13.4 Enzyme Nomenclature and Classification, Cofactors, Coenzymes, and Vitamin Precursors

13.4 Enzyme Nomenclature and Classification, Cofactors, Coenzymes, and Vitamin Precursors

Quick Answer: The protein area of the Biochemistry TOS (14 items) names enzyme naming and classification and coenzymes with their precursors alongside kinetics and inhibition (Section 13.5). Know the seven EC classes with an example of each, the metal and coenzyme cofactors, which vitamin each coenzyme comes from and which reaction it supports, and the unit arithmetic of spectrophotometric enzyme assays.

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Enzyme Nomenclature and the EC Classes

Common names usually add -ase to the substrate or reaction (urease, lactate dehydrogenase). The IUBMB Enzyme Commission (EC) number has four parts: class, subclass, sub-subclass, and serial number. For example, alcohol dehydrogenase is EC 1.1.1.1.

Related terms:

• Isozymes catalyse the same reaction but differ in sequence and properties. Lactate dehydrogenase has five tetrameric isozymes (H4 to M4), useful in diagnosing tissue damage.
• Ribozymes are catalytic RNAs, such as the peptidyl transferase centre of the ribosome and self-splicing introns.
• Enzyme activity units: 1 unit (U) converts 1 µmol of substrate per minute; the SI unit, the katal, is 1 mol/s, so 1 U = 16.67 nkat. Specific activity is units per mg of protein.

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Cofactors and Coenzymes

An inactive apoenzyme plus its cofactor forms the active holoenzyme.

Metal-Ion Cofactors

Coenzymes

Cosubstrates such as $NAD^+$ and coenzyme A bind transiently and leave changed, so they must be regenerated by another reaction. Prosthetic groups such as FAD in succinate dehydrogenase, heme, biotin, and lipoamide stay tightly or covalently bound.

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Vitamins and Their Coenzyme Forms

Fat-soluble vitamins: A (retinal in rhodopsin for vision; deficiency causes night blindness), D (converted to calcitriol, which raises calcium absorption; deficiency causes rickets and osteomalacia), E (tocopherol, a lipid antioxidant), and K (cofactor for $\gamma$-carboxylation of glutamate in clotting factors II, VII, IX, and X; warfarin is its antagonist).

Methotrexate inhibits dihydrofolate reductase, and sulfonamide antibiotics block bacterial folate synthesis, which humans do not perform.

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Coenzyme Mechanisms

• $NAD^+$ and $NADP^+$: accept a hydride ion at C-4 of the nicotinamide ring. NADH absorbs at 340 nm ($\varepsilon = 6220\ M^{-1}cm^{-1}$) and $NAD^+$ does not, so dehydrogenase rates can be followed spectrophotometrically. $NADPH$ serves biosynthesis; $NADH$ feeds the electron transport chain.
• FAD and FMN: accept one or two electrons with protons (semiquinone, then hydroquinone), linking two-electron and one-electron carriers.
• PLP: forms a Schiff base with an active-site lysine (internal aldimine), then with the substrate amino acid (external aldimine). The pyridinium ring acts as an electron sink.
• TPP: the C-2 carbanion (ylide) of the thiazolium ring attacks $\alpha$-keto acids and stabilizes the acyl carbanion after decarboxylation.
• Biotin: ATP-dependent carboxylation at N-1' forms carboxybiotin, which swings on a lysine arm to carry $CO_2$ to the substrate.
• Coenzyme A: its thiol forms high-energy thioesters (acetyl-CoA, $\Delta G^{\circ\prime}$ of hydrolysis about $-31.4$ kJ/mol).

Worked assay: NADH formation raises $A_{340}$ by 0.311 per minute in a 1.00 cm cuvette holding 1.00 mL. The rate is $\frac{0.311}{6220} = 5.0 \times 10^{-5}$ M/min (50 µM/min), which in 1.00 mL is 0.050 µmol/min, or 0.050 U.