Enzyme Classification and Nomenclature

Enzyme Essentials - Name Game Gurus

• Enzymes: Biological catalysts, typically proteins, accelerating biochemical reactions without being consumed.
• Active Site: Specific 3D pocket on the enzyme where the substrate binds and catalysis occurs.
• Substrate (S): The reactant molecule(s) upon which an enzyme acts.
• Enzyme Components:
  • Apoenzyme: The protein part of an enzyme; inactive on its own.
  • Cofactor: Non-protein chemical compound (ion or molecule) required for an enzyme's activity.
    • Coenzyme: Organic, loosely bound cofactor (e.g., vitamins like NAD+, FAD+).
    • Prosthetic Group: Organic or inorganic cofactor, tightly bound to the apoenzyme (e.g., heme, FMN).
  • Holoenzyme: The complete, catalytically active enzyme, consisting of an apoenzyme and its cofactor. 📌 Holo = Whole (active).
• Nomenclature:
  • Trivial names: Common, often historical (e.g., Pepsin, Trypsin).
  • Systematic names: Based on the substrate and type of reaction catalyzed, ending with the suffix "-ase" (e.g., Lactate dehydrogenase).

⭐ Ribozymes are catalytic RNAs, an exception to the general rule that enzymes are proteins.

Enzyme Classes 1 & 2 - Redox & Group Shuttlers

📌 Mnemonic for 6 enzyme classes: OTHLIL (Oscar The Hairy LILy)

📌 Mnemonic for 6 enzyme classes: OTHLIL (Oscar The Hairy LILy)

| Dehydrogenases (remove H), oxidases (use $O_2$ as acceptor), peroxidases. | NAD+/NADP+, FAD/FMN as coenzymes. | | Transferases | EC 2 | Transfer functional groups (e.g., methyl, amino, phosphate). $G-X + A \rightleftharpoons G-A + X## Enzyme Classes 1 & 2 - Redox & Group Shuttlers

📌 Mnemonic for 6 enzyme classes: OTHLIL (Oscar The Hairy LILy)

| Kinases (transfer $PO_4^{3-}$), transaminases (e.g., ALT, AST; transfer amino group). | C, N, P-containing groups. |

⭐ Alanine aminotransferase (ALT) is a more specific indicator of liver damage than Aspartate aminotransferase (AST).

Enzyme Classes 3 & 4 - Water Breakers & Bond Splitters

| Peptidases, lipases, nucleases, glycosidases | | EC 4 | Lyases | Non-hydrolytic/oxidative cleavage of C-C, C-O, C-N bonds; forms double bonds/rings. $X-A-B-Y \rightarrow A=B + X-Y## Enzyme Classes 3 & 4 - Water Breakers & Bond Splitters

| Decarboxylases, aldolases, dehydratases, synthases* |* 📌 OTHLIL: Hydrolases, Lyases.

• Synthases (Lyases) cleave bonds; Synthetases (Ligases, EC 6) join molecules (ATP-dependent).

⭐ Many digestive enzymes (e.g., pepsin, amylase, lipase) are hydrolases, crucial for nutrient breakdown.

Enzyme Classes 5 & 6 & EC Codes - Shifters, Joiners & ID Tags

📌 OTHLIL: Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases.

EC 5: Isomerases ("Shifters")

• Intramolecular rearrangements (geometry/structure change). Reaction: $A-B-C \rightarrow A-C-B$.
• E.g., L-alanine $\leftrightarrow$ D-alanine. Types: Epimerases, racemases, mutases.

EC 6: Ligases ("Joiners")

• Join two molecules; form new C-O, C-S, C-N, C-C bonds; ATP-dependent. Reaction: $A + B + ATP \rightarrow A-B + ADP + P_i$.
• Types: Synthetases, carboxylases. E.g., DNA ligase.

⭐ DNA Ligase (EC 6), essential for DNA replication and repair by joining DNA fragments, requires ATP.

EC Number System (ID Tags): EC W.X.Y.Z

• W: Main class (enzyme's broad category, 1-7).
• X: Subclass (type of bond/group acted upon).
• Y: Sub-subclass (further details like cofactor/acceptor).
• Z: Serial number (specific enzyme's unique ID).

High‑Yield Points - ⚡ Biggest Takeaways

• Six major enzyme classes (EC 1-6) are defined by the Enzyme Commission (IUBMB): Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases (OTHLIL).
• Each enzyme has a unique four-digit EC number (Class.Subclass.Sub-subclass.Specific enzyme).
• Oxidoreductases (EC 1) catalyze redox reactions; Transferases (EC 2) move functional groups.
• Hydrolases (EC 3) cleave bonds using water; Lyases (EC 4) cleave bonds non-hydrolytically, often forming double bonds.
• Isomerases (EC 5) rearrange atoms within a molecule.
• Ligases (EC 6) join two molecules, typically using ATP hydrolysis.