Proteins and Enzymes
Proteins
Proteins are polymers of amino acids. There are 20 common amino acids, each with the same basic structure — a central carbon bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen, and a variable R group that gives each amino acid its properties.
Amino acids join by condensation, forming a peptide bond (releasing water) to make dipeptides and polypeptides.
The four levels of protein structure
| Level | Description |
|---|---|
| Primary | The sequence of amino acids in the polypeptide chain (determined by the gene) |
| Secondary | Local folding into α-helices and β-pleated sheets, held by hydrogen bonds |
| Tertiary | The overall 3D shape of the chain, held by hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions |
| Quaternary | Two or more polypeptide chains joined together (e.g. haemoglobin has 4 chains) |
The precise 3D shape determines a protein's function — especially for enzymes and receptors.
Types of protein
- Fibrous (e.g. collagen) — long, structural, insoluble.
- Globular (e.g. enzymes, haemoglobin) — rounded, soluble, functional.
Test for proteins: the Biuret test — add Biuret reagent → turns purple/lilac if protein is present.
Enzymes
Enzymes are globular proteins that act as biological catalysts, lowering the activation energy of reactions. The substrate binds to the enzyme's active site.
- Lock and key model: the substrate fits a rigid, complementary active site.
- Induced fit model (more accurate): the active site changes shape slightly to mould around the substrate, straining bonds and lowering activation energy further.
Factors affecting enzyme activity
- Temperature: rate rises to an optimum, then the enzyme denatures (tertiary structure/active site destroyed).
- pH: each enzyme has an optimum pH; extremes denature it.
- Substrate concentration: rate rises until all active sites are saturated (Vmax).
- Inhibitors: competitive inhibitors bind the active site (overcome by more substrate); non-competitive inhibitors bind elsewhere, changing the active site's shape (not overcome by more substrate).
Worked example
Why does a change in a single amino acid (primary structure) alter a protein's function?
- The primary sequence determines how the chain folds, so one change can alter the hydrogen/ionic/disulfide bonds in the tertiary structure, changing the 3D shape — and for an enzyme, its active site. ✓
Common mistakes
- Confusing the bonds at each level (secondary = H-bonds; tertiary adds ionic, disulfide, hydrophobic).
- Saying enzymes are "used up" — they are catalysts and are reused.
- Mixing up competitive (active site) vs non-competitive (elsewhere) inhibition.
Exam tips
- Learn the four structure levels and the bonds holding each.
- Explain enzyme action via induced fit and lowering activation energy.
- Distinguish competitive vs non-competitive inhibitors, including the effect of adding more substrate.
Key facts to remember
- Proteins = amino acids joined by peptide bonds; structure levels primary → secondary (H-bonds) → tertiary (ionic/disulfide/hydrophobic) → quaternary.
- 3D shape determines function; the Biuret test goes purple for protein.
- Enzymes lower activation energy via induced fit; affected by temperature, pH, substrate concentration and competitive/non-competitive inhibitors.