Stomach acid protects us from the effects of biologically active proteins (enzymes and hormones) by denaturing them (change shape). When denatured, they are no longer active. Pepsin and other digestive enzymes break these proteins into amino acids, which are then absorbed and used by the body to make new proteins.
Why is the presence of bovine growth hormone in milk, or any other protein-based hormone or enzyme from a plant or animal, not of great concern for human health?
While food proteins are denatured, what happens to pepsin?