Editing Digestion

{{short description|Biological process of breaking down food}}
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{{for-multi|the industrial process|Anaerobic digestion|the treatment of precipitates in analytical chemistry|Precipitation (chemistry)#Digestion|the journal|Digestion (journal)|the term in alchemy|Digestion (alchemy)}}
{{Infobox anatomy
|Name         = Digestive system
|Latin        = systema digestorium
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'''Digestion''' is the breakdown of large insoluble [[food]] compounds into small water-soluble components so that they can be absorbed into the [[blood plasma]]. In certain organisms, these smaller substances are absorbed through the [[small intestine]] into the [[blood stream]]. Digestion is a form of [[catabolism]] that is often divided into two processes based on how food is broken down: mechanical and chemical digestion. The term '''mechanical digestion''' refers to the physical breakdown of large pieces of food into smaller pieces which can subsequently be accessed by [[digestive enzyme]]s. Mechanical digestion takes place in the [[mouth]] through [[Chewing|mastication]] and in the small intestine through [[segmentation contractions]]. In '''chemical digestion''', [[enzyme]]s break down food into the small compounds that the body can use.

In the [[human digestive system]], food enters the mouth and mechanical digestion of the food starts by the action of mastication (chewing), a form of mechanical digestion, and the wetting contact of [[saliva]]. Saliva, a liquid secreted by the [[salivary glands]], contains [[salivary amylase]], an enzyme which starts the digestion of [[starch]] in the food.<ref>{{Cite book |title=The Digestive System |last=Avraham |first=Regina |publisher=Chelsea House |year=1989 |isbn=0-7910-0015-X |location=New York |pages=[https://archive.org/details/digestivesyste00avra/page/48/mode/2up 49] |url=https://archive.org/details/digestivesyste00avra |others=Introduction by C. Everett Koop |ol=2055854M |access-date=2024-03-20}}</ref> The saliva also contains [[mucus]], which lubricates the food; the [[electrolyte]] hydrogencarbonate ({{chem2|HCO-3|link=Bicarbonate#Physiological role}}), which provides the ideal conditions of pH for amylase to work; and other electrolytes ({{chem2|Na+|link=Sodium in biology}}, {{chem2|K+|link=Potassium in biology}}, {{chem2|Cl-|link=Chloride#Role in biology}}).<ref>{{Cite book |title=Principles of Physiology |last1=Berne |first1=Robert M. |publisher=[[Mosby (imprint)|Mosby]] |year=2000 |isbn=0-323-00813-5 |edition=3rd |location=St. Louis |pages=[https://archive.org/details/principlesofphys00cvmo/page/372/mode/2up 373-374] |url=https://archive.org/details/principlesofphys00cvmo |last2=Levy |first2=Matthew N. |ol=9840795M |author-link=Robert M. Berne |author-link2=Matthew N. Levy |access-date=2024-03-20}}</ref> About 30% of starch is [[hydrolyzed]] into [[disaccharide]] in the oral cavity (mouth). After undergoing mastication and starch digestion, the food will be in the form of a small, round slurry mass called a [[Bolus (digestion)|bolus]]. It will then travel down the [[esophagus]] and into the [[stomach]] by the action of [[peristalsis]]. [[Gastric juice]] in the stomach starts [[proteolysis|protein digestion]]. Gastric juice mainly contains [[hydrochloric acid]] and [[pepsin]]. In [[infants]] and [[toddlers]], gastric juice also contains [[rennin]] to digest milk proteins. As the first two chemicals may damage the stomach wall, mucus and bicarbonates are secreted by the stomach. They provide a slimy layer that acts as a shield against the damaging effects of chemicals like concentrated hydrochloric acid while also aiding lubrication.<ref>{{Cite journal|last1=Allen|first1=Adrian|last2=Flemström|first2=Gunnar|date=January 2005|title=Gastroduodenal mucus bicarbonate barrier: protection against acid and pepsin|url=https://pubmed.ncbi.nlm.nih.gov/15591243/|journal=American Journal of Physiology. Cell Physiology|volume=288|issue=1|pages=C1–19|doi=10.1152/ajpcell.00102.2004|issn=0363-6143|pmid=15591243}}</ref> Hydrochloric acid provides acidic pH for pepsin. At the same time protein digestion is occurring, mechanical mixing occurs by peristalsis, which is waves of muscular contractions that move along the stomach wall. This allows the mass of food to further mix with the digestive enzymes. Pepsin breaks down proteins into [[peptides]] or [[proteose]]s, which is further broken down into dipeptides and [[amino acid]]s by enzymes in the small intestine. Studies suggest that increasing the number of chews per bite increases relevant gut hormones and may decrease self-reported hunger and food intake.<ref>{{Cite journal|last1=Miquel-Kergoat|first1=Sophie|last2=Azais-Braesco|first2=Veronique|last3=Burton-Freeman|first3=Britt|last4=Hetherington|first4=Marion M.|date=2015-11-01|title=Effects of chewing on appetite, food intake and gut hormones: A systematic review and meta-analysis|journal=Physiology & Behavior|volume=151|pages=88–96|doi=10.1016/j.physbeh.2015.07.017|issn=1873-507X|pmid=26188140|doi-access=free}}</ref>

When the [[Pylorus|pyloric sphincter valve]] opens, partially digested food ([[chyme]]) enters the [[duodenum]] where it mixes with digestive enzymes from the [[pancreas]] and bile juice from the [[liver]] 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 nutrient absorption occurs in the small intestine. Water and minerals are reabsorbed back into the blood in the [[Colon (anatomy)|colon]] (large intestine) where the pH is slightly acidic (about 5.6 ~ 6.9). Some vitamins, such as [[biotin]] and [[vitamin K]] (K<sub>2</sub>MK7) produced by bacteria in the colon are also absorbed into the blood in the colon. Absorption of water, simple sugar and alcohol also takes place in stomach. Waste material ([[feces]]) is eliminated from the [[rectum]] during [[defecation]].<ref name=Maton>{{cite book| last = Maton| first = Anthea| author2 = Jean Hopkins| author3 = Charles William McLaughlin| author4 = Susan Johnson| author5 = Maryanna Quon Warner| author6 = David LaHart| author7 = Jill D. Wright| title = Human Biology and Health| publisher = Prentice Hall| year = 1993| location = Englewood Cliffs, NJ| isbn = 978-0-13-981176-0| oclc = 32308337| url-access = registration| url = https://archive.org/details/humanbiologyheal00scho}}</ref>

==Digestive system==

Digestive systems take many forms. There is a fundamental distinction between internal and external digestion. External digestion developed earlier in evolutionary history, and most [[fungi]] still rely on it.<ref>Dusenbery, David B. (1996). "Life at Small Scale", pp. 113–115. Scientific American Library, New York. {{ISBN|0-7167-5060-0}}.</ref> In this process, [[enzyme]]s are [[Secretion|secreted]] into the environment surrounding the organism, where they break down an organic material, and some of the products [[Molecular diffusion|diffuse]] back to the organism. [[Animal]]s have a tube ([[gastrointestinal tract]]) 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.<ref>Dusenbery, David B. (2009). ''Living at Micro Scale'', p. 280. Harvard University Press, Cambridge, MA {{ISBN|978-0-674-03116-6}}.</ref>

Some organisms, including nearly all [[spiders]], 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 (biology)|vesicle]] or a sac-like structure, through a tube, or through several specialized organs aimed at making the absorption of nutrients more efficient.

[[Image:Conjugation.svg|right|thumb|250px|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===
{{Main|Secretion#Secretion in Gram negative bacteria}}

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

====Channel transport system====

In a channel transport 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 [[ATP-binding cassette family|ABC protein]], [[membrane fusion protein]] (MFP), and [[outer membrane protein]].{{Specify|date=May 2011}} This secretion system transports various chemical species, from ions, drugs, to proteins of various sizes (20–900 kDa). The chemical species 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.<ref name= Wooldridge>{{cite book |editor= Wooldridge K | year=2009 |title=Bacterial Secreted Proteins: Secretory Mechanisms and Role in Pathogenesis | publisher=Caister Academic Press | isbn= 978-1-904455-42-4}}</ref>

====Molecular syringe====

A [[type III secretion system]] means that a 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 be secreted into the extracellular medium.<ref name=Salyers>Salyers, A.A. & Whitt, D.D. (2002). ''Bacterial Pathogenesis: A Molecular Approach'', 2nd ed., Washington, DC: ASM Press. {{ISBN|1-55581-171-X}}</ref>

====Conjugation machinery====
The [[Bacterial conjugation|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).<ref name=Cascales>{{cite journal |vauthors=Cascales E, Christie PJ |title=The versatile Type IV secretion systems |journal=Nature Reviews Microbiology |volume=1 |issue=2 |pages=137–149 |year=2003 |doi=10.1038/nrmicro753 |pmid=15035043|pmc=3873781 }}</ref> The VirB complex of ''Agrobacterium tumefaciens'' is the prototypic system.<ref name=Christie>{{cite journal |author1=Christie PJ |author2=Atmakuri K |author3=Jabubowski S |author4=Krishnamoorthy V |author5=Cascales E. |title=Biogenesis, architecture, and function of bacterial Type IV secretion systems |journal=Annu Rev Microbiol |volume=59 |pages=451–485 |year=2005 |issue=1 |doi=10.1146/annurev.micro.58.030603.123630 |pmid=16153176|pmc=3872966 }}</ref>

In the [[Diazotroph|nitrogen-fixing]] ''[[Rhizobia]]'', conjugative elements naturally engage in inter-[[Kingdom (biology)|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 [[Agrobacterium tumefaciens|crown gall]] or [[Agrobacterium rhizogenes|root tumors]]. The Ti and Ri plasmids are thus [[endosymbiont]]s 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 vesicle]]s.<ref name=Chatterjee>{{Cite journal
 | pmid = 4168882|doi=10.1099/00221287-49-1-1
| year = 1967
| last1 = Chatterjee
| first1 = S.N.
| title = Electron microscopic observations on the excretion of cell-wall material by ''Vibrio cholerae''
| journal = Journal of General Microbiology
| volume = 49
| issue = 1
| pages = 1–11
| last2 = Das
| first2 = J
| doi-access = free
}}</ref><ref>{{Cite journal
 | pmid = 16291643
| year = 2005
| last1 = Kuehn
| first1 = M.J.
| title = Bacterial outer membrane vesicles and the host-pathogen interaction
| journal = Genes & Development
| volume = 19
| issue = 22
| pages = 2645–2655
| last2 = Kesty
| first2 = N.C.
| doi = 10.1101/gad.1299905
| doi-access = free
}}</ref>  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.<ref name=McBrrom>{{Cite journal
| last1 = McBroom | first1 = A.J.
| last2 = Kuehn | first2 = M.J.
| doi = 10.1111/j.1365-2958.2006.05522.x
| title = Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response
| journal = Molecular Microbiology
| volume = 63
| issue = 2
| pages = 545–558
| year = 2007
| pmid = 17163978
| pmc =1868505
}}</ref>

[[Image:Venus Flytrap showing trigger hairs.jpg|thumb|right|125px|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 (anatomy)|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.<ref name=Leege>{{cite web | url = http://www.sciam.com/article.cfm?id=how-does-the-venus-flytra | work = Scientific American | author = Leege, Lissa | title = How does the Venus flytrap digest flies? | access-date= 2008-08-20 }}</ref>

[[Image:Trophozoites of Entamoeba histolytica with ingested erythrocytes.JPG|thumb|125px|left|[[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 [[phagolysosome]]s. In humans, ''[[Entamoeba histolytica]]'' can phagocytose [[red blood cell]]s.<ref name=Boettner>{{Cite journal | doi = 10.1371/journal.ppat.0040008| pmid = 18208324| pmc = 2211552| title = Entamoeba histolytica Phagocytosis of Human Erythrocytes Involves PATMK, a Member of the Transmembrane Kinase Family| journal = PLOS Pathogens| volume = 4| issue = 1| pages = e8| year = 2008| last1 = Boettner | first1 = D.R. | last2 = Huston | first2 = C.D. | last3 = Linford | first3 = A.S. | last4 = Buss | first4 = S.N. | last5 = Houpt | first5 = E. | last6 = Sherman | first6 = N.E. | last7 = Petri | first7 = W.A. | doi-access = free}}</ref>

===Specialised organs and behaviours===
To aid in the digestion of their food, animals evolved organs such as beaks, [[tongue]]s, [[radula]]e, teeth, crops, gizzards, and others.

{{multiple image
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| caption1  = A [[Bird Hybrids|Catalina Macaw]]'s seed-shearing beak
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| caption2  = Squid beak with ruler for size comparison
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====Beaks====
[[Bird]]s have bony [[beak]]s that are specialised according to the bird's [[ecological niche]]. For example, [[macaw]]s primarily eat seeds, nuts, and fruit, using their 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.<ref name=Miserez>{{cite journal |last=Miserez|first=A|author2=Li, Y |author3=Waite, H |author4= Zok, F  |year=2007|title=Jumbo squid beaks: Inspiration for design of robust organic composites |journal=[[Acta Biomaterialia]] |volume=3 |issue= 1|pages=139–149 |doi=10.1016/j.actbio.2006.09.004 |pmid=17113369 }}</ref> The beak is the only indigestible part of the squid.

====Tongue====
{{Main|Tongue}}
The '''tongue''' is skeletal muscle on the floor of the [[mouth]] of most vertebrates, 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 used to roll food particles into a [[Bolus (digestion)|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 [[Blood vessel|vascular]] quality of the oral cavity, and allows for the speedy application of medication into the cardiovascular system, bypassing the gastrointestinal tract.

====Teeth====
{{Main|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, such as enamel, dentine and cementum. Human teeth have a blood and nerve supply which enables proprioception. This is the ability of sensation when chewing, for example if we were to bite into something too hard for our teeth, such as a chipped plate mixed in food, our teeth send a message to our brain and we realise that it cannot be chewed, so we stop trying.

The shapes, sizes and numbers of types of animals' teeth are related to their diets. For example, herbivores have a number of molars which are used to grind plant matter, which is difficult to digest. [[Carnivore]]s have [[canine tooth|canine teeth]] which are used to kill and tear meat.

====Crop====
A [[Crop (anatomy)|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.<ref name=Gordon>{{cite web | title=The Alimentary Canal in Birds | url=http://www.earthlife.net/birds/digestion.html | author=Gordon John Larkman Ramel | date=2008-09-29 | access-date=2008-12-16}}</ref>

Certain insects may have a crop or enlarged [[esophagus]].

[[Image:Abomasum-en.svg|150px|thumb|Rough illustration of a ruminant digestive system]]

====Abomasum====
{{Main|Digestive system of ruminants}}

[[Herbivore]]s have evolved [[cecum]]s (or an [[abomasum]] in the case of [[ruminant]]s). Ruminants have a fore-stomach with four chambers. These are the [[rumen]], [[Reticulum (anatomy)|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 (digestion)|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.

====Specialised behaviours====
[[File:Flesh fly concentrating food.jpg|thumb|A flesh fly "blowing a bubble", possibly to concentrate its food by evaporating water]]
[[Regurgitation (digestion)|Regurgitation]] has been mentioned above under abomasum and crop, referring to crop milk, a secretion from the lining of the crop of [[Columbidae|pigeons and doves]] with which the parents feed their young by regurgitation.<ref name="Levi">{{cite book |last=Levi |first=Wendell |title= The Pigeon|year= 1977|publisher= Levi Publishing Co, Inc|location= Sumter, SC|isbn=978-0-85390-013-9 }}</ref>

Many [[Physical characteristics of sharks|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]], produce [[Cecotrope|cecotropes]] to re-digest food, especially in the case of roughage. Capybaras, rabbits, hamsters, and other related species do not have a complex digestive system as ruminants. They instead extract more [[nutrition]] by giving their food a second pass through the [[gut (anatomy)|gut]]. Soft cecotropes 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 [[vertebrate]]s, digestion is a multistage 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:
# [[Ingestion]]: placing food into the mouth (entry of food in the digestive system),
# Mechanical and chemical breakdown:  mastication and the mixing of the resulting [[Bolus (digestion)|bolus]] with water, [[acid]]s, [[bile]] and enzymes in the stomach and intestine to break down complex chemical species into simple structures,
# Absorption: of nutrients from the digestive system to the circulatory and lymphatic capillaries through [[osmosis]], [[active transport]], and [[diffusion]], and
# 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 (anatomy)|gut]] bacteria and for resorption of water from digests before excretion.

In [[mammal]]s, preparation for digestion begins with the [[cephalic phase]] in which saliva is produced in the mouth and [[digestive enzyme]]s are produced in the [[stomach]].  Mechanical and chemical digestion begin in the mouth where food is [[Mastication|chewed]], and mixed with saliva to begin enzymatic processing of [[starch]]es.  The stomach continues to break food down mechanically and chemically through churning and mixing with both acids and enzymes. [[Small intestine#Absorptions|Absorption]] occurs in the stomach and [[gastrointestinal tract]], and the process finishes with defecation.<ref name=Maton/>

==Human digestion process==
{{Main|Human digestive system}}
{{Digestive system diagram}}

The [[human gastrointestinal tract]] is around {{Convert|9|m|abbr=off}} long. Food digestion physiology varies between individuals and upon other factors such as the characteristics of the food and size of the meal, and the process of digestion normally takes between 24 and 72 hours.<ref name=KongSingh2008>{{cite journal |vauthors=Kong F, Singh RP |title=Disintegration of solid foods in human stomach |journal=J. Food Sci. |volume=73 |issue=5 |pages=R67–80 |date=June 2008 |pmid=18577009 |doi=10.1111/j.1750-3841.2008.00766.x |doi-access=free }}</ref>

Digestion begins in the [[human mouth|mouth]] with the secretion of saliva and its digestive enzymes. Food is formed into a [[bolus (digestion)|bolus]] by the mechanical [[mastication]] and swallowed into the [[esophagus]] from where it enters the stomach through the action of [[peristalsis]]. [[Gastric juice]] contains [[hydrochloric acid]] and [[pepsin]] which could damage the stomach lining, but [[mucus]] and bicarbonates are secreted for protection. In the stomach further release of enzymes break down the food further and this is combined with the churning action of the stomach. Mainly proteins are digested in stomach. The partially digested food enters the [[duodenum]] as a thick semi-liquid [[chyme]]. In the small intestine, the larger part of digestion takes place and this is helped by the secretions of [[bile]], [[pancreatic juice]] and [[intestinal juice]].  The intestinal walls are lined with [[intestinal villus|villi]], and their [[epithelial cells]] are covered with numerous [[Microvillus|microvilli]] to improve the absorption of nutrients by increasing the [[surface area]] of the intestine. Bile helps in emulsification of fats and also activates lipases.

In the large intestine, the passage of food is slower to enable fermentation by the [[gut flora]] to take place. Here, water is absorbed and waste material stored as [[Human feces|feces]] to be removed by defecation via the [[anal canal]] and [[Human anus|anus]].

=== Neural and biochemical control mechanisms ===
Different [[phases of digestion]] take place including: the [[cephalic phase]], [[gastric phase]], and [[intestinal phase]].

The cephalic phase occurs at the sight, thought and smell of food, which stimulate the [[cerebral cortex]]. Taste and smell stimuli are sent to the [[hypothalamus]] and [[medulla oblongata]]. After this it is routed through the [[vagus nerve]] and release of acetylcholine. Gastric secretion at this phase rises to 40% of maximum rate. Acidity in the stomach is not buffered by food at this point and thus acts to inhibit parietal (secretes acid) and [[G cell]] (secretes gastrin) activity via [[D cell (biology)|D cell]] secretion of [[somatostatin]].

The gastric phase takes 3 to 4 hours. It is stimulated by [[Gastric distension|distension]] of the stomach, presence of food in stomach and decrease in [[pH]]. Distention activates long and myenteric reflexes. This activates the release of [[acetylcholine]], which stimulates the release of more gastric juices. As protein enters the stomach, it binds to [[hydrogen]] ions, which raises the pH of the stomach. Inhibition of gastrin and [[gastric acid]] secretion is lifted. This triggers G cells to release [[gastrin]], which in turn stimulates [[parietal cell]]s to secrete gastric acid.  Gastric acid is about 0.5% [[hydrochloric acid]], which lowers the pH to the desired pH of 1–3.  Acid release is also triggered by [[acetylcholine]] and [[histamine]].

The intestinal phase has two parts, the excitatory and the inhibitory. Partially digested food fills the [[duodenum]]. This triggers intestinal gastrin to be released. Enterogastric reflex inhibits vagal nuclei, activating [[Sympathetic nervous system|sympathetic fibers]] causing the [[Pylorus|pyloric sphincter]] to tighten to prevent more food from entering, and inhibits local reflexes.

==Breakdown into nutrients==
{{Expand section|digestion of other substances|date=August 2011}}

===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 [[protein]]s to smaller polypeptides.

===Fat digestion=== <!--Fat digestion redirects here-->
{{Main|Fatty acid metabolism#Dietary sources of fatty acids, their digestion, absorption, transport in the blood and storage}}
Digestion of some fats can begin in the mouth where [[lingual lipase]] breaks down some short chain lipids into [[diglyceride]]s. However fats are mainly digested in the small intestine.<ref name="mehta">[http://pharmaxchange.info/press/2013/10/digestion-of-fats-triacylglycerols/ Digestion of fats (triacylglycerols)]</ref>  The presence of fat in the small intestine produces hormones that stimulate the release of [[pancreatic lipase]] from the pancreas and [[Bile acid|bile]] from the liver which helps in the emulsification of fats for absorption of [[fatty acids]].<ref name="mehta" />  Complete digestion of one molecule of fat (a [[triglyceride]]) results a mixture of fatty acids, mono- and di-glycerides, but no [[glycerol]].<ref name="mehta" />

===Carbohydrate digestion===
{{further|Carbohydrate metabolism|Carbohydrate catabolism}}
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 65 percent of the adult population produce only small amounts of lactase and are unable to eat [[Fermentation|unfermented]] milk-based foods.  This is commonly known as [[lactose intolerance]].  Lactose intolerance varies widely by genetic heritage;  more than 90 percent of peoples of east Asian descent are lactose intolerant, in contrast to about 5 percent of people of northern European descent.<ref>{{cite web|title=Genetics Home Reference|url=http://ghr.nlm.nih.gov/condition/lactose-intolerance|website=US National Library of Medicine|publisher=US National Institutes of Health|access-date=27 June 2015}}</ref>

[[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===
{{main|nucleic acid metabolism}}
DNA and RNA are broken down into [[Nucleotide|mononucleotides]] by the [[nuclease]]s [[deoxyribonuclease]] and [[ribonuclease]] (DNase and RNase) from the pancreas.

==Non-destructive digestion==
Some nutrients are complex molecules (for example [[vitamin B12|vitamin B<sub>12</sub>]]) which would be destroyed if they were broken down into their [[functional groups]].  To digest vitamin B<sub>12</sub> non-destructively, [[haptocorrin]] in saliva strongly binds and protects the B<sub>12</sub> molecules from stomach acid as they enter the stomach and are cleaved from their protein complexes.<ref name="pmid21593496">{{cite journal |vauthors=Nexo E, Hoffmann-Lücke E | title = Holotranscobalamin, a marker of vitamin B-12 status: analytical aspects and clinical utility | journal = Am. J. Clin. Nutr. | volume = 94 | issue = 1 | pages = 359S–365S |date=July 2011 | pmid = 21593496 | pmc = 3127504 | doi = 10.3945/ajcn.111.013458 }}</ref>

After the B<sub>12</sub>-haptocorrin complexes pass from the stomach via the pylorus to the duodenum, pancreatic proteases cleave haptocorrin from the B<sub>12</sub> molecules which rebind to [[intrinsic factor]] (IF).  These B<sub>12</sub>-IF complexes travel to the ileum portion of the small intestine where [[cubilin]] receptors enable [[Assimilation (biology)|assimilation]] and circulation of B<sub>12</sub>-IF complexes in the blood.<ref name="pmid19627091">{{cite journal |vauthors=Viola-Villegas N, Rabideau AE, Bartholomä M, Zubieta J, Doyle RP | title = Targeting the cubilin receptor through the vitamin B(12) uptake pathway: cytotoxicity and mechanistic insight through fluorescent Re(I) delivery | journal = J. Med. Chem. | volume = 52 | issue = 16 | pages = 5253–5261 |date=August 2009 | pmid = 19627091 | doi = 10.1021/jm900777v }}</ref>

==Digestive hormones==
[[Image:Digestive hormones.jpg|right|thumb|350px|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. Connections to metabolic control (largely the glucose-insulin system) have been uncovered.
* [[Gastrin]] – is in the stomach and stimulates the [[gastric gland]]s to secrete [[pepsinogen]] (an inactive form of the enzyme pepsin) and [[hydrochloric acid]]. Secretion of gastrin is stimulated by food arriving in stomach. The secretion is inhibited by low pH.
* [[Secretin]] – is in the [[duodenum]] and signals the secretion of sodium bicarbonate in the [[pancreas]] and it stimulates the bile secretion in the [[liver]].  This hormone responds to the acidity of the chyme.
* [[Cholecystokinin]] (CCK) – is in the duodenum and stimulates the release of digestive enzymes in the pancreas and stimulates the emptying of bile in the [[gall bladder]]. This hormone is secreted in response to fat in chyme.
* [[Gastric inhibitory peptide]] (GIP) – is in the duodenum and decreases the stomach churning in turn slowing the emptying in the stomach. Another function is to induce [[Insulin#Release|insulin secretion.]]
* [[Motilin]] – is in the duodenum and increases the [[migrating myoelectric complex]] component of gastrointestinal motility and stimulates the production of pepsin.

==Significance of pH==

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 [[Denaturation (biochemistry)|denatures]] proteins for further digestion in the small intestines, and provides [[Innate immune system|non-specific immunity]], damaging or eliminating various [[pathogens]].<ref>{{cite journal |last1=Beasley |first1=DeAnna E. |last2=Koltz |first2=Amanda M. |last3=Lambert |first3=Johanna E. |last4=Fierer |first4=Noah |last5=Dunn |first5=Rob R. |editor1-last=Li |editor1-first=Xiangzhen |title=The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome |journal=PLOS ONE |date=July 2015 |volume=10 |issue=7 |pages=e0134116 |doi=10.1371/journal.pone.0134116 |pmid=26222383 |pmc=4519257 |bibcode=2015PLoSO..1034116B |doi-access=free }}</ref>

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|date=May 2011}}

==See also==
* [[Digestive system of gastropods]]
* [[Digestive system of humpback whales]]
* [[Evolution of the mammalian digestive system]]
* [[Discovery and development of proton pump inhibitors]]
* [[Erepsin]]
* [[Gastroesophageal reflux disease]]

==References==
{{reflist}}

==External links==
* [http://homepage.ufp.pt/pedros/qfisio/digestion.htm Human Physiology – Digestion]
* [https://web.archive.org/web/20060810184706/http://digestive.niddk.nih.gov/ddiseases/pubs/yrdd/index.htm NIH guide to digestive system]
* [https://web.archive.org/web/20110521043014/http://www.biology-innovation.co.uk/digestive_system.php The Digestive System]
* [http://www.medical-reference.net/2012/07/how-does-digestive-system-work.html How does the Digestive System Work?]

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[[Category:Digestive system]]
[[Category:Metabolism]]