PDB-101 Enzyme Notes

  • Enzymes Overview

    • Enzymes are proteins that catalyze chemical reactions in living cells.

    • They initiate reactions, speed up their progress, and ensure consistent end products.

    • Enzymes work collaboratively to form metabolic pathways, like the Citric Acid Cycle (Krebs Cycle).

  • Role of Enzymes in Metabolism

    • Enzymes regulate vital life functions:

    • Metabolism: Chemical reactions to generate energy.

    • Protein Synthesis: Formation of proteins from amino acids.

    • Cell Growth & Renewal: Cell division and repair processes.

    • Function effectively under mild conditions (neutral pH, moderate temperature, atmospheric pressure).

    • Catalyzed reactions occur millions to trillions times faster than uncatalyzed reactions.

  • Energy and Activation

    • Without enzymes, reactions require additional energy to proceed, often provided as heat.

    • Unstable transition states form during reactions, leading to product formation.

  • Mechanism of Enzyme Action

    • Enzymes provide a template for reactions, binding substrates in optimal positions.

    • They surround substrates with reactive groups to stabilize transition states.

  • Case Study: Aconitase in the Citric Acid Cycle

    • Aconitase catalyzes a reaction involving citrate:

    • Binds to citrate, removes a hydroxyl and hydrogen to generate cis-aconitate.

    • Repositions the hydroxyl to create isocitrate.

    • Active Site Composition:

    • Specific amino acids in the active site:

      • Histidine 101: Acts as an acid (donates protons).

      • Serine 642: Acts as a base (accepts protons).

      • Iron-sulfur cluster stabilizes electrostatically.

    • Reaction Steps:

    1. Dehydration: Histidine protonates hydroxyl, enabling it to leave as water.

    2. Serine extracts hydrogen, yielding intermediate cis-aconitate.

    3. Hydration: Histidine acquires hydrogen from water; Serine returns hydrogen, producing isocitrate.

    • Catalytic Characteristics:

    • The enzyme remains unchanged post-reaction and is ready for subsequent reactions.

    • Enzymes often have flexible active sites that encase substrates to enhance reaction conditions.

  • Significance of Enzymes

    • Essential for sustaining life on Earth by maintaining cellular and bodily functions continuously.

    • Enzymes perform innumerable reactions for various biological processes daily.