Comprehensive Biochemistry Study Guide: Enzyme Fundamentals and Enzyme Classes

Study Requirements and Assigned Materials

• Reading assignment: Vol. 132–141 covering Metabolic Pathways and Enzymes.
• Recommended practice: Complete all end-of-chapter problems and Lehninger's chapter examples.
• Optional resource: PowerPoint presentation on Enzymes.

Fundamentals of Enzymes

• Definition: Enzymes are biological catalysts that increase chemical reaction rates without being consumed or spent up in the process.
• Reversibility: Enzyme-catalyzed reactions are generally reversible.
• Protein structure:
  • Most enzymes are globular proteins.
  • Globular protein architecture features hydrophilic amino acid residues on the exterior surface and hydrophobic amino acid residues on the interior core.
• Non-protein catalysts:
  • Some RNA molecules, termed ribozymes, possess catalytic properties and function as non-protein biological catalysts (RNA ribozymes are catalytic RNA).

Enzyme Nomenclature

• Substrate-based naming: Most commonly used enzyme names utilize the suffix -ase attached to the name of the substrate or bond linkage involved (e.g., glucosidase, lactase).
• Reaction description: Enzyme names may be derived from a specific description of the chemical reaction catalyzed (e.g., transaminase, dehydrogenase).
• Trivial naming: Certain enzymes retain historical, non-systematic trivial names (e.g., Trypsin).

Major Classes of Enzymes

1. Oxidoreductases

• Catalytic mechanism: Catalyze oxidation-reduction reactions by transferring organic hydrogen ions ($H^+$) and electrons ($e^-$ / hydride ion) from a substrate donor to an acceptor molecule such as $NAD^+$..
• Biological context: Functions in the cytosol and plays a key role in cellular respiration and the electron transport chain (ETC). Hydrogen atoms extracted from carbohydrate food sources are transferred to $NAD^+$ to yield $NADH$.
• Reaction equation (Lactate Dehydrogenase): $\text{L-Lactate} + NAD^+ \rightleftharpoons \text{Pyruvate} + NADH + H^+$
  • Substrates: L-Lactate ($HO-C(H)(COO^-)-CH_3$) and $NAD^+$
  • Products: Pyruvate ($O=C(COO^-)-CH_3$), $NADH$, and $H^+$
  • Enzyme: Lactate dehydrogenase

2. Transferases

• Catalytic mechanism: Catalyze the transfer of a specific functional group from a donor molecule to an acceptor substrate molecule.
• Reaction equation (Alanine Aminotransferase): $\text{L-Alanine} + \alpha\text{-Ketoglutarate} \rightleftharpoons \text{Pyruvate} + \text{L-Glutamate}$
  • Functional group transferred: Amino group ($-NH_3^+$)
  • Substrates: L-Alanine ($H_3N^+-C(H)(COO^-)-CH_3$) and $\alpha\text{-Ketoglutarate}$ ($O=C(COO^-)-CH_2-CH_2-COO^-$)
  • Products: Pyruvate ($O=C(COO^-)-CH_3$) and L-Glutamate ($H_3N^+-C(H)(COO^-)-CH_2-CH_2-COO^-$)
  • Enzyme: Alanine aminotransferase

3. Hydrolases

• Catalytic mechanism: Catalyze the cleavage of chemical bonds in larger substrate molecules through the addition of water ($H_2O$), transferring functional groups to water to break down complex molecules into smaller units.
• Reaction equation (Pyrophosphatase): $\text{Pyrophosphate} + H_2O \rightarrow 2\,\text{Phosphate}$
  • Substrates: Pyrophosphate ($^{-}O_3P-O-PO_3^{2-}$) and water ($H_2O$)
  • Products: 2 equivalents of Inorganic Phosphate ($HO-PO_3^{2-}$ / $PO_4^{3-}$)
  • Enzyme: Pyrophosphatase