Active sites, induced fit, collisions and denaturation

Molecules (Interaction and interdependence) · Enzymes and metabolism · note 2 of 4

Spec C1.1.4, C1.1.5, C1.1.6, C1.1.7Download all Enzymes and metabolism notes (PDF)Download all notes (PDF)6 pages

Active sites, induced fit, collisions and denaturationSpec C1.1.4, C1.1.5, C1.1.6, C1.1.7

In short

Enzymes are globular proteins with an active site, a small region of a few amino acids where the substrate binds and catalysis happens. Binding is by induced fit: the substrate and the enzyme both change shape. Substrate and active site must collide, so molecular motion matters. Specificity depends on active site shape and chemistry, and denaturation destroys both.

Enzymes are globular proteins. The polypeptide is folded into a compact, roughly spherical shape that is usually soluble in water. Part of the surface forms the active site, the region where the substrate binds and the reaction is catalysed.

The active site is made of only a few amino acids. Their R groups give it a particular shape and chemical properties (charge, polarity, hydrophobic areas). But these few amino acids are held in exactly the right positions by interactions between amino acids throughout the rest of the protein (hydrogen bonds, ionic bonds, disulfide bonds and hydrophobic interactions). The whole three-dimensional structure is needed for the active site to work.

Induced-fit binding

The substrate binds to the active site by chemical attraction between them. In the induced-fit model, both the substrate and the enzyme change shape when binding occurs. The active site moulds more tightly around the substrate, which stresses bonds in the substrate and makes them easier to break or form. The products are then released and the active site returns to its original shape.

Three panels of the induced-fit model: a substrate approaches an enzyme whose active site is not quite the same shape; in the enzyme–substrate complex the active site moulds around the substrate and both change shape; the products are released and the enzyme is unchanged and can be reused. — Induced fit: both the enzyme and the substrate change shape as the substrate binds to the active site.

Molecular motion and collisions

For a reaction to be catalysed, a substrate molecule and an active site must collide, in a suitable orientation. Enzymes and substrates dissolved in water move randomly, and these collisions happen by chance. Sometimes only one of them moves: large substrate molecules (such as starch in a starch grain or cellulose in a cell wall) may be immobilised while enzymes move to them, and some enzymes are immobilised by being embedded in membranes while their substrates move to them.

Specificity and denaturation

Enzyme–substrate specificity exists because only a substrate with a shape and chemical properties that match the active site can bind to it. Change the structure of the active site and binding fails.

Denaturation is a change to the three-dimensional structure of the protein, caused by high temperature or extreme pH. Bonds holding the tertiary structure break, so the active site changes shape and its chemical properties change. The substrate can no longer bind, so the enzyme cannot catalyse the reaction. Denaturation is usually permanent.

Exam tip:

When explaining denaturation, link the chain: bonds in the tertiary structure break, the active site changes shape, the substrate no longer fits or binds, so no enzyme–substrate complexes form.

Written and checked against the IB Biology SL specification · Updated October 2026

Frequently asked questions

Why do enzymes denature at high temperatures?

Enzymes denature at high temperatures because extra vibration breaks the bonds holding the protein's three-dimensional structure. The active site changes shape and chemical properties, so the substrate can no longer bind and no enzyme–substrate complexes form. This is why the rate falls steeply above the optimum temperature, and the change is usually permanent.

What is the induced-fit model of enzyme action?

The induced-fit model says that both the substrate and the enzyme change shape when the substrate binds to the active site. The active site moulds more tightly around the substrate, which stresses bonds in the substrate and lowers the activation energy. After the products leave, the active site returns to its original shape.

Why does the rate of an enzyme reaction level off at high substrate concentration?

The rate levels off because nearly all the active sites are occupied at any moment. Adding more substrate cannot increase the number of successful substrate–active site collisions, so enzyme concentration becomes the limiting factor. At low substrate concentrations, by contrast, more substrate means more frequent collisions and a faster rate.