Digestive System

∞ generated and posted on 2018.10.08 ∞

Basics of alimentary canal physiology and structures from the mouth to just above the stomach, i.e., the initial preparation of food for digestion.

The anatomy, starting from the lips and ending just prior to the stomach, is charged with obtaining, physically processing, and then translocating food to the primary location of protein digestion within the body, the stomach.

This page contains the following terms: Alimentary canal, Lumen, Peritoneum, Mesentery, Brunner's glands, Crypt of Lieberkühn, Mucosa, Lamina propria, Muscularis mucosa, Submucosa, Peristalsis, Oral cavity, Uvula, Salivary gland, Salivary amylase, Pharynx, Esophagus, Lower esophageal sphincter

The above video is one of Hank Green's more inspired efforts. ☺

Alimentary canal

Tube that begins with the mouth and ends with the anus that is employed by many animals for digestion.
The alimentary canal consists of, going from top to bottom or front to back (or upstream to downstream):

The mouth, the pharynx (i.e., the throat), the esophagus, the lower esophageal sphincter (there also is an upper esophageal sphincter at the top of the esophagus), the stomach, the pyloric sphincter, the small intestine (duodenum, jejunum, and the ileum), the ileocecal valve, the large intestine (cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and rectum as well as anal canal), and then the anus and the anal sphincters.

Though some excretion occurs into the alimentary canal, that is, removal of wastes especially from the blood that ultimately leave the body via the anus, the primary function of the alimentary canal is food digestion and absorption, and in most land vertebrates water conservation as well. Other names for the alimentary canal include the gastrointestinal tract (GI tract) and, simply, gut.

Links to terms of possible interest: Accessory organs, Anal canal, Anus, Appendix, Ascending colon, Cecum, Chyme, Descending colon, Duodenum, Esophagus, Gallbladder, Hepatic portal vein, Ileum, Jejunum, Large intestine, Liver, Motility, Mouth, Oral cavity, Pancreas, Parotid gland, Pharynx, Rectum, Salivary glands, Sigmoid colon, Small intestine, Spleen, Stomach, Sublingual gland, Submandibular gland, Tongue, Transverse colon

I'm not sure that I would have worded everything in quite the same way, but the above video provides a fascinating step-by-step discussion of the process of food digestion and movement through our alimentary canal.

The above video walks you through the layers and other tissues making up the wall of alimentary canal at numerous points.


Separate interior volume of a biological structure.
Lumen is used to describe the interior volume found within the alimentary canal, especially within the intestine (as in intestinal lumen).

Lumen is also used to describe the interior portion of the blood vessels (as in vascular lumen).

The word lumen is also used to describe the interior of a cell's endomembrane system (as in the lumen of the endoplasmic reticulum).

Lumen thus is a useful anatomical term, and one that is used rather often to distinguish, for example, the intestine, the wall of the intestine, and the volume that is contained within the intestine, i.e., the lumen of the gastrointestinal tract is the volume in which food digestion and movement towards the anus actually occurs.

Links to terms of possible interest: Alimentary canal, Brunner's gland, Circular muscle, Exocrine gland, Lieberkuhn gland, Longitudinal muscle, Lumen, Mesentery, Mucosa, Muscularis, Peritoneum, Salivary gland, Serosa, Submucosa, Tubular gland, Villi

The above video does a nice job of walking us through the non-accessory organ portion of the alimentary canal proper, with emphasis on the layers making up the canal and also multiple mention of the associated lumen.


Serous membrane covering the interior of abdominal cavity and the exterior of the abdominal organs.
The peritoneum thus covers the organs of the alimentary canal, particularly as those organs are found within the abdominal cavity.

The above video provides a really nice anatomical introduction to the peritoneum and peritoneal cavity.


Tissue connecting together the back wall of the abdominal cavity and the intestines.
This connection is especially to the jejunum and ileum of the small intestine or more broadly portions of the large intestine as well. Within the mesentery are found the blood supply and nerves.

The mesentery is intimately associated with the peritoneum and it is through the mesentery that absorbed nutrients are delivered to the hepatic portal vein and otherwise within lymph.

Links to terms of possible interest: Ileum, Jejunum, Mesentery, Mesocolon, Paracolic sulcus, Sigmoid colon

The above video is not ideal for introducing the concept of mesenteries – the previous video introducing peritoneum in fact does a better job – but nevertheless does indicate the anatomical placement of some mesentery; it's just important to realize that mesentery is being referred to in association with the description of the various arteries and veins.

Brunner's glands

Secretors of mucus and bicarbonate into, and to protect the duodenum from gastric juices and chyme.
The Brunner's glands, a.k.a., duodenal glands, are located below the pyloric sphincter. The glands themselves are described as submucosal meaning that they are embedded within the wall of the duodenum, that is, rather than serving as accessory organs.

The mucus lubricates the walls of the duodenum while the bicarbonate neutralizes stomach acids. Additional protection is afforded via the inhibition of additional gastric juice production during stomach emptying via secretion of the signaling molecule, urogastrone (see also epidermal growth factor).

Crypt of Lieberkühn

Secreting, digesting, and absorbing structures found in association with the intestinal mucosa.
Also known as intestinal glands or intestinal crypts, these structures secrete mucus (via goblet cells), absorb water (as well as electrolytes), and, within the small intestine, also secrete antimicrobial peptides.

The latter, presumably, are secreted so as to kill off bacteria that have managed to survive the gastric juices of the stomach and which might otherwise invade the gland as well as infect the intestine more generally.

In addition, enteroendocrine cells are present which secrete hormones from these crypts/glands into the blood.


Tissue membrane that lines the alimentary canal along with other non-skin exposed surfaces of the body.
The mucosa represents the outer layer of the tissue layers that form the wall of the alimentary canal. Most of the alimentary canal possesses four such layers, with the exception of the mouth. All of the alimentary canal, however, includes the mucosa as one of its layers.

The mucosa is referred to as the outer layer because technically the lumen of alimentary canal, which the mucosa contacts via its basal side, is found outside the body, albeit a part of the outside world that is otherwise surrounded by the body.

Food absorption as well as some of the digestive process itself is effected by the mucosa. That is, as the tissue layer separating the extracellular digestion of food from the rest of the body's tissues, digested food must cross especially the intestinal mucosa to reach the rest of the body's tissues, and the process of crossing from the lumen of the alimentary canal into body tissues is called absorption.

The above video is a bit heavy duty on the immunology along with discussion of inflammatory bowel disease, but nonetheless provides a reasonably good introduction to what the mucosa of alimentary canal is all about, at least on its surface.

Lamina propria

The connective tissue underlying epithelial tissue together making up mucosa.
Mucosa lines more than just the alimentary canal, e.g., also the respiratory tract, the mouth (though which technically is a part of the alimentary canal), the nasal cavity, etc. These are all mucous membranes which, like the skin, consist of a combination of epithelial tissue and underlying connective tissue.

It is this connective tissue that is described as the lamina propria. The lamina propria therefore is the connective tissue component of mucosa.

Links to terms of possible interest: Basement membrane, Lamina propria, Mouth, Mucosa, Stratified squamous epithelium

Muscularis mucosa

Agitating muscle found just below the epithelial layer.
The muscularis mucosa, also known as the lamina muscularis mucosa, is a thin layer of smooth muscle that is found between the mucosa and submucosa of the alimentary canal. Its function is to agitate the mucosa so as to gently move about luminal contents relative to the mucosa as well as to disperse secretions from glands.

Think of a dog shaking itself dry, only in super slow motion, and that's more or less the function of the muscularis mucosa, that is, to scatter materials that otherwise would remain in association with the mucosal surface (though keep in mind that all of this is happening "under water", that is, within fluids of the gastrointestinal lumen, rather than in the air).

Links to terms of possible interest: Circular muscle, Connective tissue, Duct of gland, Epithelium, Lamina propria, Longitudinal muscle, Lumen, Mesentery, Mucosa, Mucosa-associated lymphoid tissue, Muscularis externa, Muscularis mucosae, Myenteric nerve plexus, Serosa, Submucosa, Submucosal nerve plexus


Lamina propria- or muscularis- underlying connective tissue.
The submucosa is found beneath the tissue membrane, the mucosa, that lines the alimentary canal. It is mostly found beneath the muscularis mucosa, which in turn is found beneath the lamina propria.

The submucosa essentially is dense irregular connective tissue or instead loose connective tissue that is connects the mucosa to the muscularis propria, which in turn are the muscles of peristalsis.

Links to terms of possible interest: Colorectal cancer, Mucosa, polyp, Serosa, Submucosa


Involuntary contractions of muscles found in the wall of the alimentary canal that serve both to mix digesting food and to move that food forward towards the anus.
Peristalsis is a rhythmic, ongoing contraction during digestion. This is a muscle contraction that you are not aware of, however, except (to a degree) in the course of swallowing and also (to a degree) especially when trying to avoid defecating (despite strong peristaltic urges otherwise to do so). Peristalsis nevertheless occurs all along in between in the alimentary canal, mixing and otherwise moving the contents of lumen of the alimentary canal literally towards the anus.

Note that in addition to peristalsis, swallowing also involves skeletal muscles, that is, which are under voluntary control. Swallowing thus can be viewed as a handoff between voluntary control over movement of the food you are consuming to involuntary control, with defecation then returning, to some degree, voluntary control again over that movement.

The smooth musculature responsible for peristalsis is known as the muscularis, though more formally, muscularis propria or muscularis externa, etc.

Links to terms of possible interest: Food bolus, Muscularis, Peristalsis, Smooth muscle

Peristalsis as seen from the inside; definitely an "Oh wow!" kind of video.

The above video shows peristalsis as seen from the inside and from the outside.

Pathological peristalsis as seen from the outside looking in.

Oral cavity

Initial chamber of the animal alimentary canal.
Our oral cavity is closed by the jaw, lips, and cheeks. It contains teeth, tongue, and both a hard palate and a soft palate. It includes the pharynx, that is, the throat, and passes into the esophagus.

It also has associated salivary glands, which secrete saliva into the mouth. Note too the uvula and tonsils (the tonsils consist of immune system tissue).

Links to terms of possible interest: Hard palate, Mouth, Oral cavity, Soft palate, Taste buds, Tongue, Tonsils, Uvula

The above video provides a quick overview of the function of the mouth, that is, the oral cavity.


Singular, hanging, posterior extension of our soft palate.
The uvula consists a combination of connective tissue, muscle tissue, epithelial tissue, and glandular tissue. Among many possible explanations of the function of the uvula, one proposed in a review by Back et al. is that it "bastes" the pharynx, thereby preventing our throat from drying out.

The above video provides a quick overview of the uvula and its potential functions.

If you've ever wondered what a uvula looks like in slow motion

Salivary gland

Various sites of production of a watery, lubricating, enzymatic, and immunologically protective substance secreted into the mouth.
There are three pairs of major salivary glands within humans as well as various minor salivary glands. The largest of these glands is the parotid gland, and salivary glands otherwise are a form of exocrine gland.

Salivary glands of course produce saliva. The digestive function of saliva is a combination of providing moisture as well as lubrication to foods and their enzymatic function is one of beginning the digestion of starches found in food via the action of the enzyme, salivary amylase.

Protective functions of salivary glands include the secretion of antibodies (IgA) along with secretion of the antibacterial enzyme, lysozyme.

Links to terms of possible interest: Parotid gland, Salivary glands, Sublingual gland, Submandibular gland

And introduction to the parotid salivary gland, our largest salivary glands.

Salivary amylase

Enzyme that digests starch as found in the mouth.
As the name implies, salivary amylase is a component of saliva. The -ase ending implies that it is an enzyme, and amylose is the carbohydrate, the starch, that the enzyme is named after in terms of what it acts upon. That is, amylose is the substrate of amylase and amylose technically is an unbranched starch, that is, an unbranched polymer of glucose.

Because of salivary amylase, the digestion of the starch component of food can begin in the mouth, thereby potentially allowing very starchy foods that don't happen to also be terribly sugary foods to taste at least a little bit sweet, and particularly so during very long bouts of chewing (thereby serving as a means of starch detection in otherwise barely palatable foods, such as may be consumed under otherwise starvation conditions while "living off of the land").

The digestion mediated by salivary amylase also can be viewed as a means of beginning the solubilization of otherwise very large and not very water-soluble starch molecules. This enzymatic activity is in addition to the mechanical breaking up of food that occurs in the mouth as a consequence of mastication (that is, chewing) as well as the addition of the other components of saliva, including moisture, to the chewed (masticated) food.

Indeed, perhaps salivary amylase is particularly useful given a not-so-modern diet that once-upon-a-time required the chewing of wild, uncooked tubers for hours to extract reasonable amounts of energy, during which salivary amylase, over those long chewing time spans, may have helped towards the otherwise difficult task of extracting available starch while at the same time providing at least a modicum of tastiness.


The back of the mouth, also known as the throat.
Food as well as air, both coming and going, pass through the pharynx either after or before passing through the mouth. This results, particularly in humans, in a potential conflict, as movement especially of food or water into the trachea (which leads to the lungs) is neither a good idea nor pleasant.

As a consequence of this conflict in functions, we have what is known as the epiglottis, which is found at the entrance to the trachea within the pharynx (atop a structure known as the glottis). The epiglottis folds to close this entrance during swallowing, thereby allowing movement of food and water exclusively to the esophagus, to which the pharynx otherwise connects.

Links to terms of possible interest: Epiglottis, Esophagus, Glottis, Larynx, Pharynx, Throat, Trachea

The above vide begins discussing the mouth at 2:20 and the pharynx around 4:45.


The muscular tube connecting the throat to the stomach.
The muscle found at the top of the esophagus is skeletal muscle and is under voluntary control. It nonetheless is reflexive in its action, that is, we don't normally think about using the muscles in our esophagus to swallow. We instead just do it. This voluntary control allows us to reverse the process of swallowing if swallowing has not proceeded beyond this skeletal muscle.

Further onward, muscle is still present but is instead not under voluntary control and it is at this point that involuntary, smooth muscle-associated peristalsis commences. Thus, to the extent that you are aware of food coursing down the length of your esophagus to your stomach, then you are aware of the directed-movement aspect of peristalsis.

Note that alternative words describing the esophagus are the alternative spelling, oesophagus, and the common name, gullet. Note too that the upper terminus of the esophagus is the pharynx, that is, the throat, while the lower terminus is the esophageal sphincter, as located at what is known as the gastroesophageal junction.

Links to terms of possible interest: Esophagus, Lower esophageal sphincter, Small intestine, Stomach

The above video does a reasonably good job of describing peristalsis within the context of the passage of food down the esophagus.

Lower esophageal sphincter

The valve found at the entrance to the stomach that prevents movement backwards in the alimentary canal, out of the stomach.
Sphincters are circular muscular bands that control the passage of materials from one compartment to another within the alimentary canal (think, for example, of the anal sphincter).

The lower esophageal sphincter – which is located at what is known as the gastroesophageal junction – prevents food and gastric juices (together, chyme or at least chyme that is in the process of forming) from moving out of the stomach and back up into the esophagus.

Low-level malfunctioning of the lower esophageal sphincter can result in heartburn. Opening of the lower esophageal sphincter to a substantial extent is associated with puking/throwing up.

The lower esophageal sphincter thus serves as a one-way valve, working with gravity to keep food along with gastric juices in your stomach. Hiatal hernias are especially problematic if they occur in combination with poor functioning of the lower esophageal sphincter.

Links to terms of possible interest: Bolus, Esophagus, Lower esophageal sphincter, Peristalsis, Stomach

"That most people call heartburn", or at least that's how the above video might have ended; otherwise this video dwells mostly on the lower esophageal sphincter and associated issues. Note that GERD stands for GastroEsophageal Reflux Disease.