Proteases are enzymes that break peptide bonds. One class of proteases are the serine proteases, which you may have studied at some point. Chymotrypsin is an example of a serine protease. Serine is an amino acid in which the side-chain has a hydroxyl group. Why would a group of proteases be named after serine? The reason that a serine residue in the active site is crucial to the functioning of these enzymes. The serine oxygen of the enzyme acts as a nucleophile in forming an acyl enzyme intermediate in the hydrolytic mechanism.