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The alimentary canal is the principal part of the digestive system. It includes the mouth, pharynx, esophagus, stomach, small intestine, cecum, and large intestine. Food is masticated in the mouth where it is mixed with digestive fluids in saliva before passing through the pharynx and esophagus by a wave-like action called peristalsis into the stomach. The esophageal sphincter is the first of several muscles that act as one-way valves to prevent the food from moving back toward the mouth. When in the stomach, muscles rhythmically contract and mix the stomach content, called chyme, with gastric juices to assist in its decomposition. The small intestine uses peristalsis to move the chyme. During this time, the liver secretes bile into the small intestine through its approximately 20 foot length. During the transit, bile breaks large fat globules into small droplets which enzymes in the small intestine act upon and pancreatic juice enters the small intestine through the pancreatic duct. The pancreatic juice contains enzymes that break down sugars and starches into simple sugars, fats into fatty acids and glycerol, and proteins into amino acids. Glands in the intestinal walls secrete additional enzymes that break down starches and complex sugars into nutrients that the intestine absorbs. Structures called Brunner's glands secrete mucus to protect the intestinal walls from the acid effects of digestive juices. The chyme then passes through the cecum and enters the large intestine where about six liters of water are removed daily, as well as dissolved salts. In addition, bacteria in the large intestine break down undigested materials and make several vitamins. The large intestine moves its remaining contents toward the rectum, which makes up the final 6 to 8 inches of the alimentary canal. The rectum stores the feces until elimination when muscle contractions in the walls of the rectum push the feces toward the anus. When sphincters between the rectum and anus relax, the feces pass out of the body.

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