Protein is digested by the enzyme called pepsin. The stomach has naturally produced the enzyme. Pepsin is considered to be a digestive protease that breaks down dietary protein into simpler forms. Together with chymotrypsin and trypsin, pepsin is the main protein – digesting enzyme. Specifically, pepsin is most effective in breaking down the bonds of certain simple protein molecules like phenylalanine, tryptophan, and tyrosine.