Flexi Says: Chemical digestion is the biochemical process in which macromolecules in food are changed into smaller molecules that can be absorbed into body fluids and transported to cells throughout the body. Substances in food that must be chemically digested include carbohydrates, proteins, lipids, and nucleic acids. Carbohydrates must be broken down into simple sugars, proteins into amino acids, lipids into fatty acids and glycerol, and nucleic acids into nitrogen bases and sugars. Some chemical digestion takes place in the mouth and stomach, but most of it occurs in the first part of the small intestine (duodenum).