When you eat the body's digestive enzymes and acids break the foods down into smaller molecules. These then pass through to the small intestine into the blood stream.
Once in the bloodstream they go all around the body and nutrients are absorbed, waste disposed, toxins are cleaned by the liver and excreted out. Anything that is unrecognisable is either stored as fat or if seen as a threat it alerts the immune system and an inflammatory response occurs.
The immune system then does its best to destroy the invader, creating antigens and telling its support troops to watch out for these invaders in future. If you name is on the list you are not coming in!