In general, polypeptides are unbranched polymers, so their primary structure can often be specified by the sequence of amino acids along their backbone. However, proteins can become cross-linked, most commonly by disulfide bonds, and the primary structure also requires specifying the cross-linking atoms, e.g., specifying the cysteines involved in the protein's disulfide bonds. Other crosslinks include desmosine.
The chiral centers of a polypeptide chain can undergo racemization. In particular, the L-amino acids normally found in proteins can spontaneously isomerize at the mathrm{C^{alpha}} atom to form D-amino acids, which cannot be cleaved by most proteases.
Finally, the protein can undergo a variety of posttranslational modifications, which are briefly summarized here.
The N-terminal amino group of a polypeptide can be modified covalently, e.g.,