C1.1 Enzymes and metabolism

Enzymes as catalysts

Metabolism is the full set of chemical reactions in an organism. Most would be far too slow at body temperature without enzymes, globular proteins that speed reactions without being used up. Each enzyme has an active site, a region whose shape and chemical properties match a particular substrate, which gives enzymes their specificity. Metabolism includes anabolic reactions that build larger molecules and catabolic reactions that break them down.

Collisions and induced fit

For a reaction to happen, substrate and enzyme must collide with the right orientation. Substrate and enzyme molecules move randomly in solution (substrates usually move more, though large enzymes may be fixed in membranes). In the induced-fit model, the active site is not a perfectly rigid lock: as the substrate binds, both the enzyme and substrate change shape slightly, giving a tighter fit that stresses bonds in the substrate.

flowchart LR
  A["Substrate collides with active site"] --> B["Enzyme-substrate complex forms"]
  B --> C["Induced fit: shape change strains bonds"]
  C --> D["Activation energy lowered"]
  D --> E["Products form and are released"]
  E --> F["Enzyme unchanged and reused"]

Activation energy

Every reaction needs an initial input of energy to break bonds, the activation energy. Enzymes lower it, so a much larger fraction of collisions lead to reaction at normal temperatures. The overall energy change of the reaction is not altered.

Factors affecting rate

• Temperature: as it rises, molecules move faster and collide more often, so rate increases up to an optimum. Above the optimum, vibrations break the bonds holding the active site's shape, the enzyme denatures and the rate falls steeply.
• pH: each enzyme has an optimum pH. Away from it, charges on R-groups in the active site change, reducing binding; extreme pH denatures the enzyme.
• Substrate concentration: rate rises as more collisions occur, then levels off when all active sites are occupied at any moment (saturation), so enzyme concentration becomes limiting.

Measuring rates

Rate is the amount of product formed or substrate used per unit time. Practical examples include measuring oxygen from catalase breaking down hydrogen peroxide, or the time for starch to disappear when amylase acts. The initial rate is found from the gradient of a tangent at the start of a product-time curve, before substrate runs low.

Metabolic pathways (HL)

Many reactions occur as chains or cycles, each step catalysed by its own enzyme, with the product of one step becoming the substrate of the next. Glycolysis and the Krebs cycle are examples.

Inhibition (HL)

End-product inhibition is negative feedback: the final product of a pathway binds to an allosteric site on the first enzyme, slowing the whole pathway when product is plentiful. An example is isoleucine inhibiting threonine deaminase. Some drugs act as mechanism-based inhibitors: penicillin binds irreversibly to a bacterial enzyme that builds cell walls.

Common mistakes

• Saying enzymes are "killed" by heat. They are denatured; they were never alive.
• Saying enzymes "provide energy". They lower the activation energy.
• Claiming temperature above the optimum "slows molecules down". It denatures the enzyme.
• Mixing up which inhibitor is overcome by extra substrate.

Exam tips

• Describe a rate graph by quoting values at key points, then explain using collisions, saturation or denaturation.
• Deduce inhibitor type from graphs: same plateau at high substrate means competitive; lower plateau means non-competitive.
• Calculate initial rate from a tangent and include units such as cm³ s⁻¹.
• In practical designs, name controlled variables (temperature, pH, enzyme concentration) and how each is kept constant.