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Six classes of enzymes. Factors affecting enzyme activity. Post-transcriptional modification/ Regulatory events pH Temperature Enzyme or Substrate concentration Cofactors. What do enzymes do?. A catalyst is a substance that accelerates a chemical reaction without itself

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factors affecting enzyme activity
Factors affecting enzyme activity
  • Post-transcriptional modification/ Regulatory events
  • pH
  • Temperature
  • Enzyme or Substrate concentration
  • Cofactors

What do enzymes do?

A catalyst is a substance

that accelerates a chemical

reaction without itself

undergoing any net change


dynamic equilibria
Dynamic Equilibria
  • Consider: A   B
  • The rate of the forward reaction (kf) is


  • The rate of the back reaction (kb) is 10-6sec-1
  • K = [B]/[A] or kf/kb = 100
  • At equilibrium, there is 100X B than A
  • Enzymes accelerate these rates
activation energy
Activation energy
  • The starting point for a reaction is called the ground state, which reflects the contribution to the free energy of the system by the reactant
  • Equilibrium between reactants (substrates; S) and products (P) reflects the difference in free energies of their ground states
  • In the previous example, free energy of P is lower than that of S, so the free energy is negative and equilibrium favors products (look at the y-axis)
  • Activation energy is the energy need to reach the transition state
the transition state is an energetic barrier
The transition state is an energetic barrier
  • A favorable equilibrium does not meant that a reaction occurs at a detectable rate
  • The rate is dependent on crossing the energy barrier for alignment of reacting groups, formation of transient intermediates, bond rearrangements, etc.
  • The molecules are raised to a higher energy level to overcome this level.
  • The peak of the “hill” is called the transition state
enzymes are catalysts
Enzymes are catalysts
  • Catalysts enhance reaction rates by lowering activation energies
  • Intermediates can

be observed

  • Do not affect

reaction equilibria


How do enzymes work?

Transition state vs. Ground State theory

Do enzymes accelerate catalysis by putting substrates

in close proximity?


As Pauling, among others, suggested is catalysis a

result of an enzyme having a higher affinity for the

transition state

Still to this day a topic of debate, but presently it seems to be

a little of both

the catalytic power of enzymes
The catalytic power of enzymes
  • The ability of enzymes to catalyze reactions lies in
    • 1. Chemical reactions of many types occur between substrates and enzyme function groups (amino acids, metal ions, cofactors). These reactions allow the rearrangement of covalent bonds during enzyme-mediated reactions
    • 2. Binding energy
binding energy is optimized for the transition state
Binding energy is optimized for the transition state
  • Some weak interactions are formed in the ES complex, but the full complement of interactions are only met in the transition state.
  • The transition state exists as a brief point in time
  • These interactions also provide specificity!


E + S E + (S)*

E + S ES (ES)*




= [E][S]*/[ES]* = [(kcat/Km)/knon]-1

Affinity for the Transition state


For Triosephosphate isomerase KTS = 10-12, and Km = 10-4

Thus, this enzyme binds the transition state eight orders of magnitude

more strongly than the substrate.


Recognition of transition state effects have led to

developments in analogs and catalytic antibodies


Components of catalytic mechanisms

General acid-base catalysis

Covalent catalysis

Metal Ion catalysis (nucleophile,


covalent catalysis
Covalent catalysis
  • A transient covalent bond is formed between enzyme and substrate
  • Covalent complexes undergo regeneration to give back free enzyme
  • Combo of

Acid-base and

Covalent 

metal ion catalysis
Metal Ion catalysis
  • Ionic interactions assist in orientation of substrate and stabilize charged transition states
  • Mediate oxidation-reduction reactions
  • Nearly 1/3 of all enzymes are metalloenzymes
examples of enzymatic reactions
Examples of enzymatic reactions
  • Chymotrypsin – covalent catalysis; general acid-base catalysis
  • Hexokinase – induced fit
  • Enolase – metal dependence
  • Lysozyme – an unproven mechanism

Hexokinase catalytic mechanism illustrates an additional important principle

  • Catalyzes the conversion of glucose and ATP to G6P and ADP; the hydroxyl group at C6 of glucose is similar in reactivity to water, how does this enzyme discriminate?

Hexokinase undergoes a conformational change upon substrate binding

  • Specific for glucose binding not water

Hexokinase a nice model for Koshland’s induced-fit mechanism

  • When glucose is not present, the enzyme is in an open, inactive form with catalytic amino acids out of position.
  • When glucose (not water), and ATP bind, the binding energy induces the conformational change to catalytically active form