Anatomy and Physiology of the GI Tract and Accessory Organs


  • Digestion is an incredibly complex process involving multiple organs and organ systems
  • Most of the digestion/absorption of nutrients occurs in the small intestine, however additional critical processes occur in the large intestine
  • Other critical functions including immunity and processes involving the microbiome occur in the small and large intestine as well

Table of Contents


  • Learn how digestion occurs, and what organs are involved
  • Understand the symbiotic relationship between the body and the microbiome
  • Learn how to modify nutrition, supplements and lifestyle to optimize gut health around your/your clients’ goals


  • Name the critical functions of the gastrointestinal tract
  • Understand the function of the major organs involves in digestion
    • Liver, salivary glands, gallbladder, pancreas, stomach, small and large intestine
  • Recognize and describe the folded structure of the small intestine
  • Understand where the gut lumen, epithelial layer and lamina propria are in relation to one another
  • Describe the journey of food from our mouth, through the stomach, into the small and large intestine as it relates to what stages of digestion occur in what locations
  • Explain how protein, fat and carbs are broken down and absorbed into the body
  • Have a basic understanding of how hormones regulate digestion

Review terms here: Gut Biology Key Terms

Introduction to the Gastrointestinal System

Key points

  • The gastrointestinal system is an extremely complicated conglomerate of organ systems
  • Key roles include digestion and excretion of waste, and housing of the GI microbiome
  • Billions of bacteria that live in your gut

System 1 – Gastrointestinal tract aka Alimentary Canal


avg length 5-7m Small and large Intestine - Lumen Like to think of the Lumen as outside of the body – You really want to keep your food away from your body.


  • Absorption of nutrients
  • Elimination of waste
  • Home of the microbiome


  • Pharynx and Esophagus: receive and transport food from mouth to stomach
  • Stomach Initiates the process.. doesn’t do the full thing Not involved in absorption of nutrients other than B12
    • Combine saliva, food, & gastric juices
    • initiates protein digestion
    • Kill microbes in food
    • Absorbs some vitamin B12
  • Small Intestine Tries to fold itself on itself to increase surface area to absorb as much nutrients as possible holds much of our immune system

Parts of the small Intestine: Duodenum jejunum ileum

  • Mixes “Chyme” with secretions from the small Intestine, Pancreas, & Liver (through the Gallbladder) to complete the digestion of carbohydrates, proteins, lipids, & nucleic acids

  • Circular folds, villi, & microvilli help absorb about 90 percent of digested nutrients

  • Large [Intestine]]

    • Resistant Starch: we don’t possess the enzymes to break it down but there is bacteria in the Large Intestine that can. By product of that is short chain fatty acids – important!
    • Reabsorption of water, ions and vitamins occurs
    • Production/absorption of B and K vitamins by bacteria
  1. Muscosal Structure and Function

    • The tissues of the GI tract
    • Epithelium
      • The layer of tissue that separates the ‘inside’ and ‘outside’ of the body and GI tract. Nutrients are broken down to be asborbed through the Epithelium
      • Mouth, pharynx, esophagus, & anal canal use stratified squamous epithelium more square like
      • Stomach & intestine use simple columnar epithelium more long-like
      • Integrated into the epithelium are several types of endocrine cells which secrete hormones, immune cells
    • Lamina Propria
      • A connective tissue containing many blood & lymphatic vessels, immune cells
    • Muscularis mucosae
      • Pulls the mucous membrane of small intestine into small folds to increase the surface area for digestion & absorption outside of this border is where the bacteria live
  2. Sub Mucosal Structure and Function

    • Connective Tissue to bind mucosa to muscularis
    • Blood vessels and lymphatic vessels
    • Extensive network of neurons known as the submucosal plexus
  3. Muscularis

    • Mouth, pharynx, & most of the esophagus contain skeletal muscle that produces voluntary swallowing
    • The middle parts of the digestive tract contact smooth muscle layered in two sheets Inner circular fibers and outer longitudinal fibers
    • Muscularis also contains a second set of nerve bundles (plexus) called the myenteric plexus

System 2 – Accessory digestive organs

  • Teeth: Maneuvers food and mastication
  • Tongue
  • Salivary glands: Initiates digestion of starches through enzymes


  • Buffers acidic gastric juice in chyme
  • Stops the action of pepsin from the stomach
  • Creates the proper pH for digestion in the small intestine
  • Participates in the digestion of carbohydrates, proteins, triglycerides
  1. Function
    • Makes pancreatic juices called enzymes
    • Hormones
      • Insulin
      • Glucagon
      • Gastrin
      • Amylin

Liver :: - Produces Bile, which is required for the emulsification & absorption of lipids in the small intestine

  • The liver is responsible for a large number of functions, but specific to digestion its responsible for the production of bile
  • Bile is then sent to the Gall Bladder for storage
  • Bile is partially responsible for the digestion of fats to fatty acids

Gallbladder :: Stores & concentrates Bile & releases it into the small intestine

Central and Enteric Nervous System

Complex system that stimulates multiple organs involved in digestion More neurons in your gut than a cat has in its entire brain! Direct cross-talk between your gut and brain.

Digestion and Absorption

  • Basic chemical units of our food & our tissue are the same
    • Our food looks so different from the tissue because the units are arranged very differently
  • In order to achieve rearrangement of the building blocks of our food, it is first necessary to break the food molecules into their basic constituents

Saliva (Food >>> Food Bolus)

Seconds to minutes

  • Salivary amylase which starts breaking down starches
  • Mucus for food lubrication
  • Hydrogen carbonate for alkaline pH

Stomach (Bolus >>> Chyme)

1-2 hours

  • Gastric juices start protein digestion
    • Pepsin, hydrochloric acid
  • Mixing of the bolus occurs through peristalsis

Small Intestine (duodenum, jejunum, ileum)

1-3 hours

  • Pancreatic (Pancreas) and Liver enzymes (bile) mix with the Chyme further breaking down the protein, fat and carbs
  • After chyme is fully broken down, absorption occurs through the intestinal Epithelium

Large Intestine

Up to 36 hours

  • Water and mineral (re)absorption
  • Bacterial production of additional nutrients (ie, SCFAs – short chain fatty acids)

Protein Digestion

  • Occurs in the stomach and duodenum
  • Pepsin secreted by the stomach, trypsin and chymotrypsin secreted by the Pancreas
    • Break proteins down into shorter polypeptides
  • Polypeptides are then broken down by various exopeptidases and dipeptidases into amino acids

Fat Digestion

Similar process to protein digestion but different enzymes. Purpose of breaking the fat is so that they can be absorbed by the Epithelium cells

  • Dietary triglycerides cannot be absorbed by the Intestine
  • The presence of fat in the small intestine produces hormones that stimulate the release of pancreatic lipase and Bile from the liver which helps in the emulsification of fats for absorption of fatty acids
  • The mixture of bile salts and the free fatty acids plus some mono and diglycerides for micelles in the duodenum
  • The micelles enter into the epithelial cells of the intestine (enterocytes) where triglycerides are reformed, packaged into chylomicrons and then released into the blood stream

Carb Digestion

Glycogen is when starches are in long chains

  • Most dietary carbs come in the form of starches composed of glucose units arranged into long chains, which are often called amylose
  • During digestion, salivary and pancreatic amylase break the bonds between the glucose molecules, resulting in progressively smaller chains of glucose. This results in simple sugars glucose and maltose (2 glucose molecules) that can be absorbed by the small intestine
  • Lactose is broken down by lactase into glucose and galactose which can both be absorbed by the enterocytes
  • Sucrose is broken down by sucrase into fructose and glucose which can also be absorbed by the enterocytes

The resulting glucose, fructose, galactose get absorbed by the Epithelial (Epithelium) wall

Regulation of Digestion - Hormones

  • Gastrin: stimulates the gastric glands to secrete pepsinogen and hydrochloric acid. Secretion of gastrin is stimulated by food arriving in stomach. The secretion is inhibited by low pH
  • Secretin: signals the secretion of sodium bicarbonate in the pancreas and Bile secretion in the liver
  • Cholecystokinin (CCK): stimulates the release of digestive enzymes in the pancreas and stimulates the emptying of bile in the gall bladder
  • Gastric inhibitory peptide (GIP): slows the emptying of the stomach. Another function is to induce insulin secretion

Regulation of Digestion - Enteric nervous system

Sensory, motor and interneurons respond to a number of signals producing an incredible array of neurotransmitters, such as acetylcholine and norepinephrine which have opposing effects

The enteric system functions autonomously but also requires communication with the central nervous system which occurs through the parasympathetic and sympathetic nervous system

Sympathetic signaling = inhibition of digestion Parasympathetic signaling = stimulation of digestive factors

rest and digest - feed and breath

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