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Physiology of the Small Intestine, Part 1: Jon Barron

Date: 03/08/2010   Posted By: Jon Barron

Physiology of the Small Intestine, Part 1

spongeAnd now we reach the heart of the intestinal tract. Everything so far has been preparation for this discussion. Digestion, or breaking food down into smaller bits, is certainly important -- crucial even -- but to what purpose? The purpose, quite simply, is to get the nutrition inherent in the food you ate ready so that it can be absorbed into your body where it can be used by each and every single cell to survive and carry on its individual function. When it comes to the intestinal tract, the key is absorption. It's not what you eat or digest that matters; it's what you absorb. And when it comes to absorption, the small intestine is the portal for virtually all nutrients that enter into the bloodstream.

Note: much of this discussion is easy to understand, but the core of it, the actual act of absorption is quite technical and involves some chemistry. As always, I will only deal with as much chemistry as is absolutely necessary -- and will present it in such a way as to make it comprehensible.

Digestion -- setting up absorption

Before we can get to absorption, we have to cover the final stages of digestion that take place in the small intestine. In fact, you get a combination of mechanical and chemical digestion and some absorption in the small intestine. Early in the intestine it is mostly digestion, very little absorption. However, the further on you move down the digestive tract, the more the ratio swings in favor of absorption. Effectively, the entire small bowel (duodenum, jejunum, and ileum) is devoted to these two processes: digestion and absorption. Digestion itself is divided into mechanical and chemical phases.

Mechanical digestion

Mechanical digestion, as we alluded to in our exploration of the anatomy of the small intestine, is the result of two very different, but complementary actions:

  • Segmentation contractions chop, mix, and roll the chyme (the mixture of food and digestive juices).
  • Peristalsis slowly propels the chyme forward toward the large intestine.

Segmentation represents localized activity in the small intestine, whereas peristalsis represents the more global movement that takes place throughout the entire intestinal tract.

In segmentation, circular muscles constrict and divide the small bowel into segments -- each about 3-4 inches long. A muscle then contracts between the two other muscles and subdivides the segment. This is repeated many times per minute so that the chyme is moved back and forth in the same area of the segment. Localized contractions crush and mix food within that segment alone. This action mixes the chyme with intestinal juices and prolongs its contact with the absorptive surface of the small intestine. Relaxation allows the segments to coalesce, thus allowing chyme to move on down the intestinal tract -- pushed by peristalsis.

Peristaltic contractions represent a global movement that is designed to move chyme through the entire length of the small intestine and ultimately complement the mechanical process of segmentation that holds chyme in individual segments of the intestinal tract. Peristalsis is completely under the control of the autonomic nervous system and is coordinated by the myenteric plexi (plexuses).  The myenteric plexus, also known as Auerbach's plexus, is a network of nerves between the circular and longitudinal layers of the muscles surrounding the intestinal tract.

Segmentation in a sheep's small intestine

It should be noted that peristaltic activity is weak (as opposed to segmentation), which means that food stays in the small bowel for a relatively long time (4-6 hours). And it should also be noted that peristalsis can be fairly easily slowed or even stopped by outside factors. Culprits include appendicitis, surgery, medication, and even very large meals. On the other hand, there are certain things that can increase peristalsis such as laxatives and certain kinds of illness or toxicity. As anyone who has experienced food poisoning or stomach flu would know, peristalsis is quite capable of shooting food through the intestinal tract when required. In simple terms, the body responds to toxins in the intestinal tract by adhering to the old bromide, "The solution to pollution is dilution." In effect, the body pours fluid into the intestines and increases peristalsis to eject and weaken toxins in cases such as bacterial contamination. In extreme situations such as presented by cholera, victims may actually die of dehydration from massive diarrhea. Note:  in cases of massive diarrhea, you cannot drink enough water to compensate for the loss of fluids. Without the use of massive IV's, you will die of dehydration.

It should also be noted that in the period between meals, when the small intestine is for the most part empty, peristaltic contractions continue throughout the entire small intestine. Think of it as housekeeping activity, designed to sweep the small bowel clear of debris. This movement is the cause of "growling" that can be heard when people have not eaten for awhile.

Chemical digestion

By the time chyme reaches the small bowel, it is a mix of partially digested carbohydrates, lipids, and proteins -- not yet ready for absorption. Digestion must be completed in the small intestine, because the colon will not absorb nutrients to any significant degree. As I mentioned earlier, the ratio of digestion to absorption changes dramatically as the chyme moves through the small intestine and is exposed to ever more chemical digestion. Specifically, digestion for each type of nutrient proceeds as follows.


Proteins are denatured (unwound) by acid and broken down by pepsin in the stomach. For the most part, they arrive as polypeptides (short-chain amino acids) in the small intestine. The extent of breakdown into polypeptides is dependent on several factors such as:

  • The amount of proteases that arrive undamaged with the food to significantly break down proteins before being neutralized by the release of stomach acid (about 45 minutes after food enters the stomach) -- or the use of supplemental digestive enzymes to make up the difference.
  • The ability of the stomach to produce sufficient stomach acid to denature the protein. If the protein is not unwound from its tight ball-like structure into a long chain, pepsin won't be able to work on it.
  • Sufficient pepsin production to chop up the protein into its smaller component chunks.
  • Any use of antacids or proton pump inhibitor drugs, of course, totally compromise the ability of the body to break down proteins in the stomach since they suppress the stomach acid required to unwind the protein.

protein structure

Any breakdown not accomplished in the stomach must now be compensated for in the small intestine -- in addition to the small intestine's role in breaking down short-chain amino acids into even smaller molecules capable of being absorbed into the bloodstream. In either case, after proteins leave the stomach, breakdown continues in the small bowel by activated pancreatic enzymes, including trypsin, chymotrypsin, and elastase (which breaks down elastin fibers). All three are necessary because they each act at different places in the amino acid sequences.

In addition, brush border cells of the small bowel excrete more peptidases -- enzymes such as aminopeptidase and dipeptidase -- that complete the splitting of the amino acids into ever smaller components. Ultimately, this creates molecules small enough to transport across the brush border cells and into the bloodstream.

Lipids (fats)

Some lingual and gastric lipases (fat digesting enzymes) have already been at work, but the major job of fat digestion takes place in the small bowel. Again, if fats are consumed uncooked or unprocessed or if supplemental digestive enzymes are consumed with the meal, the equation changes. But in lieu of that, at this point in the process, fats are composed mainly of triglycerides (three fatty acids bound to glycerine). It is the action of pancreatic lipase in the small bowel that breaks them down into smaller, potentially absorbable components. Specifically, pancreatic lipase splits off a monoglyceride, leaving two of the lipids still attached to the glycerine.

bileTo a significant degree, the ability of pancreatic lipase to break down lipids is regulated by how soluble those fats have become. It should be noted that lipids in their natural state are not water-soluble (that is, they do not dissolve in water). This is where bile, regulated by the gallbladder, comes into play. Bile salts (from the liver and gallbladder) emulsify (break into small droplets) the fat for easier entry into water solutions -- or more technically, into water suspensions. If you have gallstones, or have had your gallbladder removed, you will tend to have incomplete breakdown of lipids in your small intestine, resulting in fatty stools and a tendency to intestinal discomfort. In addition, and even more important, malabsorption of lipids prevents the body from receiving any of the nutrients dissolved in the fat. We're talking about vitamins A, E, and D, tocotrienols, and Omega-3 fatty acids to name some of the more familiar ones.


Unless you chewed your food properly (to pick up amylase from your saliva), or took supplemental enzymes with your meal, carbohydrates, for the most part, enter the small intestine intact. Once there, however, they are cleaved into sugars by pancreatic amylase. Further down the small bowel, maltase, sucrase, lactase, isomaltase and alpha dextrinas, secreted by the brush border cells, act on the remaining carbohydrates, cleaving off the component simple sugars one sugar at a time. For example:

  • Maltase acts on maltose -- cleaving it into its component parts, glucose and glucose.
  • Sucrase acts on sucrose -- cleaving it into glucose and fructose.
  • Lactase acts on lactose -- cleaving it into its component parts, glucose and galactose. Note: if lactase levels are insufficient, lactose intolerance develops. Bacteria ferment the unbroken lactose, and excess gas is produced.

Note: pancreatic lipase and amylase in the blood are used to measure abnormal function of damaged pancreatic cells.


Again, everything we've talked about so far is about preparing the chyme for absorption into the bloodstream. Ninety to ninety-five percent of nutrition is absorbed in the small bowel. By the time chyme has reached the small intestine, it has been mechanically broken down and reduced to a liquid by chewing and by mechanical grinding in the stomach. In addition, partial chemical digestion may already have taken place as the result of enzymes in the food itself and enzymes found in saliva. As discussed previously, the effect of those enzymes can be extensive (up to 70% of total digestion) or virtually non-existent depending on how cooked and processed the food is and how much it is chewed. The use of supplemental digestive enzymes, of course, can change that equation dramatically. And finally, the action of stomach acids and pepsin serve to denature proteins and begin the process of breaking them down, making them readily amenable to final breakdown in the small intestine.

Thus, once inside the small intestine, the "partially" digested chyme is exposed to pancreatic enzymes and bile, which ultimately break down the chyme into "component" forms of protein, carbohydrates, and fats capable of being absorbed.

By the end of its passage through the small intestine, virtually everything of value to the body has been extracted from the chyme. We're talking about:

  • Water
  • Electrolytes (sodium, chloride, potassium)
  • Proteins, carbohydrates, and fats (which have been broken down respectively into amino acids, glucose, and fatty acids)
  • Vitamins, minerals, antioxidants, and phytochemicals

Let's now look at this process in detail.

The absorption of water in the intestinal tract

Virtually all of the water that enters your intestinal tract, in whatever form, is absorbed into the body across the walls of the small intestine -- primarily through the action of osmosis. Incidentally, osmosis is defined as the movement of water across a semi-permeable membrane from an area of high water potential (closer to distilled water) to an area of low water potential (water that contains a lot of dissolved osmotically active molecules such as electrolytes and some nutrients). Incidentally, since its molecules are so large, the chyme that enters the intestinal tract from the stomach has only a minimal impact on osmotic pressure. However, as it is progressively broken down, its ability to increase osmotic pressure rises dramatically. For example, undigested starch has little effect on osmotic pressure, but as it is digested, each starch molecule breaks down into thousands of molecules of maltose, each of which is as osmotically active as the single original starch molecule. The net effect is to increase the osmotic pressure by a factor of several thousand times over the original starch molecule. Thus, as digestion proceeds, the osmotic pressure increases dramatically, thereby pulling water into the small intestine. In addition, crypt cells at the base of each villus (in the duodenum and jejunum) secrete electrolytes (chloride, sodium, and potassium) into the small intestine which further increases the osmotic pressure to pull water into the lumen (the empty space in the small intestine). On the other hand, as the osmotically active molecules (maltose, glucose, amino acids, and electrolytes) are absorbed out of the lumen and into the bloodstream, osmotic pressure decreases relative to the electrolyte rich water of the bloodstream, and water is thus reabsorbed back into the body.

The bottom line is that if the secretion and absorption of water doesn't balance, we become either bloated or dehydrated. With that in mind, we can take a look at a water balance sheet.

Production and intake:





1.0 liter


Swallowed liquids

2.3 liters (most contained in the food we eat)


Gastric juice

2.0 liters



1.0 liter


Pancreatic juice

2.0 liters


Intestinal juice

1.0 liter (primarily from brush border cells)



9.3 liters (average 154 lb man)




Recycled and excreted:




Small intestine reabsorption

8.3 liters


Colon reabsorption

1.0 liter


Excreted in feces

0.1 liter



9.3 liters (average 154 lb man)


drinking waterThus we can see that the water that enters the digestive tract and that is used in the digestive process is matched to a remarkable degree by the water that is recycled and excreted. In a healthy body, they are perfectly balanced, give or take a tenth of a liter. Keep in mind that the water lost through other means needs to be accounted for in balancing intake and outflow for the entire body. Sweat, for example, can account for anywhere from 100 to 8,000 ml (about 8.5 quarts) lost per day. You lose another quart as water vapor that passes out of your body as you breathe each day -- as anyone knows who watches their breath on a cold day. The amount lost in your urine will pretty much balance out the difference between the amount above and beyond the bare 2.3 liters you consume in your drink and food and the tenth of a liter lost in your feces and what you lose in your perspiration and breath. The bottom line is that your body will seek to balance the intake and outflow of the water it deals with every day -- to prevent bloating or dehydration. At any point it fails to do so, you will end up visiting your doctor.

Keep in mind that even small imbalances between fluid intake and output can cause major problems. Diarrhea is a common symptom of disease and can kill patients through dehydration. On the other hand, rapid over-consumption of water or other liquids, though rare, can cause a rapid drop in sodium and electrolyte levels in the bloodstream and can cause death. Or if your body loses the ability to effectively pass water through your kidneys, you suffer from edema (swelling in your legs), which puts an added burden on your heart.

So, how much water should you drink in addition to what you get in your food? Despite some medical claims to the contrary, I'm still a big fan of 64 ounces a day -- give or take, as circumstances dictate (body weight, temperature, how much you perspire, etc.).


Let's break here for now. In our next issue of the newsletter, we will focus on the fascinating topic of how your small intestine actually recognizes and absorbs specific nutrients after preparation by the digestive process. We will also discuss some of the things that can go wrong and what you can do to prevent or even reverse them.

Physiology of the Small Intestine, Part 2