Rucete ✏ Lehninger Principles of Biochemistry In a Nutshell
6.2 How Enzymes Work
This chapter explains the essential mechanisms by which enzymes catalyze biochemical reactions, covering the nature of active sites, the effect on reaction rates and equilibria, the concept of activation energy, the role of binding energy, and the major catalytic strategies (including acid-base, covalent, and metal ion catalysis).
The Nature of Enzyme Catalysis and the Active Site
• Enzymatic reactions are central to life, enabling essential processes (digestion, nerve signals, muscle contraction) that would otherwise proceed far too slowly under physiological conditions.
• Each enzyme-catalyzed reaction occurs within a specialized pocket called the active site, lined with amino acid residues that bind the substrate and promote its transformation.
• The substrate binds to the enzyme at the active site, forming an enzyme-substrate (ES) complex that is central to both the mechanism and the mathematical description of enzymatic catalysis.
Enzymes Affect Reaction Rates, Not Equilibria
• Enzymes function as catalysts by increasing the rate of reactions without affecting their equilibrium positions.
• A reaction’s equilibrium depends on the difference in free energy (ΔG) between reactants and products, while the rate depends on the activation energy (ΔG‡)—the energy barrier required to reach the transition state.
• Catalysts (including enzymes) lower activation energy, allowing reactions to proceed more rapidly, but do not alter the overall free-energy change or the equilibrium constant.
• Enzymes accelerate both forward and reverse reactions, helping the system reach equilibrium faster.
• Biological reactions often involve multiple steps and intermediates, and the rate-limiting step is the one with the highest activation energy barrier.
• Activation energies are critical for maintaining biological order; without them, macromolecules would spontaneously break down.
Thermodynamics of Reaction Rates and Equilibria
• Reaction equilibria are defined by the equilibrium constant (K_eq), which relates to the standard free-energy change (ΔG°’); reaction rates are described by rate constants (k), which are exponentially related to activation energy.
• A large, negative ΔG°’ reflects a favorable equilibrium but says nothing about how fast the reaction will proceed.
• The rate of a reaction depends on reactant concentration and the magnitude of k; lowering activation energy (ΔG‡) greatly increases k and the reaction rate.
The Source of Catalytic Power and Specificity
• Enzymes achieve extraordinary rate enhancements and substrate specificity primarily through noncovalent interactions with the substrate in the transition state, releasing binding energy (ΔGb).
• The active site is not a static, perfectly shaped "lock" for the substrate; rather, optimal binding occurs with the transition state (not the ground state), which lowers activation energy—an insight known as transition-state stabilization.
• Specificity arises because the active site is arranged to form multiple weak interactions only with the correct substrate in its transition state, discriminating even between very similar molecules.
• Binding energy also helps: (1) precisely orient substrates, (2) desolvate the substrate (replace water-shell H-bonds), (3) compensate for energy costs of substrate distortion, and (4) induce conformational changes (induced fit) that enhance catalysis.
• The requirement for numerous weak interactions partly explains why enzymes are large, complex molecules.
• Quantitatively, lowering ΔG‡ by only 5.7 kJ/mol increases reaction rate tenfold, and the combined energy from multiple weak interactions can account for the huge rate enhancements seen in enzymes.
Major Catalytic Strategies Used by Enzymes
• Most enzymes use several catalytic mechanisms in concert, including:
• General acid-base catalysis: Amino acid side chains or cofactors donate or accept protons, stabilizing charged intermediates and enabling reaction in environments where water is not available.
• Covalent catalysis: The enzyme forms a transient covalent bond with the substrate, creating a new reaction pathway with lower activation energy; enzyme functional groups act as nucleophiles or accept transferred groups.
• Metal ion catalysis: Metal ions facilitate catalysis by orienting substrates, stabilizing charges, or mediating redox reactions; about a third of all enzymes require metal ions for activity.
• These mechanisms often work together, as in the case of chymotrypsin, which employs acid-base, covalent, and transition-state stabilization.
In a Nutshell
• Enzymes are extraordinarily effective and specific catalysts because their active sites form multiple weak interactions with substrates in the transition state, releasing binding energy to lower activation energy.
• Enzymes increase the rates of reactions, not their equilibria, by providing alternative pathways with lower activation energy through strategies like acid-base catalysis, covalent catalysis, and metal ion catalysis.
• The interplay of precise substrate orientation, transition-state stabilization, and catalytic chemistry underpins both the speed and specificity of enzymatic reactions essential for life.