The goal of protein digestion is to disassemble proteins to their constituent amino acids and smaller peptides that can be absorbed. Protein digestion begins in our stomach, as swallowed food is bathed in the acidic juice. In fact, the presence of protein/amino acids along with distension of the stomach causes stomach juice to ooze from glands in the wall of the stomach. The acid serves to straighten out the complex three-dimensional design characteristic of many proteins. Scientists refer to this as denaturing the protein or changing its natural three-dimensional design. This will make it easier for protein-digesting enzymes in the stomach and small intestine to do their job. This is analogous to straightening out a ball of yawn so that you can cut small lengths.
An enzyme called pepsin is found in stomach juice and begins to break the bonds between amino acids. The impact of pepsin is significant yet incomplete, as most of the bulk of protein digestion takes place further along in the small intestine. As partially digested proteins make their way into the small intestine, a battery of protein-digesting enzymes attack and break down protein into very small amino acid links and individual amino acids. Most of these enzymes come from the pancreas and include trypsin, chymotrypsin, carboxypeptidase A and B, elastase, and collagenase. These enzymes are made, packaged, and released by our pancreas in an inactive form. It is not till they reach the small intestine that these enzymes are activated by another enzyme produced by the small intestinal called enterokinase (enteropeptidase). The reason for this complex system is to protect the pancreas and the duct that connect to the stomach from the protein-digesting activity of these enzymes.
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