CH 6: Enzymes

6.1 Enzymes Are Powerful and Highly Specific Catalysts

• Enzymes are protein catalysts that accelerate reaction rates by factors of a million or more.
• Reactants in enzyme-catalyzed reactions are called substrates.
• Enzymes exhibit high specificity for their substrates.
  • Examples include proteolytic enzymes like trypsin (A) and thrombin (B).
• Even simple reactions like adding water to carbon dioxide require an enzyme, carbonic anhydrase, in red blood cells.

Six Major Classes of Enzymes

1. Oxidoreductases: Catalyze oxidation-reduction reactions.
2. Transferases: Move functional groups between molecules.
3. Hydrolyases: Cleave bonds with the addition of water.
   • Hydrolyase Example
4. Lyases: Remove atoms to form double bonds or add atoms to double bonds.
5. Isomerases: Move functional groups within a molecule.
6. Ligases: Join two molecules, coupled with ATP hydrolysis.

6.2 Many Enzymes Require Cofactors for Activity

• Cofactors are small molecules required by some enzymes for activity.
  • Two main classes:
    • Coenzymes: Organic molecules, often derived from vitamins.
    • Metals: Metallic elements, usually with full charges.
• Cofactors tightly bound to enzymes are called prosthetic groups.
• An enzyme with its cofactor is a holoenzyme.
• Without the cofactor, the enzyme is called an apoenzyme.

6.3 Gibbs Free Energy is a Useful Thermodynamic Function

• Free energy (G) is a measure of energy capable of doing work.
• The change in free energy when a reaction occurs is symbolized by ΔG.
  • \Delta G = \Delta H - T \Delta S

Free-Energy Change and Reaction Spontaneity

• ΔG of a reaction:
  • Depends on the free energy difference between reactants and products.
  • Is independent of how the reaction occurs.
  • Provides no information about the rate of the reaction.
• Enzymes do not alter the ΔG of a reaction.

Equilibrium and Spontaneity

• At equilibrium, there is no net change in the amount of reactant or product, and ΔG = 0.
• A reaction will occur spontaneously only if ΔG is negative (exergonic).
• A reaction will not occur without added energy if the ΔG is positive (endergonic).

Standard Free-Energy Change and Equilibrium Constant

• For a reaction, the free energy change is given by:\Delta G = \Delta G^o + RT \ln{([C][D])/([A][B])}

  • ΔGo is the standard free energy.
  • R is the gas constant (0.0083145 KJ ⋅ mol-1 ⋅ K-1 = 8.3145 J ⋅ mol-1 ⋅ K-1).
  • T is 298 Kelvin.
  • Brackets denote concentration in moles.

• ΔGo' symbolizes the standard free energy change at pH 7.

• At equilibrium, ΔG = 0, so:0 = \Delta G'^o + RT \ln{K'_{eq}}

• Knowing that\Delta G'^o = -RT \ln{K'_{eq}}

• And that the equilibrium constant for the reaction under standard conditions isK'_{eq} = e^{\frac{-\Delta G'^o}{RT}}

• The more exergonic a reaction is, the larger the equilibrium constant will be.

• The more endergonic a reaction is, the smaller the equilibrium constant will be.

Quick Quiz

• Which of the following two reactions will take place spontaneously?
  • A → B ΔG°’ = –10 kJ mol–1
  • C → D ΔG°’ = +10 kJ mol–1
• What are the ΔG°’ values for the reverse reactions?
  • B → A ΔG°’ = +10 kJ mol–1
  • D → C ΔG°’ = -10 kJ mol–1

Enzymes and Reaction Equilibrium

• The reaction equilibrium is determined only by the free energy difference between the products and reactants.
• Enzymes cannot alter this difference.

ATP Hydrolysis

• Will the hydrolysis of ATP happen spontaneously under standard conditions?
• What is K’eq for this reaction?
• ATP + H2O \rightleftharpoons ADP + Pi
• At pH 7.0, 25°C, K’eq = 2.23 x 105
• K'{eq} = \frac{[ADP][Pi]}{[ATP]}

6.4 Enzymes Facilitate the Formation of the Transition State

• A chemical reaction proceeds through a transition state (X‡), which is neither substrate nor product: S ⇌ X‡ → P
• The energy required to form the transition state from the substrate is called the activation energy, symbolized by ΔG‡.
  • \Delta G^\ddagger = G{X^\ddagger} − GS
• Enzymes facilitate the formation of the transition state by lowering activation energy.

Graph Model of How Enzymes Decrease the Activation Energy

• Diagram illustrating the free energy changes during a reaction, comparing catalyzed and uncatalyzed reactions. The enzyme lowers the activation energy (ΔG‡).

Common Features of Enzyme Active Sites

1. The active site is a three-dimensional cleft or crevice created by amino acids from different parts of the primary structure.
2. The active site constitutes a small portion of the enzyme volume.
3. Active sites create unique microenvironments.
4. The interaction of the enzyme and substrate at the active site involves multiple weak interactions.
5. Enzyme specificity depends on the molecular architecture at the active site.
   • Lock-and-Key Model

• Enzymes do not interact with their substrates like a lock and key.
• Rather, the enzyme changes shape upon substrate binding, a phenomenon called induced fit.
  • Induced Fit Model

Transition-State Analogs

• Transition-state analogs are potent inhibitors of enzymes.
• Example:
  • Proline racemase catalyzes the isomerization of proline. The reaction proceeds through a planar transition state in which the α carbon has trigonal geometry.
  • Pyrrole 2-carboxylate mimics that trigonal geometry. The similarity to the transition-state means pyrrole 2-carboxylate is a transition-state analog and is a potent inhibitor of proline racemase.

Problem-Solving Strategies

• Reaction in the glycolytic pathway:
  • Fructose 1,6-bisphosphate ⇌ dihydroxyacetone phosphate + glyceraldehyde 3-phosphate
  • The ΔG°’ of the reaction is 23.8 kJ/mol.
• Inside a cell performing glycolysis, the concentrations are as follows:
  • Dihydroxyacetone phosphate (DHAP) = 4.3 × 10–6 M
  • Fructose 1,6-bisphosphate (FBP) = 1.5 × 10–4 M
  • Glyceraldehyde 3-phosphate (G3P) = 9.6 × 10–5 M
• Calculate the ΔG value under these intracellular conditions.