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The digestive tract (alimentary canal) supplies the body with water, electrolytes, and nutrients.  In order for this to be accomplished, five basic processes must occur in a synchronized fashion with far more complexity than is comprehensible.

These simultaneous, exquisitely orchestrated processes include:

(1) movement of food through the canal

(2) secretion of digestive juices and mechanical and chemical simplification of the food

(3) absorption of the digestive products, water and electrolytes

(4) circulation of blood through the all the organs involved to carry away the absorbed substances as well as sustain the organs, themselves

(5) control of all these functions by the nervous and hormonal systems

These processes begin in the mouth, (although the olfactory system (nose) and visual systems are extremely important accessory organ systems) and the unusable contents are ultimately defecated through the anus, about 22 to 30 feet (7 to 10 meters) later.

What occur between these two openings of “the tube” is the subject of volumes upon volumes of material hence we will limit our current discussion through great simplification to include only the very basics of motility and chemical modification of orally ingested substances.

Along the duration of this tube, there are two locations where mechanical digestion is of primary import; the mouth and stomach.   Additionally, chemical processing occurs during these phases of digestion with very specific pH and secretory volume requirements.  In other areas chemical processing is primary although peristaltic movement must occur in proper sequence.

The brain stem has multiple “centers” involved in the secretion of organic substances as well as water and electrolytes throughout “the tube” which have direct connections from both the eyes and nose, such as when one’s favorite food is seen or smelled salivary secretions will increase whereas when a something extremely repulsive is seen or smelled, nausea is experienced while reverse peristalsis (gag reflex) is initiated.

As previously stated, the gastrointestinal system is controlled by the nervous and the endocrine (hormonal) systems.  The enteric nervous system lies completely in the wall of the gut.  It begins in the esophagus and ends at the anus.  The number of neurons involved is approximately 100 million (approximately the same number as the spinal cord!) demonstrating the importance of the enteric system, which controls both gastrointestinal movement and secretions.  Like all neural functions, this system operates by the incredibly complex harmonic modulation of excitatory and inhibitory stimuli functioning in both afferent (incoming) and efferent (outgoing) directions whose ultimate consequence is the processing and absorption of exogenous substances necessary for not only survival, but optimal functioning of the human organism.

There are approximately 12 (or more) neurotransmitter substances that are released within this system to coordinate these vital requirements for life. 1) acetylcholine, 2) norepinephrine, 3) adenosine triphosphate, 4) serotonin, 5) dopamine, 6) cholecystokinin,   7) substance P,  8) vasoactive intestinal polypeptide, 9) somatostatin, 10) leu-enkephalin, 11) met-enkephalin, and 12) bombesin.

Many of these same neurotransmitters are found in the brain which may account for what is termed, a “gut feeling”. Although identified, the specific functions of these are not completely understood, at present. All of these neurotransmitters in the gut stimulate specific responses depending upon the receptor and are secreted in response to a central coordinating effort requiring continuous input (afferent) all along “the tube”.

The enteric nervous system consists of nerve nets (plexuses) and peripheral nerves lining the tube.

Although motility effects are less important in the hormonal control of “the tube”, three are of paramount importance:

1) cholecystokinin is secreted by the “I” cells in the duodenum and jejunum (small intestines) in response to fat.  It both stimulate gall bladder contraction of bile and decreases stomach emptying

2) Secretin is produced in the duodenum (small intestines) in response to acid emptying from the stomach and it acts to slow down the entire gastrointestinal tract (GI Tract)

3) Gastric inhibitory peptide also secreted by the duodenum acts to slow stomach emptying and does this in response to fats, amino acids and carbohydrates.

Propulsion and Mixing of Food

Hunger is the intrinsic desire to eat while appetite selects what will be eaten and in what quantities.  Hunger is easily satisfied, while appetite is never satisfied.  Hunger is a state that has rarely been experienced by most people in Western cultures; rather it is appetite that is attended to and fed.

Chewing (Mastication)

The muscles involved in chewing can exert a pressure of 55 pounds on the incisors (front four teeth) and 200 pounds on the molars (rear, grinding teeth).  Chewing involves both voluntary and involuntary functions of the fifth cranial nerve, hypothalamus, brain stem nuclei and cerebral cortex with continual feedback from sensory nerves involved in touch (tactile), smell and taste.

Although chewing is important for the digestion of all food, it is essential  for raw plant material, including fruit because they have cell walls made of cellulose, which prevents most of the nutrients from being exposed to digestive enzymes and other secretions.  Since digestive enzymes can only affect the surfaces of food particles, the rate and thoroughness of digestion is dependent on the total surface area of the food that is exposed to digestive secretions. Therefore the more that plant materials are mechanically broken apart by the teeth, jaw muscles and cheeks, the more can be chemically prepared and ultimately absorbed as a nutrient.

Both starch and cellulose consist of glucose molecules bound together however the glucose molecules in starch are connected by alpha bonds while the glucose molecules in cellulose are connected by beta bonds.  Only certain bacteria and fungi have the enzymes necessary to cleave beta bonds (cellulose) while most mammals, including humans can easily break down starch into maltose and then into glucose which is readily absorbed and serves as the primary fuel source for the body to make energy.

For this reason, cellulose is indigestible and considered “fiber” which performs the incredibly important function of increasing transit time of digestive materials through “the tube” and thereby decreasing the amount of time that waste products remain in contact with the walls of the small and large intestines (colon).  This has the direct benefit of decreasing the risk of colon cancer and systemic toxemia, which leads to all other degenerative conditions (diseases).

Although, these two polysaccharides differ only in the type of linkage between their glucose molecules, they are very different molecules.

Starch is soluble in water, cellulose is insoluble; starch is pasty, cellulose is fibrous; starch is digestible while cellulose is indigestible, starch is a food rich in calories, while cellulose is roughage.  This demonstrates the precise nature of enzymes.  Most hormones and other biologically active chemicals have a variety of actions, while enzymes are specific to only one type of reaction.

Moving on….

Chewed food passes through the esophagus rapidly to the stomach.  The mechanism by which this movement occurs is termed, peristalsis which is a coordinated wave of contractions followed by relaxation resulting in the bolus of food being propelled forward.

The motor functions of the stomach include:

1) storage

2) mixing of food with gastric secretions to form a semi fluid mixture, called chyme

3) slowing the emptying of the chyme from the stomach into the small intestine at an appropriate rate.

The stomach empties it’s contents into duodenum (first part of small intesines) at varying rates regulated by factors in both the stomach and the duodenum.  The duodenum has the greatest degree of control over the rate of emptying and maintains a rate that allows for the most efficient digestion and absorption of the chyme by the small intestine.

The duodenum, both inhibits and stimulates the pyloric sphincter (control “valve”) through nerves (enteric, autonomic and spinal) and hormones.

Thus the duodenum continually monitors and regulates the quantity and quality of chyme based upon the following:

  1. Degree of distension
  2. Irritation of mucosal lining
  3. pH  (degree of acidity/alkalinity)
  4. Osmolality  (concentration of particles that contribute to the strength of absorbing or excreting water) of chyme.
  5. Presence of breakdown products of protein and fats.

The small intestines also propels the chyme through the small intestines by peristaltic waves at a velocity which ranges from 0.5 to 2.0 cm/sec., slowing down after about 10 cm so that the net movement is approximately 1 cm/sec.

Peristaltic movements of the small intestines increases after a meal due to chyme entering the duodenum as well as the gastroenteric reflex. This reflex is very similar to the reflex that one observes when their patellar tendon is tapped, just below their patella (knee-cap), at which point their lower leg extends forward without voluntary effort.  This reflex (gastroenteric) is initiated by distention of the stomach by food.

Several hormones, as well, are involved in the coordination of the peristaltic movements occurring in the small intestines.  Gastrin, CCK, insulin and serotonin enhance intestinal motility and are secreted at different phases of food processing.  Secretin and glucagon, on the other hand, inhibit intestinal motility.

The function of the peristaltic waves is not only to propel the products of digestion forward, toward the ileocecal valve but also to disperse the chyme all along the intestinal mucosa for processing and absorption, as appropriate.

The last portion of the small intestines (ileum) connects to the cecum (first part of the colon) by way of the ileocecal valve.  The chyme is often kept in the ileum by a closed ileocecal valve for several hours until more food is taken, producing the gastroileal reflex which increases the pressure necessary to allow the ileal contents to pass into the colon.    The ileocecal sphincter is usually in a state of constriction except after food is eaten resulting in the gastroileal reflex.  The chyme is, therefore, spread out along the ileal mucosa for extended periods of time to allow for maximal absorption.  Usually about 1500 cc of chyme enter the colon daily.  The other, extremely important function of this valve is to prevent backflow of feces into the small intestines.

Pressure and chemical irritation in the ileum both relax the ileocecal sphincter and stimulate perstalsis as does fluidity of the chyme  all of which promote emptying of the ileal contents.  Pressure and chemical irritation in the cecum, on the other hand, inhibit emptying of the chyme from the ileum into the colon.  Clearly, the harder the feces becomes, due to decreased emptying, the less chyme enters the cecum and hence a viscious cycle is perpetuated, called constipation.  By the way, 90% or more of people in the “civilized” world are constipated.

The principal functions of the colon include absorption of water and electrolytes, temporary storage of feces (hours, not days ! ) and provision of an environment for billions of microorganisms that produce, among other things,  biochemicals necessary for immunity, blood clotting, fuel for colonic tissues and maintenance of appropriate pH requirements.

Haustrations (mixing and propelling movements) that occur in the colon last about 60 seconds and are repeated again each few minutes.  This has the effect of causing the fecal material to be slowly dug into and rolled over, gradually exposing different parts of the feces to the surface of the colon so that fluid and dissolved substances can be continually absorbed until only about 80 to 200 milliliters of feces are expelled each day.  A total of approximately 6 hours is required for the remaining 10 to 15% of the water to be reabsorbed. These are the quantities that have been observed in the average person who has a poor diet, of chemicals and lifeless animal and plant material, most of which has been so processed as to no longer resemble its original form, in both appearance and chemical structure.

The rectum is usually empty since it is angulated away from the descending colon in a sigmoid (S) shaped area separated by a sharp turn.  Therefore, as feces enters the rectal vault, the urge to defecate becomes intense.  The external sphincter is under voluntary control so that defecation requires the conscious, relaxation of those muscles as well as the muscles in the pelvic floor in order for defecation to occur smoothly and quickly.  Other aspects of defecation involve closing of the glottis and contraction of the abdominal muscles, which result in increased pressure towards the rectum.   When combined with the relaxation at the distal end of “the tube”, emptying occurs quite easily.  The most anatomically efficient position for complete emptying of the rectum and descending colon is the squatting position, not sitting on a chair with an opening in it, reading a magazine.

In addition to the duodenocolic, gastrocolic, gastroileal, enterogastric and defecation reflexes, there are the perioneointestinal, renointestinal, vesicoinntestinal, and somatointestinal reflexes which will not be discussed at this time.

Chemical Digestion

Digestion can be summarized as a number of specific stages that occur in sequence so that the interaction of fluid, pH, emulsifying agents and enzymes can process ingested material for absorption of appropriate material and elimination of unnecessary/toxic materials.  This requires a delicately precise, coordination of secretions from the salivary glands, liver, gall bladder, pancreas and intestinal mucosa (lining).

  1. Lubrication and mixing of ingested material with secreted fluids by glands throughout the intestinal tract beginning with the mouth.
  2. Secretion of enzymes to breakdown large molecules to smaller molecules that can be acted upon further or absorbed.
  3. Secretion of hydrogen and bicarbonate ions, as well as electrolytes, within different parts of “the tube” to establish the appropriate pH necessary to activate specific enzymes required at that point.
  4. Secretion of bile acids required to process (emulsify) fats for further enzymatic processing and absorption.
  5. Further enzymatic processing at the level of the jejunum by membrane-bound surface enzymes.
  6. Specific transport of digested material into intestinal cells and thence into blood or lymph.

The optimal pH requirements for different parts of the gastrointestinal tract vary depending upon the function and biochemical requirements of that part.


Daily Volume            pH

Saliva                         6.0-7.0         (necessary for function of salivary amylase)                                1000 ml      

Stomach                    1.0-3.5         (necessary for function of pepsin and protein digestion)        1500 ml

Pancreatic                8.0-8.3         (necessary for function of pancreatic enzymes)                         1000 ml

Bile                                 7.8              (necessary for emulsification of fats)                                              1000 ml

Small Intestine        7.5-8.0        (necessary for function enzymes and absorption)                2000 ml                                 

Colon                          7.5-8.0        (necessary for production of many bioactive chemicals and  the life of colonic bacteria)      


Most digestive enzymes are secreted as inactive precursors (zymogens).   The only exceptions are salivary amylase (breakdown starch) and certain oral lipases (breakdown fat).

Proteases (breakdown proteins) and certain lipases are synthesized by glands as zymogens which become activated as they reach the inside of “the tube”  (lumen) where the pH has been appropriately prepared for activation.  Pepsinogen (inactive), for example, in the stomach is converted to pepsin (active) only when the pH is below 4.0.

All enzymes have specific pH and temperature requirements to become active and, of course, there are optimal pH and temperature requirements for optimal functioning.  Certainly, as can be understood by that requirement, someone who has an underactive thyroid gland and is usually feeling ‘cold’, will not have the enzymes in their body functioning in an optimal fashion and hence, all operations of the body will be diminished.

Since it is beyond the scope of this discussion to elaborate with detail of each gland as it relates to chemical digestion, the stomach will be briefly detailed, as an example.

The mucosal lining of the stomach has a variety of glands.  “Chief cells” secrete pepsinogen which is activated isnto pepsin when the pH decreases below 4.0, a condition maintained by the parietal cells which produce hydrogen ions (acid).  Gastrin (hormone) is secreted by G-cells in the stomach triggered by food entering. Oxyntic glands (acid producing) which constitute 80% of the glands in the proximal (first part) of the stomach have several functions including…PRODUCE ACID (HCl).  Stomach cells also secrete intrinsic factor (IF), which is required for vitamin B12 to be absorbed further down “the tube” in the ileum.  Finally, cells in the stomach secrete an alkaline mucus which protects the lining of the stomach from the effects of the strong acid (low pH).


Dietary  carbohydrates enter “the tube” as sugar molecules connected in different lengths; polysaccharides (many sugars), di-saccharides (two sugars) and mono-saccharides (one sugar).   Enzymes secreted by the pancreas and others produced by the lining of the small intestines break down these sugars into the three basic mono-saccharides, glucose, fructose and galactose.  These single sugars are then, absorbed directly into the blood through the small intestinal mucosa.

Lipids (Fats)

Lipids are not soluble in water so they require several steps so that they can eventually be transported in the blood which is made of cells and plasma.  Plasma is 55% of blood volume and consists of 95% water so clearly, it can be understood that blood is a water transport system.

The change in the physical nature of lipids begins in the stomach where the core body temperature helps to liquefy while the stomach churns and begins the process of emulsification (break down into very small subunits).  What should be clear from the foregoing is that the fat of animals is solid at room temperature while the fat of plants (oil) is liquid hence the much greater ease of digestion and assimilation.

The emulsification process is carried further by the acid-stable lipases (enzymes that process fat) that are present in saliva and gastric (stomach) secretions.

As the lipid emulsion enters the small intestines, bile salts are released by the gall bladder in response to the hormone cholecystokinin and are activated by an alkaline pH produced by pancreatic secretions.  Both pancreatic co-lipase and lipase along with the bile salts are responsible for the majority of lipid processing and the end result is the formation of micelles  (tiny aggregates of fat with water soluble connections to the blood), which are then absorbed into circulation.  This is an extreme simplification of the process and much has been omitted for purposes of this discussion.

Proteins (Poly Peptides)

Proteins enter “the tube” as part of the diet in the form of amino acids or more complex polypeptides through eating (5% of the coloric intake/day) or are produced by the body (35-200 g), mostly digestive enzymes secreted directly into “the tube” or are shed from the cells lining the GI tract as a result of cellular turnover.

In the stomach, the pH is reduced to 1-2 by hydrochloric acid (HCl) production and acts to denature dietary polypeptides (proteins).  As proteins denature, they unfold becoming more susceptible to the actions of proteases released in the stomach.  These proteases are not fully activated until the pH drops below 2.0.  Gastric protein fragments stimulate, much like fat fragments, the release of CCK (cholecystokinin), which triggers the release of many pancreatic enzymes.

Pancreatic enzymes are released as are stomach enzymes, that is, in their zymogen (inactive) form and are then activated appropriately either by pH factors or other enzymes.  Enzymes produced by cells lining the GI tract (“the tube”) all work in synchrony to break down large polypeptides (proteins) to smaller polypeptides, tripeptides and dipeptides.  For example, enteropeptidase, produced by the cells lining the first portion of the small intestine convert trypsinogen into trypsin which, by auto-activation is then capable of activating several other proteases.  Trypsin, chymotrypsin and elastase (pancreatic proteases), then produce an abundance of free amino acids and small 2-8 residue peptides (proteins).

These protein fragments are then, further broken down by enzymes produced by the small intestines. Finally, what occurs is the transfer of these amino acids and small peptides into the enterocytes (cells lining “the tube”) where they are broken down to their final, single amino acid products and then transferred into the blood destined for the liver.


As a reminder, food entering the duodenum stimulates the secretion of CCK, which stimulates pancreatic enzyme production and secretion.  The acidity of stomach contents stimulates the release of secretin, as it enters the duodenum, which in turn triggers bicarbonate-rich pancreatic fluid, necessary for activation of pancreatic enzymes. The pancreas secretes enzymes which digest carbohydrates, lipids and proteins as discussed previously.


Not Self ?

Colonized within and upon us are approximately 100 trillion micro-organisms (slightly more than the number of cells comprising our bodies)…they are required for our basic functioning.  Approximately 10% of these organisms are yeast (fungi) while the remainder are a multitude of bacterial species that produce everything from B12 (in health) to blood clotting factors to immune enhancers to fuel sources for the cellular constituents of the gastrointestinal tract to essential components of the reproductive process…human life would not be possible without “friendly” bacteria and indeed, IT IS A MATTER OF PERSPECTIVE AS TO WHETHER ONE SHOULD CONSIDER THESE AS SEPARATE ORGANISMS OR AS FUNCTIONAL UNITS OF THE HUMAN ORGANISM.  THIS SITUATION IS NOT RESTRICTED TO HUMANS BUT EXISTS IN ALL HIGHER LIFE FORMS FROM INSECTS TO MAMMALS.