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Digestive System Notes

Functions of the Digestive System

  • The primary function is to extract energy from ingested biomolecules by breaking chemical bonds.

  • It also obtains basic building blocks for synthesizing enzymes and energy storage.

  • Additionally, the digestive system plays a crucial role in immunity due to constant exposure to the external environment.

Mass Balance in the Digestive System

  • The digestive system maintains mass balance, meaning the fluid entering the GI tract equals the fluid leaving it. For instance, if 9 liters enter, 9 liters must exit.

Anatomy of the Digestive System

  • Oral Cavity

  • Esophagus: Connects the oral cavity to the stomach

  • Stomach: Includes the fundus, body, antrum, and pylorus with the pyloric valve controlling the release of stomach contents into the small intestine.

  • Small Intestine: Consists of the duodenum, jejunum, and ileum.

  • Large Intestine: Includes the cecum, ascending colon, transverse colon, descending colon, and rectum.

  • Accessory Organs: Liver and Pancreas

Four Processes of the Digestive System

  • Digestion: Breaking down chemical bonds to extract energy.

    • Mechanical Digestion: Physical breakdown of food particles to increase surface area.

    • Chemical Digestion: Using digestive enzymes to break down food. Enzymes are present in secretions from accessory organs. These processes break down food into absorbable units.


    • Significance of Absorbable Units: The digestive system breaks down food into smaller units that can be absorbed into the bloodstream but doesn't extract all possible energy from them. A polysaccharide (e.g., bread) is broken down into monosaccharides (e.g., glucose) , which the body can absorb and use later. While further energy can be extracted in the form of CO2 and H2O from monosaccharides, such as glucose, it doesn't happen in the GI tract.

  • Secretion: Includes digestive enzymes and fluids from the GI tract and waste materials. Some secreted substances, like insulin, facilitate the absorption of molecules by cells.

  • Absorption: Uptake of digested units into the blood (extracellular fluid).

  • Motility: Movement of the bolus through the GI tract, facilitated by muscle contractions eventually leading to defecation.

Anatomical Layers of the GI Tract

  • Layers (Inside to Outside):

    • Mucosa (innermost layer): involved in secretion and absorption, contains glands to increase surface area, although not as much in the stomach.

      • Absorption of alcohol and aspirin occurs here.

    • Submucosa: Underneath the mucosa; contains blood vessels, lymph vessels, and nerves.

    • Muscularis Externa: Consists of circular and longitudinal muscle layers responsible for motility.

      • The circular muscle layer squeezes the contents.

      • The longitudinal muscle layer moves the contents forward.

      • These muscles are smooth muscles, which means that you have no control over them, controlled by reflexes.

      • Myenteric Plexus: Neuronal network between the muscle layers that controls GI tract segments; part of the Enteric Nervous System (ENS).

      • Short reflexes (GI and ENS) and long reflexes (GI tract and CNS) regulate movement.

    • Serosa (outermost layer)


  • Small Intestine: Has villi to increase surface area for nutrient absorption.

  • Large Intestine: Reabsorbs water and ions.

  • GALT (Gut Associated Lymphoid Tissue): includes Peyer's patches that are large lymph node structures in the body; part of what is absorbed include complex fat molecules which cannot be uploaded to the blood vessels, therefore are transfer to the lymphatic system


  • Muscularis Externa: Composed of circular (squeezing) and longitudinal (forward movement) muscle layers. Controlled by the myenteric plexus which is between the two muscles.

Movements in the GI Tract

  • Peristalsis: Propels the bolus of food via alternating contraction and relaxation controlled by ganglia. Segment contraction is controlled by one ganglion and the relaxed segment is controlled by the next ganglion. Bolus of food moves from contracted segment to a relaxed segment

    • Hirschsprung's Disease: Disease characterized by missing ganglia in segments and missing the myenteric plexus which leads to inability to contract and obstruction therefore results in food bolus getting stuck and dehydrated.

  • Segmental Contraction: Responsible for mixing the bolus with digestive enzymes.

  • Tonic Contractions: Sustained contractions in sphincters and the anterior stomach to prevent backward movement.

  • Phasic Contractions: Last a few seconds and occur in the posterior stomach and small intestine.

  • Slow Wave Potentials: Originate from the cells of Cajal.

Stomach Functions and Cells

  • Important Functions: Storage, protein and lipid digestion.

  • Protection Mechanism: Hydrochloric acid (cleans food) and mucus production.

  • Cells and Their Functions:

    • Chief Cells: Produce pepsinogen (inactive form) and gastric lipase. Pepsinogen \longrightarrow pepsin, digests proteins; lipase digests fats.

    • Parietal Cells: Produce hydrochloric acid (kills bacteria, activates pepsin) and intrinsic factor (IF) for B12 absorption. Destruction of parietal cells leads to pernicious anemia.

    • D Cells: Produce somatostatin, which inhibits gastric acid secretion.

    • G Cells: Produce gastrin, which stimulates gastric acid secretion.

Digestive Enzymes

  • Specific enzymes digest each of the four major biomolecules.

  • Digestive enzymes are secreted in the mouth, stomach, and intestine.

  • Mucus cells, serous cells and goblet cells produce mucins which is an immunity mechanism.

Liver and Bile

  • The liver detoxifies bilirubin into conjugated form as a result of hemolisis of red blood cells in the spleen, then makes bile (bile salt, bile pigment, and cholesterol).

  • The gallbladder stores and concentrates bile, it does not make it.

Digestion of Biomolecules

  • Carbohydrates: Polysaccharides are digested to disaccharides and then monosaccharides using amylase (salivary and pancreatic).

  • Lipids: Bile emulsifies fats, and lipase (pancreatic) breaks them down into monoglycerides and fatty acids.

  • Proteins: Pepsin(stomach) or trypsin helps breaks down pepsin.

  • Nucleic Acids: Digested into nitrogenous bases and monosaccharides. .Examples are DNA and RNA.

Intestinal Absorption

  • Vitamins and Minerals: Can be fat-soluble (absorbed with fat) or water-soluble (absorbed with water).

  • Vitamin B12: Requires intrinsic factor (IF) produced by parietal cells in the stomach for absorption. Lack of IF (destroyed parietal cells) causes pernicious anemia.

  • Mineral Absorption: Occurs via active transport. Iron and calcium are actively regulated. Sodium is absorbed by enterocytes and colonocytes.

Reflexes and Hormones

  • Reflexes: Short reflexes involve GI and ENS; long reflexes involve GI tract and CNS.

  • Phases of Digestion: Cephalic, gastric, and intestinal.

  • Digestive Hormones: Gastrin family (gastrin and cholecystokinin), secretin family, and others like motilin.

Digestion, Secretion, Absorption, and Motility in Different parts of the GI Tract

  • For the stomach:

    • It can absorb lipid-soluble substances such as alcohol and aspirin.

    • It can secrete hydrochloric acid (from the parietal cells).

    • Produces pepsinogen and gastrin and lipase from their cells

    • Starts the protein digestion because of pepsin secreted

  • Small intestine is mainly involved in absorption.

    • Active transport of amino acid.

    • Active absorption of glucose.

  • Large intestine is mainly involved in absorbing ions and water and minerals.

Phases of Digestion

  • Cephalic Phase: Initiated by the thought, smell, or sight of food. Ends with the swallowing reflex, which is integrated in the brainstem and involves cranial nerves.

  • Gastric Phase: Involves storage and digestion of proteins and lipids triggered by distention of the stomach.

  • Intestinal Phase: protective functionalities over here related to diarrhea and controlled by reflexes.

Hepatic Portal System

  • All blood from the GI tract goes to the liver for filtration before entering the systemic circulation.

  • The liver receives dual blood supply: oxygenated blood from the heart and blood from the GI tract for filtration.

  • Route of administration of medication: Oral medications are absorbed and go to the liver to get detoxified, thus have a lower potency compared to IV medications that directly enter the circulatory system.

Defecation Reflex

  • Similar to the urination reflex.

  • Receptors in the rectum send signals to the sacral area of the spinal cord.

  • Response: rectum contracts, internal sphincter (smooth muscle) relaxes, and external sphincter (skeletal muscle) controls the release.

Functions of the Digestive System

  • The primary function is to extract energy from ingested biomolecules by breaking chemical bonds, ensuring the body has sufficient energy to perform its vital functions.

  • It also obtains basic building blocks (amino acids, monosaccharides, fatty acids) for synthesizing enzymes, structural proteins, and energy storage molecules like glycogen and triglycerides. These building blocks are crucial for growth, repair, and maintenance of bodily functions.

  • Additionally, the digestive system plays a crucial role in immunity by acting as a barrier against pathogens and toxins ingested with food. It houses Gut Associated Lymphoid Tissue (GALT) and promotes the production of antibodies to neutralize harmful substances due to constant exposure to the external environment.

Mass Balance in the Digestive System

  • The digestive system maintains mass balance, meaning the fluid entering the GI tract equals the fluid leaving it. For instance, if 9 liters enter (from ingested liquids and secretions), 9 liters must exit (through absorption or excretion). This balance is crucial for maintaining proper hydration and preventing dehydration or edema.

Anatomy of the Digestive System

  • Oral Cavity: The entry point for food, where mechanical digestion (chewing) and chemical digestion (salivary amylase) begin.

  • Esophagus: Connects the oral cavity to the stomach, transporting food via peristaltic contractions.

  • Stomach: A muscular organ that includes the fundus (stores undigested food), body (primary site of digestion), antrum (mixes food with gastric secretions), and pylorus with the pyloric valve (controls the release of chyme - partially digested food - into the small intestine).The stomach is where protein digestion begins.

  • Small Intestine: Consists of three segments:

    • Duodenum: Receives chyme from the stomach and digestive enzymes from the pancreas and bile from the liver/gallbladder; primary site of chemical digestion.

    • Jejunum: The middle segment, characterized by extensive nutrient absorption due to its large surface area (villi and microvilli increase surface area massively).

    • Ileum: The final segment, absorbs vitamin B12 and bile salts, and connects to the large intestine.

  • Large Intestine: Includes the cecum (receives undigested material from the small intestine), ascending colon, transverse colon, descending colon, sigmoid colon, rectum (stores feces), and anus (eliminates feces).

  • Accessory Organs:

    • Liver: Produces bile, detoxifies blood, and metabolizes nutrients.

    • Pancreas: Secretes digestive enzymes (amylase, lipase, proteases) and bicarbonate (to neutralize stomach acid) into the small intestine.

Four Processes of the Digestive System

  • Digestion: Breaking down chemical bonds to extract energy.

    • Mechanical Digestion: Physical breakdown of food particles to increase surface area for enzyme action; includes chewing (mouth) and churning (stomach).

    • Chemical Digestion: Using digestive enzymes to break down food. Enzymes are present in secretions from accessory organs (e.g., salivary glands, pancreas, liver/gallbladder). These processes break down food into absorbable units.


    Significance of Absorbable Units: The digestive system breaks down food into smaller units that can be absorbed into the bloodstream but doesn't extract all possible energy from them. A polysaccharide (e.g., bread) is broken down into monosaccharides (e.g., glucose) , which the body can absorb and use later. While further energy can be extracted in the form of CO2 and H2O from monosaccharides, such as glucose, it doesn't happen in the GI tract. Cellular respiration is responsible for extracting more energy not in the GI tract.

  • Secretion: Includes digestive enzymes (e.g., amylase, lipase, proteases) and fluids (e.g., hydrochloric acid, bile) from the GI tract and waste materials. Some secreted substances, like insulin, facilitate the absorption of molecules by cells. Secretions are regulated by hormonal and neural mechanisms.

  • Absorption: Uptake of digested units (monosaccharides, amino acids, fatty acids, vitamins, minerals) into the blood (extracellular fluid). Most nutrients are absorbed in the small intestine.

  • Motility: Movement of the bolus through the GI tract, facilitated by muscle contractions (peristalsis and segmentation) eventually leading to defecation. Motility is controlled by smooth muscles and regulated by neural and hormonal signals.

Anatomical Layers of the GI Tract

  • Layers (Inside to Outside):

    • Mucosa (innermost layer): involved in secretion (enzymes, hormones, mucus) and absorption, contains glands to increase surface area, although not as much in the stomach. The mucosa contains:

      • Epithelium: Innermost lining, responsible for absorption and secretion.

      • Lamina Propria: Connective tissue layer containing blood vessels, lymph vessels, and immune cells.

      • Muscularis Mucosae: Thin layer of smooth muscle that contributes to the folding of the mucosa.

      • Absorption of alcohol and aspirin occurs here.These substances bypass first-pass metabolism because the stomach empties more slowly when they are consumed in higher concentrations.

    • Submucosa: Underneath the mucosa; contains blood vessels, lymph vessels, and nerves. This layer supports the mucosa and provides vascular supply.

    • Muscularis Externa: Consists of circular and longitudinal muscle layers responsible for motility.

      • The circular muscle layer squeezes the contents, reducing the diameter of the lumen.

      • The longitudinal muscle layer moves the contents forward, shortening the length of the GI tract.

      • These muscles are smooth muscles, which means that you have no control over them, controlled by reflexes. These muscles are responsible for peristalsis and segmentation.

      • Myenteric Plexus: Neuronal network between the muscle layers that controls GI tract segments; part of the Enteric Nervous System (ENS). It regulates the activity of the muscularis externa.

      • Short reflexes (GI and ENS) and long reflexes (GI tract and CNS) regulate movement. Short reflexes are local responses, while long reflexes involve the central nervous system.

    • Serosa (outermost layer): A serous membrane that protects the GI tract and reduces friction between organs. It is also known as the visceral peritoneum. Layers that are not covered by the serosa has an adventitia layer.


Small Intestine: Has villi to increase surface area for nutrient absorption; microvilli on the surface of the villi further increase surface area.

  • Large Intestine: Reabsorbs water and ions, compacting undigested material into feces. It also houses a large population of gut microbiota that ferment undigested carbohydrates.

  • GALT (Gut Associated Lymphoid Tissue): includes Peyer's patches that are large lymph node structures in the body; part of what is absorbed include complex fat molecules which cannot be uploaded to the blood vessels, therefore are transfer to the lymphatic system(lacteals). GALT plays a critical role in immune surveillance and response within the GI tract.


Muscularis Externa: Composed of circular (squeezing) and longitudinal (forward movement) muscle layers. Controlled by the myenteric plexus which is between the two muscles. The balance of activity in these layers determines the type of motility patterns.

Movements in the GI Tract

  • Peristalsis: Propels the bolus of food via alternating contraction and relaxation controlled by ganglia. Segment contraction is controlled by one ganglion and the relaxed segment is controlled by the next ganglion. Bolus of food moves from contracted segment to a relaxed segmentThis coordinated movement is essential for moving food along the digestive tract.

    • Hirschsprung's Disease: Disease characterized by missing ganglia in segments and missing the myenteric plexus which leads to inability to contract and obstruction therefore results in food bolus getting stuck and dehydrated. This condition requires surgical intervention to remove the affected segments.

  • Segmental Contraction: Responsible for mixing the bolus with digestive enzymes and exposing all parts of the bolus to the absorptive surfaces of the intestinal wall. It occurs mainly in the small intestine.

  • Tonic Contractions: Sustained contractions in sphincters (e.g., pyloric sphincter, ileocecal valve) and the anterior stomach to prevent backward movement and regulate the flow of chyme. These contractions are important for controlling the rate at which food moves through the GI tract.

  • Phasic Contractions: Last a few seconds and occur in the posterior stomach and small intestine to propel and mix the contents.

  • Slow Wave Potentials: Originate from the interstitial cells of Cajal (ICC), which act as pacemaker cells for GI motility. These potentials determine the frequency of contractions in different regions of the GI tract.

Stomach Functions and Cells

  • Important Functions: Storage (holding food until it can be processed), protein and lipid digestion (initiated by pepsin and gastric lipase, respectively).

  • Protection Mechanism: Hydrochloric acid (cleans food by killing bacteria) and mucus production (protects the stomach lining from acid and enzymes).

  • Cells and Their Functions:

    • Chief Cells: Produce pepsinogen (inactive form) and gastric lipase. Pepsinogen \longrightarrow pepsin (activated by HCl), digests proteins; lipase digests fats.

    • Parietal Cells: Produce hydrochloric acid (kills bacteria, activates pepsin) and intrinsic factor (IF) for B12 absorption. Destruction of parietal cells leads to pernicious anemia. Intrinsic factor is essential for the absorption of vitamin B12 in the ileum.

    • D Cells: Produce somatostatin, which inhibits gastric acid secretion. Somatostatin helps regulate gastric activity and prevent excessive acid production.

    • G Cells: Produce gastrin, which stimulates gastric acid secretion and gastric motility. Gastrin release is stimulated by the presence of peptides and amino acids in the stomach.

Digestive Enzymes

  • Specific enzymes digest each of the four major biomolecules (carbohydrates, lipids, proteins, nucleic acids).

  • Digestive enzymes are secreted in the mouth (salivary amylase), stomach (pepsin, gastric lipase), and intestine (pancreatic enzymes, brush border enzymes).

  • Mucus cells, serous cells and goblet cells produce mucins which is an immunity mechanism. Mucin hydrates to form mucus that protects and lubricates the GI tract lining. Goblet cells also helps absorbs excess nutrients

Liver and Bile

  • The liver detoxifies bilirubin into conjugated form as a result of hemolysis of red blood cells in the spleen, then makes bile (bile salt, bile pigment, and cholesterol). Conjugated bilirubin is water-soluble and can be excreted.

  • The gallbladder stores and concentrates bile, it does not make it. The release of bile is stimulated by cholecystokinin (CCK).

Digestion of Biomolecules

  • Carbohydrates: Polysaccharides are digested to disaccharides and then monosaccharides using amylase (salivary and pancreatic). Brush border enzymes (e.g., lactase, maltase, sucrase) further break down disaccharides into monosaccharides.

  • Lipids: Bile emulsifies fats, and lipase (pancreatic) breaks them down into monoglycerides and fatty acids. Colipase helps lipase bind to the emulsion droplets.

  • Proteins: Pepsin(stomach) or trypsin helps breaks down pepsin. The digestion of proteins continues in the small intestine, with pancreatic proteases (e.g., trypsin, chymotrypsin, carboxypeptidase) and brush border peptidases breaking down peptides into amino acids.

  • Nucleic Acids: Digested into nitrogenous bases and monosaccharides. .Examples are DNA and RNA. Nucleases (pancreatic) and nucleosidases (brush border) are involved in the digestion of nucleic acids.

Intestinal Absorption

  • Vitamins and Minerals: Can be fat-soluble (A, D, E, K - absorbed with fat) or water-soluble (absorbed with water). Fat-soluble vitamins require micelles for absorption; water-soluble vitamins are absorbed directly into the blood.

  • Vitamin B12: Requires intrinsic factor (IF) produced by parietal cells in the stomach for absorption. Lack of IF (destroyed parietal cells) causes pernicious anemia. The B12-IF complex is absorbed in the ileum.

  • Mineral Absorption: Occurs via active transport. Iron and calcium are actively regulated. Sodium is absorbed by enterocytes and colonocytes. The absorption of iron and calcium is influenced by hormones and physiological needs.

Reflexes and Hormones

  • Reflexes: Short reflexes involve GI and ENS; long reflexes involve GI tract and CNS. Short reflexes are local responses, while long reflexes involve the brain.

  • Phases of Digestion: Cephalic, gastric, and intestinal. Each phase is characterized by specific stimuli and responses.

  • Digestive Hormones: Gastrin family (gastrin and cholecystokinin), secretin family, and others like motilin. These hormones regulate secretion, motility, and other digestive processes.

Digestion, Secretion, Absorption, and Motility in Different parts of the GI Tract

  • For the stomach:

    • It can absorb lipid-soluble substances such as alcohol and aspirin. The stomach's absorptive capacity is limited; most absorption occurs in the small intestine.

    • It can secrete hydrochloric acid (from the parietal cells), which aids in protein digestion and kills bacteria.

    • Produces pepsinogen and gastrin and lipase from their cells that helps digests protein within the cell.

    • Starts the protein digestion because of pepsin secreted

  • Small intestine is mainly involved in absorption. The small intestine's structure (villi, microvilli) maximizes surface area for absorption.

    • Active transport of amino acid.

    • Active absorption of glucose.

  • Large intestine is mainly involved in absorbing ions and water and minerals. This process helps to solidify feces and maintain electrolyte balance.

Phases of Digestion

  • Cephalic Phase: Initiated by the thought, smell, or sight of food. Ends with the swallowing reflex, which is integrated in the brainstem and involves cranial nerves. This phase prepares the digestive system for food.

  • Gastric Phase: Involves storage and digestion of proteins and lipids triggered by distention of the stomach. Gastric secretions (HCl, pepsinogen) are stimulated.

  • Intestinal Phase: protective functionalities over here related to diarrhea and controlled by reflexes. The intestinal phase regulates the rate of gastric emptying and stimulates the release of intestinal hormones.

Hepatic Portal System

  • All blood from the GI tract goes to the liver for filtration before entering the systemic circulation. This ensures that nutrients and toxins are processed by the liver before reaching other parts of the body.

  • The liver receives dual blood supply: oxygenated blood from the heart (via the hepatic artery) and nutrient-rich blood from the GI tract for filtration (via the hepatic portal vein).

  • Route of administration of medication: Oral medications are absorbed and go to the liver to get detoxified, thus have a lower potency compared to IV medications that directly enter the circulatory system. This is known as the first-pass effect.

Defecation Reflex

  • Similar to the urination reflex. This reflex is controlled by the parasympathetic nervous system.

  • Receptors in the rectum send signals to the sacral area of the spinal cord. This triggers the defecation reflex.

  • Response: rectum contracts, internal sphincter (smooth muscle) relaxes, and external sphincter (skeletal muscle) controls the release. Voluntary control of the external sphincter allows for conscious control of defecation.