Protein's chemical breakdown begins in the stomach. Here, hydrochloric acid and an enzyme called pepsin starts to break apart protein. Then, in the small intestines, four different enzymes that are created by the pancreas break the protein pieces all the way down to individual amino acids to be absorbed. Most of the protein has made it through to the bloodstream by the time it makes it half way down the small intestines. The amino acids and nitrogen are carried into the blood to be delivered to all cells.