Inside the alimentary canal, each protein molecule is broken down into smaller molecules.

What are these smaller molecules

Each protein molecule is broken down into smaller molecules called amino acids through chemical digestion in order to be assimilated by the alimentary canal.

Explanation:

Chemical digestion of protein molecules present in the food starts in the stomach and ends in the small intestine. This takes place through hydrolysis of protein molecules by enzymes present in the alimentary canal.

The enzymes break the polypeptide bonds of the larger protein molecules into its respective amino acids like alanine, glycine etc. The enzymes that act on proteins include:

Pepsin - stomach

Peptidase - small intestine

Elastase - pancreas

Trypsin - pancrease