Secondary Structure of Proteins

The secondary structure is the way a polypeptide chain coils or folds in regular patterns, held in place by hydrogen bonds between peptide links.Each peptide link contains an N-H group and a C=O group. The δ+ H of an N-H is attracted to a lone pair on the δ− O of a C=O further along the chain or in a neighbouring section. These hydrogen bonds are between atoms of the backbone (the peptide links), not the side chains.There are two main types:α-helix: the chain coils into a spiral. The C=O of each peptide link hydrogen bonds to the N-H of the peptide link four amino acids further along, so the hydrogen bonds run roughly parallel to the axis of the helix. The side chains point outwards.β-pleated sheet: sections of chain lie side by side and are linked by hydrogen bonds between the C=O groups of one section and the N-H groups of the next, giving a flat, folded (pleated) sheet.Individual hydrogen bonds are weak, but there are very many of them, so together they hold the shape firmly. Because each one is weak, they are broken by heating or by a change in pH. This is one reason proteins lose their shape (are denatured) under these conditions.Worked example. In an α-helix, which group does the C=O of amino acid 1 hydrogen bond to? It bonds to the N-H of amino acid 5, four residues further along the chain.Many proteins contain both α-helix and β-sheet regions, linked by less regular sections of chain.