Part Two

• Enzymatic catalysis


  Essential to living systems
• Under biologically relevant conditions, uncatalyzed reactions tend to be slow because most biological molecules are quite stable in neutral pH, mild temperature, aqueous environment inside cells
• Reactions needed to digest food, send nerve signals, or contract a muscle simply would not occur without enzymatic catalysis
• Distinguishing feature of an enzyme catalyzed reaction

  • It takes place within the confines of a pocket on the enzyme called the active site
  • It provides a specific environment, customized by evolution, in which a given reaction can occur more rapidly
• Substrate

  The molecule that is bound to the active site and acted upon by the enzyme
• The surface of the active site is lined with amino acid residues with substituent groups that bind to the substrate and catalyze its chemical transformation
• The active site often encloses a substrate, sequestering it completely from a solution
• Enzyme substrate complex

  • Central to the action of enzymes
  • Starting point for mathematical treatments that define the kinetic behavior of enzyme catalyzed reactions and for theoretical descriptions of enzyme mechanisms
• Simple enzymatic equation


  E + S ES EP E + P
• Enzymes affect reaction rates, not equilibria
• The function of a catalyst is to increase the rate of a reaction, but they do not affect the equilibria
• The reaction is at equilibrium when there is no net change in concentrations of reactants or products
• Reaction coordinate diagram

  A picture of energy changes during the reaction
• Free energy, G

  Energy in a biological systems is described in this term
• The starting point for either the forward or reverse reaction is called the ground state, the contribution to the free energy of the system by the average molecule (S or P) under a given set of conditions
• The equilibrium between S and P reflects the difference in free energies of their ground states
• Delta G' degree


  The standard free energy change for a reacting system under standard conditions (temperature of 298K, partial pressure of each gas, 1 atm, or 101.3 kPa; concentration of each solute, 1 M)
• Delta G' degree


  The biochemical standard free energy change, the standard free energy change at pH 7
• A favorable equilibrium does not mean that S P conversion will occur at a rapid or even detectable rate
• Activation energy

  The energy barrier between S and P, consisting of the energy required for alignment of reacting group, formation of transient unstable changes, bond rearrangements, and other transformations required for the reaction to proceed in either direction
• To undergo reaction, the molecules must overcome this activation energy barrier and be raised to a higher energy level
• Transition state


  • The point at the top of the energy hill where decay to the S or P state is equally probable
  • Not a chemical species with any significant stability and should not be confused with a reaction intermediate (such as ES or EP)
  • A fleeting molecular moment in which events such as bond breakage, bond formation, and charge development proceeded to the precise point at which decay to substrate and decay to product are equally likely
• Activation energy

  The difference between the energy level of the ground state and the energy level of the transition state
• The rate of reaction reflects the activation energy, a higher activation energy corresponds to a slower reaction
• Lowering the activation energy increases the rate of reaction
• Reaction rates can be increased by raising the temperature and/or pressure, thereby increasing the number of molecules with sufficient energy to overcome the energy barrier
• Alternatively, the activation energy can be lowered and the reaction rate can be increased by adding a catalyst
• Catalysts do not affect the reaction equilibria
• Any enzyme that catalyzes the reaction S P also catalyzes the reaction P S
• Role of enzymes

  • To accelerate the interconversion of S and P
  • They are not used up in the process, and the equilibrium point is unaffected
  • The reaction reaches equilibrium much faster when the appropriate enzyme is present, because the rate of the reaction is increased
• Conversion of sucrose and oxygen to carbon dioxide and water

  • C12H22O11 + 12 O2 12 CO2 + 11 H2O
• This conversion takes place through a series of separate reactions, had a very large and very negative delta G' degree, and at equilibrium the amount of sucrose present is negligible
• Yet, sucrose is a stable compound, because the activation barrier must be overcome before sucrose reacts with oxygen is quite high
• In cells, however, sucrose is readily broken down to CO2 and H2O in a series of reactions catalyzed by enzymes
• These enzymes not only accelerate the reactions, they organize and control them so that much of the energy released is recovered in other chemical forms and made available to the cell for other tasks
• The reaction pathway by which sucrose (and other sugars) is broken down is the primary energy yielding pathway for cells, and the enzymes of this pathway allow the reaction sequence to proceed on a biologically useful time scale
• Reaction intermediate

  • Any species on the reaction pathway that has a finite chemical lifetime
  • When S P reaction is catalyzed by an enzyme, the ES and EP complexes can be considered intermediates, even though S and P are stable chemical species; the ES and EP complexes occupy valleys in the reaction coordinate diagram
  • Additional, less stable intermediates often exist in the course of an enzyme catalyzed reaction
• Reaction step

  The interconversion of two sequential reaction intermediates
• When several steps occur in a reaction, the overall rate is determined by the step, or steps, with the highest activation energy, or the rate limiting step
• In the simplest case, the rate limiting step is the highest energy point in the diagram for the interconversion of S and P