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A: The enzymes that break down protein include trypsin, chymotrypsin, pepsin, thermolysin, glutamyl endopeptidase, elastase, bromelain and papain. Trypsin, pepsin, elastase, thermolysin, glutamyl, endopeptidase and chymotrypsin are made in the human body. Bromelain comes from pineapples and papain comes from papayas.
Proteins are broken down in the stomach by pepsin and in the small intestine by chymtrypsin, trypsin, and carboxypeptidase among others. Proteases are enzymes that degrade proteins. Pepsin is a protease that breaks down large proteins into smaller polypeptides.