In protein degradation, the primary structure is destroyed, which means the covalent peptide bonds are broken. However, denaturation only involves the unfolding of a protein, where quaternary, tertiary and secondary structures are disrupted but primary structure remains intact.

Degraded proteins can still have a secondary or tertiary structure and can even still have their biological activity in some cases, whereas denatured proteins lose its biological function because the function is directly dependent on its structure.