Enzymes Chapter 8

Important Group of Proteins Catalytic power can incr rates of rxn > 10 6 Specific Often regulated to control catalysis Coupling  biological pathway

Catalysis Happens… Enzymes use many intermolecular forces –At enzyme active site –From R grps of aa’s Substrates brought together Optimal orientation Making/breaking bonds facilitated –Transition state stabilization –Allows high energy transition state Enzyme native conformation crucial

Additional Chemical Components Prosthetic Groups –Cofactors (Table 8-1) –Coenzymes (Table 8-2) Bound to apoenzyme  holoenzyme

Table 8-1

Table 8-2

Rxns Occur at Enzyme Active Sites (8-1) Physical clefts “Lined” w/ aa funct’l grps Stabilize transition state S  P Complex ES forms (reversible)

Fig. 8-1

Energetics For any (cat’d) rxn involving S:  G =  H - T  S  G: –If negative –If = 0 –If positive  G: –Depends on free energy prod’s – free energy reactants –Independent on path of rxn (so catalysis doesn’t alter) –No info on rate of rxn

For S P at Equilibrium Keq = [P] / [S]  G =  G’ o + RT ln [P] / [S], and  G = 0, so  G’ o = - RT ln [P] / [S]  G’ o = - RT ln Keq ’ –So Keq directly related to  G for rxn (Table 8-4)

Table 8-4

 G’ o = diff in free energy between S, P Enzymes do NOT effect Keq ’,  G’ o Enzymes impt when energy must be added for rxn to proceed

S* = Transition State = High Energy Intermediate Must add energy for S S* Common rxn intermediate “Fleeting molecular moment” Can go to S or P (8-2)  G*(S  P) = Activation Energy –Diff in energy S to S* –Enzymes lower  G*

Fig. 8-2

ES* = Enzyme Substrate Complex Must add energy for E + S ES* BUT less energy So lower rxn pathway Can go to E + S or E + P (8-3) Note: E is always regenerated  G*(cat’d) –Diff in energy S to ES* –So rxn more energetically favorable in presence of catalyst

Fig. 8-3

Enzymes Effect Rxn Rate Use rate constant (k) to describe rate S P Velocity (V) of rxn dependent on [S], k –V = k [S] –First order rxn Can relate k to  G* –Eq’n 8-6 –Relationship between k and  G* is inverse and exponential

Table 8-5

Summary Enzymes don’t change overall energy difference, equilibrium Enzymes do lower EA Enzymes do increase k

Source of Energy from within Enzyme to Facilitate Rxn S P Most impt: ES complex Existence proven experimentally, theoretically Enzyme active site –Aa residues directly participate (catalytic grps) –Only small part of total volume –Catalytic grps may be far apart in primary structure Folding is important!

Fig. 8-4

Substrate Binding to Enzyme Active Site Multiple weak interactions –What are these? Must have proper orientation between atoms Substrate, active site have complementary shapes Commonly crevice is nonpolar –Polar residues at site commonly participate –Water excluded unless it participates So: microenvironment w/ aa funct’l grps that have particular properties essential for catalysis of rxn

Binding Specificity DNA evolution  protein w/ optimal aa sequence  optimal E/S interactions  lowering energy nec for rxn So, depends on precisely arranged atoms in active site

Two theories of E/S “match” Lock & key (Fisher, 1894) (8-4) –If precise match to S, why  S* or P? Complementarity to S* –Enz active site complementary to transition state –So weak interactions encourage S*, then stabilize it Best energetically when S* fits best into enz active site –Must expend energy for rxn to take place –BUT overall many weak interactions lower net activation energy E/S “match” also confers specificity

Fig. 8-5

Fig cont’d

Other Factors that Reduce Activation Energy Besides multiple weak atom-atom interactions Physical, thermodynamic factors influence energy, rate of catalyzed rxn –Entropy reduction (8-7) S held in proper orientation Don’t rely on random, productive collisions

Fig. 8-7

–Desolvation H-bonds between S and solvent decreased Incr’s productive collisions –Induced fit Enzyme conformation changes when S binds Brings impt funct’l grps to proper sites Now has enhanced catalytic abilities