Sinh học - Chapter 6: Mechanisms of enzyme action

Chapter 6Mechanisms of Enzyme ActionActivation Energy (AE) – The energy require to reach transition state from ground state.AE barrier must be exceeded for rxn to proceed.Lower AE barrier, the more stable the transition state (TS)The higher [TS], the move likely the rxn will proceed.Enzymatic CatalysisS  Ts  P Enzymatic CatalysisTransition (TS) State IntermediateTransition state = unstable high-energy intermediateRate of rxn depends on the frequency at which reactants collide and form the TS Reactants must be in the correct orientation and collide with sufficient energy to form TSBonds are in the process of being formed and broken in TSShort lived (10–14 to 10-13 secs)IntermediatesIntermediates are stable.In rxns w/ intermediates, 2 TS’s are involved.The slowest step (rate determining) has the highest AE barrier. Formation of intermediate is the slowest step.Enzyme binding of substrates decrease activation energy by increasing the initial ground state (brings reactants into correct orientation, decrease entropy)Need to stabilize TS to lower activation energy barrier.ES complex must not be too stableRaising the energy of ES will increase the catalyzed rate This is accomplished by loss of entropy due to formation of ES and destabilization of ES by strain distortion desolvationTransition State StabilizationTransition state analogEquilibrium between ES TS, enzyme drives equilibrium towards TSEnzyme binds more tightly to TS than substrate Mechanistic Strategies Polar AA Residues in Active SitesCommon types of enzymatic mechanismsSubstitutions rxnsBond cleavage rxnsRedox rxnsAcid base catalysisCovalent catalysisSubstitution RxnsNucleophillic Substitution– Direct Substitutiontransition stateNucleophillic = e- rich Electrophillic = e- poorOxidation reduction (Redox) RxnsLoose e- = oxidation (LEO)Gain e- = reduction (GER)Central to energy productionIf something oxidized something must be reduced (reducing agent donates e- to oxidizing agent)Oxidations = removal of hydrogen or addition of oxygen or removal of e-In biological systems reducing agent is usually a co-factor (NADH of NADPH)Heterolytic vs homolytic cleavageCarbanion formation (retains both e-) R3-C-H  R3-C:- + H+Carbocation formation (lose both e-) R3-C-H  R3-C+ + H:-Free radical formation (lose single e-) R1-O-O-R2  R1-O* + *O-R2 Cleavage RxnsHydride ionAccelerates rxn by catalytic transfer of a protonInvolves AA residues that can accept a protonCan remove proton from –OH, -NH, -CH, or –XHCreates a strong nucleophillic reactant (i.e. X:-) Acid-Base Catalysis::Acid-Base Catalysiscarbanion intermediateCovalent Catalysis20% of all enzymes employ covalent catalysis A-X + B + E BX + E + AA group from a substrate binds covalently to enzyme (A-X + E A + X-E)The intermediate enzyme substrate complex (A-X) then donates the group (X) to a second substrate (B) (B + X-E B-X + E)Covalent CatalysisProtein KinasesATP + E + Protein ADP + E + Protein-PA-P-P-P(ATP) + E-OH A-P-P (ADP) + E-O-PO4-E-O-PO4- + Protein-OH E + Protein-O- PO4- The Serine ProteasesTrypsin, chymotrypsin, elastase, thrombin, subtilisin, plasmin, TPAAll involve a serine in catalysis - thus the name Ser is part of a "catalytic triad" of Ser, His, Asp (show over head)Serine proteases are homologous, but locations of the three crucial residues differ somewhat Substrate specificity determined by binding pocketSerine Proteases are structurally Similar Chymotrpsin Trypsin ElastaseSubstrate binding specificity