The gastrointestinal or digestive tract, also referred to as the GI tract or the alimentary canal or the gut, is the system of organs within multicellular animals which takes in food, digests it to extract energy and nutrients, and expels the remaining waste.

The GI tract differs substantially from animal to animal. For instance, some animals have multi-chambered stomachs but humans only have one stomach, so much better.

BASIC ANATOMY
In a normal human adult male, the GI tract is approximately 7½ meters long (25 feet) and consists of the following components:

Upper gastrointestinal tract

Mouth (buccal cavity; includes salivary glands, mucosa, teeth and tongue)
Pharynx
Esophagus and cardia
Stomach, which includes the antrum and pylorus and pyloric sphincter

Lower gastrointestinal tract

Bowel or intestine:
Small intestine, which has three parts:
Duodenum
Jejunum
Ileum
Large intestine, which has three parts:
Cecum (the vermiform appendix is attached to the cecum).
Colon (ascending colon, transverse colon, descending colon and sigmoid flexure)
Rectum
Anus

Related organs
The liver secretes bile into the small intestine via the biliary system, employing the gallbladder as a reservoir. The pancreas secretes an isosmotic fluid containing bicarbonate and several enzymes, including trypsin, chymotrypsin, lipase, and pancreatic amylase, as well as nucleolytic enzymes, into the small intestine. Both these secretory organs aid in digestion.

Physiology

Digestion and excretion

Food, after being mostly mechanically broken down in the mouth by the teeth and tongue, and slightly chemically broken down by the saliva, passes through the esophagus by means of peristalsis to the stomach, where the process of breakdown continues, mostly mechanical, as relatively large parts of food (now called "bolus") are minimized into smaller portions, and slight amounts of chemical processing takes place, especially on protein, by the enzymes present in the stomach. It then passes to the small intestine where further breakdown occurs, by enzymes and with the aid of bacteria, and the useful particles are absorbed into the bloodstream. The remaining particles pass through the large intestine and are ultimately expelled as feces.

Digestion is regulated both hormonally and by the autonomic nervous system:

The major hormones that control the functions of the digestive system are produced and released by cells in the mucosa of the stomach and small intestine. These hormones, such as secretin, gastrin and cholecystokinin, are released into the blood by the digestive tract and stimulate digestive juices and cause organ movement.

The two arms of the autonomic nervous system both influence the digestive process; parasympathetic nerves stimulate secretions and peristalsis while the sympathetic influence is more inhibitory.

Immune function

The gastrointestinal tract is also a prominent part of the immune system. The low pH (ranging from 1 to 4) of the stomach kills many microorganisms that enter it. Similarly, mucus (containing IgA antibodies) neutralizes many of these microorganisms. Other factors in the GI tract help with immune function as well, including enzyme in the saliva and bile enhancing intestinal bacteria serve to prevent the overgrowth of potentially harmful bacteria in the gut.

The whole digestive system comprises of:
Mouth - Pharynx - Crop - Esophagus - Stomach - Pancreas - Gallbladder - Liver - Small intestine (duodenum, jejunum, ileum) - Colon - Cecum - Rectum – Anus

MOUTH
The mouth, also known as the buccal cavity or the oral cavity, is the opening through which an animal or human takes in food.

The human mouth is covered by an upper and lower lip. They play an important role in speech, facial expression, kissing, drinking (especially with a straw), and smoking. Infants are born with a sucking reflex, by which they instinctively know to suck for nourishment using their lips and jaw. Lips are often adorned with lipstick or lip gloss. The philtrum is the vertical groove in the upper lip, formed where the nasomedial and maxillary processes meet during embryo development. When these processes fail to fuse fully, a hare lip and/or Cleft palate can result.

According to etiquette the mouth is kept closed, especially when chewing.

ESOPHAGUS

The esophagus (also spelled oesophagus/esophagus), or gullet is the muscular tube in vertebrates through which ingested food passes from the mouth area to the stomach. Food is passed through the esophagus by using the process of peristalsis. Specifically, in mammals, it connects the pharynx, which is the body cavity that is common to the digestive system and respiratory system behind the mouth (buccal cavity), with the stomach, where the second stage of digestion is initiated (the first stage of digestion is in the mouth, with teeth and tongue masticating food and mixing it with saliva).

The esophagus is lined with mucous membrane, and is more deeply lined with muscle that acts with peristaltic action to move swallowed food down to the stomach.

The junction between the esophagus and the stomach is not actually considered a valve, although it is sometimes called the cardiac valve, cardia or cardias, but is actually more of a stricture. Many people experience acid reflux, where stomach acid gets pushed up into the esophagus, causing a burning sensation, commonly termed heartburn. Extended exposure to heartburn may erode the lining of the esophagus, leading to a potentially cancerous condition called Barrett's Esophagus.

Some people also experience a sensation known as globus esophagus, where it feels as if a ball is lodged in the lower part of the esophagus.

The word "esophagus" is the result of the "o" being dropped from the typographic œ (oe) in "œsophagus".

Esophageal diseases and conditions:
The following are diseases and conditions that affect the esophagus:

Achalasia
Bleeding varices
Chagas disease
Caustic injury to the esophagus
Esophageal cancer
Esophageal web
Esophageal speech
Esophageal spasm
Esophageal stricture
Esophagitis
GERD
Mallory-Weiss syndrome
Neurogenic dysphasia
Plummer-Vinson syndrome
Schatzki's ring
Zenker's diverticulum

STOMACH

In anatomy, the stomach is an organ in the alimentary canal used to digest food. Generally, the stomach's primary function is not the absorption of nutrients from digested food; this task is usually performed by the intestine. The main job of the stomach is to break down large food molecules into smaller ones, so that they can be absorbed into the blood more easily. Latin names for the stomach include Ventriculus and Gaster; many medical terms related to the stomach start in "gastro-" or "gastric". The stomach is a highly acidic environment (maintained by the secretion of hydrochloric acid) with peptidase digestive enzymes. In fact, the stomach's interior can secrete 2 to 3 liters of gastric fluid per day.

Anatomy of the human stomach
The stomach lies between the esophagus and the first part of the small intestine (the duodenum). It is on the left side of the abdominal cavity, the fundus of the stomach lying against the diaphragm. Lying beneath the stomach is the pancreas, and the greater omentum hangs from the greater curvature.

It is divided into five sections, each of which have different cells and functions. The gastric juice, which is in the stomach, has a pH of 1-3. The pH (power of hydrogen) scale goes from 1 to 14; the lower the pH, the more acidic a substance is. Sometimes gastric juice erodes the stomach wall or its layer of mucus, causing an ulcer.

Diseases

Curling ulcer
Cushing ulcer
Stomach cancer
Gastritis
Linitis plastica
Peptic ulcer
Zollinger-Ellison syndrome

PANCREAS
The pancreas is a retroperitoneal organ that serves two functions:

Exocrine - it produces pancreatic juice containing digestive enzymes
Endocrine - it produces several important hormones, namely insulin

Anatomy
The pancreas is a retroperitoneal organ located posterior to the stomach on the posterior abdominal wall.

In humans the pancreas is a small, elongated organ in the abdomen. It is described as having a head, body and tail. The pancreatic head abuts the second part of the duodenum while the tail extends towards the spleen. The pancreatic duct runs the length of the pancreas and empties into the second part of the duodenum at the ampulla of Vater. The common bile duct commonly joins the pancreatic duct at or near this point.

It is supplied arterially by the pancreaticoduodenal arteries, themselves branches of the superior mesenteric artery. Venous drainage is via the pancreaticoduodenal veins, which end up in the portal vein. The splenic vein passes posterior to the pancreas but is said to not drain the pancreas itself. The portal vein is formed by the union of the superior mesenteric vein and splenic vein posterior to the body of the pancreas.

Function
The pancreas produces enzymes that break down all categories of digestible foods (exocrine pancreas) and secretes hormones that affect carbohydrate metabolism (endocrine pancreas).

Diseases of the pancreas

Benign tumors
Carcinoma of pancreas
Cystic fibrosis
Diabetes
Pancreatitis
Acute pancreatitis
Chronic pancreatitis
Pancreatic pseudocyst

GALLBLADDER

The gallbladder (or cholecyst) is a pear-shaped organ that stores bile (or "gall") until the body needs it for digestion. It is connected to the liver and the duodenum by the biliary tract.

Function
The gallbladder stores bile, which is released when food containing fat enters the digestive tract, stimulating the secretion of cholecystokinin (CCK).

Role in disease

Cholestasis
Cholestasis is the blockage in the supply of bile into the digestive tract. It can be "intrahepatic" (the obstruction is in the liver) or "extrahepatic" (outside the liver). It can lead to jaundice, and is identified by the presence of elevated bilirubin level that is mainly conjugated.

Cholelithiasis
Up to 25% of all people have gallstones (cholelithiasis), composed of cholesterol, lecithin and bile acids. These can cause colicky shooting abdominal pain, usually in relation with the meal, as the gallbladder contracts and gallstones pass through the bile duct. Surgery (cholecystectomy, removal of the gallbladder) is the most common treatment for gallstones. It can be performed laparoscopically, and it is in fact one of the most common procedures done through the laparoscope.

People traditionally considered at an increased risk of cholelithiasis are people who are 5 F's:

Female
Fat (obesity)
Fair (Caucasian, but this is disputed by recent studies)
Forty (middle-aged)
Fertile (the risk is increased in pregnancy)

Cholecystitis
Acute or chronic inflammation of the gall bladder causes abdominal pain. 90% of cases of acute cholecystitis are caused by the presence of gallstones.

Choledocholithiasis
When gallstones obstruct the common bile duct, the patient develops jaundice and liver cell damage. It is a medical emergency, requiring endoscopic or surgical treatment.

Gallstone ileus
A rare clinical entity is ileus (bowel obstruction) by a large gallstone, or gallstone ileus. This condition develops in patients with longstanding gallstone disease, in which the gallbladder forms a fistula with the digestive tract. Large stones pass into the bowel, and generally block the gut at the level of Treitz' ligament or the ileocecal valve, two narrow points in the digestive tract. Therapy is surgical.

LIVER

The liver is an organ in vertebrates, including humans. It plays a major role in metabolism and has a number of functions in the body including drug detoxification, glycogen storage, and plasma protein synthesis. It also produces bile, which is important for digestion. Medical terms related to the liver often start in hepato- or hepatic from the Greek word for liver, hepar.

Anatomy
The adult human liver normally weighs between 1.0 - 2.5 kilograms, and is a soft, pinkish-brown "boomerang shaped" organ. It is the second largest organ (the largest organ being the skin) Its anatomical position in the body is : immediately under the diaphragm on the right side of the upper abdomen. The liver lies on the right of the stomach and makes a kind of bed for the gallbladder (which stores bile).

The liver is supplied by two major blood vessels: the hepatic artery and the portal vein. The hepatic artery normally comes off the celiac trunk. The portal vein brings venous blood from the spleen, pancreas, and small intestines, so that the liver can process the nutrients and byproducts of food digestion. The hepatic veins drain directly into the inferior vena cava.

The bile produced in the liver is collected in bile canaliculi, which merge to form bile ducts. These eventually drain into the right and left hepatic ducts, which in turn merge to form the common hepatic duct. The cystic duct (from the gallbladder) joins with the common hepatic duct to form the common bile duct. Bile can either drain directly into the duodenum via the common bile duct or be temporarily stored in the gallbladder via the cystic duct. The common bile duct and the pancreatic duct enter the duodenum together at the ampulla of Vater. The branchings of the bile ducts resemble those of a tree, and indeed the term "biliary tree" is commonly used in this setting.

The liver is one of the only internal human organs capable of natural regeneration of lost tissue; as little as 25% of remaining liver can regenerate into a whole liver again. This is predominantly due to the hepatocytes acting as unipotential stem cells. There is also some evidence of bipotential stem cells, called oval cells, which can differentiate into either hepatocytes or cholangiocytes (cells that line the bile ducts).

Physiology
The various functions of the liver are carried out by the liver cells or hepatocytes.

The liver produces and excretes bile required for food digestion. Some of the bile drains directly into the duodenum, and some is stored in the gallbladder.
The liver performs several roles in carbohydrate metabolism:
Gluconeogenesis (the formation of glucose from certain amino acids, lactate or glycerol)
Glycogenolysis (the formation of glucose from glycogen)
Glycogenesis (the formation of glycogen from glucose)
The breakdown of insulin and other hormones
The liver also performs several roles in lipid metabolism:
Cholesterol synthesis
The production of triglycerides (fats).
The liver produces coagulation factors I (fibrinogen), II (prothrombin), V, VII, IX, and XI, as well as protein C, protein S and antithrombin.
The liver breaks down hemoglobin (bile pigments are its metabolites), toxic substances and most medicinal products. This sometimes results in toxication, when the metabolite is more toxic than its precursor.
The liver converts ammonia to urea.
The liver stores a multitude of substances, including glucose in the form of glycogen, vitamin B12, iron, and copper.
In the first trimester fetus, the liver is the main site of red blood cell production. By the 42nd week of gestation, the bone marrow has almost completely taken over that task.
Producing an artificial organ or device capable of emulating all functions of the liver is outside the reach of science in the foreseeable future. Some functions can be emulated by liver dialysis, an experimental treatment for liver failure.

Diseases of the liver
Many diseases of the liver are accompanied by jaundice caused by increased levels of bilirubin in the system. The bilirubin results from the breakup of the hemoglobin of dead red blood cells; normally, the liver removes bilirubin from the blood and excretes it through bile.

Hepatitis, inflammation of the liver, caused mainly by various viruses but also by some poisons, autoimmunity or hereditary conditions.
Cirrhosis is the formation of fibrous tissue in the liver, replacing dead liver cells. The death of the liver cells can for example be caused by viral hepatitis, alcoholism or contact with other liver-toxic chemicals.
Hemochromatosis, a hereditary disease causing the accumulation of iron in the body, eventually leading to liver damage.
Cancer of the liver (primary hepatocellular carcinoma or cholangiocarcinoma and metastatic cancers, usually from other parts of the gastrointestinal tract) Wilson's disease, a hereditary disease which causes the body to retain copper.
Primary sclerosing cholangitis, an inflammatory disease of the bile duct, autoimmune in nature.
Primary biliary cirrhosis, autoimmune disease of small bile ducts.
Budd-Chiari syndrome, obstruction of the hepatic vein.

A number of liver function tests are available to test the proper function of the liver. These are enzymes that are most abundant in liver tissue, metabolites or products.

SMALL INTESTINE

In human biology, the small intestine is the part of the gastrointestinal tract between the stomach and the large intestine (colon). In humans over 5 years old it is about 7 m long. It is divided into three structural parts: duodenum, jejunum and ileum. Food from the stomach is allowed in to the duodenum by a muscle called the pylorus, or pyloric sphincter, and is then pushed through the small intestine by a process of muscular contractions called peristalsis.

The small intestine is the site where most of the nutrients from ingested food are absorbed. There are microscopic finger-like projections called villi covering the small intestinal walls, which increase surface area for absorption. Each villus contains a lacteal and capillaries. The lacteal absorbs the digested fat into the lymphatic system, which will eventually drain into the circulatory system. The capillaries absorb all other digested nutrients.

Functions
In the small intestine, proteins are changed into amino acids; fats are changed into fatty acids; and carbohydrates are changed into sugars. The small intestine is also where most of the nutrients from ingested food are absorbed.

Small Intestine Disorders

Small intestine obstruction ("high" mechanic ileus)
Volvulus
Obstruction from external pressure
Obstruction by masses in the lumen (foreign bodies, bezoar, gallstones)
Paralytic ileus
Crohn's disease
Celiac disease
Carcinoid
Meckel's diverticulum
Gastric dumping syndrome
Infectious diseases
Giardiasis
Ascaridosis
Tropical sprue
Tapeworm infection
Mesenteric ischemia
Short bowel syndrome

DUODENUM
In anatomy of the digestive system, the duodenum is a hollow jointed tube connecting the stomach to the jejunum. It is the first part of the small intestine. It starts with the duodenal bulb and ends at the ligament of Treitz. Two very important ducts open into the duodenum, namely the bile duct and the pancreatic duct.

The duodenum is largely responsible for the breakdown of food in the small intestine. Brunner’s glands are only found in the duodenum and they secrete mucus.

The duodenum is divided into four sections for the purposes of description. The duodenum is almost all retroperitoneal.

JEJUNUM
In anatomy of the digestive system, the jejunum is the central of the three divisions of the small intestine and lies between the duodenum and the ileum. In adult humans, it is usually between 2-8m (06' 07"-26' 03") long. The pH in the jejunum is usually between 7 and 8 (neutral or slightly alkaline). The jejunum and the ileum are suspended by mesentery which gives the bowel great mobility within the abdomen.

The inner surface of the jejunum, its mucous membrane, is covered in projections called villi, which increase the surface area of tissue available to absorb nutrients from the gut contents. It differs from the duodenum due to lack of Brunner's glands. It is also different from the ileum due to less goblet cells and generally lacks Peyer's patches.

ILEUM
In anatomy of the digestive system, the ileum (not to be confused with the ilium, a pelvic bone), is the final section of the small intestine. It is about 4m long in humans, follows the jejunum and duodenum, and is separated from the cecum by the ileocecal valve (ICV). The pH in the ileum is usually between 7 and 8 (neutral or slightly alkaline).

Its function is to absorb vitamin B12 and bile salts.

COLON (ANATOMY)
In anatomy of the digestive system, the colon, also called the large intestine or large bowel, is the part of the intestine from the cecum to the rectum. Its primary purpose is to extract water from feces. In mammals, it consists of the cecum, ascending colon and approximately the first two-thirds of the transverse colon on the right (or proximal) side and the last third of the transverse colon to the splenic flexure, the descending colon, the sigmoid colon, and the rectum on the left (or distal) side.

Role in digestion
The large intestine comes after the small intestine in the digestive tract and measures approximately 1.5 meters in length. Although there are differences in the large intestine between different organisms, the large intestine is mainly responsible for storing waste, reclaiming water, maintaining the water balance, and absorbing some vitamins, such as vitamin K.

By the time the chyme has reached this tube, almost all nutrients have been absorbed by the body and only water and some electrolytes like sodium and chloride are left. As the chyme moves through the large intestine, water is removed, while the chyme is mixed with mucus and bacteria known as gut flora, and becomes feces. The large intestine produces no digestive enzymes - chemical digestion is completed in the small intestine before the chyme reaches the large intestine. The pH in the colon varies between 5.5 and 7 (slightly acidic to neutral).

Diseases of the colon

Angiodysplasia of the colon
Colitis
Colon cancer
Constipation
Crohn’s disease
Diarrhea
Diverticulitis
Hirschsprung's disease (aganglionosis)
Irritable bowel syndrome (spastic colon)
Polyposis (see also polyp)
Pseudomembranous colitis
Ulcerative colitis and toxic megacolon

CECUM
In anatomy of the digestive system, the cecum or caecum is a pouch connected to the large intestine between the ileum. It is separated from the ileum by the ileocecal valve (ICV) or Bauhin's valve, and is considered to be the beginning of the large intestine and part of the colon.

Its primary function is to absorb water and salts from undigested food. It has a muscular wall that can knead the contents to enhance absorption.

The appendix is a branch of the cecum. Like the appendix, the cecum was once believed to have no function.

RECTUM

The rectum (from the Latin verb regere "to straighten, correct, rule" hence the rectum is "that which is ruled, controlled") is the final straight portion of the large intestine in some mammals, and the gut in others, terminating in the anus.

For the diagnosis of certain ailments, a rectal exam may be done. Suppositories may be inserted into the rectum as a route of administration for medicine.

Body temperature can also be taken in the rectum. Rectal temperature can be taken by inserting a mercury thermometer for 3 to 5 minutes,

ANUS
In anatomy, the anus (from Latin anus "ring, anus") is the external opening of the rectum. Closure is controlled by sphincter muscles. Feces are expelled from the body through the anus during the act of defecation, which is the primary function of the anus.

Role in defecation
When the rectum is full the increase in intrarectal pressure forces the walls of the anal canal apart allowing the fecal matter to enter the canal. The rectum shortens as material is forced into the anal canal and peristaltic waves propel the feces out of the rectum. The internal and external sphincters of the anus allow the feces to be passed by muscles pulling the anus up over the exiting feces.

Pathology
Anal cancer, abscess, warts, fistula, fissure, itching and hemorrhoids are among the diseases of the anus that benefit from medical intervention. Birth defects of the anus include stenosis and imperforation. The anus is also a frequent site of sexually transmitted infections.

Vocabulary

Some Common pathological conditions of Digestive system:

Laboratory tests, clinical procedures and abbreviations

Practical applications

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