3.1.4 Proteins and Enzymes

Why this matters

Almost every process you study at A-Level depends on proteins. Haemoglobin (a transport protein) carries oxygen because its quaternary structure has four haem groups in exactly the right place. Antibodies bind one specific antigen because their tertiary structure produces a complementary binding site. Channel proteins and carrier proteins move substances across membranes because their shape opens, closes or rotates in response to binding. Enzymes — the most heavily examined sub-topic — control the rate of every metabolic reaction from photosynthesis to respiration. AQA rewards two ideas relentlessly here: that structure determines function, and that shape (especially of an active site) is the mechanism behind specificity. Get those two right and you score the bulk of the marks across this whole section.

How to learn this topic

Build on what you already know

• Atoms, ions and covalent bonds (GCSE Chemistry)
• Polymers and monomers (3.1.1)
• Condensation and hydrolysis reactions (3.1.2 carbohydrates, where the same chemistry is met first)
• Hydrogen bonding (covered briefly in 3.1.5 nucleic acids)
• Activation energy and the energy profile of a reaction (GCSE Chemistry)

1. Recap amino acid structure: a central carbon, an amine group, a carboxylic acid group, a hydrogen, and a variable R group
2. Condensation: two amino acids join with loss of water to form a peptide bond; hydrolysis breaks it with addition of water
3. Levels of protein structure — primary (sequence), secondary (alpha-helix / beta-pleated sheet from hydrogen bonds), tertiary (3-D shape from H-bonds, ionic, disulfide and hydrophobic interactions between R groups), quaternary (more than one polypeptide chain, sometimes plus a prosthetic group)
4. Introduce enzymes as proteins with a precisely shaped active site, and define them as biological catalysts that lower activation energy
5. Induced fit: substrate binding causes a small change in the active site so the substrate is held more tightly, then converted into product(s)
6. Apply: how temperature, pH, substrate concentration, enzyme concentration, competitive inhibitors and non-competitive inhibitors each affect the rate of reaction — and crucially, explain WHY in terms of active-site shape and enzyme-substrate complex formation

Notes

Amino acids and the peptide bond

Amino acids are the monomers of proteins. Every amino acid has the same skeleton — a central carbon bonded to an amine group (-NH₂), a carboxylic acid group (-COOH), a hydrogen, and a variable R group (the side chain). The 20 amino acids that build human proteins differ only in their R group, which is what gives each protein its individual chemistry.

Two amino acids join in a condensation reaction: the -OH of one carboxylic acid and an -H from the next amine group are lost as water (H₂O), forming a covalent peptide bond. The product is a dipeptide. Many amino acids joined this way make a polypeptide. The reverse reaction — hydrolysis — splits a peptide bond by adding water back across it.

Four levels of protein structure

• Primary — the sequence of amino acids in the polypeptide. Determined directly by the DNA base sequence of the gene.
• Secondary — local folding of the polypeptide chain into an alpha-helix or beta-pleated sheet, held in place by hydrogen bonds between the C=O of one amino acid and the N-H of another.
• Tertiary — the full three-dimensional shape of a single polypeptide, fixed by interactions between R groups: hydrogen bonds, ionic bonds, hydrophobic interactions, and (where two cysteine R groups are nearby) covalent disulfide bridges.
• Quaternary — present only when a protein has more than one polypeptide chain (e.g. haemoglobin's four). May also include a non-protein prosthetic group (e.g. the iron-containing haem in haemoglobin).

The key idea AQA hammers: the shape of a protein is determined by the sequence of amino acids, and the shape determines the function. Change one amino acid and you can change the shape; change the shape and you change the function.

Enzymes as biological catalysts

Enzymes are proteins that speed up the rate of chemical reactions without being used up. They do this by lowering the activation energy of the reaction — the minimum energy collisions need before the reaction can happen. Each enzyme has an active site — a small region on its surface whose shape is complementary to its substrate.

The induced fit model

The substrate binds to the active site, forming an enzyme-substrate complex. As it binds, the active site changes shape slightly so it fits the substrate more closely — putting strain on the substrate's bonds and so lowering the activation energy. The substrate is converted to products, which no longer fit the active site and so leave. The enzyme is unchanged and can catalyse the same reaction again.

What changes the rate of an enzyme-controlled reaction

• Temperature — higher temperature gives molecules more kinetic energy, so more frequent collisions and more enzyme-substrate complexes form. Above the optimum, vibrations break the hydrogen and ionic bonds holding the tertiary structure together; the active site changes shape and the enzyme is denatured — irreversible.
• pH — extremes alter the charges on R groups, breaking the ionic and hydrogen bonds in the tertiary structure. Active site changes shape, substrate no longer fits.
• Substrate concentration — more substrate means more collisions with active sites, so rate rises. Once all active sites are occupied (enzymes saturated), adding more substrate has no effect.
• Enzyme concentration — more enzyme means more active sites. Rate rises until substrate becomes limiting.
• Competitive inhibitors — similar shape to the substrate, occupy the active site. Increasing substrate concentration overcomes the inhibition.
• Non-competitive inhibitors — bind to the enzyme away from the active site, changing the tertiary structure and so the active-site shape. Adding more substrate does not overcome the inhibition.

Mark-scheme phrasing

Common misconceptions

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Worked example

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Frequently asked questions