Enzymes: Protein Catalysts

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Enzymes Protein Catalysts

• Increase rates of reaction, but not consumed.
• Enable reactions to occur under mild conditions
  e.g. temperature, pH.
• High reaction specificity no side products.
• Activity of enzymes can be regulated.
• Substrate
• Availability of enzyme (expression,
  localization)
• Reversible covalent modification
• Allosteric control (other proteins or co-factors)

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Enzyme Cofactors

• Simple Enzymes only protein chain(s)
• Complex Enzymes require additional molecules
  (co-factors) for functioning
• Co-enzyme non-covalently bound
• Prosthetic Group covalently bound to protein

Prosthetic groups/co-enzymes usually
VITAMINS! Vitamin deficiency diseases
malfunction of enzymes
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Enzyme Classes/Reactions

• Oxidoreductases. Act on many chemical groupings
  to add or remove hydrogen atoms.
• Transferases. Transfer functional groups between
  donor and acceptor molecules (e.g. kinases that
  transfer phosphate from ATP to other molecules).
• Hydrolases. Add water across a bond, hydrolyzing
  it.
• Lyases. Add H2O, NH2, or CO2 across double
  bonds, or remove these elements to produce double
  bonds.
• Isomerases. Carry out stereochemical, geometric
  and other types of isomerization.
• Ligases. Catalyze reactions in which two
  chemical groups are joined (ligated) with the use
  of energy from ATP.

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Catalytic Mechanisms

• Bond Strain Strains substrate bonds, which
  facilitates attaining the transition state.
• Proximity and Orientation Binding brings
  molecules into proximity and helps to properly
  orients reactive groups.
• Acid/Base Catalysis Required catalytic proton
  donors (acids) or acceptors (bases) are supplied
  by catalyst.
• Covalent Catalysis The reaction is facilitated
  by formation of a covalent intermediate between
  the enzyme (or coenzyme) and the substrate.

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Catalytic Mechanisms (cont.)

• Metal Ions (metalloenzymes) Orients substrates
  stabilizes charge in the transition state
  supplies or captures electrons during the course
  of the reaction.
• Electrostatic Exclusion of solvent changes
  environment to facilitate reactions
  stabilization of charge in the transition state.
• Preferential Binding of the Transition State
  Binding of the transition state is PREFERRED over
  the reactants and products, greatly stabilizing
  this species at the critical moment it is formed.

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Enzymes Protein Catalysts

• Catalysts increase rate of reaction, but not
  consumed.
• Enzymes bind substrates to increase the rate of a
  biochemical reaction that converts the substrate
  (reactant) into a desired product.
• Reactions occur once sufficient energy has been
  supplied to overcome the energy barrier that
  prevents the reaction from occurring
  spontaneously.
• Each reaction has a transition state where the
  substrate is in an unstable, short-lived
  chemical/structural state.
• A-H B ? A?H?B ? A H-B

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Reaction Coordinate Diagrams

• The progress of the reaction can be viewed in
  terms of the energy of the system reaction
  coordinate. Fig. 11-3
• The transition state is the highest point on the
  reaction coordinate diagram.
• The height of the energy barrier is the Free
  Energy of Activation and is symbolized by DG.
• Reactions can go forward and backward. The
  height of the energy barrier to go backwards may
  be higher than to go forward, because the product
  may be more stable than the substrate. The
  difference in energy between substrate and
  product is the Free Energy of Reaction.

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Multi-Step Reactions

• A reaction may have more than one step S ? I ?
  P.
• Two step reaction have two transition states.
  Fig. 11-4
• If the energy barrier is higher for one step than
  the other, than the rate of this step will be
  slower.
• In multi-step reactions, the step with the
  highest transition state free energy (the highest
  point on the reaction coordinate diagram) is the
  Rate Determining Step of the reaction.
• The overall rate of the reaction, kinetics, can
  only be as fast as the slowest step.

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The Catalytic Effect of Enzymes

• Enzymes act by lowering the free energy of the
  transition state, thereby reducing the free
  energy of activation (DG). Fig. 11-5
• The catalytic efficiency (DDGcat) is the
  difference in DG for the catalyzed reaction
  versus the uncatalyzed reaction.
• The catalytic efficiency can be viewed in terms
  of the kinetic parameters rate enhancement for
  the reaction.
• Enzymes allow huge enhancements of rates, in many
  cases, enabling reactions to occur that would
  almost never occur spontaneously because DG is
  so high.

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Enzymes Affect Rates, Not Outcome

• The lowering of the free energy barrier and
  increase in rate is equal for the forward and the
  reverse reactions.
• Ultimately, the reaction will settle to
  equilibrium. The time required to come to
  equilibrium depends on the rates of the forward
  and reverse reactions. Enzymes facilitate this
  process.
• Enzymes increase the kinetic parameter velocity
  with which products are produced from reactants.
  This is equally true for the forward and reverse
  reactions.
• At equilibrium, the preference for substrate
  versus product is determined by the difference in
  energy between substrate and product- NOT BY THE
  RATES.

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Simple Kinetics
S ------gt P Reaction Velocity the instantaneous
rate (k) at which product is produced (or
substrate disappears) mulitplied by the amount of
substrate present v kS The rate of
production of product rate of consumption of
substrate. The rate constant for the forward
reaction is defined as kf or k1 and for the
reverse reaction as kr or k-1 The velocity of
the forward reaction is vforward k1S The
velocity of the reverse reaction is vreverse
k-1P
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Kinetics at Equilibrium
At equilibrium, the velocity of the forward
reaction is equal to the reverse reaction k1S
k-1P, so there is no overall change in the
distribution of S and P. An equilibrium constant
of the reaction can be defined Keq P/S
k1/k-1 This equation demonstrates that at
equilibrium, the concentration of S and P
reflects the relative stability (free energy
difference) between S and P.