Our bodies secrete enzymes to speed up the chemical processes in a variety of situation, with digestion being one such incidence that is repeated several times daily. In the stomach, food and beverages containing protein are greeted with pepsin, which, along with mucus, hydrochloric acid, and the grinding motion of the stomach muscles, helps to make the initial chunks of food into more of a liquid stew that empties into the small intestine where it is more easily absorbed. The pancreas then dribbles into duodenum lipase to break down fats and amylase to break starch. Other digestive enzymes work to further break down certain sugars throughout the small intestine; for example, the milk sugar lactose is degraded by the digestive enzyme lactase in the small and large intestine. All of this metabolic action is essential to allow the body to properly absorb the specific nutrients.
The vast majority of people in the world secrete enough such enzymes that supplementation is unnecessary. However, some people lack enough of a certain enzyme or enzymes and must supplement their diets with synthetically produced enzymes. For example, those with cystic fibrosis take supplements to help digest foods while those with lactose intolerance may take a pill to allow them to consume ice-cream or milk without a wicked case of gas that would follow if they didn't. Many people with pancreatic disease such as pancreatic cancer must take enzymes as the pancreas is impaired; those with gastroparesis may have to take supplemental enzymes as well.
Currently, there are no well-controlled studies to support a theory that supplementing with digestive enzymes would improve symptoms of reflux because it would aid in digestion, thus making things move along more quickly through the stomach. Many of the supplemental enzymes are not acid-resistant and must be protected in some fashion to keep them from releasing in the stomach; once in the intestine, the enzymes are released and do their work.