Amino acids and protein structureEdexcel A-Level Biology A: Revision notes

All proteins are polymers of amino acids, of which 20 different ones are commonly found in living organisms. Every amino acid has the same general structure around a central carbon atom:

• an amino group, –NH₂
• a carboxyl group, –COOH
• a hydrogen atom, –H
• a variable R group

It is the R group that differs between amino acids. R groups can be hydrophobic or hydrophilic, charged or uncharged, and some contain sulfur (as in cysteine). You do not need to learn the structures of specific amino acids.

Two amino acids join in a condensation reaction. The –OH from the carboxyl group of one amino acid and an –H from the amino group of the other are removed, forming a molecule of water. The two amino acids are now linked by a peptide bond (–CO–NH–) and form a dipeptide.

Repeating this many times forms a polypeptide. A protein is one or more polypeptides folded into a functional shape. Peptide bonds are broken by hydrolysis, which adds water, as in digestion.

• Primary structure: the sequence of amino acids in the polypeptide, held by peptide bonds.
• Secondary structure: regular coiling or folding of the chain, such as the α-helix and β-pleated sheet, held by hydrogen bonds between the –NH and –C=O groups of the backbone.
• Tertiary structure: the further folding of the whole chain into a specific three-dimensional shape.
• Quaternary structure: two or more polypeptide chains held together in one protein.

The primary structure determines everything else. It fixes where the R groups are, which decides where bonds form between them, so it determines the three-dimensional shape and therefore the properties of the protein.

Bonds between R groups hold a polypeptide in its tertiary shape:

• Hydrogen bonds: weak but numerous, between polar groups.
• Ionic bonds: between oppositely charged R groups (such as –NH₃⁺ and –COO⁻); broken by changes in pH.
• Disulfide bridges: strong covalent S–S bonds between two cysteine R groups.
• Hydrophobic interactions: hydrophobic R groups cluster together away from water, usually in the centre of a globular protein.

Globular proteins are folded into compact, roughly spherical shapes. Hydrophilic R groups are on the outside and hydrophobic R groups are in the centre, so they are soluble and suited to metabolic roles such as enzymes and transport.

Haemoglobin has quaternary structure: four polypeptide chains (two α and two β). Each chain contains a haem group with an iron(II) ion, Fe²⁺, that binds one oxygen molecule, so one haemoglobin molecule can carry four O₂ molecules. Its solubility lets it pack into red blood cells at high concentration.

Fibrous proteins are long and narrow, with regular, repetitive primary structures. They are usually insoluble and provide strength or support.

Collagen is made of three polypeptide chains wound into a triple helix. About every third amino acid is glycine, whose very small R group lets the chains pack tightly. Hydrogen bonds hold the chains together, and covalent cross-links join neighbouring molecules into fibrils and fibres. This gives collagen high tensile strength, which is needed in tendons, skin and artery walls.