# A-level Biology/Mammalian Physiology and Behavior/Mammalian Nutrition
## Overview

In mammalian physiology, the alimentary canal is the location of all digestion. The alimentary canal is most easily described as a long tube which runs from the mouth, through the body to the anus. In an adult human, it can be up to 6 metres long, and is obviously coiled to preserve space. This canal, in addition to organs which secrete various substances into it make up the digestive system.
You may remember from your work on blood vessels, for example, that the space inside the tube is known as a lumen. The lumen of the alimentary canal goes straight from the mouth to the anus without obstruction and thus substances can pass right through without ever entering a cell, and the lumen is thus considered a part of the outside world. The process of absorption is what moves food substances from the lumen into cells and usually into the blood stream.
Eating food and thus entering it into the alimentary canal is known as ingestion, followed by digestion and then absorption. Any food that cannot be digested for whatever reason (cellulose is a good example), passes all the way through the alimentary canal and out the anus in the form of faeces, the removal of which is known as egestion. Remember, egestion is not excretion, since excretion is the removal of metabolism waste products, but egestion deals with material that has not been absorbed and therefore cannot have been part of metabolism.
Due to requirements of absorption in the alimentary canal (very small size), usually only small molecules (e.g. iron, calcium, vitamins, amino acids, monosaccharides) and water can be absorbed immediately. Other molecules (known as macromolecules) such as starch and proteins cannot be absorbed and they must first be broken down into smaller molecules - the less complex monomers from which they are constructed.
Mechanical digestion is the process of chewing (also, the churning of the stomach), breaking larger pieces of food into smaller ones, providing a larger surface area for the digestive enzymes to act on during chemical digestion. The macromolecules we discussed in the previous paragraphs can then be more easily broken down - via hydrolysis reactions catalysed by a variety of enzymes.

## Enzymes in Digestion

All digestive reactions are hydrolysis - breaking down complex molecules into simple ones with the addition of water, and thus all digestive enzymes are hydrolases.
A table detailing the enzyme activity in a human alimentary canal can be found below;

### Protein Digestion

Protein digestion takes place in the stomach, duodenum and ileum. The stomach has the protease pepsin which catalyses the hydrolysis of peptide bonds within protein molecules, splitting them into smaller chains, and is thus known as an endopeptidase. In the duodenum, trypsin and chymotrypsin do the same thing. An exopeptidase is one which cleaves off single amino acids from the end of a chain, and the one in the ileum is the carboxypeptidase, producing amino acids which are then absorbed into the blood capillaries.

## Gastroinestinal Tract

The alimentary canal, a canal that travels from mouth to the anus, has the same structure throughout, a wall with four main layers - the mucosa, submucosa, muscularis externa and serosa.
The mucosa is the layer nearest the lumen and on its inner surface is a thin epithelium, which contains goblet cells. These secrete mucus to lubricate and protect the cells from abrasion by food. It also stops damage by digestive enzymes. Except for this common factor, the epithelium differs in various parts of the alimentary canal. Beneath the epithelium is a layer of connective tissue, and beneath that is a layer of smooth muscle called the muscularis mucosa. It is smooth muscle which allows it to contract slowly and rhythmically for long periods without tiring.
The submucosa consists of connective tissue lying within blood vessels and nerves. It contains a high proportion of collagen and elastin (fibrous proteins).
The musclurais externa, again smooth muscle, is made up of two bands - longitudinal muscle and circular muscle. Longitudinal lies lengthwise along the wall of the canal, whereas circular muscle lies around the wall. Their combined contraction and relaxation moves food through the alimentary canal via peristalsis.
The serosa is a thin layer of connective tissue that makes up the outer layer of the wall

### Mouth/Oesophagus

Food is ingested and then masticated (chewed) using the broad ridges/grooves on molars/premolars which breaks solid food into smaller pieces, increasing its surface area. Saliva is also secreted into the mouth - being mostly water it helps dissolve any soluble components, and the enzyme amylase begins the breakdown of starch to maltose. Swallowing takes the food into the top of the oesophagus, and peristalsis takes it to the stomach.

### Stomach

The stomach is a small sac with muscles at either end (sphincters), which control the entry and exit of food. When a bolus (ball of food) arrives at the stomach, the cardiac sphincter relaxes to allow food to enter, whilst the pyloric sphincter remains contracted so that food can remain there for several hours. It then allows the partially digested food to pass, now called chyme, into the duodenum.
The mucosa in the stomach is very folded, forming gastric pits, which secrete gastric juice. The epithelium is made up of columnar cells. It also contains chief cells and oxyntic cells, the former of which produce pepsinogen and the latter of which produce hydrochloric acid. Oxyntic cells have many mitochondria and deep invaginations on their surface.

#### Digestion

Gastric juice is mostly water but also contains hydrochloric acid from oxyntic cells. This hydrochloric acid gives gastric juice a pH of <1.0, which kills a high proportion of bacteria that is present in food. Chief cells secrete pepsinogen, which does not function as an enzyme and is converted to its active form (pepsin) by the removal of a short length of amino acids. This is achieved by both hydrochloric acid and pepsin itself.
Gastric juice also contains lipases to break down fats. The walls of the stomach lining is protected by alkaline mucus, coating the entire stomach wall.

#### Absorption

Only a few substances can be absorbed here, small, lipid-soluble molecules, for example alcohol, and aspirin.

### Liver/Pancreas

The mix of enzymes, hydrochloric acid and chyme (partially digested food) passes into the small intestine when the pyloric sphincter relaxes, and this coincides with the liver and the pancreas releasing juices into the small intestine. One of the liver's functions is to produce bile, which is stored in the gall bladder and then carried along the bile duct into the dueodenum. Bile contains bile salts which help emulsify fats, and are then reabsorbed (mostly) and go back to the liver, where they are then resecreted. Bile also contains hydrogencarbonate ions which help neutralise the acidic mixture of the duodenum.
The pancreas is both an endocrine and exocrine gland - its endocrine functon is to secrete insulin and glucagon (produced by the islets of Langerhans). Its exocrine function, the one we'll discuss most here, is the secretion of pancreatic juice into the pancreatic duct.
Pancreatic juice consists of enzymes and enzyme precursors. Trypsin and chymotrypsin are secreted in an inactive form, trypsoinogen and chymotrypsinogen. The former gradually changes to trypsin, and is speeded up by an enzyme enterokinase. Trypsin can then act on trypsoinogen and chymotripsinogen to activate them. Other enzymes include carboxypeptidase (secreted in inactive form, trypsin sorts it out), lipase and amylase. It also contains hydrogen carbonate ions to neutralise the acidic mixture of food and gastric juice in the duodenum.

### Small Intestine

The small intestine consists of three regions - the duodenum, jejunum and the ileum. The structure of the ileum has many numerous tiny folds in the walls, known as villi, made from the mucosa layer, and each villus is around 1mm tall. These villi all have their own microvilli which combined have a great surface area available for absorption. The smooth muscle in the musclaris mucosa can make them contract and sway around for great contact with the food in the lumen, and the villus also have a network of blood capillaries for absorption and transport of food.
Beneath the villi are glands called the crypts of Lieberkuhn, which contain goblet cells to secrete mucus.

#### Digestion

The enzymes from the duodenum continue to act, and enzymes that act in the ileum do so while attached to the surface of the epithelial cells of the villi. Some enzymes from the duodenum become adsorbed onto the surface of the cells, ensuring that the products of digestion are concentrated right next to the cells which will absorb them. In fact the majority of the digestion in the ileum happens right next to the plasma membranes of epithelial cells.

#### Absorption

The products of digestion; amino acids, fatty acids, glycerol and monosaccharides, can all cross the plasma membranes of the epithelial cells on the villi, passing through these cells to enter either the blood or lymphatic capillaries. Monosaccharides and amino acids go straight into the blood stream, whilst fatty acids and glycerol go into the lymphatic system.
Monosaccharides are absorbed in the same way as amino acids - sodium ions are continually pumped out of the base of the epithelial cells into the surrounding tissue fluid, resulting in sodium ions travelling down this created concentration gradient, carrying glucose and amino acids with them - co-transport.
Fatty acids and glycerol are able to diffuse through the phospholipid bi-layer (lipid-soluble), and are converted back to triglycerides on the smooth endoplasmic reticulum of an epithelium cell, transferred to the Golgi and then surrounded by a protein to create a chylomicron.
Water, inorganic ions and vitamins are also absorbed in the ileum, via osmosis, active transport, facilitated diffusion or plain diffusion (lipid-soluble only).

### Colon

The colon, caecum, appendix and rectum make up the large intestine, and the colon's function is to absorb inorganic ions and water, what remains anyway. The epithelium does not contain villi but it does have columnar cells with microvilli, providing a relatively large surface area for absorption. The material that reaches the rectum is mostly indigestible material - cellulose and lignin as well as mucus and cells that have been shed form the canal - it is passed out as faeces.

## Control of Digestion
### Endocrine system

The secretion of the digestive juices from the stomach/pancreas and the bile from the gall bladder is controlled by hormones. The arrival of action potentials at the stomach wall causes the secretion of a hormone called gastrin, which is released into the blood causing gastric glands to produce large quantities of gastric juice. This is also stimulated by the presence of food in the stomach.
The secretion of pancreatic juice is largely controlled by the arrival of food in the duodenum. The contact with acidic substances stimulates cells of the wall to secrete a hormone called secretin, which stimulates exocrine cells in the pancreas to release a hydrogencarbondate rich juice into the pancreatic duct.
The duodenum epithelial cells react to products of fat or protein digestion by secreting CCK which acts on the exocrine cells of the pancreas, stimulating the secretion of an enzyme rich juice, and causing the gall bladder (by forcing it to contract its smooth muscles) to force bile along the bile duct.

### Nervous system

The taste, sight and smell of food all feed into the nervous system, and the medulla oblongata carries impulses from it to the salivary glands as part of the autonomic nervous system. Gastric juice secretion is also stimulated by nerve impulses sent from the brain to the stomach wall (see above)

## Digestion and Dentition in other animals
### Herbivores

The food herbivores eat is not surrounded by cellulose cell walls that cannot be digested by enzymes, and are so have to be masticated by molars etc. A herbivore, such as a cow, may not have any canines at all, a diastema (gap), instead allows the long flexible tongue to move grass around the mouth. The chewing is done by premolars and molars, which have broad surfaces with ridges and cusps which move side to side and fit into each other. The cow does have incisors, but they are only on the lower surface, with a horny pad on the top where the upper incisors should be - these two act as a kind of clamp for the cow to pull grass from the ground. Cow's teeth continue to grow throughout life, since they are continually ground down by all the chewing.
A cow has a four chambered stomach - the largest chamber, the rumen (and also the reticulum), has a community of anaerobic microorganisms that produce enzymes to break down cellulose to glucose. Other enzymes break down this sugar to a fatty acid, thus many tissues in a cow are adapted to use fatty acids as their main respiratory substrate.
Plant material is passed up from the rumen and reticulum back into the mouth peridocally until it is completely chewed up, and is known as chewing the cud. Material is then passed from the rumen and reticulum into the omasum and abomason. Here hydrochloric acid and protease is secreted, as in a human stomach. Then the material continues into the small intestine.

### Carnivores

Carnivores, in contrast to herbivores, are meat eating animals and thus have very different dentistry and digestion. The wolf, for example, has long pointed teeth known as canines at the front of its mouth, which allow the wolf to stab the body of its prey when it bites it, killing it. Behind the canines are premolars and molars with extremely sharp edges, and are known as carnassial teeth because they slice past each other with the jaw is closed in a scissor like action that cracks, crushes bones and cuts meat into smaller pieces.
The inciscors at the front of the wolf's mouth are used in scraping meat from the surface of the bones. Since meat does not contain starch or cellulose cell walls, amylase is not required, and dogs do not have to chew very much. However, compensating for the lack of chemical digestion in the mouth is a very concentrated acid in the dogs stomach, allowing a dog to eat 'dangerous' food that is rotten without harm.