Once the food or "ingesta" as it is now called moves into the stomach the excitement really begins. Gastric juices begin their task of digesting food as the stomach churns. Gastric juices include hydrochloric acid (HCl) and enzymes called proteases and lipases. Hydrochloric acid is secreted by the parietal cells. The acidic environment in the stomach is also useful in killing off potential pathogens (harmful bacteria and fungi) before they can cause us harm. As we enter later adulthood, our production of stomach acid generally diminishes, making us more susceptible to food borne pathogens and toxins. This is just one of the reasons why Food Safety should be an important part of our daily routine. We examine Food Safety later in this website. Proteases, like pepsin, for example, are enzymes that help breakdown proteins into peptides (small protein molecules) and amino acids.

The acidified ingesta entering the small intestine stimulates the release of secretin a hormone secreted by epithelial cells in the wall of the small intestine, which in turn stimulates the release of bicarbonate-rich fluids from the pancreas and liver. The bicarbonate solution neutralizes the acidic ingesta in the same way that sodium bicarbonate (NaHCO₃ or "baking soda") from an Alka-Seltzer tablet neutralizes stomach acid. Interestingly, the mucous cells lining the stomach wall also secrete bicarbonate-rich mucus, which protects the stomach itself from being digested by hydrochloric acid.

The final stages of the enzymatic digestion of food (ingesta) occur in the small intestine. It is through the small intestine that the nutrients we obtain from foods are absorbed. The small intestine (as shown by the figure above) comprises three sections, which in order of appearance from the stomach are the duodenum, jejunum and ileum.

The duodenum is just a short section, but it receives important secretions including an assortment of pancreatic enzymes and bile from the liver via common bile ducts. The jejunum is roughly 40% of the small intestine in humans. The ileum is the remainder of the small intestine and empties into the large intestine.

Bile is a complex mixture of water, various salts (electrolytes), bile acids, cholesterol, phospholipids and bilirubin. Bilirubin is a waste product resulting from the breakdown of hemoglobin molecules from old red blood cells (erythrocytes). Bile acids (also called bile salts) are important cholesterol derivatives synthesized in the liver. Their importance comes from the fact that bile acids behave much like a detergent does in dissolving fats in water solutions. Once the fats are dissolved in a process known as emulsification they can be digested by lipases secreted by the pancreas and absorbed by the small intestine.

Bile acids also facilitate the absorption of fat-soluble vitamins through the small intestine and aid in the elimination of excess cholesterol from the body as well as other waste products. About 5% of bile acids end up in the feces while the remainder is recycled through the ileum.

The small intestine is where amino acids and monosaccharides (simple sugars) are absorbed. The bulk of the minerals that we need are also absorbed via the small intestine.

Trypsin and chymotrypsin are two of the major proteolytic (meaning protein digesting) enzymes secreted by the pancreas. They digest proteins into medium-sized to small peptides, which can be cleaved into small peptides and amino acids by a family of aminopeptidase enzymes that are also secreted into the small intestine by the pancreas.

Pancreatic amylase converts polysaccharide sugars (starch) into disaccharides such as maltose, sucrose and lactose. These sugars are then cleaved into monosaccharides by the enzymes specific to the task, namely maltase, sucrase and lactase. People who are lactose (milk sugar) intolerent either lack the enzyme lactase or have too little of it for the proper conversion of lactose into glucose and galactose.

Glucose is absorbed through the epithelial cells lining the villi of the small intestine. Actually, glucose is absorbed along with sodium, which binds to glucose via a sodium-dependent hexose transporter in a process known as active transport. Pumping glucose molecules and sodium ions (Na⁺) across the epithelial cell membrane and against a change in solution concentration (known as a gradient or "slope") is active transport and it requires energy in the form of ATP (adenosine triphosphate). From here, glucose enters the bloodstream and is carried to individual cells of the body.

The inner surface (called the lumen) of the small intestine is not smooth, but instead is covered with millions of finger-like projections called villi, which significantly increase the surface area of the small intestine.

The large intestine must reclaim much of the water used in the digestion process in order to avoid dehydration of the body. In the case of diarrhea, for example, the large intestine is forced to discharge waste products before the water reabsorption process is complete. People with prolonged episodes of diarrhea can quickly become dehydrated. Recurrent diarrhea in children and adults can lead to serious problems such malnutrition. Constipation, on the other hand, occurs when the large intestine retains waste products for too long. Waste materials basically dry out to the point where they become hard to pass. When Mother Nature calls we struggle to get the job done. It is then that we truly need intestinal fortitude.

The large intestine is a miniature ecosystem teeming with various bacteria, intestinal yeasts and fungi along with a host or other microbes, which come together to produce the "intestinal flora" as it is called. Many of the intestinal bacteria are "friendly" like lactobacillus acidophilus and bifidobacteria (bifidus), which are also known as probiotic bacteria. Probiotics has been defined as the ingestion by the host (person) live microorganisms in amounts that produce a health benefit for the host. Although most probiotic microorganisms are bacteria the yeast Saccharomyces boulardii has been given probiotic status. Saccharomyces boulardii (S. boulardii) is used, for example, to prevent diarrhea linked to the use of antibiotics.

We need these friendly intestinal microorganisms to help defend us against harmful bacteria and other pathogenic organisms and toxins. A healthy intestinal flora not only boosts our immune system, there is also evidence to suggest that friendly intestinal microbes aid in the elimination of pre-carcinogenic or mutagenic compounds from the body. Intestinal bacteria can also affect the synthesis and metabolism of certain vitamins (K, B₁₂, biotin and folic acid). Vitamin K is known as the anti-hemorrhagic vitamin and is synthesized by intestinal bacteria.

Step 3: Nutrients are transported via the blood to all parts of your body where they are taken up by the cells and used as energy or for the construction or "synthesis" as it is called, of other compounds needed by the body.