How are secondary structures in proteins such as alpha-helixes formed?

Secondary structures in proteins, such as alpha-helices, are primarily formed through hydrogen bonding between backbone atoms of the polypeptide chain. In particular, the carbonyl oxygen of one amino acid forms a hydrogen bond with the amide hydrogen of another amino acid that is typically four residues away in the sequence. This pattern of hydrogen bonding stabilizes the helical structure, allowing the polypeptide to coil into the characteristic spiral shape of an alpha-helix.

In addition to hydrogen bonds, the formation of secondary structures does not rely on covalent bonds between amino acids, which are typically found in the primary structure of proteins. Similarly, while the environment can influence protein folding, secondary structures themselves are specifically defined by these hydrogen bonds. Ionic bonds, which may occur between side chains of amino acids, play a more significant role in the tertiary or quaternary structures of proteins rather than in maintaining secondary structures.