International A Level Biology / Proteins and DNA

Active sites, specificity and induced fit

Edexcel International A Level Biology (YBI11), chapter 5: Proteins and DNA, specification point 2.7. Free lesson.

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An enzyme’s tertiary structure gives its active site a specific shape, so only suitable substrates bind and form an enzyme-substrate complex. The shape can change during induced fit, while denaturation changes the active site by disrupting the tertiary structure.

How an enzyme acts

An enzyme is a globular protein folded into a precise tertiary structure. This folding creates a pocket called the active site. Although only a few amino acids form the site, the folding of the whole protein chain determines its shape. A substrate binds if its shape is complementary to the active site. Temporary bonds with the amino acids’ R groups hold it there, forming an enzyme-substrate complex. Binding lowers the activation energy. The enzyme may strain bonds in the substrate so they break more easily, or hold two substrates close enough to join. The reaction happens in…

Why enzymes are specific

In the lock and key model, the active site is rigid and has a fixed shape. A substrate with a complementary shape fits, but a differently shaped molecule does not. Without a fit, no enzyme-substrate complex forms and no reaction takes place. The enzyme’s amino acid sequence leads to its tertiary structure, which gives the active site its shape. Products have a different shape from the substrate, so they no longer fit the active site and are released.

How induced fit works

The induced fit model treats the active site as flexible, rather than rigid. The substrate is not quite complementary to the site before binding. As it binds, it causes the site to change shape and mould around it. This creates a tight fit that strains bonds in the substrate, helping to lower the activation energy. When the products leave, the active site returns to its original shape. The enzyme is still specific: only the right substrate can bind and cause the active site to change shape.

What denaturation does to the active site

Denaturation changes the enzyme’s tertiary structure. High temperature or extreme pH breaks bonds that hold this structure, such as hydrogen and ionic bonds between R groups. Peptide bonds stay intact, so the primary structure is unchanged. The active site changes shape. The substrate is no longer complementary, so an enzyme-substrate complex cannot form.

Using specificity to explain a reaction

For a three-mark explanation, link the active site’s shape to complex formation, then state what happens when the substrate does not fit. Be precise: a substrate is complementary to the active site, not to the whole enzyme. Amylase’s tertiary structure gives its active site a specific shape. Starch is complementary to the active site, so it binds and forms an enzyme-substrate complex. A protein is not complementary, so no complex forms and its peptide bonds are not hydrolysed.

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