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How Does Protein Digest in the Digestive System?

author image Jan Annigan
A writer since 1985, Jan Annigan is published in "Plant Physiology," "Proceedings of the National Academy of Sciences," "Journal of Biological Chemistry" and on various websites. She holds a sports medicine and human performance certificate from the University of Washington, as well as a Bachelor of Science in animal sciences from Purdue University.
How Does Protein Digest in the Digestive System?
A woman is slicing a chicken breast. Photo Credit mettus/iStock/Getty Images

A protein molecule comprises a string of linked amino acids, folded into a complex globular shape. Digesting the protein in the foods you eat involves unfolding the protein chain and then unlinking the amino acids it contains. These amino acids, once your body absorbs them, become incorporated into new proteins that your body synthesizes as needed. Digestion of protein occurs in your stomach and small intestine with the help of enzymes secreted by your pancreas.


After you chew and swallow your food, the low pH of your stomach acid begins to denature, or unfold, the proteins you consume. This unfolding is important because it allows digestive enzymes to access the bonds holding the individual amino acids together. The gastric juice in your stomach contains a protease, or protein-degrading enzyme, called pepsin, and pepsin cleaves the large, bulky, unfolded protein molecule into smaller pieces of protein known as peptides. The microorganisms you may inadvertently consume with your food usually die in the presence of your stomach acid, and the proteins they contain join your pool of food proteins in the digestive process.


Although no protein digestion occurs within your pancreas, this organ is essential in the digestion process. Your pancreas secretes a bicarbonate-containing buffer that serves to neutralize your gastric contents as they move out of your stomach and into your small intestine. This matters because, with the exception of pepsin, your digestive proteases and peptidases are not active at the low pH of your stomach acid. The digestive enzymes trypsin, chymotrypsin and carboxypeptidase, secreted by your pancreatic cells, empty into your small intestine.

Small Intestine

Now at a neutral pH of about 7, the peptide mixture in your small intestine is ready for further degradation. Your pancreatic enzymes function to cleave the peptide mixture into even smaller peptides and finally into individual amino acids. Each digestive enzyme works by separating specific amino acids from the short peptide chains until a pool of free amino acids remains. The walls of your small intestine consist of structures called villi, a collection of folds that greatly increases the surface area of your small intestine. The pool of individual amino acids becomes absorbed through your intestinal villi, where they enter your bloodstream and then your cells as needed.


The small intestine comprises the duodenum, the ileum and the jejunum. Protein digestion occurs in the duodenum, while absorption takes place in the ileum and the jejunum. Health issues affecting any portion of your small intestine may impact your ability to digest and absorb dietary proteins.

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