What Is the Structure of Proteins?

Proteins have up to four levels of structure: primary is the amino acid sequence; secondary is local folding into helices or sheets; tertiary is the overall three-dimensional shape of one polypeptide; and quaternary is the arrangement of two or more polypeptide chains. Not every protein has quaternary structure.

How the levels build

Primary structure is the order of amino acids in a polypeptide chain. Amino acids are joined by peptide bonds, formed in condensation reactions. The sequence matters because each amino acid has an R group (side chain) with particular properties, which influences how the chain folds.

Secondary structure forms when parts of the chain fold into an alpha helix or a beta pleated sheet. These shapes are held by hydrogen bonds between groups in the polypeptide backbone.

Tertiary structure is the further folding of a polypeptide into its overall three-dimensional shape. Interactions between R groups help hold this shape in place, including hydrogen bonds, ionic bonds and disulfide bridges. A protein’s shape is important to its function: for example, an enzyme’s tertiary structure determines the shape of its active site.

For example, if a change in the amino acid sequence places a different R group in the chain, the interactions holding the tertiary structure may change. The enzyme’s active site may then have a different shape, so its substrate may no longer bind as effectively.

Quaternary structure exists when a protein contains more than one polypeptide chain. Haemoglobin is an example: it contains four polypeptide chains, each associated with a haem group. A protein made from just one polypeptide can have tertiary structure without having quaternary structure.

Exam mistake to avoid

Do not describe secondary structure as the whole protein’s three-dimensional shape: that is tertiary structure. Also distinguish peptide bonds, which join amino acids in the primary structure, from the bonds and interactions that help maintain folding.