Digestion

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Digestion is the mechanical and chemical breakdown of food into smaller components that are more easily absorbed into a blood stream, for instance. Digestion is a form of catabolism: a breakdown of large food molecules to smaller ones.

When food enters the mouth, its digestion starts by the action of mastication, a form of mechanical digestion, and the contact of saliva. Saliva, which is secreted by the salivary glands, contains salivary amylase, an enzyme which starts the digestion of starch in the food. After undergoing mastication and starch digestion, the food will be in the form of a small, round slurry mass called a bolus. It will then travel down the esophagus and into the stomach by the action of peristalsis. Gastric juice in the stomach starts protein digestion. Gastric juice mainly contains hydrochloric acid and pepsin. As these two chemicals may damage the stomach wall, mucus is secreted by the stomach, providing a slimy layer that acts as a shield against the damaging effects of the chemicals. At the same time protein digestion is occurring, mechanical mixing occurs by peristalsis, which are waves of muscular contractions that move along the stomach wall. This allows the mass of food to further mix with the digestive enzymes. After some time (typically an hour or two in humans, 4–6 hours in dogs, somewhat shorter duration in house cats), the resulting thick liquid is called chyme. When the pyloric sphincter valve opens, chyme enters the duodenum where it mixes with digestive enzymes from the pancreas, and then passes through the small intestine, in which digestion continues. When the chyme is fully digested, it is absorbed into the blood. 95% of absorption of nutrients occurs in the small intestine. Water and minerals are reabsorbed back into the blood in the colon (large intestine) where the pH is slightly acidic about 5.6 ~ 6.9. Some vitamins, such as biotin and vitamin K (K2MK7) produced by bacteria in the colon are also absorbed into the blood in the colon.[1] Waste material is eliminated from the rectum during defecation.[2]

Contents

Digestive systems

Digestive systems take many forms. There is a fundamental distinction between internal and external digestion. External digestion is more primitive, and most fungi still rely on it.[3] In this process, enzymes are secreted into the environment surrounding the organism, where they break down an organic material, and some of the products diffuse back to the organism. Later, animals form a tube in which internal digestion occurs, which is more efficient because more of the broken down products can be captured, and the internal chemical environment can be more efficiently controlled.[4]

Some organisms, including nearly all spiders, simply secrete biotoxins and digestive chemicals (e.g., enzymes) into the extracellular environment prior to ingestion of the consequent "soup". In others, once potential nutrients or food is inside the organism, digestion can be conducted to a vesicle or a sac-like structure, through a tube, or through several specialized organs aimed at making the absorption of nutrients more efficient.

Schematic drawing of bacterial conjugation. 1- Donor cell produces pilus. 2- Pilus attaches to recipient cell, bringing the two cells together. 3- The mobile plasmid is nicked and a single strand of DNA is transferred to the recipient cell. 4- Both cells recircularize their plasmids, synthesize second strands, and reproduce pili; both cells are now viable donors.

Secretion systems

Bacteria use several systems to obtain nutrients from other organisms in the environments.

Channel transport system

In a channel transupport system, several proteins form a contiguous channel traversing the inner and outer membranes of the bacteria. It is a simple system, which consists of only three protein subunits: the ABC protein, membrane fusion protein (MFP), and outer membrane protein (OMP)[specify]. This secretion system transports various molecules, from ions, drugs, to proteins of various sizes (20 - 900 kDa). The molecules secreted vary in size from the small Escherichia coli peptide colicin V, (10 kDa) to the Pseudomonas fluorescens cell adhesion protein LapA of 900 kDa.[5]

Molecular syringe

One molecular syringe is used through which a bacterium (e.g. certain types of Salmonella, Shigella, Yersinia) can inject nutrients into protist cells. One such mechanism was first discovered in Y. pestis and showed that toxins could be injected directly from the bacterial cytoplasm into the cytoplasm of its host's cells rather than simply be secreted into the extracellular medium.[6]

Conjugation machinery

The conjugation machinery of some bacteria (and archaeal flagella) is capable of transporting both DNA and proteins. It was discovered in Agrobacterium tumefaciens, which uses this system to introduce the Ti plasmid and proteins into the host, which develops the crown gall (tumor).[7] The VirB complex of Agrobacterium tumefaciens is the prototypic system.[8]

The nitrogen fixing Rhizobia are an interesting case, wherein conjugative elements naturally engage in inter-kingdom conjugation. Such elements as the Agrobacterium Ti or Ri plasmids contain elements that can transfer to plant cells. Transferred genes enter the plant cell nucleus and effectively transform the plant cells into factories for the production of opines, which the bacteria use as carbon and energy sources. Infected plant cells form crown gall or root tumors. The Ti and Ri plasmids are thus endosymbionts of the bacteria, which are in turn endosymbionts (or parasites) of the infected plant.

The Ti and Ri plasmids are themselves conjugative. Ti and Ri transfer between bacteria uses an independent system (the tra, or transfer, operon) from that for inter-kingdom transfer (the vir, or virulence, operon). Such transfer creates virulent strains from previously avirulent Agrobacteria.

Release of outer membrane vesicles

In addition to the use of the multiprotein complexes listed above, Gram-negative bacteria possess another method for release of material: the formation of outer membrane vesicles.[9] Portions of the outer membrane pinch off, forming spherical structures made of a lipid bilayer enclosing periplasmic materials. Vesicles from a number of bacterial species have been found to contain virulence factors, some have immunomodulatory effects, and some can directly adhere to and intoxicate host cells. While release of vesicles has been demonstrated as a general response to stress conditions, the process of loading cargo proteins seems to be selective.[10]

Venus Flytrap (Dionaea muscipula) leaf

Gastrovascular cavity

The gastrovascular cavity functions as a stomach in both digestion and the distribution of nutrients to all parts of the body. Extracellular digestion takes place within this central cavity, which is lined with the gastrodermis, the internal layer of epithelium. This cavity has only one opening to the outside that functions as both a mouth and an anus: waste and undigested matter is excreted through the mouth/anus, which can be described as an incomplete gut.

In a plant such as the Venus Flytrap that can make its own food through photosynthesis, it does not eat and digest its prey for the traditional objectives of harvesting energy and carbon, but mines prey primarily for essential nutrients (nitrogen and phosphorus in particular) that are in short supply in its boggy, acidic habitat.[11]

Trophozoites of Entamoeba histolytica with ingested erythrocytes

Phagosome

A phagosome is a vacuole formed around a particle absorbed by phagocytosis. The vacuole is formed by the fusion of the cell membrane around the particle. A phagosome is a cellular compartment in which pathogenic microorganisms can be killed and digested. Phagosomes fuse with lysosomes in their maturation process, forming phagolysosomes. In humans, Entamoeba histolytica can phagocytose red blood cells.[12]

Specialised organs and behaviours

To aid in the digestion of their food animals evolved organs such as beaks, tongues, teeth, a crop, gizzard, and others.

A Catalina Macaw's seed-shearing beak
Squid beak with ruler for size comparison

Beaks

Birds have beaks that are specialised according to the bird's ecological niche. For example, macaws primarily eat seeds, nuts, and fruit, using their impressive beaks to open even the toughest seed. First they scratch a thin line with the sharp point of the beak, then they shear the seed open with the sides of the beak.

The mouth of the squid is equipped with a sharp horny beak mainly made of cross-linked proteins. It is used to kill and tear prey into manageable pieces. The beak is very robust, but does not contain any minerals, unlike the teeth and jaws of many other organisms, including marine species.[13] The beak is the only indigestible part of the squid.

Tongue

The tongue is skeletal muscle on the floor of the mouth that manipulates food for chewing (mastication) and swallowing (deglutition). It is sensitive and kept moist by saliva. The underside of the tongue is covered with a smooth mucous membrane. The tongue also has a touch sense for locating and positioning food particles that require further chewing. The tongue is utilized to roll food particles into a bolus before being transported down the esophagus through peristalsis.

The sublingual region underneath the front of the tongue is a location where the oral mucosa is very thin, and underlain by a plexus of veins. This is an ideal location for introducing certain medications to the body. The sublingual route takes advantage of the highly vascular quality of the oral cavity, and allows for the speedy application of medication into the cardiovascular system, bypassing the gastrointestinal tract.

Teeth

Teeth (singular tooth) are small whitish structures found in the jaws (or mouths) of many vertebrates that are used to tear, scrape, milk and chew food. Teeth are not made of bone, but rather of tissues of varying density and hardness. The shape of an animal's teeth is related to its diet. For example, plant matter is hard to digest, so herbivores have many molars for chewing.

The teeth of carnivores are shaped to kill and tear meat, using specially shaped canine teeth. Herbivores' teeth are made for grinding food materials, in this case, plant parts.

Crop

A crop, or croup, is a thin-walled expanded portion of the alimentary tract used for the storage of food prior to digestion. In some birds it is an expanded, muscular pouch near the gullet or throat. In adult doves and pigeons, the crop can produce crop milk to feed newly hatched birds.[14]

Certain insects may have a crop or enlarged esophagus.

Rough illustration of a ruminant digestive system

Abomasum

Herbivores have evolved cecums (or an abomasum in the case of ruminants). Ruminants have a fore-stomach with four chambers. These are the rumen, reticulum, omasum, and abomasum. In the first two chambers, the rumen and the reticulum, the food is mixed with saliva and separates into layers of solid and liquid material. Solids clump together to form the cud (or bolus). The cud is then regurgitated, chewed slowly to completely mix it with saliva and to break down the particle size.

Fibre, especially cellulose and hemi-cellulose, is primarily broken down into the volatile fatty acids, acetic acid, propionic acid and butyric acid in these chambers (the reticulo-rumen) by microbes: (bacteria, protozoa, and fungi). In the omasum water and many of the inorganic mineral elements are absorbed into the blood stream.

The abomasum is the fourth and final stomach compartment in ruminants. It is a close equivalent of a monogastric stomach (e.g., those in humans or pigs), and digesta is processed here in much the same way. It serves primarily as a site for acid hydrolysis of microbial and dietary protein, preparing these protein sources for further digestion and absorption in the small intestine. Digesta is finally moved into the small intestine, where the digestion and absorption of nutrients occurs. Microbes produced in the reticulo-rumen are also digested in the small intestine.

A flesh fly "blowing a bubble", possibly to concentrate its food by evaporating water

Specialised behaviours

Regurgitation has been mentioned above under abomasum and crop, referring to crop milk, a secretion from the lining of the crop of pigeons and doves with which the parents feed their young by regurgitation.[15]

Many sharks have the ability to turn their stomachs inside out and evert it out of their mouths in order to get rid of unwanted contents (perhaps developed as a way to reduce exposure to toxins).

Other animals, such as rabbits and rodents, practise coprophagia behaviours - eating specialised faeces in order to re-digest food, especially in the case of roughage. Capybara, rabbits, hamsters and other related species do not have a complex digestive system as do, for example, ruminants. Instead they extract more nutrition from grass by giving their food a second pass through the gut. Soft faecal pellets of partially digested food are excreted and generally consumed immediately. They also produce normal droppings, which are not eaten.

Young elephants, pandas, koalas, and hippos eat the faeces of their mother, probably to obtain the bacteria required to properly digest vegetation. When they are born, their intestines do not contain these bacteria (they are completely sterile). Without them, they would be unable to get any nutritional value from many plant components.

In earthworms

An earthworm's digestive system consists of a mouth, pharynx, esophagus, crop, gizzard, and intestine. The mouth is surrounded by strong lips, which act like a hand to grab pieces of dead grass, leaves, and weeds, with bits of soil to help chew. The lips break the food down into smaller pieces. In the pharynx, the food is lubricated by mucus secretions for easier passage. The esophagus adds calcium carbonate to neutralize the acids formed by food matter decay. Temporary storage occurs in the crop where food and calcium carbonate are mixed. The powerful muscles of the gizzard churn and mix the mass of food and dirt. When the churning is complete, the glands in the walls of the gizzard add enzymes to the thick paste, which helps chemically breakdown the organic matter. By peristalsis, the mixture is sent to the intestine where friendly bacteria continue chemical breakdown. This releases carbohydrates, protein, fat, and various vitamins and minerals for absorption into the body.

Overview of vertebrate digestion

In most vertebrates, digestion is a multi-stage process in the digestive system, starting from ingestion of raw materials, most often other organisms. Ingestion usually involves some type of mechanical and chemical processing. Digestion is separated into four steps:

  1. Ingestion: placing food into the mouth (entry of food in the digestive system),
  2. Mechanical and chemical breakdown: mastication and the mixing of the resulting bolus with water, acids, bile and enzymes in the stomach and intestine to break down complex molecules into simple structures,
  3. Absorption: of nutrients from the digestive system to the circulatory and lymphatic capillaries through osmosis, active transport, and diffusion, and
  4. Egestion (Excretion): Removal of undigested materials from the digestive tract through defecation.

Underlying the process is muscle movement throughout the system through swallowing and peristalsis. Each step in digestion requires energy, and thus imposes an "overhead charge" on the energy made available from absorbed substances. Differences in that overhead cost are important influences on lifestyle, behavior, and even physical structures. Examples may be seen in humans, who differ considerably from other hominids (lack of hair, smaller jaws and musculature, different dentition, length of intestines, cooking, etc.).

The major part of digestion takes place in the small intestine. The large intestine primarily serves as a site for fermentation of indigestible matter by gut bacteria and for resorption of water from digesta before excretion.

In mammals, preparation for digestion begins with the cephalic phase in which saliva is produced in the mouth and digestive enzymes are produced in the stomach. Mechanical and chemical digestion begin in the mouth where food is chewed, and mixed with saliva to begin enzymatic processing of starches. The stomach continues to break food down mechanically and chemically through churning and mixing with both acids and enzymes. Absorption occurs in the stomach and gastrointestinal tract, and the process finishes with defecation.[2]

Human digestion process

Salivary glandsParotid glandSubmandibular glandSublingual glandpharynxTongueEsophagusPancreasStomachPancreatic ductIleumAnusRectumVermiform appendixCecumDescending colonAscending colonTransverse colonColon (anatomy)Bile ductDuodenumGallbladderLiveroral cavity
Upper and Lower human gastrointestinal tract

The whole digestive system is around 9 meters long. In a healthy human adult this process can take between 24 and 72 hours. Food digestion physiology varies between individuals and upon other factors such as the characteristics of the food and size of the meal.[16]

Phases of gastric secretion

Oral cavity

In humans, digestion begins in the Mouth, otherwise known as the "Buccal Cavity", where food is chewed. Saliva is secreted in large amounts (1-1.5 litres/day) by three pairs of exocrine salivary glands (parotid, submandibular, and sublingual) in the oral cavity, and is mixed with the chewed food by the tongue. Saliva cleans the oral cavity, moistens the food, and contains digestive enzymes such as salivary amylase, which aids in the chemical breakdown of polysaccharides such as starch into disaccharides such as maltose. It also contains mucus, a glycoprotein that helps soften the food and form it into a bolus. An additional enzyme, lingual lipase, hydrolyzes long-chain triglycerides into partial glycerides and free fatty acids.

Swallowing transports the chewed food into the esophagus, passing through the oropharynx and hypopharynx. The mechanism for swallowing is coordinated by the swallowing center in the medulla oblongata and pons. The reflex is initiated by touch receptors in the pharynx as the bolus of food is pushed to the back of the mouth.

Pharynx

The pharynx is the part of the neck and throat situated immediately behind the mouth and nasal cavity, and cranial, or superior, to the esophagus. It is part of the digestive system and respiratory system. Because both food and air pass through the pharynx, a flap of connective tissue, the epiglottis closes over the trachea when food is swallowed to prevent choking or asphyxiation.

The oropharynx is that part of the pharynx behind the oral cavity. It is lined with stratified squamous epithelium. The nasopharynx lies behind the nasal cavity and like the nasal passages is lined with ciliated columnar pseudostratified epithelium.

Like the oropharynx above it the hypopharynx (laryngopharynx) serves as a passageway for food and air and is lined with a stratified squamous epithelium. It lies inferior to the upright epiglottis and extends to the larynx, where the respiratory and digestive pathways diverge. At that point, the laryngopharynx is continuous with the esophagus. During swallowing, food has the "right of way", and air passage temporarily stops.

Esophagus

The esophagus is a narrow muscular tube about 20-30 centimeters long, which starts at the pharynx at the back of the mouth, passes through the thoracic diaphragm, and ends at the cardiac orifice of the stomach. The wall of the esophagus is made up of two layers of smooth muscles, which form a continuous layer from the esophagus to the colon and contract slowly, over long periods of time. The inner layer of muscles is arranged circularly in a series of descending rings, while the outer layer is arranged longitudinally. At the top of the esophagus, is a flap of tissue called the epiglottis that closes during swallowing to prevent food from entering the trachea (windpipe). The chewed food is pushed down the esophagus to the stomach through peristaltic contraction of these muscles. It takes only about seven seconds for food to pass through the esophagus and now digestion takes place.


Stomach

The stomach is a small, 'J'-shaped pouch with walls made of thick, distensible muscles, which stores and helps break down food. Food reduced to very small particles is more likely to be fully digested in the small intestine, and stomach churning has the effect of assisting the physical disassembly begun in the mouth. Ruminants, who are able to digest fibrous material (primarily cellulose), use fore-stomachs and repeated chewing to further the disassembly. Rabbits and some other animals pass some material through their entire digestive systems twice. Most birds ingest small stones to assist in mechanical processing in gizzards.

Food enters the stomach through the cardiac orifice where it is further broken apart and thoroughly mixed with gastric acid, pepsin and other digestive enzymes to break down proteins. The enzymes in the stomach also have an optimum conditions, meaning that they work at a specific pH and temperature better than any others. The acid itself does not break down food molecules, rather it provides an optimum pH for the reaction of the enzyme pepsin and kills many microorganisms that are ingested with the food. It can also denature proteins. This is the process of reducing polypeptide bonds and disrupting salt bridges, which in turn causes a loss of secondary, tertiary, or quaternary protein structure. The parietal cells of the stomach also secrete a glycoprotein called intrinsic factor, which enables the absorption of vitamin B-12. Mucus neck cells are present in the gastric glands of the stomach. They secrete mucus, which along with gastric juice plays an important role in lubrication and protection of the mucosal epithelium from excoriation by the highly concentrated hydrochloric acid. Other small molecules such as alcohol are absorbed in the stomach, passing through the membrane of the stomach and entering the circulatory system directly. Food in the stomach is in semi-liquid form, which upon completion is known as chyme.

After consumption of food, digestive "tonic" and peristaltic contractions begin, which helps break down the food and move it onward.[16] When the chyme reaches the opening to the duodenum known as the pylorus, contractions "squirt" the food back into the stomach through a process called retropulsion, which exerts additional force and further grinds down food into smaller particles.[16] Gastric emptying is the release of food from the stomach into the duodenum; the process is tightly controlled with liquids being emptied much more quickly than solids.[16] Gastric emptying has attracted medical interest as rapid gastric emptying is related to obesity and delayed gastric emptying syndrome is associated with diabetes mellitus, aging, and gastroesophageal reflux.[16]

The transverse section of the alimentary canal reveals four (or five, see description under mucosa) distinct and well developed layers within the stomach:

Small intestine

It has three parts: the Duodenum, Jejunum, and Ileum.

After being processed in the stomach, food is passed to the small intestine via the pyloric sphincter. The majority of digestion and absorption occurs here after the milky chyme enters the duodenum. Here it is further mixed with three different liquids:

The pH level increases in the small intestine as all three fluids are alkaline. A more basic environment causes more helpful enzymes to activate and begin to help in the breakdown of molecules such as fat globules. Small, finger-like structures called villi, and their epithelial cells is covered with numerous microvilli to improve the absorption of nutrients by increasing the surface area of the intestine and enhancing speed at which nutrients are absorbed. Blood containing the absorbed nutrients is carried away from the small intestine via the hepatic portal vein and goes to the liver for filtering, removal of toxins, and nutrient processing.

The small intestine and remainder of the digestive tract undergoes peristalsis to transport food from the stomach to the rectum and allow food to be mixed with the digestive juices and absorbed. The circular muscles and longitudinal muscles are antagonistic muscles, with one contracting as the other relaxes. When the circular muscles contract, the lumen becomes narrower and longer and the food is squeezed and pushed forward. When the longitudinal muscles contract, the circular muscles relax and the gut dilates to become wider and shorter to allow food to enter.

Large intestine

After the food has been passed through the small intestine, the food enters the large intestine. Within it, digestion is retained long enough to allow fermentation due to the action of gut bacteria, which breaks down some of the substances that remain after processing in the small intestine; some of the breakdown products are absorbed. In humans, these include most complex saccharides (at most three disaccharides are digestible in humans). In addition, in many vertebrates, the large intestine reabsorbs fluid; in a few, with desert lifestyles, this reabsorbtion makes continued existence possible.

In general, the large intestine is less vigorous in absorptive activity. It produces sacculation, renews epithelial cells, and provides protective mucus and mucosal immunity. In humans, the large intestine is roughly 1.5 meters long, with three parts: the cecum at the junction with the small intestine, the colon, and the rectum. The colon itself has four parts: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon. The large intestine absorbs water from the chyme and stores feces until it can be egested. Food products that cannot go through the villi, such as cellulose (dietary fiber), are mixed with other waste products from the body and become hard and concentrated feces. The feces is stored in the rectum for a certain period and then the stored feces is eliminated from the body due to the contraction and relaxation through the anus. The exit of this waste material is regulated by the anal sphincter.

Breakdown into nutrients

Protein digestion

Protein digestion occurs in the stomach and duodenum in which 3 main enzymes, pepsin secreted by the stomach and trypsin and chymotrypsin secreted by the pancreas, break down food proteins into polypeptides that are then broken down by various exopeptidases and dipeptidases into amino acids. The digestive enzymes however are mostly secreted as their inactive precursors, the zymogens. For example, trypsin is secreted by pancreas in the form of trypsinogen, which is activated in the duodenum by enterokinase to form trypsin. Trypsin then cleaves proteins to smaller polypeptides.

Fat digestion

Digestion of some fats can begin in the mouth where lingual lipase breaks down some short chain lipids into diglycerides. The presence of fat in the small intestine produces hormones that stimulate the release of pancreatic lipase from the pancreas and bile from the liver for breakdown of fats into fatty acids. Complete digestion of one molecule of fat (a triglyceride) results in 3 fatty acid molecules and one glycerol molecule.

Carbohydrate digestion

In humans, dietary starches are composed of glucose units arranged in long chains called amylose, a polysaccharide. During digestion, bonds between glucose molecules are broken by salivary and pancreatic amylase, 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.

Lactase is an enzyme that breaks down the disaccharide lactose to its component parts, glucose and galactose. Glucose and galactose can be absorbed by the small intestine. Approximately half of the adult population produce only small amounts of lactase and are unable to eat milk-based foods. This is commonly known as lactose intolerance.

Sucrase is an enzyme that breaks down the disaccharide sucrose, commonly known as table sugar, cane sugar, or beet sugar. Sucrose digestion yields the sugars fructose and glucose which are readily absorbed by the small intestine.

DNA and RNA digestion

DNA and RNA are broken down into mononucleotides by the nucleases deoxyribonuclease and ribonuclease (DNase and RNase) from the pancreas.

Digestive hormones

Action of the major digestive hormones

There are at least five hormones that aid and regulate the digestive system in mammals. There are variations across the vertebrates, as for instance in birds. Arrangements are complex and additional details are regularly discovered. For instance, more connections to metabolic control (largely the glucose-insulin system) have been uncovered in recent years.

Significance of pH in digestion

Digestion is a complex process controlled by several factors. pH plays a crucial role in a normally functioning digestive tract. In the mouth, pharynx, and esophagus, pH is typically about 6.8, very weakly acidic. Saliva controls pH in this region of the digestive tract. Salivary amylase is contained in saliva and starts the breakdown of carbohydrates into monosaccharides. Most digestive enzymes are sensitive to pH and will denature in a high or low pH environment.

The stomach's high acidity inhibits the breakdown of carbohydrates within it. This acidity confers two benefits: it denatures proteins for further digestion in the small intestines, and provides non-specific immunity, damaging or eliminating various pathogens.[citation needed]

In the small intestines, the duodenum provides critical pH balancing to activate digestive enzymes. The liver secretes bile into the duodenum to neutralize the acidic conditions from the stomach, and the pancreatic duct empties into the duodenum, adding bicarbonate to neutralize the acidic chyme, thus creating a neutral environment. The mucosal tissue of the small intestines is alkaline with a pH of about 8.5.[citation needed]

Uses of animal gut by humans

See also

References

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