Enzyme Notes

Definition: Enzymes are biological catalysts that facilitate biochemical reactions.
Types:
- Mostly proteins, though some RNA molecules called ribozymes act as enzymes.
- Originally extracted from yeast.

Substrate Interaction: Act on a variety of substrates but have a limited range of reactions.
Classification of Enzymes:
- Oxidoreductases: Catalyze electron transfer (e.g., hydride ions, H atoms).
- Transferases: Catalyze group transfer reactions.
- Hydrolases: Catalyze hydrolysis reactions (functional groups transferred to water).
- Lyases: Add groups to double bonds or remove groups to form double bonds.
- Isomerases: Rearrange molecules to yield isomers.
- Ligases: Form C-C, C-S, C-O, and C-N bonds via condensation reactions coupled with ATP cleavage.

Cofactors: Many enzymes require additional molecules called cofactors for activity.
Coenzymes: Can be prosthetic (tightly bound) or loosely bound.
Apoenzymes: Enzymes without their cofactors are termed apoenzymes.
Holoenzymes: The enzyme-cofactor complex is referred to as holoenzyme.

Substrate Binding: The substrate binds to the active site of the enzyme, where catalysis occurs.
Reaction Rate: Enzymes change the reaction rate but do not affect the equilibria; they facilitate the movement from reactants to products via a transition state.

Transition State: This state has a high energy barrier compared to the energy gain from catalysis.
Activation Energy: Represented as ΔG‡; the energy required to reach the transition state.
Biochemical Standard Free Energy Change: ΔG’_0 indicates energy changes during the reaction at pH 7.0.

Concentration Dependence: The reaction rate depends on the concentration of substrates.
Rate Equations: Measure velocity of reaction, e.g., for first-order reactions V = k[S] (where k is a rate constant) and for second-order reactions V = k[S1][S2].
Maximal Velocity (Vmax): Indicates the maximum rate an enzyme can achieve, where V_0 will be constant despite changes in substrate concentration at this point.

Steady-State Approximation: Assumes constant concentration of enzyme-substrate complex, leading to the Michaelis-Menten equation: V0 = \frac{V{max} [S]}{K_m + [S]}.
Km: The substrate concentration when V0 is half of V{max}; a measure of enzyme affinity for substrate.

Types of Inhibition:
- Competitive: Inhibitor competes for active site, alters Km: V0 = \frac{V{max}[S]}{αK_m + [S]}.
- Noncompetitive: Binds E or ES complex, affecting both Km and Vmax.
- Irreversible: Kills enzyme activity, often via covalent bonding.

Feedback Inhibition: Final product inhibits an earlier step, influencing the pathway.
Allosteric Regulation: Enzymes can be positively or negatively regulated, often through reversible changes that modify activity via covalent modifications (commonly phosphorylation).
Proteolytic Regulation: Enzymes are synthesized in inactive forms (proenzymes or zymogens), activated by proteolytic cleavage.

Chymotrypsin: A serine protease that cuts after aromatic amino acids and requires specific amino acids in the active site for function.
RNase A: Utilizes acid-base catalysis without forming a covalent intermediate for RNA cleavage.
Lysozyme: Catalyzes the cleavage of peptidoglycan in bacterial cell walls through a two-step displacement mechanism.
Enolase: Utilizes metal ion catalysis to assist dehydration reactions in glycolysis, featuring Mg2+ at the active site.

Specificity Constant: k{cat}/Km represents enzyme efficiency, indicating turnover rates for different substrates.
Multisubstrate Reactions: Reactions involving multiple substrates can follow sequential (random/ordered) mechanisms or without forming a ternary complex.