Explain the secondary structure of proteins.
The term secondary structure refers to the interaction of the hydrogen bond donor and acceptor residues of the repeating peptide unit. The secondary structure is defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.
The secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Most common secondary structures are the alpha-helices and the beta-sheets. Beta turns and omega loops occur as well.
Protein secondary structure can be used to aid in multiple sequence alignment.