Unit 3_Enzymes & Catalysis_Introduction to Enzymes_BIOC2200

Introduction to Enzymes

  • Enzymes (biocatalysts) accelerate biochemical reactions in living organisms.

  • Catalysis significantly reduces the time for reactions that would otherwise take a long time (years) when uncatalyzed.

  • Enzymatic reactions are faster compared to chemical catalysts (e.g., platinum).

Fundamental Concepts

  • Energy in Reactions: Chemical reactions tend to move towards lower energy states but often have energy barriers. Catalysts lower these energy barriers, increasing reaction rates.

  • Before class, review:

    • Chemical Equilibria and Catalysis (CHEM 1302)

    • Bioenergetics and Enzymes (BIOL 1103)

The Nature and Classification of Enzymes

  • Definition: Enzymes are biological catalysts that speed up biochemical reactions.

  • Applications: They are used in producing sweeteners, modifying antibiotics, and in various cleaning products and analytical devices.

  • Origin of the Term: First used by Wilhelm Kühne in 1878 from Greek roots 'en' (within) and 'zume' (yeast).

  • Historical Advances: Significant breakthroughs in the 19th-20th centuries led to extracting, characterizing, and commercializing enzymes.

  • It was discovered in the 1920s that catalytic activity is associated with proteins.

  • Ribozymes: RNA molecules that have catalytic properties, significant in gene expression.

  • Abzymes: Antibodies with catalytic abilities that may serve industrial and therapeutic roles.

Enzymatic Properties

Potent Catalysts

  • Enzymes work in low concentrations and are not consumed in reactions.

  • Turnover Rate (kcat): Amount of substrate converted to product per enzyme per time unit, indicative of enzyme efficiency.

    • Example: Carbonic anhydrase can convert over 600,000 molecules of CO2 and H2O into bicarbonate per second.

Specific Catalysts

  • Enzymes generally convert only one type or a few closely related substrate molecules into products.

  • Group Specificity: Example - Alkaline phosphatase removes phosphate from various substrates.

  • Absolute Specificity: Example - Glucose oxidase specifically acts only on β-D-glucose.

Enzyme Names and Classification

  • Naming Convention: Most enzymes use the suffix '–ase' (e.g., oxidase) indicating their reaction type or substrate.

  • EC System: Established by the International Union of Biochemistry to systematically name enzymes. Each enzyme has a four-part Enzyme Commission number indicating the reaction type and substrate.

    • Example: Lactate dehydrogenase (EC 1.1.1.27) is an oxidoreductase with specific donor and acceptor details in its EC number.

Enzyme Classification

Main Classes of Enzymes (Table 2)

  1. Oxidoreductases: Catalyze oxidation/reduction reactions.

  2. Transferases: Transfer atoms or groups.

  3. Hydrolases: Catalyze hydrolysis.

  4. Lyases: Remove groups without hydrolysis.

  5. Isomerases: Catalyze isomerization.

  6. Ligases: Join molecules linked to breaking a pyrophosphate bond.

Secondary and Tertiary Classes of Oxidoreductases (Tables 3 & 4)

  • The second digit in the EC number denotes the type of electron donor.

  • The third digit indicates the electron acceptor.

Enzyme Structure and Substrate Binding

  • Enzymes are globular proteins made from amino acids that can fold into specific three-dimensional shapes.

  • Active Site: The region where substrate binds, often consisting of less than 10 amino acids.

  • Lock and Key Hypothesis: Proposed by Emil Fischer; proposed that only the correct substrate fits the enzyme’s active site.

  • Induced Fit Model: Extended by Daniel Koshland; enzymes adjust shape to fit the substrate, enhancing binding.

Enzyme Cofactors

  • Many enzymes require non-protein components (cofactors) for catalytic activity.

    • Cofactors can be organic (coenzymes) or inorganic (metal ions).

    • Prosthetic group: Coenzyme that tightly binds to the enzyme.

    • Apoenzyme: Inactive enzyme without its cofactor; Holoenzyme: Active enzyme with its cofactor.

Enzymes and Reaction Equilibrium

  • Enzymes do not change equilibrium: They enable reactions to reach equilibrium more quickly but don't alter the position of equilibrium.

  • Example of Reaction Dynamics: Adding enzyme speeds the conversion from substrate to product but does not alter final amounts at equilibrium.

Complex Formation and Reaction Pathway

  • Enzyme-catalyzed reactions involve:

    1. Enzyme-Substrate (ES) complex formation

    2. Conversion to product

    3. Product release, enzyme ready for another substrate.

  • Enzymes lower the activation energy (Ea), facilitating transition state formation without altering energy levels of substrates/products.

Effects of pH and Temperature

  • Optimum pH: Each enzyme has a pH at which its activity is maximal; deviations can reduce activity.

  • Extreme pH can denature enzymes, altering their structure.

  • Temperature effects: Higher temperatures increase reaction rates but also risk protein denaturation. Enzymes from microbial sources tend to show higher thermal stability.

Enzyme Regulation

  • Regulating enzyme activity is key to controlling metabolic pathways.

    • Competitive Inhibition: Inhibitor competes with substrate for the active site.

    • Allosteric Regulation: Inhibitors or activators bind to sites away from the active site affecting enzyme function.

    • Feedback Inhibition: End product of a pathway inhibits an earlier enzyme (allosteric inhibition).

References

  1. Ahern K., et al. Principles of Catalysis.

  2. Biochemistry Free for All, (CC BY-NC-SA 4.0).

  3. Flatt, P.M. Enzyme Principles and Applications.

  4. Jakubowski H. and Flatt P., Enzyme Activity Fundamentals.

  5. Robinson, P. Enzymes: Principles and Applications.