Chapter 6

Mechanisms of Enzyme Action

• Activation 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 Catalysis

S Ts P

Enzymatic Catalysis

Transition (TS) State Intermediate

• Transition state = unstable high-energy intermediate

• Rate 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 TS

• Bonds are in the process of being formed and broken in TS

• Short lived (10–14 to 10-13 secs)

Intermediates• Intermediates 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 stable

Raising 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

•desolvation

Transition State Stabilization

Transition state analog

• Equilibrium between ES <-> TS, enzyme drives equilibrium towards TS

• Enzyme binds more tightly to TS than substrate

Mechanistic Strategies

Polar AA Residues in Active Sites

Common types of enzymatic mechanisms

• Substitutions rxns• Bond cleavage rxns• Redox rxns• Acid base catalysis• Covalent catalysis

Substitution Rxns

• Nucleophillic Substitution–

• Direct Substitution

C

O

XR

Y

C

O

XR

Y

C

O

YR+ X

CR1 R2

R3 YCX Y

R1 R2

R3X

CR1 R2

X R3

+ Y

transition state

Nucleophillic = e- rich Electrophillic = e- poor

Oxidation reduction (Redox) Rxns

• Loose e- = oxidation (LEO)• Gain e- = reduction (GER)• Central to energy production• If 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 cleavage• Carbanion 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 Rxns

Hydride ion

• Accelerates rxn by catalytic transfer of a proton• Involves AA residues that can accept a proton• Can remove proton from –OH, -NH, -CH, or –XH• Creates a strong nucleophillic reactant (i.e. X:-)

Acid-Base CatalysisX H : B X: H B

X H : B X: H B

C

O

N

O

H H : B

C

O

OH

N

HB

C

O

OH HN

: B

:

:

Acid-Base Catalysis

carbanion intermediate

Covalent Catalysis• 20% of all enzymes employ covalent

catalysisA-X + B + E <-> BX + E + A

• A 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-P

1) A-P-P-P(ATP) + E-OH <-> A-P-P (ADP) + E-O-PO4

-

2) E-O-PO4- + Protein-OH <-> E + Protein-O- PO4

-

The Serine ProteasesTrypsin, chymotrypsin, elastase, thrombin, subtilisin, plasmin, TPA

• All 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 pocket

Serine Proteases are structurally Similar

Chymotrpsin Trypsin Elastase

Substrate binding specificity