Your Gastrointestinal Exam




Anatomy of the GI Tract

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The GI tract is essentially a hollow tube connecting the mouth to the anus. The GI tract has a similar layout through out its length:

  • An inner mucosal layer with an epithelial lining
  • A submucosal layer
  • A thin layer of muscle , the Muscularis Mucosa is at the junction of the mucosal and sub mucosal layers, outside this are the nerves of the mucosal plexus
  • A muscular layer with an inner circular muscle layer and an outer longitudinal layer
  • Between the muscles are the nerves of the myenteric plexus
  • A serosal layer which is continuous with the mesentry

This is illustrated graphically here:

Smallintestine layers2.png

 General Anatomy


Layers of Intestine as illustrated in the stomach
villi (from Grays anatomy)

The mucosal layer consists of a Epithelial layer, and its underlying suportive tissue, the Lamina Propria. It is separated from the Submucosal layer by the Muscularis Mucosa. The epithelial layer varies from section to section of the Gut. In the oesophagus it is a non-cornified stratified squamous epithelium; in the stomach it is mainly mucosal cells; the small intestine and large intestine are characterized by absorptive cells, with many mucous producing goblet cells. In the absorptive sections of the intestine, the surface are for absorbtion is greatly increased by finger like projections into the lumen called villi, and the absorptive cells themselves also have small projections of microvilli giving them the appearence of a brush border when viewed with a light microscope.

The lamina propria contains lymph and blood vessels which drain into larger vessels in the submucosal layer. Also in the lamina propria, particularly in the absorptive layers are numerous immune cells, wandering macrophages and lymphocytes, as well as agregations of lymphoid tissue called called Peyers patches. By some estimates 80% of the body's lymphoid tissue is in the intestine.

The cell to cell junctions are of the epithelia are mainly tight junctions. In the stomach there are very little or no gaps between the epithelial cells, but in the absorptive sections there is a certain amount of 'leakiness' so that water and some solutes can go between the cells rather than through them. The degree of leakiness is variable and is to some extent under hormonal control.


The submucosa consists of connective tissue with larger blood and lymph vessels. It is separated from the mucosa by the muscularis mucosa. Also in the the submucosal layer is the submucosal plexus, part of the enteric nervous system. The muscularis mucosa probably acts to propel the contents of the mucosal glandular lumens and crypts (see below) into the lumen and also to enhance contact of the cells with the contents of the lumen.

 Muscular Layers

Consists of an inner circular muscle, and an outer longitudinal musle. Between the two layers is the mesenteric plexus', also part of the enteric nervous system. In the stomach there is also an oblique layer of muscle fibers interior to these two. The musclar layers work in harmony to produce peristaltic contractions and segmental contractions.


The serosa is a continuation of the peritoneal membrane. It is useful to think of the gut as being evaginated into the peritoneal membrane until it completely surounds it. The double layer of membrane as it attaches to the gut is called the mesentry, and contains the main vessels and the non-intrinsic nerve supply to the gut.


Stomach diagram.svg

Each section of the intestine has a variation on this theme. A brief review of the anatomy and function of each section follows.

 Mouth & Pharynx

anatomy of mouth and pharynx

Digestion starts in the oral cavity. Food is taken into the mouth and masticated by the teeth, being mixed with saliva from the parotid, sub-mandibular, and sublingual glands. Saliva contains amylase and lipase enzymes, and these are mixed with the food. As these enzymes are deactivated on reaching the stomach, the more thoroughly food is masticated, the longer they have to act. When mastication is complete, the food is swallowed, a three part process, only the first part of which is under voluntary control. (see Motility). The epithelia lining of the mouth and pharynx is non-cornifed squamous epithelium.

Plate from Grays anatomy showing Salivary glands


The esophagus extends from the pharynx to the stomach and is about ten inches in length. It traverses three regional anatomical areas, the neck, the thorax, and the abdominal cavity. At the upper and lower ends of the esophagus the musclar layers act like sphincters - they are in tonic contraction, and these have been known as the esophageal and the cardiac sphincters. Although the esophagus is outside the abdomen, and thus does not have a serosal layer, it has the same basic layout as the rest of the system

The epithelium of the mucosal layer is non-cornified stratified squamous epithelium. The lamina propria is not copious and contains aggregates of lymphoid tissue.

The oesophageal glands are scattered throughout the length of the esophagus and are located in the submucosa. There are also cardiac glands - similar in microscopic appearance to those in the stomach, but with no enzymes in their secretions - at the proximal and distal ends of the esophagus. These glands are confined to the mucosal layer. The longitudinal rugae disappear on swallowing. The sub-mucosal layer consists of loose fibrous tissue and elastic tissue allowing expansion. No new digestive enzymes are added nor does absorption take place in the esophagus.

 Clinical Note - Barrets esophagitis

Barrett's esophagus Alcian blue stain. The characteristic goblet cells are stained blue. Normal stratified squamous epithelium is seen on the right of the image

In Barrets esophagitis the stratified squamous epithelium at the lower end of the esophagus is replaced by intestinal-type lining (columnar epithelium), due to reflux esophagitis. It is considered a pre-malignant condition as about 0.5% per year of patients will go on to develop esophageal cancer (adenocarcinoma of the esophagus). Wikipedia Article


 Gross Anatomy

Illu stomach.jpg

1. Body of stomach 2. Fundus 3. Anterior wall 4. Greater curvature 5. Lesser curvature 6. Cardia 9. Pyloric sphincter 10. Pyloric antrum 11. Pyloric canal 12. Angular notch 13. Gastric Canal 14. Rugal folds

Food enters the stomach from the esophagus at the at the cardia and passes into the stomach. In the fasting state the stomach is kept in a state of contraction, but the presence of food causes it to expand. The rugae of the stomach are folds in the mucosa seen in the fasting state, unlike the small intestine they are not there to increase surface area for absorption. Numerous pores are seen, the openings to the gastric glands which secrete enzyme persinogen and Hydrocloric Acid as well as mucous. The Hydrochloric Acid produces a pH of about 2. This highly acidic environment serves two purposes - to provide an environment hostile to bacteria and other pathogens; to denature protein, causing it to unfold, and thus increasing the area that pepsins can attack (see digestion below)

The stomach is divided into three parts, the fundus,; the main body; and the pyloric antrum. Stored food is mixed with enzymes and HCl to form chyme. The muscles feed the the chyme down to the pyloric anrum, where it is thoroughly mixed, and fed in small amounts into the small intestine by relaxation of the pyloric valve.

The Arterial Supply to the stomach is from the Coeliac Artery. The venous drainage of the stomach drains into the venous portal system

 Microscopic Anatomy

Gastric anatomy.png

The basic layout pattern holds true in the stomach, although the stomach has a third inner layer of oblique muscle fibers. The mucosal layer has numerous pits opening into the lumen, the mouths of the gastric glands. Some of these glands penetrate down into the submucosal layer.

 Gastric Glands

The gastric glands secrete mucous, hydrochloric acid and enzymes into the stomach. They are located for the most part in the mucosal layer of the stomach, but some of the deeper gland penetrate into the submucosal layer, and secrete into the lumen via. ducts. Several different secretory cells are found: mucous; parietal; chief cells; D cells; enterochafin cells; and G cells.

Mucous cells secrete both mucous and bicarbonate, substances that protect the stomach from auto-digestion. Parietal cells secrete Hydrochloric acid, 1-3 liters a day which cause the pH in the stomach to fall as low as 1. Chief cells secrete the enzyme pepsinogen, which is activated to pepsin by the pH of the stomach. G cells produce gastrin, a hormone that promotes gastric acid secretions and stimulates the growth of the gastric mucosa.

Gastric gland.pngc_gland.png">


Gray1053.png Gray1054.png Gray1055.png
Cardiac glands (at cardia) Pyloric glands (at pylorus) Fundic glands

(at fundus)

The composition of the gastric glands varies throughout the stomach. In the fundus, the glands are more branched and contain all the different kinds of secretory cells. In the pyloric part of the stomach the glands are deeper and contain more mucous cells. The Chief cells are only found in the fundus of the stomach,G cells are found mainly in the Antrum, the other cells are found in all areas.  Not much absorption of nutrients take place in the stomach, although many fluids, particularly alcohol, can be absorbed from here.

 Small Intestine

The small intestine is divided into three sections, the duodenum, the jejunum, and the ilium. In is the area of the intstine where most of the absorption takes place. In all three sections the layers follow the general pattern:
Intestinal layers.png

The surface for absorption is increased in many ways: the mucosa of the small intestine is thrown into folds called rugae; the mucosa itself has numerous finger like projections called villi, and the epithelial cells are also covered with numerous projections called microvilli. this later gives the appearance of a 'brush' on light microscopy, hence the term brush border. the following illustration shows the anatomy of a villi: Villi1.png
Mucous is secreted by numerous goblet cells, the other cells are specialized for absorption and are known as absorptive cells. In the base of the crypts are numerous secretory cells which secrete the digestive enzymes of the small intestine. Some of the cryts will penetrate into the submucosal layer forming digestive glands which will communicate with the mucosa via. a secretory duct. The length of the small intestine is about 12-13 ft. in the living adult, although after death, due to the loss of longitudinal muscle tonicity, this length will double.


epithelia of duodenum

Release of chyme into the duodenum is controlled by a number of factors that ensure that there is a controlled release into the small intestine for processing.

The duodenum is itself divided into three parts, the first, second, and third part. Small portions of highly acidic chime is released into the first part of the duodenum. This part secretes the hormone Secretin from the mucosal cells (as do the other parts of the doudenum)in response to the presence of acidic chyme leaving the stomach. This stimulates the pancreas to secrete copious amounts to neutralizing Sodium Bicarbonate, so the pH of the chyme is nearer 7 when it leaves the duodenum. the digestive enzymes of the pancreas and small intestine operate maximally at this pH. This also means that any pepsin from the stomach is also deactivated. The first part of the duodenum does not have plicae and folds, indicating that this part is probably not important for absorption.

In the Second part of the duodenum bile and pancreatic enzymes are secreted via the common duct into the lumen see (Biliary System & Pancreas) below. Absorption of food starts in the second part of the duodenum.

 Jejunum & Ilium

Transmission electron microscope image of a thin section cut through a human jejunum(segment of small intestine) epithelial cell. Image shows apical end of absorptive cell with some of the densely packed microvilli that make up the striated border. Each microvillus is approximately 1um long by 0.1um in diameter and contains a core of actin microfilaments.

The jejunum comprises about the upper two fifths and the ilium the lower three fifths of the small intestine past the duodenum. The jejunum and ilium are classified according to various anatomical differences. These differences include the arrangement of the cascade of vessels in mesentry mesentry; the distribution of Peyers patches - more numerous in the ilium; the mucosa is thicker and has more blood supply in the jejunum; and the incidence of surface area increasing plicae are more prevalent in the jejunum. Physiologically they have more or less the same functions, although probably more digestive enzymes are produced in the proximal portions of the small intestine. In any case, when we consider absorption and digestion we shall just consider them all 'small intestine'.


 Epithelial Regeneration

Epithelial cells have a life-time of 5-7 days. New cells are continuously being generated in the crypts, and migrate up the sides of the villi. These cells differentiate into either goblet cells (10-25%) or absorptive cells. Old cells are shedded from the tips of the villi. Epithelial shedding.png

 Bilary System & Pancreas

From Grays Anatomy: The anterior part of the pancreas has been removed to show the pancreatic duct

Bile and bile salts are manufactured by the liver and fed into the second part of the duodenum via the common duct. Bile salts are important in fat digestion.

The pancrease is a retro-peritoneal gland that is both an endocrine - producing the hormones insulin and glucagon, and an exocrine gland - producing digestive enzymes. The enzymes are secreted in a deactivated form - to prevent auto-digestion - and are activated in the lumen of the duodenum.

The following illustration indicates the relationships of the pancreas and bilary systems.

Pancrease biliary1.png

 Large Intestine

The large intestine extends from the ileo-caecal junction to the recum and anus. The microscopic appearence is similar to that of the small intestine. In is divided into the caecum, ascending, transverse, descending and sigmoid colon. In the colon electrolytes and water are removed, and faeces are formed. These are propelled fowards by a form of movement called mass movement. (see Motility). The colon is populated with bacteria, which usually operate in a symbiotic mode. Any food that has not been processed may be digested by these bacteria, and the products will then be absorbed by the Large Intestine.

The microscopic appearence is similar to the small intestine with the following exceptions:

  • Goblet cells are more numerous.
  • Villi are few or absent.
  • The muscularis mucosa has both a circular and a longitudinal layer.
  • The Crypts of Lieberkuhn are larger and do not branch.
  • The longitudinal muscle layer is condensed in the colonic portion of the Large Intestine into three longitudinal bands called the teniae coli.


 Rectum and Anus

Illustrating the Internal and External anal sphincters

The faeces are now passed to the rectum where they await elimination. The process of elimination is controlled by two sphinctae, the Internal and external Anal sphinctae. The former is under involuntary control, the latter under voluntary control. The functioning of these are discussed in the section on motility

 Splanchnic Circulation

This includes the blood supply and drainage - via. the portal system - of the Gut as well as the pancreas, liver and spleen. The liver is drained by the hepatic vein.

 Gastrointestinal blood supply

Blood supply comes from three arteries branching off the aorta:the coeliac artery; the superior mesenteric artery; and the inferior mesenteric artery.

 Coeliac Artery

Supplies blood to the stomach, liver, pancreas and spleen as well as the duodenum.


 Superior Mesenteric Artery

Supplies blood to the small intestine as well as the superior part of the Colon. Notice the system of arching anastemoses that is a feature of The splanchnic arteries.


 Inferior Mesenteric Artery

Supplies blood to the Colon. Again notice the system of arching anastemoses.


 Hepatic Portal System

The Hepatic Portal Vein

All the blood from the GI system below the esophagus drains into the Hepatic Portal Vein, the Portal system also drains the spleen and pancreas. Blood is conveyed to the liver for processing where it passes through millions of liver sinusoids. This allows the reticuloendithelial cells that line the sinusoids to remove bacteria and other particulate matter. Blood finally leaves the liver via. the Hepatic vein where it drains into the Inferior Vena Cava.

The total blood flow to the liver is about 1.5 Liters per minute of which two-thirds is carried by the portal vein. The Blood in the portal vein is more oxygen saturated than blood in the Systemic Venous System - about 80-90% saturated, and provides about 70% of the oxygen requirements of the liver.


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