The Chemistry of Digestion: Exposing the True Secrets of the Stomach and Intestines

Digestion can be simply put as a catabolic process of breaking down the foods we eat, filtering out nutrients necessary in the body, and expelling waste material. This process is important because it provides all of the energy we use to function daily. even when organisms consisted of a mouth and anus with an esophagus connecting the two, digestion was crucial in providing the organism with energy, eventually allowing organisms to develop more complicated features. 95% of nutrients get absorbed in the small intestine. Digestion takes on average about 53 hours, with around 40 hours spent in the large intestine.

The different processes of digestion for types of biomolecules

The Chemistry of Digestion

There are many chemicals that play crucial roles in digestion in order to break down food and separate the nutrients our body needs to absorb from the waste material which will eventually be removed from the body. Digestion can be broken down into mechanical and chemical digestion. They occur in conjunction at certain times, and alternately at other times. The major components of mechanical digestion are the chewing of the teeth, peristalsis in the intestines, churning of the stomach, and the separation of fat by bile in the small intestine. Initially, the mouth performs mechanical digestion, or mechanically breaks down the foods we eat by using the teeth to chew them into smaller pieces.The food is also exposed to saliva in the mouth, which contains amylase.This catalyzes the reaction that breaks down starch into sugars. This could form smaller disaccharides such as maltose, or even monosaccharides such as glucose. Whatever the case, this enzyme consists of three domains, where the A domain the hydrolysis of starch.


This is the use of a water molecule to break bonds. In the stomach, multiple enzymes are added which break down the food, around 400-800 mL of stomach acid per meal. This “gastric” juice consists of hydrochloric acid at concentration 0.1M, as well as some sodium chloride and potassium chloride. One of the most critical of these enzymes is pepsin, which is initially added as pepsinogen by the “chief cells” and converted to pepsin as the pH is lowered to around 2 by hydrochloric acid released by the parietal cells, which also stops the activity of amylase. This is important since pepsin is initially secreted as a zymogen, an inactive form. Otherwise, the enzyme would digest parts of your body. Thus, it is only activated when inside the confines of the stomach where the pH is low enough to turn pepsinogen into pepsin.Thus chemical reactions not only help digest the food, but also control when and where it occurs.

Caption: Pepsinogen and Pepsin

Salivary amylase

Bile AcidsParietal cells also release the protein intrinsic factor, which aids the large intestine in the absorption of Vitamin B12. Other cells secrete mucous which protects the cells lining the stomach from activity of pepsin.

Yet another class of chemicals that aid in digestion are the bile acids. Found naturally in bile, a digestive fluid produced by the liver that helps the small intestines digest lipids, the bile acids play two important roles in digesting food: Bile acids are amphipathic, meaning that they can both donate and accept protons due to the bile acids. One known effect of bile in the digestive process is the “emulsification of lipid aggregates.” Here, similar to how washing detergent acts, the bile acids break fat molecules down into microscopic droplets. Another astounding property of bile acids is their ability to solubilize a great variety of lipids. Essentially, the bile acids solubilize normally insoluble compounds by surrounding them similarly to the chemical structure of a  micelle. Thus, bile acid is extremely important as it aids in digestion in more ways than one.

The Intestines

In the small intestine, wrinkles in the walls called villi release intestinal enzymes which finish the digestion of proteins and carbohydrates. In the duodenum, the first part of the small intestine, sodium bicarbonate from the pancreas neutralize the pepsin, chyme (basically food stuff mixture), and HCl from the stomach while watery mucous released by the duodenum protects the intestine. Bile from the liver emulsifies or break down fat molecules until fat-digesting enzymes (Lipase) can act upon them and also help neutralize the acids from the stomach. Other intestinal enzymes (Protease-proteins, amylase-carbohydrates, maltase sucrase lactase -sugars, peptidase -peptides, nuclease – nucleic acids in sugars) break down sugars and peptides, eventually finishing the digestion of carbohydrates and proteins. Hormonal secretions are released in the intestine in order to control the flow of food and ensure all of the nutrient can be absorbed. Secretine, released by the duodenum and triggered by food passing into the small intestine, controls the secretion of sodium bicarbonate and stops the addition of stomach content into the intestine until the previous content can be neutralized, protecting the intestine from the stomach’s acidic conditions. Gastrin in the stomach is triggered by proteins entering the stomach and triggers the addition of gastric enzymes into the stomach. Cholecystokinin (CCK) in released by the small intestine and triggers the release of bile and pancreatic enzymes into the small intestine.

Finally, in the large intestine, any remaining nutrients such as vitamins and any water is absorbed, and the waste material is expelled from the body as bowel movement.

The different parts of the digestive system


From the moment food enters your mouth, to the moment it leaves your body as waste material, a large variety of chemical reactions are occurring. Mechanical and chemical digestion break down the food you consume, allowing for it to be used by your body. Food is broken down, increasing the total surface area, allowing for contact with the enzymes. Nutrients and minerals are absorbed through various processes, made possible by the cohort of enzymes catalyzing reactions. Without the well-coordinated series of chemical processes that must happen, food would merely pass through your body without acting as sustenance.


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