C1.1 Enzymes and metabolismIB Biology HL: Revision notes

Enzymes are catalysts that speed up reactions in cells. Metabolism is the network of interdependent reactions in an organism; because enzymes are specific, many are needed, and metabolism is controlled through them.

• Anabolism: building macromolecules from monomers by condensation (protein synthesis, glycogen formation, photosynthesis).
• Catabolism: hydrolysis of macromolecules in digestion; oxidation of substrates in respiration.

Enzymes are globular proteins. The active site is made of a few amino acids whose properties depend on the whole 3D structure. In induced fit, both enzyme and substrate change shape on binding. Substrate and active site must collide; one may be immobilised (large substrates, or enzymes embedded in membranes).

Specificity comes from a complementary shape and chemistry. Denaturation by heat or extreme pH changes the active site so the substrate cannot bind.

Enzymes lower the activation energy (energy to break bonds in the substrate) but do not change the energy released when product bonds form.

Rate rises with temperature (more collisions) up to an optimum, then falls as the enzyme denatures. Each enzyme has an optimum pH. Rate rises with substrate concentration until all active sites are occupied (saturation). Sketch graphs are models; evaluate them against real results. Rate = amount of product ÷ time, or 1/time for endpoint experiments.

Intracellular enzymes act inside cells, for example in glycolysis (cytoplasm) and the Krebs cycle (mitochondrial matrix). Extracellular enzymes are secreted and act outside cells, as in chemical digestion in the gut.

Metabolic reactions are not 100% efficient in transferring energy, so heat is inevitably generated. Mammals and birds (and some other animals) use this heat to maintain a constant body temperature.

Pathways may be linear (glycolysis: glucose → pyruvate) or cyclical, where the final product regenerates the starting molecule (Krebs cycle, Calvin cycle).

An allosteric site is a binding site away from the active site; only specific substances bind there. Binding causes a conformational change that alters the active site enough to prevent catalysis. Binding is reversible. This is non-competitive inhibition: raising substrate concentration does not overcome it.

Competitive inhibitors resemble the substrate and bind reversibly to the active site, so substrate and inhibitor compete. At high substrate concentration the inhibition is largely overcome. Statins competitively inhibit HMG-CoA reductase, reducing cholesterol synthesis.

In feedback inhibition, the end product of a pathway inhibits an enzyme early in the pathway, usually by binding to an allosteric site. In bacteria, isoleucine inhibits threonine deaminase, the first enzyme of the pathway from threonine. When isoleucine is plentiful the pathway slows; when it is used up the inhibitor detaches and production resumes.

Mechanism-based inhibition is irreversible: the inhibitor binds to the active site and causes a chemical change to it. Penicillin binds covalently to transpeptidases, which cross-link peptidoglycan in bacterial cell walls, so walls weaken and growing bacteria burst. Some bacteria are resistant because they make a modified transpeptidase to which penicillin does not bind.