Enzymes

Chapter 6

Important Group of Proteins

• Catalytic power can incr rates of rxn > 1017

• Specific

• Often regulated to control catalysis

• Coupling biological pathway

Catalysis Happens…• Enzymes use many intermolecular

forces

– At enzyme active site

– From atoms making up R grps of aa’s

• Substrates brought together

– Optimal orientation

• Making/breaking bonds facilitated

– Transition state stabilization

– Allows high energy transition state

• Enzyme native conform’n crucial

Additional Chemical Components

• Prosthetic Groups– Cofactors (Table 6-1)

– Coenzymes (Table 6-2)

• Bound to apoenzyme (apoprotein)

Holoenzyme

Rxns Occur at Enzyme

Active Sites

• Physical clefts

• “Lined” w/ atoms that make up aa R grps

• Stabilize transition state S P

• Complex ES forms (reversible)

G Calc’d for Any Rxn S P

G = Diff in free energy between S, P

• REMEMBER: G = H _ T S

– What are these terms??

Energetics G = H _ T S

G:

– If negative

– If = 0

– If positive

G:

– Depends on free energy prod’s – free energy reactants

– Independent of path of rxn

• Catalysis doesn’t alter

– No info on rate of rxn

S* = Transition State = High Energy Intermediate• Must add energy for S S*

• Common rxn intermediate

• “Fleeting molecular moment”

• Can go to S or P

G*(SP) = Activation Energy

– Diff in energy S to S*

– Enzymes lower G*

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

• Note: E is always regenerated

G*(cat’d)

– Diff in energy S to ES*

– So rxn more energetically favorable in presence of catalyst

For S P at Equilibrium

• Keq = [P] / [S]G = G’o + RT ln [P] / [S],

andG = 0, soG’o = - RT ln [P] / [S]G’o = - RT ln Keq’

– So Keq directly related to G for rxn

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

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 6-6

– Relationship between k and G* is inverse and exponential

Summary

• Enzymes don’t change overall energy difference (S P), equilibrium (Keq)

• Enzymes do lower EA

• Enzymes do increase rate (k)

Source of Energy from within Enz to Facilitate Rxn S P

• Most impt: ES complex

• ES proven experimentally, theoretically

• Enzyme active site

– Aa’s directly participate (catalytic grps)

– Only small part of total volume

– Catalytic grps may be far apart in primary structure

•Folding impt!

Substr Binding to Enz Active Site• Multiple weak interactions

–What are these?

Binding energy (GB)•Stabilizes ES*

• Must have proper orientation between atoms

• Substrate, active site have complementary shapes

• Commonly crevice nonpolar

– If polar aa’s, often participate

– Water excluded unless participates in rxn

• So: microenvironment w/ aa funct’l grps that have partic prop’s 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)

– 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 act’n energy

• E/S “match” also confers specificity

Other Factors that Reduce

Act’n Energy• Besides multiple, weak, atom-atom

interactions

• Physical, thermodynamic factors influence energy, rate of catalyzed rxn

– Entropy reduction

•S held in proper orientation

•Random, productive collisions not nec

– Desolvation

•H-bonds between S and solvent decr’d

• Incr’s productive collisions

– Induced fit

•Enzyme conform’n changes when S binds

•Brings impt funct’l grps to proper sites

•Now has enhanced catalytic abilities

http://www.blobs.org/science/enzyme/imgs/active2.gif