The human body makes about twenty-two different digestive enzymes, capable of digesting protein, carbohydrates, sugars, and fats. People digest food in stages: beginning in the mouth, moving to the stomach, and finally through the small intestine. At each step, specific enzymes break down different types of food. An enzyme designed to digest protein, for example, has no effect on starch, and an enzyme active in the mouth will not be active in the stomach. This process is balanced through acidity; each site along the digestive track has a different degree of acidity that allows certain enzymes to function while inhibiting others.

  As enzymes begin digesting food in the mouth and continue their work in the stomach, plant enzymes (derived from food itself or taken as a supplement) also join in and become active. The food then enters the upper portion of the small intestine where the pancreas (a digestive organ that feeds enzymes into the gut) provides pancreatic enzymes to further break down the food. Final breakdown of remaining small molecules of food occurs in the lower small intestine. Ideally, these enzymes can work together, digesting food and delivering nutrients to cells to maintain their health. Protocols in enzyme therapy are based on this sequence of events.