Part Two: How Enzymes Work

• Enzyme catalyzed reactions take place within the active site.
• An active site provides a specific environment in which a given reaction can occur more rapidly.
• A substrate is the molecule that is bound to the active site and is acted upon by the enzyme.
• Simple enzymatic reactions can be written as E + S -> ES -> EP -> E + P. Here, E, S, and P represent the enzyme, substrate, and product and ES and EP are transient complexes of the enzyme.
• The ground state is the starting point for wither the forward or reverse reaction.
• The transition state is the point at which decay to substrate or product are equally likely.
• Biochemical standard free energy change, or delta G prime degree, is the standard free energy change at pH 7.
• Activation energy, delta G transition state, is the difference between the ground state energy level and the transition state energy level.
• Catalysts lower the activation energy and increase reaction rate.
• Diagram

  A) Reaction coordinate

  B) Free energy

  C) Substrates

  D) Transition state

  E) Products

  F) ES

  G) ES transition state

  H) EP

  I) Binding

  J) Catalysis

  
• Any enzyme that catalyzes the reaction S -> P also catalyzes P -> S.
• Enzymes accelerate the interconversion of S and P.
• Enzymes are not used up in the process.
• The equilibrium point is unaffected by enzymes
• A reaction intermediate is any species on the reaction pathway that has a finite chemical lifetime. For example, there are the ES and EP complexes.
• The rate limiting step is the step in a reaction with the highest activation energy that determines the overall rate of the reaction.
• Activation energies are barriers to chemical reactions.
• Enzymes have developed to lower activation energies selectively to increase rates for reactions needed for cell survival.
• Reaction equilibria are linked to the standard free energy change for the reaction, delta G prime degree.
• Reaction rates are linked to the activation energy, delta G transitiion state.
• The equilibrium constant, Keq, describes an equilibrium such as S and P.
• Under standard conditions Keq' = [P] / [S].
• From thermodynamics, delta G prime degree = -RT X lnK'eq
• The rate of any reaction is determined by the concentration of reactant(s) and the rate constant, k.
• For the unimolar reaction S -> P, a rate equation expresses the rate of reaction V= k X [S] where V is the velocity or the rate of the reaction and [S] is the concentration of the substrate.
• In first order reactions, the rate depends only on the concentration of S and k has units of reciprocal time, such as s^-1.
• In second order reactions, rate depends on the concentration of two different compounds or the reaction is between two molecules of the same compound. k has units of M^-1 X s^-1.
• In second order reactions, V = k [S1] X [S2].
• For transition state theory, k = (kt / h) X e^-delta G transition state/ RT where K is Boltzmann constant and h is Planck's constant.
• The relationship between the rate constant k and activation energy delta G transition state is inverse and exponential.
• Enzymes enhance rates in the ranges of 5 to 17 orders of magnitude.
• Binding energy, delta G_B, is the energy derived from noncovalent enzyme substrate interaction.
• Binding energy is mediated by hydrogen bonds, ionic interactions, and the hydrophobic effect.
• Binding energy is the major source of free energy used by enzymes to lower the activation energy.
• Covalent interactions between enzymes and substrate lower the activation energy.
• The lock and key hypothesis says that enzymes are structurally complementary to their substrates, which would make for a poor enzyme.
• The full complement of interactions between substrate and enzyme is formed only when the substrate reaches the transition state.
• The sum of unfavorable activation energy, delta G transition state, and the favorable binding energy, delta G_B, results in a lower net activation energy.
• Weak binding interactions between the enzyme and the substrate drive enzymatic catalysis.
• Optimized binding energy in the transition state is accomplished by positioning a substrate in the active site, removed from water.