Biology

Enzymes

3,181 words, 7 sections

This chapter is Biology unit 6 of the PMDC MDCAT-2025 uniform curriculum, inside a subject worth 81 of the 180 marks. Enzymes have been asked 231 times across 74 official papers between 2000 and 2026, and the bank holds 889 active questions on the chapter at a mean difficulty of 1.48. A student who has mastered it can define $E_a$ , walk the catalytic cycle in order, name where a substrate binds, give the optimum temperature and $pH$ of a named enzyme with figures, and separate competitive, non-competitive and irreversible inhibition on sight.

Enzymes are organic substances, synthesised in the cell, that catalyse specific chemical reactions. Almost all are proteins, folded from hundreds of amino acids into a compact globular shape and soluble in water, and the term itself dates to Friedrich Wilhelm Kuhn in 1878. The exception to the protein rule is ribozymes, catalytic RNA discovered by Thomas Cech and Sidney Altman in the 1980s, and the papers still ask what they are made of.

What the enzyme does is narrow. It lowers $E_a$ , the barrier separating reactants from the transition state they must pass through, by stabilising that state through specific interactions inside the active site. It changes neither the equilibrium, the direction nor the overall energy change, and it leaves the cycle unchanged and reusable.

The active site is a small part of the enzyme: a few amino acids arranged by the folding of the polypeptide within the globular symmetry. The active site is charge-bearing and splits into a binding site, whose amino acids make temporary bonds with the substrate, and a catalytic site, whose amino acids convert substrate into product. Those temporary bonds are hydrogen bonds.

Others need a non-protein part, and the final shape of the active site is established only once the cofactor attaches, so without it the substrate does not fit. The complete active enzyme is the holoenzyme; strip the cofactor off and the remaining protein is catalytically inactive, the apoenzyme. The cofactor takes three forms: an inorganic metal ion such as $\mathrm{Fe}^{2+}$ or $\mathrm{Mg}^{2+}$ , detachable and so an activator; an organic molecule loosely attached, a vitamin-derived coenzyme such as $\mathrm{NAD}^{+}$ ; and a prosthetic group, covalently bonded and permanent. The boards differ on the stock example, Federal giving the cytochrome iron porphyrin and Sindh the chlorophyll magnesium porphyrin, and both fit the definition.

Worked example

The catalytic cycle is examined as a four-box diagram, so learn it: $E + S \rightarrow ES \rightarrow EP \rightarrow E + P$ Catalysis is a closed loop: the substrate binds, is converted while still attached, then leaves. Students get the third box wrong by releasing the substrate before making the product. Conversion happens while the substrate is bound, which is why the quantity and shape of the enzyme are the same before and after. Sorting a cofactor is the second routine. $\mathrm{Mg}^{2+}$ is inorganic and detachable, so an activator; $\mathrm{NAD}^{+}$ is organic and detachable, so a coenzyme; an iron porphyrin is covalently bonded, so a prosthetic group. Take the enzyme rather than its helper and hexokinase carrying $\mathrm{Mg}^{2+}$ is the holoenzyme, stripped of it the apoenzyme.

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Introduction

1. Enzyme structure, the active site and its cofactorsEnzymes are organic substances, synthesised in the cell, that catalyse specific chemical reactions. Almost all are proteins, folded from hundreds of amino acids