A Level Biology: The Digestive System

The Digestive System


Humans, like all animals, use Holozoic nutrition, which consists of these five stages: -

1. Ingestion – taking large pieces of food into the body

2. Digestion – breaking down the food by mechanical and chemical means

3. Absorption – taking up the soluble digestion products into the body's cells

4. Assimilation – using the absorbed materials

5. Egestion – eliminating the undigested material. (Do not confuse egestion, which is the elimination of material from a body cavity, with excretion, which is the elimination of waste material produced from within the body's cells.)


When you read “Digestion: think “Hydrolysis” - since the whole point of digestion is to break down (digest) i.e. “hydrolyse” large foods into the monomers from which they are made, so that the body can easily absorb and assimilate them! (Remember “Assimilate” means to put the monomers (products of digestion) to use, e.g. glucose is used in cellular respiration to produce ATP).


The Alimentary Canal


The human digestive system comprises a long tube called the alimentary canal (or digestive tract / gut) which extends from the mouth to the anus. In addition to the alimentary canal the digestive system is comprised of a number of associated glands (e.g. the salivary glands, the pancreas and the liver and the gall bladder).


[Insert Image of Digestive System]


You must also know that the digestive system is made up of different tissues doing different jobs. 


The lining wall of the alimentary canal appears different in different parts of the gut, reflecting their different roles, but always has these four basic layers: -


1. The mucosa, which secretes digestive juices and absorbs digested food. It is often folded to increase its surface area. There is a layer of columnar epithelial cells lining the mucosa. These epithelial cells contain microvilli, membrane proteins for facilitated diffusion and active transport, mitochondria, and membrane-bound enzymes. Epithelial cells are constantly worn away by friction with food moving through the gut, so are constantly being replaced.


2. The submucosa, which contains blood vessels, lymph vessels and nerves to control the muscles. It may also contain secretory glands.


3. The muscle layer, which is made of smooth muscle, under involuntary control. It can be subdivided into circular muscle (which squeezes the gut when it contracts) and longitudinal muscle (which shortens the gut when it contracts). These two muscles therefore have opposite effects and so are antagonistic. The combination of these two muscles allows food to be pushed along the gut by peristalsis.


4. The serosa, which is a thin, tough layer of connective tissue that holds the gut together, and attaches it to the abdomen.

[insert image showing tissue layers]


Overview of the Digestive system - a journey from mouth to large intestine.


Every time you eat, the food that is masticated (chewed) in the month follows the same journey through the digestive system…


Digestion begins in the mouth.


The Mouth (Buccal cavity). The teeth and tongue physically break up the food into small pieces with a larger surface area, and form it into a ball or bolus. The salivary glands secrete saliva, which contains water to dissolve soluble substances, mucus for lubrication, lysozymes to kill bacteria and salivary amylase to digest starch. The food bolus is swallowed by an involuntary reflex action through the pharynx (the back of the mouth). During swallowing the trachea is blocked off by the epiglottis to stop food entering the lungs.


From the mouth to the Oesophagus (gullet).


Oesophagus (gullet). This is a simple tube through the thorax, which connects the mouth to the rest of the gut. No digestion takes place in the Oesophagus!. 


There is an epithelium, no villi, a few glands secreting mucus, and a thick layer of circular and longitudinal muscle to propel the food (bolus) via peristalsis. 


What is Peristalsis?


Peristalsis is a wave of circular muscle contraction. This Muscular contraction passes down the gut and is completely involuntary. 


The oesophagus is a soft tube that can be closed. (Unlike the trachea, which is a hard tube, held open by rings of cartilage).


[insert image of peristalsis]


From Oesophagus and into the Stomach.


The Stomach is an expandable ‘bag’ where the food is stored for up to a few hours. 


There are three layers of muscle to churn the food (bolus) into a liquid called chyme. 


This chime is gradually released in to the small intestine via the pyloric sphincter, a region of thick circular muscle that acts as a valve. 


The mucosa of the stomach wall has no villi, but does have numerous gastric pits (104 cm-2) leading to gastric glands in the mucosa layer. 

These glands secrete gastric juice, which contains: -


Hydrochloric acid (pH 1): The main function of Hydrochloric acid is to to kill bacteria! The acid does not aid digestion, in fact it hinders digestion because the low pH (acidic pH 1) denatures most enzymes. Thus, Carbohydrate digestion stops and protein digestion begins.


Mucus: Mucus lubricates food and coats the epithelium to protect it from the acidic conditions of the stomach and some protease enzymes. 


Only protein digestion takes place in the stomach!



From the stomach to the small intestine.


The Small Intestine is about 6.5M long, and is typically be divided into three sections: -

1. The duodenum (30 cm long). 

2. The jejunum (2 m long)

3. The ileum (4 m long). 


Note: Since the jejunum and ileum are similar in humans, and are the site of final digestion and all absorption (at A-level they are both typically considered as “the Ileum” i..e the rest of the small intestine after the duodenum.



The duodenum 

The first 30cm of the small intestine is called the duodenum. Although this is short,

almost all the digestion takes place here, due to two secretions: pancreatic juice and bile. 


Pancreatic juice is secreted by the pancreas into the duodenum through the pancreatic duct. 


Pancreatic juice contains numerous amylase, protease and lipase enzymes. 


Bile is secreted by the liver, stored in the gall bladder, and released into the duodenum through the bile duct. 


Bile doesn’t contain any enzymes, but it does contain bile salts to aid lipid digestion, and the alkali sodium hydrogen carbonate to neutralise the stomach acid. 


This alkali gives chyme in the duodenum a pH of around 7.5, so the pancreatic enzymes can work at their optimum pH. 


The mucosa of the duodenum has few villi, (since there is no absorption), but the submucosa contains glands secreting mucus and sodium hydrogen carbonate.


The rest of the small intestine is called the Ileum. (jejunum and ileum).


The Ileum is the site of final digestion and absorption. There are numerous glands in the mucosa and submucosa secreting enzymes, mucus and sodium hydrogen carbonate. To maximise the rate of absorption the ileum has the three features which are dictated by Fick’s law!


1. Large Surface Area. The ileum has a huge surface area. It is over 6m long; the mucosa has large circular folds, villi and the epithelial cells have microvilli. Don't confuse these two: villi are large structures composed of hundreds of cells that can easily be seen with a light microscope, while microvilli are small subcellular structures formed by the folding of the plasma membrane of individual epithelial cells.


Microvilli can only be seen clearly with an electron microscope, and appear as a fuzzy brush border under the light microscope. The total internal surface area of the ileum is over 2000m2.


2. Short diffusion pathway. There is a network of blood capillaries in the submucosa of

each villus, so between the lumen of the gut and the blood there is just one layer of epithelium

lining the mucosa and one layer of endothelium lining the capillaries.


3. A high concentration gradient is maintained by mixing the fluids on either side of the exchange surface. On the lumen side, the circular and longitudinal muscles propel the chyme by peristalsis, and mix the contents by pendular movements (bi-directional peristalsis). The microvilli can also wave to stir the contents near the epithelial cells. On the blood side, the blood flow ensures there is always a low concentration of nutrients.


[insert images of small intestine, villi, microvilli etc.]

From the Small intestine to the Large Intestine. 


The large intestine comprises the caecum, appendix, colon and rectum. 

Food can spend around 36 hours in the large intestine, while water is absorbed to form semi-solid faeces. 


The mucosa contains villi but no microvilli, and there are numerous glands secreting mucus. Faeces is made up of plant fibre (cellulose mainly), cholesterol, bile, mucus, mucosa cells (around 250 g of cells are lost each day!), bacteria and water, and is released by the anal sphincter.



How (and where) are Carbohydrates Digested?


By far the most abundant carbohydrate in the human diet is starch (in bread, potatoes, cereal, rice, pasta, biscuits, cake, etc). 


Starch is digested (broken down / hydrolysed) into glucose in two stages: -


[insert images - flow diagram of starch-maltose-glucose]


1. the digestion (hydrolysis) of starch into the disaccharide maltose

2. the digestion (hydrolysis) of maltose into glucose.


Carbohydrate digestion begins in the mouth.


Mastication (chewing your food!) is of massive importance, since mastication helps in the production of Salivary amylase. 


Salivary amylase begins the digestion of starch in the mouth. Albeit, very little digestion actually takes place, and as the chewed up food (now called a bolus) passes into the stomach, salivary amylase is quickly denatured! 


However, salivary amylase in the mouth also helps to clean the mouth of bits of starch and reduce bacterial infection!


Carbohydrate digestion continues in the Duodenum.


Since no carbohydrate digestion takes place in the stomach due to amylase enzyme being denatured (low, acidic pH denatures salivary amylase enzymes). We continue carbohydrate digestion in the small intestine, specifically the duodenum.


The Pancreas secretes pancreatic amylase into the small intestine (duodenum) which digests all the remaining starch (in the duodenum). 


Pancreatic Amylase digests starch molecules from the ends of the chains in two-glucose units, forming the disaccharide maltose. Glycogen is also digested here.



Disaccharides in the Ilium.

Starch has been digested (hydrolysed) into the disaccharide maltose in the beginning section of the small intestine (the duodenum). Now, these disaccharides continue their journey into the ileum where membrane bound enzymes complete the hydrolysis of maltose into glucose.


Disaccharidases in the membrane of the ileum epithelial cells complete the digestion of disaccharides to monosaccharides. This includes maltose from starch digestion as well as any sucrose and lactose in the diet. 


There are three important disaccharidase enzymes you must know:


  1. Maltase: Hydrolyses the disaccharide Maltose into Glucose.

  2. Sucrase: Hydrolyses the disaccharide sucrose into Glucose + Fructose

  3. Lactase: Hydrolyses the disaccharide Lactose into Glucose + Galactose.


(Now you should be beginning to understand why the basic biochemistry stuff is of such vital importance!)


These enzymes (maltase, sucrase and lactase) are unusual in that they are located in the membrane of the ileum epithelial cells (thus, they are membrane bound enzymes). 


(Insert diagram showing membrane bound enzymes and hydrolysis). 


This is an important adaptation as it means glucose can be produced at the cells where it needs to be absorbed into the body.


How is Glucose Absorbed into the body?


Glucose (and the other monosaccharides) are absorbed from the gut by a special kind of active transport called coupled active transport. 


In coupled active transport the monosaccharides are transported by a facilitated diffusion protein, which is coupled to an active transport protein.


1. The active transport protein is the sodium-potassium ATPase which is present in all animal cell membranes. 


This protein continuously pumps sodium ions out of the epithelial cell and potassium ions into the cell, using the energy from the hydrolysis of ATP to do so. Because this is active transport, the ions are pumped against their concentration gradients, which results in a large build-up of sodium ions in the lumen of the gut.


2. A facilitated diffusion protein called the sodium-glucose co-transporter protein, (which is only found in the membrane of the epithelial cells of the ileum), has two binding sites: 

1. A binding site for glucose and

2. A binding site for sodium ions.


It is important that you know, both molecules (sodium and glucose) must be carried together. 


However, since the process is diffusion, the molecules are only carried down their concentration gradients. But how, if glucose is being used (assimilated) and the concentration gradient is low for glucose? (i.e. glucose is being idffused against is concentrations gradient!)


Well, the very large concentration gradient of sodium ions across the epithelial cell membrane drives the sodium-glucose co-transporter in one direction only – carrying both molecules into the cell. So, whilst the sodium ions are diffusing down their concentration gradient, the glucose molecules can be carried across, against their concentration gradient!


3. The sodium ions are pumped out again by the Na/K ATPase to restore the sodium gradient. The potassium ions diffuse out through a potassium ion channel, doing no work in the process. So both ions constantly cycle in and out of the epithelial cell.



4. There is now a high concentration of glucose inside the epithelial cell. The glucose diffuses through the epithelial cell and diffuses into the tissue fluid of the villus via facilitated diffusion, through a glucose carrier protein that is only found on the inner surface of the epithelial cell.


5. The glucose enters the blood capillary by diffusing through gaps between the capillary endothelial cells. The glucose is carried in the blood to every cell in the body, where it is used for cellular respiration.



The combination of steps 1 and 2 is the transport of glucose against its concentration gradient into the epithelial cell, together with the hydrolysis of ATP. So, in effect the energy released by splitting ATP is used to pump glucose into the cell, though indirectly. 


Hence This is called “Coupled Active Transport”.



The Digestion of Proteins


Rennin (in gastric juice) converts the soluble milk protein caesin into its insoluble calcium salt. This keeps in the stomach longer so that pepsin can digest it. Rennin is normally only produced by infant mammals. (It is used commercially to make cheese).


Pepsin (in gastric juice) digests proteins to peptides, 6-12 amino acids long. Pepsin is an endopeptidase, which means it hydrolyses peptide bonds in the middle of a polypeptide chain. It is unusual in that it has an optimum pH of about 2 and stops working at neutral pH.


Pancreatic endopeptidases continue to digest proteins and peptides to short peptides in the duodenum. Different endopeptidase enzymes cut at different places on a peptide chain because they have different target amino acid sequences, so this is an efficient way to cut a long chain up into many short fragments, and it provides many free ends for the next enzymes to work on.


Exopeptidases in the membrane of the ileum epithelial cells complete the digestion of the short peptides to individual amino acids. Exopeptidases remove amino acids one by one from the ends of peptide chains. Carboxypeptidases work from the C-terminal end, aminopeptidases work from the N-terminal end, and dipeptidases cut dipeptides in half.


The amino acids are absorbed by active transport into the epithelial cells of the ileum, whence they diffuse into the blood capillaries of the villi. Again, the membrane-bound peptidases and the amino acid transporters are closely associated.


Protease enzymes are potentially dangerous because they can break down other enzymes (including themselves!) and other proteins in cells. To prevent this they are synthesised in the rER of their secretory cells as inactive forms, called zymogens. These are quite safe inside cells, and the enzymes are only activated in the lumen of the intestine when they are required.


Pepsin is synthesised as inactive pepsinogen, and activated by the (HCL) acid / pepsin in the stomach.


1. Rennin is synthesised as inactive pro-rennin, and activated by pepsin in the stomach

2. The pancreatic exopeptidases are activated by specific enzymes in the duodenum

3. The membrane-bound peptidase enzymes do not have this problem since they are fixed, so cannot come into contact with cell proteins.


The lining of mucus between the stomach wall and the food also protects the cells from the protease enzymes once they are activated.


[insert images of protein digestion]

[link to protein stricture and amino acids] [again an understanding of basic A-Level biochemistry is essential for answering challenging A-Level biology questions!] 

The Digestion of Lipids (Triglycerides)


Digestion of Triglycerides (lipids / fats): Lipids (fats) are emulsified by bile salts to form small oil droplets called micelles, which have a large surface area! 


Pancreatic lipase enzymes digest triglycerides to fatty acids and glycerol in the duodenum.


Fatty acids and glycerol are lipid soluble and diffuse across the membrane (by lipid diffusion) into the epithelial cells of the villi in the ileum.


In the epithelial cells of the ileum triglycerides are re-synthesised (!) and combine with proteins to form tiny lipoprotein particles called chylomicrons.


Chylomicrons diffuse into the lacteal - the lymph vessel inside each villus. The emulsified fatty droplets give lymph its milky colour, hence name lacteal.


Chylomicrons are carried through the lymphatic system to enter the bloodstream at the vena cava, and are then carried in the blood to all parts of the body. They are stored as triglycerides in adipose (fat) tissue.


Fats are not properly broken down until they needed / used for respiration in liver or muscle cells!


The Digestion of Nucleic acids and other substances.


Pancreatic nuclease enzymes digest nucleic acids (DNA and RNA) to nucleotides in the duodenum.


Membrane-bound nucleotidase enzymes in the epithelial cells of the ileum digest the nucleotides to sugar, base and phosphate, which are readily absorbed.


Many substances in the diet are composed of small molecules that need little or no digestion.


These include simple sugars, mineral ions, vitamins and water. Which are absorbed by different transport mechanisms, for example: -


Cholesterol and the fat-soluble vitamins (A, D, E, K) are absorbed into the epithelial cells of the ileum by lipid diffusion.


Mineral ions and water-soluble vitamins are absorbed by passive transport in the ileum


Dietary monosaccharides are absorbed by active transport in the ileum


Water is absorbed by osmosis in the ileum and colon.



Medical conditions of the digestive system you need to know.


Lactose Intolerance


Lactose is the sugar found in mammalian milk, and, as we’ve seen, lactose is digested by the disaccharidase enzyme lactase (in the membrane of the ileum epithelial cells) to glucose and galactose:


[insert diagram of : - Lactose hydrolysed by lactase into glucose + galactose]



Some people are lactose intolerant, which means they feel ill if they eat foods containing milk. 


The symptoms include flatulence and explosive diarrhoea. This happens because they don’t have the lactase enzyme, so they can’t digest lactose. Since lactose can’t be absorbed it remains in the gut, passing on to the large intestine, where there wouldn’t normally be any sugars. This is where the problems are caused:


1. The presence of lactose lowers the water potential of the colon lumen, so water cannot be absorbed from the faeces by osmosis, and in fact water often diffuses out of the colon mucosa cells in to the lumen down the water potential gradient. All this excess water in the gut lumen causes diarrhoea.


2. The colon is home to large numbers of bacteria (the commensal flora), who can respire lactose and increase in number. It is the fermentation products of the bacteria which produces acids and gases such as methane and carbon dioxide. These by products of fermentation cause flatulence.

In fact most adult humans (like all other adult mammals) are to some degree lactose intolerant, and this is the “normal” state. The sugar Lactose is only found in milk (hence the term of used “milk sugar”), which is produced by the mammary glands of female mammals to feed their young. 


Suckling juvenile mammals all synthesise lactase in order to digest the lactose in milk, but when they are weaned (i.e. being eating solid foods) they stop drinking milk and the gene for lactase production is switched off.


Humans are unique in that some continue to drink animal milk even as adults, at least in some human societies. These humans generally have a mutation that causes lactase to be produced throughout life, so these people are lactose tolerant and can drink milk without any ill effects. 


Societies that adopted a pastoral lifestyle (farming animals), such as most Europeans, northern Indians and some Africans, are generally lactose tolerant today. The rest (many Asian, African, Native Americans and Native Australians) remain lactose intolerant as adults.




Cholera is an infectious disease caused by the bacterium Vibrio cholerae.


V. cholerae is a typical prokaryotic cell with a slightly curved rod shape and a single flagellum. 


[insert images of Vibrio cholerae] 


[Note - This topic is also often examined / linked to prokaryotic structure and function!]



The symptoms of cholera include stomach cramps, vomiting, fever and severe diarrhoea. 


In severe cases up to 20 litres of water can be lost per day, and if untreated, leads to death in 75% of cholera patients. 


There were several serious outbreaks of cholera in the UK in the 19th century and cholera remains a major killer of small children in developing countries (several million deaths each year). However cholera can be treated simply and cheaply.


How does cholera cause diarrhoea?


The cholera bacterium adheres to the epithelium and secretes the cholera toxin CT. 

CT enters the epithelial cells and activates a chloride ion channel in the cell membrane. This causes chloride ions to diffuse out of the cells into the lumen.


The diffusion of chloride ions into the lumen lowers the water potential in the lumen of the gut.


Water is lost from cells to the lumen by osmosis, producing diarrhoea and dehydration.


[insert images of cells, and cholear and Cl- channel]


[Notice that you must fully understand osmosis - which is often examined in relation to cholera too!]


How is cholera treated? [hint oral antibiotics are no use and you often need to explain why!]


The treatment for diarrhoea was revolutionised in the 1960s, with the development of oral rehydration therapy (ORT). This simple and cheap treatment consists of drinking an oral rehydration solution (ORS) of glucose and salt (NaCl), and sometimes other ions like potassium and bicarbonate. 


ORT makes use of the sodium-glucose co-transporter protein that normally absorbs glucose into the ileum epithelial cells.


1. If both Na+ and glucose are present in the lumen, they bind to the sodium-glucose co-transporter protein. Transport only works if both molecules are present, which is why salt alone is not an effective treatment. ORS contain equimolar concentrations of glucose and salt.


2. The transporter protein carries the Na+ and glucose into the cell, down their concentration gradients.


3. This lowers the water potential inside the epithelial cells. So water diffuses from the lumen into the epithelial cells by osmosis, rehydrating cells and reducing diarrhoea.


So, why cant this bacterial disease simple be given oral antibiotics? because cholera affects the water=potential of cells causing diarrhoea - thus the antibiotics would go straight through the digestive system. As such ORT are needed.



Saprophytic digestion

Fungi (link to cell structure and function of fungal cells).


How do fungi digest, absorb and assimilate?


Fungi are not consumers like animals, but are either saprophytes (decomposers), or pathogenic.


Thus, Fungi use saprophytic nutrition. fungi are saprophytes which means they do not ingest their food, but digest it extracellularly. 




Fungi secrete digestive enzymes (carbohydrases, proteases and lipases) into the material that surrounds them and then absorb the soluble products (sugars, amino acids, etc).



[insert image of fungi - saprophytic digestions]


Fungi are usually composed of long thin threads called hyphae. These grow quickly, penetrating dead material such as leaves, as well as growing underground throughout soil. The 'cotton wool' appearance of bread mould growing on decaying bread is typical of a mass of hyphae, called a fungal mycelium. These thin hyphae give fungi a large surface area to volume ratio. They contain many nuclei, since they are formed from the fusion of many cells.

[Think about how fungal digestion links to ecology - i.e. nutrient cycles]