, products or reactants o delta G refers to the kinetics of the reaction  motion requires energy, so this dictates how fast a reaction occurs o A P v  k[A] o chemical reactions in life are catalyzed by enzymes o most but not all enzymes in life are proteins  some are RNA (ribozymes) Enzymes accelerate reaction but do not change EQ o o enzymes lower ΔG , the activation energy thereby accelerating the rate G / RT o the reaction rate is proportional to o so an enzyme does not change the thermodynamics of a reaction, but changes the kinetics  makes it faster o when delta G is decreased by a small number  big difference in rate of reaction Enzymes are names and classified by type of reaction they catalyze o each enzyme has a systematic name (International Union of Biochemistry and Molecular Biology) o it is the name of the substrates followed by a word ending in –ase specifying the type of reaction the enzyme catalyzes o example: lactate dehydrogenase o an enzyme sometimes has a common name for daily usage if systematic name is too long o each enzyme is assigned with a classification number which tells the detailed classification o example: Trypsin: EC o enzyme commission, class, subclass, sub-subclass, serial no. o if 2 enzymes are in the same sub class it does not neccesarily mean that they are structurally similar  they may enzymes from different species etc. Types of Enzymes 2 o 1 = oxireductases o 2 = transferases o 3 = hydrolases  digestive enzymes, can break larger proteins into smaller proteins o 4 = lyases o 5 = isomerases o 6 = ligases o relatice amounts of these enzymes o Hydrolases o catalyzes hydrolysis  transfeases with water serving as the acceptor of the group transferred o reaction is in one direction since EQ favours a great excess of product over substrate o example: o pyrophosphate (systematic name: diphosphate phosphohydrolase) is a high energy molecule so it is more stable broken down because it will be lower in E Lyases o catalyze lysis of substrate by generating a double bond o example: Some enzymes may need cofactors o cofactors are non protein components essential to the enzyme activity o NAD+/NADP+ are general H receptors o This kind of organic molecule cofactor is called coenzyme o Coenzyme can be permanently associated with the enzyme like a heme group in cytochrome c (called the prosthetic group) o Coenzyme must be regenerated by another reaction  NADH mst be oxidized to NAD+ o Groups of Cofactors 3 o o example of metal ions as cofactors: Fe2+, Fe3+, K+, Cu2+, etc. Vitamins – coenzyme precursors o o the vitamin is converted into a special form which aids in specific reactions as a coenzyme Chemical kinetics o the deifinition of elementary reactions o A  P or A+B  P+Q o Most real reactions can be decomposed to a series of elementary reactions o A  I1  I2  I3  P o First order reactions : only one molecule as reactant and rate is proportional to concentration of reactant o A  p and v = -d[A]/dt = d[P]/dt = k[A] o Second order reaction : 2 molecules act as reactant o A+B  P + Q - v= k[A][B] or o 2A  P - v=k[A] 2 First order reactions o A  p and v = -d[A]/dt = d[P]/dt = k[A] o t 1/2s a constant which is the half life of A o t 1/2 0.693/k o [At] = e-kt [A 0 Properties of second order reaction o 2A  P 1 t1/2 k[A0] o 4 o the half life depends on the initial concentration of A 1 1 o = +kt [At] [A 0 What happenes to an enzymatic reaction o the kinetics of enzyme reaction was first studied by Adrian Brown o 1894: the rate of sucrose fermentation by yeast is independent of the amount of sucrose o 1902: conversion of sucrose to glucose and fructose by invertase is independent of the amount of sucrose  invertase aids in the hydrolysis of sucrose o when sucrose concentration is much higher than the invertase concentration, enzyme is entirely converted to enzyme-substrate (ES) form and the reate of conversion is only dependent on the ES concentration o reaction is unlimited which means product formation is constant which means enzyme is saturated by substrate  why rate depends on ES concentration Michaelis-Menten Observation o in 1913, Michaelis and Menten noticed what Brown observed in only true when the amount of substrate is far more than the amount of the enzyme o they observed that when sucrose concentration was very low, the reaction rate becomes proportional to the concentration of substrate E + S ES o o assumption: enzyme binds to substrate and reaches EQ very quickly [E][S] k Ks  1 [ES] k1 o where Ks is the dissociation constant o v= d[P] =k [ES]=k [E T[S] dt 2 2Ks+[S] Steady state of enzymatic reaction o the equilibrium assumption is not often true (k2 is neglected) o instead of equilibrium, in 1925, Briggs and Haldane assumed that [ES] is in a steady state after the initial transient phase o 5 o so you have to have much less enzyme than reactant for this to work o therefore you have v=k [ES]= k2 1[ET][S] k2[ET][S] 2 k [S]+k +k = k-1k 2 1 -1 2 [S]+ k1 K - P + E + S k1 k 2 E o because k-1k 2 o the term k (which is equal to Ks) is termed as Michaelis ConstaMt K 1 vmaxS] o v0= This is the revised Michelis-Menten Equation [S]+K M o o the curve of the Michaelis- Menten equation is hyperbolic  as the substrate concentration increases so does the rate of the reaction but only to a certain extent because eventually there all enzyme will be saturated so increasing the substrate concentration will no longer have an effect The Significance of Michaelis Constant v max[S] Km  k2 k 1 v 0 [S] K o k1 M o the smaller the number for Km , the tighter the substrate binds to the enzyme (higher affinity)  samller Km means small Ks, which means less will dissociate, therefore tighter bond between E and S o however higher affinity of enzyme to substrate does not necessarily tell the efficiency of the enzymatic catalysis kcat/Km is a measure of the catalytic efficiency o catalytic constant (kcat) is defined as kcat = Vmax/[Et] which is the number of reaction processes per unit of time for each of the active sites
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