The term alpha chain is normally used to indicate one of the subunits of a multi-subunit protein. The term 'chain' is a general term given to any peptide sequence. It can often refer more specifically to mean: The term alpha chain is normally used to indicate one of the subunits of a multi-subunit protein. The term 'chain' is a general term given to any peptide sequence. It can often refer more specifically to mean: It should be distinguished from the term alpha helix, which refers to one of the common secondary structures found in proteins, along with beta sheet.