AP Biology
Notes: Digestive system

 The four main stages of food processing are ingestion, digestion, absorption, and elimination

     Ingestion, the act of eating, is only the first stage of food processing. Food is “packaged” 
        in bulk form and contains very complex arrays of molecules, including large polymers and 
        various substances that may be difficult to process or may even be toxic.

        Animals cannot use macromolecules like proteins, fats, and carbohydrates in the form of 
 starch or other polysaccharides.  First, polymers are too large to pass through membranes
 and enter the cells of the animal. Second, the macromolecules that make up an animal are 
 not identical to those of its food.  

    Digestion, the second stage of food processing, is the process of breaking food down into 
 molecules small enough for the body to absorb.  Digestion cleaves macromolecules into 
 their component monomers, which the animal then uses to make its own molecules or as
 fuel for ATP production.

·        Polysaccharides and disaccharides are split into simple sugars.

·        Fats are digested to glycerol and fatty acids.

·        Proteins are broken down into amino acids.

·        Nucleic acids are cleaved into nucleotides.

  Absorption   After the food is digested, the animal’s cells take up small molecules such as amino 
acids and simple sugars from the digestive compartment.

  Elimination, undigested material passes out of the digestive compartment.  

Digestion occurs in specialized compartments

Intracellular digestion
To avoid digesting their own cells and tissues, most organisms conduct digestion
in specialized compartments.   The simplest digestive compartments are food vacuoles, 
organelles in which hydrolytic enzymes break down food without digesting the cell’s 
own cytoplasm.

    This is the sole digestive strategy in heterotrophic protists and in sponges, the only animal
    that digests their food this way.  
                 (1) Heterotrophic protists engulf their food by phagocytosis or  pinocytosis 
                 (2) digest their meals in food vacuoles.
                 (3) Newly formed vacuoles are carried around the cell 
                 (4) until they fuse with lysosomes, which are organelles containing hydrolytic enzymes.
                 (5) Later, the vacuole fuses with an anal pore and its contents are eliminated.  

Extracellular digestion
 In most animals, at least some hydrolysis occurs outside cells. Extracellular digestion occurs within 
compartments that are continuous with the outside of the animal’s body. This enables organisms to 
devour much larger prey than can be ingested by phagocytosis and digested intracellularly.  

 Many animals with simple body plans, such as cnidarians and flatworms, have digestive sacs with 
single openings, called gastrovascular cavities. For example, a hydra captures its prey with 
nematocysts and stuffs the prey through the mouth into the gastrovascular cavity. The prey is then 
partially digested by enzymes secreted by gastrodermal cells.

       In contrast to cnidarians and flatworms, most animals have complete digestive tracts  
or alimentary canals with a mouth, digestive tube, and an anus.   Because food moves
 in one direction, the tube can be organized into special regions that carry out digestion
and nutrient absorption in a stepwise fashion. Food ingested through the mouth and 
pharynx passes through an esophagus that leads to a crop, gizzard, or stomach, 
depending on the species. Crops and stomachs usually serve as food storage organs,
although some digestion occurs there too. Gizzards grind and fragment food.  In the 
intestine, digestive enzymes hydrolyze the food molecules, and nutrients are absorbed 
across the lining of the tube into the blood. Undigested wastes are eliminated through the anus.

Mammalian Digestive System:

         The mammalian digestive system consists of the alimentary canal and various
 accessory glands that secrete digestive juices into the canal through ducts.

·        Peristalsis, rhythmic waves of contraction by smooth muscles in the walls of the canal, push food along.

·        Sphincters, muscular ringlike valves, regulate the passage of material between specialized chambers of the canal.

·        The accessory glands include the salivary glands, the pancreas, the liver, and the gallbladder.  

        After chewing and swallowing, it takes 5 to 10 seconds for food to 
pass down the esophagus to the stomach, where it spends 2 to 6 hours 
being partially digested. Final digestion and nutrient absorption occur in
the small intestine over a period of 5 to 6 hours. In 12 to 24 hours, any
undigested material passes through the large intestine, and feces are 
expelled through the anus.

  Main divisions in digestion:

1.  The oral cavity, pharynx, and esophagus 

        Both physical and chemical digestion of food begins in the mouth.  During chewing, teeth 
of various shapes cut, smash, and grind food, making it easier to swallow and increasing 
its surface area. The presence of food in the oral cavity triggers a nervous reflex that causes 
the salivary glands to deliver saliva through ducts to the oral cavity. Salivation may occur
 in anticipation because of learned associations between eating and the time of day, cooking
 odors, or other stimuli.  

        Saliva contains a slippery glycoprotein called mucin, which protects the soft lining of the 
mouth from abrasion and lubricates the food for easier swallowing. Saliva also contains
buffers that help prevent tooth decay by neutralizing acid in the mouth. Antibacterial agents
 in saliva kill many bacteria that enter the mouth with food. Chemical digestion of carbohydrates,
 a main source of chemical energy, begins in the oral cavity.  Saliva contains salivary amylase,
 an enzyme that hydrolyzes starch and glycogen into smaller polysaccharides and the 
disaccharide maltose.  

        The tongue tastes food, manipulates it during chewing, and helps shape the food into a 
ball called a bolus.   During swallowing, the tongue pushes a bolus back into the oral 
cavity and into the pharynx.

        The pharynx, also called the throat, is a junction that opens to both the esophagus
 and the trachea (windpipe).  When we swallow, the top of the windpipe moves up 
 such that its opening, the glottis, is blocked by a cartilaginous flap, the epiglottis.
This mechanism normally ensures that a bolus will be guided into the entrance of 
the esophagus and not directed down the windpipe.

                    (1) When not swallowing, the esophageal sphincter 
                    muscles are contracted,  the epiglottis is up, and the 
                    glottis is open, allowing airflow to the lungs.

            (2) When a food bolus reaches the pharynx, 

    (3) the larynx moves upward and the epiglottis tips over
     the glottis, closing off the trachea.

            (4) The esophageal sphincter relaxes and the bolus enters
     the esophagus.

            (5) In the meantime, the larynx moves downward and the
     trachea is opened,

    (6) and peristalsis moves the bolus down the esophagus
    to the stomach.

         The esophagus conducts food from the pharynx down to the stomach by peristalsis. The
 muscles at the very top of the esophagus are striated and therefore under voluntary control. 
 Involuntary waves of contraction by smooth muscles in the rest of the esophagus then takes 
 over.

 2.  Stomach 

        The stomach is located in the upper abdominal cavity, just below the diaphragm. With accordion
 like folds and a very elastic wall, the stomach can stretch to accommodate about 2 L of food and 
fluid, storing an entire meal.  

        Gastric Juice:

        The stomach also secretes a digestive fluid called gastric juice and mixes this secretion with the
 food by the churning action of the smooth muscles in the stomach wall. Gastric juice is secreted 
by the epithelium lining numerous deep pits in the stomach wall. With a high concentration of
 hydrochloric acid, the pH of the gastric juice is about 2—acidic enough to digest iron nails.This 
acid disrupts the extracellular matrix that binds cells together.It kills most bacteria that are 
swallowed with food.  

        Pepsin:

        Also present in gastric juice is pepsin, an enzyme that begins the hydrolysis of proteins.   
Pepsin, which works well in strongly acidic environments, breaks peptide bonds adjacent 
to specific amino acids, producing smaller polypeptides. Pepsin is secreted in an inactive 
form, called pepsinogen by specialized chief cells in gastric pits. Parietal cells, also in the pits, 
secrete hydrochloric acid which converts pepsinogen to the active pepsin only when both 
reach the lumen of the stomach, minimizing self-digestion.   Also, in a positive-feedback system, 
activated pepsin can activate more pepsinogen molecules.  

Action of  stomach  muscles:

      About every 20 seconds, the stomach contents are mixed by the churning action of smooth 
muscles. As a result of mixing and enzyme action, what begins in the stomach as a recently
swallowed meal becomes a nutrient-rich broth known as acid chyme. Most of the time the 
stomach is closed off at either end.  The opening from the esophagus to the stomach, the 
cardiac orifice, normally dilates only when a bolus driven by peristalsis arrives.  The 
occasional backflow of acid chyme from the stomach into the lower esophagus causes
 heartburn. At the opening from the stomach to the small intestine is the pyloric sphincter,
which helps regulate the passage of chyme into the intestine. A squirt at a time, it takes 
about 2 to 6 hours after a meal for the stomach to empty.

          Ulcers:

         The stomach’s second line of defense against self-digestion is a coating of mucus, secreted by 
 epithelial cells, that protects the stomach lining. Still, the epithelium is continually eroded, and 
  the epithelium is completely replaced by mitosis every three days. Gastric ulcers, lesions in the 
  stomach lining, are caused by the acid-tolerant bacterium Heliobacter pylori.  Ulcers are often 
  treated with antibiotics.  

3a.   Small Intestine (duodenum):

        With a length of over 6 m in humans, the small intestine is the longest section of the 
alimentary canal. Most of the enzymatic hydrolysis of food macromolecules and most 
of the absorption of nutrients into the blood occurs in the small intestine. In the first
25 cm or so of the small intestine, the duodenum, acid chyme from the stomach mixes 
with digestive juices from the pancreas, liver, gall bladder, and gland cells of the intestinal
 wall.

The pancreas produces several hydrolytic enzymes and an alkaline solution rich in bicarbonate
which buffers the acidity of the chyme from the stomach.

      The liver performs a wide variety of important functions in the body, including the production of
  bile. Bile is stored in the gallbladder until needed.   It contains bile salts which act as detergents 
that aid in the digestion and absorption of fats. Bile also contains pigments that are by-products 
of red blood cell destruction in the liver.  These bile pigments are eliminated from the body with 
the feces.  

3b.  Small Intestine (Jejunum/Ileum):

 Function mainly in the absorption of nutrients and water.   To enter the body, nutrients in the 
lumen must pass the lining of the digestive tract.  The small intestine has a huge surface area - 300 m2,
 roughly the size of a tennis court. The enormous surface of the small intestine is an adaptation that
 greatly increases the rate of nutrient absorption.  Large circular folds in the lining bear fingerlike
projections called villi, and each epithelial cell of a villus has many microscopic appendages called 
microvilli that are exposed to the intestinal lumen. Penetrating the core of each villus is a net of 
microscopic blood vessels (capillaries) and a single vessel of the lymphatic system called a lacteal.  
Nutrients are absorbed across the intestinal epithelium and then across the unicellular epithelium of 
capillaries or lacteals.   Only these two single layers of epithelial cells separate nutrients in the lumen 
of the intestine from the bloodstream. In some cases, such as fructose, transport of nutrients across 
the epithelial cells is passive, as molecules move down their concentration gradients from the lumen 
of the intestine into the epithelial cells, and then into capillaries.   Other nutrients, including amino 
acids, small peptides, vitamins, and glucose, are pumped against concentration gradients by epithelial 
membranes.

      The capillaries and veins that drain nutrients away from the villi converge into the hepatic portal vessel, 
      which  leads directly to the liver. Therefore, the liver—which has the metabolic versatility to interconvert 
      various organic molecules—has first access to amino acids and sugars absorbed after a meal is digested.  
      The liver modifies and regulates this varied mix before releasing materials back into the blood stream. 
       For example, the liver helps regulate the levels of glucose in the blood, ensuring that blood exiting the
       liver usually has a glucose concentration very close to 0.1%, regardless of carbohydrate content of the meal.

4.  Large Intestine:

        The large intestine, or colon, is connected to the small intestine at a T-shaped junction where a 
        sphincter controls the movement of materials. One arm of the T is a pouch called the cecum.   
        The relatively small cecum of humans has a fingerlike extension, the appendix, that makes a 
        minor contribution to body defense.  The main branch of the human colon is shaped like an
         upside-down U about 1.5 m long. 

        A major function of the colon is to recover water that has entered the alimentary canal as the 
        solvent to various digestive juices. About 7 L of fluid are secreted into the lumen of the 
        digestive tract of a person each day. Over 90% of the water is reabsorbed, most in the small 
         intestine, the rest in the colon. Digestive wastes, the feces, become more solid as they are 
        moved along the colon by peristalsis.   Movement in the colon is sluggish, requiring 12 to 
        24 hours for material to travel the length of the organ. Diarrhea results if insufficient water 
        is absorbed and constipation if too much water is absorbed.  

         Living in the large intestine is a rich flora of mostly harmless bacteria. One of the most common 
inhabitants of the humancolon is Escherichia coli, a favorite research organism. As a byproduct
of their metabolism, many colon bacteria generate gases, including methane and hydrogen sulfide.
Some bacteria produce vitamins, including biotin, folic acid, vitamin K, and several B vitamins, 
which supplement our dietary intake of vitamins. Feces contain masses of bacteria and undigested
 materials including cellulose.   Although cellulose fibers have no caloric value to humans, their 
presence in the diet helps move food along the digestive tract. The feces may also contain excess 
salts that are excreted into the lumen of the colon. The terminal portion of the colon is called the 
rectum, where feces are stored until they can be eliminated. Between the rectum and the anus 
are two sphincters, one involuntary and one voluntary.

Digestion of macromolecues

    Starch/glycogen:
The digestion of starch and glycogen, begun by salivary amylase in the oral cavity, continues in the small intestine. Pancreatic amylases hydrolyze starch, glycogen, and smaller polysaccharides into disaccharides. A family of disaccharidases hydrolyzes each disaccharide into monomers. Maltase splits maltose into two glucose molecules. Sucrase splits sucrose, a sugar found in milk, into glucose and fructose. These enzymes are built into the membranes and extracellular matrix of the intestinal epithelium which is also the site of sugar absorption.  

    Proteins:
Digestion of proteins in the small intestine completes the process begun by pepsin. Several enzymes in the duodenum dismantle polypeptides into their amino acids or into small peptides that in turn are attacked by other enzymes. Trypsin and chymotrypsin attack peptide bonds adjacent to specific amino acids, breaking larger polypeptides into shorter chains.  Dipeptidases, attached to the intestinal lining, split smaller chains. Carboxypeptidase and aminopeptidase split off one amino acid from the carboxyl or amino end of a peptide, respectively. Many of the protein-digesting enzymes, such as aminopeptidase, are secreted by the intestinal epithelium, but trypsin, chymotrypsin, and carboxypeptidase are secreted in inactive form by the pancreas. Another intestinal enzyme, enteropeptidase, converts inactive trypsinogen into active trypsin. Active trypsin then activates the other two.  

    Nucleic acid:
The digestion of nucleic acids involves a hydrolytic assault similar to that mounted on proteins. A team of enzymes called nucleases hydrolyzes DNA and RNA into their component nucleotides. Other hydrolytic enzymes then break nucleotides down further into nucleosides, nitrogenous bases, sugars, and phosphates.  

    Lipids:
Nearly all the fat in a meal reaches the small intestine undigested.  Normally fat molecules are insoluble in water, but bile salts, secreted by the gallbladder into the duodenum, coat tiny fats droplets and keep them from coalescing, a process known as emulsification. The large surface area of these small droplets is exposed to lipase, an enzyme that hydrolyzes fat molecules into glycerol, fatty acids, and glycerides.