5: Biochemical nomenclature

Biochemical Nomenclature

Biochemical nomenclature provides standardized rules for naming molecules and reactions, ensuring clarity in scientific communication. Mastery of these conventions is essential for understanding biochemical literature and pathways.

Enzymes

Enzymes are named systematically based on their catalyzed reactions and substrate specificity, often using the suffix "-ase". The Enzyme Commission (EC) system classifies enzymes into six groups (oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases) via a four-digit code (e.g., EC 1.1.1.1 for alcohol dehydrogenase). Common names persist (e.g., trypsin), but systematic names precisely describe function (e.g., ATP:glucose phosphotransferase for hexokinase).

Metabolites & Cofactors

Key metabolites use universal abbreviations:

• ATP (adenosine triphosphate), NAD$^+$ (nicotinamide adenine dinucleotide).
• Sugars: Glucose (Glc), fructose (Fru).
• Lipids: Palmitic acid (16:0), where "16" denotes carbon count and "0" double bonds.
  Cofactors like FAD (flavin adenine dinucleotide) and CoA (coenzyme A) follow similar shorthand.

Amino Acids & Nucleotides

• Amino acids use three-letter (e.g., Ala for alanine) or one-letter codes (A for alanine).
• Nucleotides are abbreviated by base (A for adenine, T for thymine) or as nucleosides/tides (AMP for adenosine monophosphate).

Stereochemistry

Stereoisomers are designated using:

• D/L system: Based on glyceraldehyde configuration (e.g., D-glucose).
• R/S system: Absolute configuration per Cahn-Ingold-Prelog rules (e.g., L-alanine is S-alanine).
  Enzymes often exhibit stereospecificity (e.g., L-amino acid oxidase acts only on L-isomers).

Prefixes/Suffixes

Common affixes convey structural or functional traits:

• Glyco- (sugar-related, e.g., glycogen), lipo- (lipid-related, e.g., lipoprotein).
• -ose (sugars, e.g., lactose), -ase (enzymes), -in (general biomolecules, e.g., insulin).

Standard Conventions

• IUPAC-IUBMB: Joint rules govern naming (e.g., fatty acids use "$\Delta$" to denote double-bond positions: linoleic acid is 18:2($\Delta^{9,12}$)).
• Reactions: Named by substrates/products (e.g., lactate dehydrogenase catalyzes lactate + NAD$^+$ $\rightleftharpoons$ pyruvate + NADH + H$^+$).

Consistent use of nomenclature prevents ambiguity, particularly in metabolic pathways (e.g., distinguishing glucose-6-phosphate from fructose-6-phosphate in glycolysis).