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Enzyme Structure and Function

  • Definition and Composition
    • Enzymes are primarily made of proteins.
    • A small subset exists as catalytic RNA molecules, referred to as ribozymes.

Enzyme Denaturation

  • If an enzyme loses its native structure, it becomes denatured.
  • When denatured, the enzyme loses its catalytic activity.

Cofactors and Coenzymes

  • Cofactor

    • Definition: A non-protein component required for enzyme activity.

    • Types of Cofactors:

      • Inorganic Ions: Examples includes ions such as Iron (Fe²⁺), Magnesium (Mg²⁺), and Zinc (Zn²⁺).
      • Organic Coenzymes: Complex organic molecules, often derived from vitamins, that act as transient carriers of specific functional groups.

    • Prosthetic Group

  • Definition: A cofactor or coenzyme that is tightly or covalently bound to the enzyme.

Holoenzyme and Apoenzyme Concept

  • Holoenzyme
    • Definition: The active enzyme which consists of the protein part (apoenzyme) along with its cofactor.
  • Apoenzyme
    • Definition: The inactive protein part of the enzyme, devoid of its cofactor.

Active Site Characteristics

  • Active Site
    • Definition: A pocket within the enzyme where the substrate binds and where catalysis occurs.
  • Factors Determining Active Site Specificity:
    • Shape
    • Polarity
    • Charge
    • Hydrophobicity
    • Cofactor compatibility

Models of Enzyme Action

  • Lock and Key Model
    • Description: The enzyme's active site is uniquely shaped to fit a specific substrate, akin to a lock and key fitting together.
  • Induced-Fit Model
    • Description: The enzyme undergoes a conformational change upon substrate binding, resulting in a more stable enzyme-substrate complex.
    • Example: Hexokinase demonstrates this model by changing its shape upon glucose binding.

Enzyme Classification

  • Enzymes are classified based on the reactions that they catalyze.
  • Seven Main Enzyme Classes:
    1. Oxidoreductases
    2. Transferases
    3. Hydrolases
    4. Lyases
    5. Isomerases
    6. Ligases
    7. Translocases

Enzyme Naming Systems

  • Recommended Naming System

    • Typically, a common name is used that ends in “-ase,” reflective of the substrate it acts upon or the type of reaction it catalyzes (e.g., lactate dehydrogenase, urease).

  • Systematic Naming System

    • This system provides a more detailed description of the full reaction, including substrates (e.g., Lactate:NAD⁺ oxidoreductase).

    • EC Number

  • An EC number is a classification number assigned by the Enzyme Commission for identification (example: 1.1.1.27 for lactate:NAD⁺ oxidoreductase).

Enzyme Kinetics and Activation Energy

  • Activation Energy (∆G‡)

    • Definition: The energy required to reach the transition state from the ground state of the reaction.

  • Effect of Enzymes on Activation Energy

    • Enzymes function to lower the activation energy, thus accelerating the rate of a reaction.

  • Equilibrium and ∆G

    • Enzymes do not affect the reaction equilibrium or the free energy change (∆G); instead, they solely increase the reaction rate.

    • Catalytic Power

  • Main sources of catalytic power stem from covalent and non-covalent interactions between the enzyme and substrate.

    • Binding Energy (∆G■)

  • Definition: The free energy released when the substrate binds to the enzyme, utilized for lowering activation energy.

    • Transition State

  • Definition: The high-energy intermediate state existing between substrate and product during a chemical reaction.

Enzyme Rate Enhancement

  • Typical rate enhancements observed with enzymes are between 10610^6 and 101210^{12} times faster compared to their uncatalyzed reaction counterparts.

Example of Enzyme Function

  • DNA Polymerase
    • Enzyme Function: Catalyzes the polymerization of deoxyribonucleotides during the process of DNA replication.
    • Reaction Rate: Approximately 50 bases incorporated into the growing DNA strand per second.