Biochemistry Lecture 9: Enzymes

Lecture 9: Enzymes

• Enzymes are specialized proteins that catalyze biological reactions.
• The active site of an enzyme contains amino acid side chains that create a three-dimensional surface complementary to the substrate.
• Enzyme + substrate → enzyme-substrate complex (ES)
• enzyme-product complex (EP) → enzyme + product
• Enzyme-catalyzed reactions are highly efficient, transforming 100-1000 substrate molecules into product each second.
• Turnover number (Kcat) is the number of substrate molecules converted to product per enzyme molecule per second.

Lecture Outline

• Properties of enzymes
• Classification of enzymes
• Cofactors, co-substrates, coenzymes
• Enzyme mechanism
• Active site of an enzyme
• Factors affecting reaction velocity
• Michaelis-Menten equation & Lineweaver-Burk plot
• Enzyme inhibitors

Enzyme Classification

• International Union of Biochemistry and Molecular Biology (IUBMB) classifies enzymes into 6 classes based on the chemical reaction they catalyze.
• 1. Oxidoreductases: Catalyze oxidation-reduction reactions (e.g., lactate dehydrogenase).
• 2. Transferases: Transfer a chemical group (containing C-, N-, or P-) from one molecule to another (e.g., kinases).
• 3. Hydrolases: Catalyze hydrolysis reactions by adding water to cleave chemical bonds (e.g., urease).
• 4. Lyases: Catalyze the cleavage of chemical bonds (C-C, C-N, C-O, C-S, P-O) to form new double bonds.
• 5. Isomerases: Rearrange atoms within a molecule to create isomers (e.g., isomerases).
• 6. Ligases: Catalyze the joining of two large molecules by forming a new chemical bond (e.g., ligases).

Coenzymes

• Coenzymes are organic, non-protein molecules that participate in enzymatic reactions but are not part of the enzyme itself.
• They can be tightly bound or covalently attached to the enzyme.
• Some coenzymes are modified during a reaction; others must participate in another reaction to return to their original state.
• Examples include NAD, NADP, FAD, coenzyme A, biotin.

Enzyme Mechanism: Binding of Substrate

• Two theories for substrate binding:
  • Lock-and-key theory: The active site of the enzyme is a rigid structure that fits the substrate like a key fits a lock.
  • Induced fit theory: The active site of the enzyme changes shape slightly upon substrate binding, to form a stable complex, allowing for a tighter and more efficient fit

Active Site of Enzymes

• Amino acid residues in the active site recognize and bind substrates.
• Interactions between enzyme and substrate include hydrogen bonds, hydrophobic interactions, temporary covalent interactions (van der Waals).
• Active site residues facilitate reaction by acting as donors or acceptors of protons or other groups on the substrate.

Transition State

• Enzymes lower the activation energy of a reaction by stabilizing the transition state.
• The transition state is the highest energy point in a reaction, where bonds are breaking and forming.
• Enzymes help stabilize the transition state, making it easier for reactants to achieve this point and proceed to products.

Factor Affecting Reaction Velocity

• Substrate concentration
• Temperature
• pH

Michaelis-Menten Equation

• Enzyme reversibly combines with its substrate to form an ES complex.
• Mathematical model describing reaction velocity (rate of enzymatic reaction) as a function of substrate concentration
• Vmax: maximum velocity at saturation.
• Km: Michaelis constant; substrate concentration at which velocity is half Vmax.

Lineweaver-Burk Plot

• Double reciprocal plot of the Michaelis-Menten equation.
• Useful for determining Km and Vmax
• Important for visualizing how enzyme inhibitors affect the reaction velocity.

Enzyme Inhibitors

• Inhibitors are molecules that reduce or block enzyme activity.
  • Irreversible inhibitors: Covalently attach to the enzyme, permanently altering its structure (e.g. nerve gas and pesticides, penicillin)
  • Reversible inhibitors: Bind non-covalently, allowing the enzyme and inhibitor to dissociate (e.g. competitive, noncompetitive, uncompetitive inhibitors, statins, methotrexate)

Explore the fascinating world of enzymes in this comprehensive quiz. From the properties and classification of enzymes to the intricacies of enzyme mechanisms, this quiz covers everything you need to know about how enzymes catalyze biological reactions. Test your knowledge on enzyme kinetics, inhibitors, and the critical role of active sites.