Editing Phosphorylation

{{Short description|Chemical process of introducing a phosphate}}
[[File:Phosporylation of a serine residue, before and after shot.png|thumb|[[Serine]] in an amino acid chain, before and after phosphorylation.]]

In [[biochemistry]], '''phosphorylation''' is described as the "transfer of a phosphate group" from a donor to an acceptor.<ref name="ana&physio">{{cite web |title=phosphorylation|url=https://goldbook.iupac.org/terms/view/PT06790|website=IUPAC Gold Book}}</ref>  A common phosphorylating agent (phosphate donor) is [[Adenosine triphosphate|ATP]] and a common family of acceptor are [[Alcohol (Chemistry)|alcohol]]s:
:{{chem2|[Adenosyl\sO\sPO2\sO\sPO2\sO\sPO3](4-)  +  ROH  ->  Adenosyl\sO\sPO2\sO\sPO3H](2-)  +  [RO\sP\sO3](2-)}}
This equation can be written in several ways that are nearly equivalent that describe the behaviors of various protonated states of ATP, ADP, and the phosphorylated product.
As is clear from the equation, a phosphate group per se is not transferred, but a phosphoryl group (PO<sub>3</sub><sup>-</sup>).  '''Phosphoryl''' is an [[electrophile]].<ref name=Ahn>{{cite journal |doi=10.1021/cr000230w |title=Kinetic and Catalytic Mechanisms of Protein Kinases |date=2001 |last1=Adams |first1=Joseph A. |journal=Chemical Reviews |volume=101 |issue=8 |pages=2271–2290 |pmid=11749373 }}</ref>
This process and its inverse, [[dephosphorylation]], are common in [[biology]].<ref name="Chen-2022">{{cite journal |vauthors=Chen J, He X, Jakovlić I |date=November 2022 |title=Positive selection-driven fixation of a hominin-specific amino acid mutation related to dephosphorylation in IRF9 |journal=BMC Ecology and Evolution |volume=22 |issue=1 |pages=132 |doi=10.1186/s12862-022-02088-5 |pmid=36357830 |pmc=9650800 |s2cid=253448972 |doi-access=free }} [[File:CC-BY_icon.svg|50x50px]]  Text was copied from this source, which is available under a [[creativecommons:by/4.0/|Creative Commons Attribution 4.0 International License]].</ref> [[Protein phosphorylation]] often activates (or deactivates) many [[enzyme]]s.<ref>{{cite journal | vauthors = Oliveira AP, Sauer U | title = The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism | journal = FEMS Yeast Research | volume = 12 | issue = 2 | pages = 104–117 | date = March 2012 | pmid = 22128902 | doi = 10.1111/j.1567-1364.2011.00765.x | doi-access = free }}</ref><ref>{{cite journal | vauthors = Tripodi F, Nicastro R, Reghellin V, Coccetti P | title = Post-translational modifications on yeast carbon metabolism: Regulatory mechanisms beyond transcriptional control | journal = Biochimica et Biophysica Acta (BBA) - General Subjects | volume = 1850 | issue = 4 | pages = 620–627 | date = April 2015 | pmid = 25512067 | doi = 10.1016/j.bbagen.2014.12.010 | hdl = 10281/138736 | hdl-access = free }}</ref>

== During respiration ==
Phosphorylation is essential to the processes of both [[Anaerobic respiration|anaerobic]] and [[aerobic respiration]], which involve the production of [[adenosine triphosphate]] (ATP), the "high-energy" exchange medium in the cell. During aerobic respiration, ATP is synthesized in the [[mitochondrion]] by addition of a third phosphate group to [[adenosine diphosphate]] (ADP) in a process referred to as [[oxidative phosphorylation]]. ATP is also synthesized by [[substrate-level phosphorylation]] during [[glycolysis]]. ATP is synthesized at the expense of solar energy by [[photophosphorylation]] in the [[chloroplast]]s of plant cells.

== Phosphorylation of glucose ==

=== Glucose metabolism ===
Phosphorylation of [[sugar]]s is often the first stage in their [[catabolism]]. Phosphorylation allows cells to accumulate sugars because the phosphate group prevents the molecules from diffusing back across their [[Transport protein|transporter]]. Phosphorylation of [[glucose]] is a key reaction in sugar metabolism. The chemical equation for the conversion of D-glucose to D-glucose-6-phosphate in the first step of [[glycolysis]] is given by:

:[[D-glucose]] + ATP → D-[[glucose 6-phosphate]] + ADP

:[[Gibbs free energy|ΔG]]° = −16.7 kJ/mol (° indicates measurement at standard condition)

==== Glycolysis ====
[[File:Glycolysis Simple Diagram.jpg|thumb|'''Glycolysis''' is a process that breaks down glucose into 2 pyruvate molecules, using ATP and NADH as well as producing it.]]
{{Main|Glycolysis}}

Glycolysis is an essential process of glucose degrading into two molecules of [[Pyruvic acid|pyruvate]], through various steps, with the help of different enzymes. It occurs in ten steps and proves that phosphorylation is a much required and necessary step to attain the end products. Phosphorylation initiates the reaction in [[Glycolysis#Preparatory phase|step 1 of the preparatory step]]<ref>{{Cite book|url=http://www.bioinfo.org.cn/book/biochemistry/chapt14/sim1.htm|title=Chapter 14: Glycolysis and the Catabolism of Hexoses|access-date=2016-05-14|archive-date=2021-10-17|archive-url=https://web.archive.org/web/20211017002355/http://www.bioinfo.org.cn/book/biochemistry/chapt14/sim1.htm|url-status=live}}</ref> (first half of glycolysis), and initiates step 6 of payoff phase (second phase of glycolysis).<ref>{{cite book|title=Biochemistry| vauthors = Garrett R |publisher=Saunders College|year=1995}}</ref>

Glucose, by nature, is a small molecule with the ability to diffuse in and out of the cell. By phosphorylating glucose (adding a phosphoryl group in order to create a negatively charged [[Phosphate|phosphate group]]<ref>{{Cite web|title=Hexokinase - Reaction|url=https://www.chem.uwec.edu/webpapers_f99/pages/Webpapers_F99/schneebm/Pages/reaction.html|access-date=2020-07-29|website=www.chem.uwec.edu|archive-date=2020-12-02|archive-url=https://web.archive.org/web/20201202023137/https://www.chem.uwec.edu/webpapers_f99/pages/Webpapers_F99/schneebm/Pages/reaction.html|url-status=live}}</ref>), glucose is converted to glucose-6-phosphate, which is trapped within the cell as the cell membrane is negatively charged. This reaction occurs due to the enzyme [[hexokinase]], an enzyme that helps phosphorylate many six-membered ring structures. Phosphorylation takes place in step 3, where fructose-6-phosphate is converted to [[fructose 1,6-bisphosphate]]. This reaction is catalyzed by [[phosphofructokinase]].

While phosphorylation is performed by ATPs during preparatory steps, phosphorylation during payoff phase is maintained by inorganic phosphate. Each molecule of [[glyceraldehyde 3-phosphate]] is phosphorylated to form [[1,3-bisphosphoglycerate]]. This reaction is catalyzed by [[glyceraldehyde-3-phosphate dehydrogenase]] (GAPDH). The cascade effect of phosphorylation eventually causes instability and allows enzymes to open the carbon bonds in glucose.

Phosphorylation functions is an extremely vital component of glycolysis, as it helps in transport, control, and efficiency.<ref>{{cite web|url=http://www.bachillerato.uchile.cl/files/Bioquimica/glycolysis/glyintro/page07.htm|vauthors=Maber J|title=Introduction to Glycolysis|access-date=18 November 2017|archive-date=6 April 2017|archive-url=https://web.archive.org/web/20170406210528/http://www.bachillerato.uchile.cl/files/Bioquimica/Glycolysis/glyintro/page07.htm|url-status=dead}}</ref>

=== Glycogen synthesis ===
[[Glycogen]] is a long-term store of glucose produced by the cells of the [[liver]]. In the [[liver]], the synthesis of [[glycogen]] is directly correlated with blood glucose concentration. High blood glucose concentration causes an increase in intracellular levels of [[glucose 6-phosphate]] in the liver, [[skeletal muscle]], and fat ([[adipose]]) tissue. Glucose 6-phosphate has role in regulating [[glycogen synthase]].

High blood glucose releases [[insulin]], stimulating the translocation of specific glucose transporters to the cell membrane; glucose is phosphorylated to glucose 6-phosphate during transport across the membrane by ATP-D-glucose 6-[[phosphotransferase]] and non-specific [[hexokinase]] (ATP-D-hexose 6-phosphotransferase).<ref name="ReferenceA" /><ref name="fasebj.org">{{cite journal | vauthors = Villar-Palasí C, Guinovart JJ | title = The role of glucose 6-phosphate in the control of glycogen synthase | journal = FASEB Journal | volume = 11 | issue = 7 | pages = 544–558 | date = June 1997 | pmid = 9212078 | doi = 10.1096/fasebj.11.7.9212078 | doi-access = free | s2cid = 2789124 }}</ref> Liver cells are freely permeable to glucose, and the initial rate of phosphorylation of glucose is the rate-limiting step in glucose metabolism by the liver.<ref name="ReferenceA">{{cite journal | vauthors = Walker DG, Rao S | title = The role of glucokinase in the phosphorylation of glucose by rat liver | journal = The Biochemical Journal | volume = 90 | issue = 2 | pages = 360–368 | date = February 1964 | pmid = 5834248 | pmc = 1202625 | doi = 10.1042/bj0900360 }}</ref>

The liver's crucial role in controlling blood sugar concentrations by breaking down glucose into carbon dioxide and glycogen is characterized by the negative [[Gibbs free energy]] (ΔG) value, which indicates that this is a point of regulation with<!-- Confusing sentence, needs rewrite -->.{{clarify|date=January 2023}} The hexokinase enzyme has a low [[Michaelis constant]] (K{{sub|m}}), indicating a high affinity for glucose, so this initial phosphorylation can proceed even when glucose levels at nanoscopic scale within the blood.

The phosphorylation of glucose can be enhanced by the binding of [[fructose 6-phosphate]] (F6P), and lessened by the binding [[fructose 1-phosphate]] (F1P). Fructose consumed in the diet is converted to F1P in the liver. This negates the action of F6P on glucokinase,<ref>{{cite journal | vauthors = Walker DG, Rao S | title = The role of glucokinase in the phosphorylation of glucose by rat liver | journal = The Biochemical Journal | volume = 90 | issue = 2 | pages = 360–368 | date = February 1964 | pmid = 5834248 | pmc = 1202625 | doi = 10.1042/bj0900360 }}</ref> which ultimately favors the forward reaction. The capacity of liver cells to phosphorylate fructose exceeds capacity to metabolize fructose-1-phosphate. Consuming excess fructose ultimately results in an imbalance in liver metabolism, which indirectly exhausts the liver cell's supply of ATP.<ref>{{cite web|url=http://cmgm.stanford.edu/biochem200/regulation/|title=Regulation of Glycolysis|website=cmgm.stanford.edu|access-date=2017-11-18|archive-date=2009-03-03|archive-url=https://web.archive.org/web/20090303224811/http://cmgm.stanford.edu/biochem200/regulation/|url-status=dead}}</ref>

[[Allosteric activation]] by glucose-6-phosphate, which acts as an effector, stimulates glycogen synthase, and glucose-6-phosphate may inhibit the phosphorylation of glycogen synthase by [[Cyclic adenosine monophosphate|cyclic AMP]]-stimulated [[protein kinase]].<ref name="fasebj.org"/>

=== Other processes ===
Phosphorylation of glucose is imperative in processes within the body. For example, phosphorylating glucose is necessary for insulin-dependent [[mechanistic target of rapamycin]] pathway activity within the heart. This further suggests a link between intermediary metabolism and cardiac growth.<ref>{{cite journal | vauthors = Sharma S, Guthrie PH, Chan SS, Haq S, Taegtmeyer H | title = Glucose phosphorylation is required for insulin-dependent mTOR signalling in the heart | journal = Cardiovascular Research | volume = 76 | issue = 1 | pages = 71–80 | date = October 2007 | pmid = 17553476 | pmc = 2257479 | doi = 10.1016/j.cardiores.2007.05.004 }}</ref>

==Protein phosphorylation==
{{Main|Protein phosphorylation}}

[[Protein phosphorylation]] is the most abundant [[posttranslational modification|post-translational modification]] in eukaryotes. Phosphorylation can occur on [[serine]], [[threonine]] and [[tyrosine]] side chains (in other words, on their residues) through [[Phosphodiester bond|phosphoester bond]] formation, on [[histidine]], [[lysine]] and [[arginine]] through [[Phosphoramidate|phosphoramidate bonds]], and on [[aspartic acid]] and [[glutamic acid]] through mixed [[Organic acid anhydride|anhydride linkages]]. Recent evidence confirms widespread histidine phosphorylation at both the 1 and 3 N-atoms of the [[imidazole]] ring.<ref name="ncbi.nlm.nih.gov">{{cite journal | vauthors = Fuhs SR, Hunter T | title = pHisphorylation: the emergence of histidine phosphorylation as a reversible regulatory modification | journal = Current Opinion in Cell Biology | volume = 45 | pages = 8–16 | date = April 2017 | pmid = 28129587 | pmc = 5482761 | doi = 10.1016/j.ceb.2016.12.010 }}</ref><ref name="https">{{cite journal | vauthors = Fuhs SR, Meisenhelder J, Aslanian A, Ma L, Zagorska A, Stankova M, Binnie A, Al-Obeidi F, Mauger J, Lemke G, Yates JR, Hunter T | display-authors = 6 | title = Monoclonal 1- and 3-Phosphohistidine Antibodies: New Tools to Study Histidine Phosphorylation | journal = Cell | volume = 162 | issue = 1 | pages = 198–210 | date = July 2015 | pmid = 26140597 | pmc = 4491144 | doi = 10.1016/j.cell.2015.05.046 }}</ref> Recent work demonstrates widespread human protein phosphorylation on multiple non-canonical amino acids, including motifs containing phosphorylated histidine, aspartate, glutamate, [[cysteine]], arginine and lysine in HeLa cell extracts.<ref name="ReferenceC">{{cite journal | vauthors = Hardman G, Perkins S, Brownridge PJ, Clarke CJ, Byrne DP, Campbell AE, Kalyuzhnyy A, Myall A, Eyers PA, Jones AR, Eyers CE | display-authors = 6 | title = Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation | journal = The EMBO Journal | volume = 38 | issue = 21 | pages = e100847 | date = October 2019 | pmid = 31433507 | pmc = 6826212 | doi = 10.15252/embj.2018100847 | doi-access = free }}</ref> However, due to the chemical lability of these phosphorylated residues, and in marked contrast to Ser, Thr and Tyr phosphorylation, the analysis of phosphorylated histidine (and other non-canonical amino acids) using standard biochemical and mass spectrometric approaches is much more challenging<ref name="ReferenceC"/><ref>{{cite journal | vauthors = Gonzalez-Sanchez MB, Lanucara F, Hardman GE, Eyers CE | title = Gas-phase intermolecular phosphate transfer within a phosphohistidine phosphopeptide dimer | journal = International Journal of Mass Spectrometry | volume = 367 | pages = 28–34 | date = June 2014 | pmid = 25844054 | pmc = 4375673 | doi = 10.1016/j.ijms.2014.04.015 | bibcode = 2014IJMSp.367...28G }}</ref><ref name="ReferenceB">{{cite journal | vauthors = Gonzalez-Sanchez MB, Lanucara F, Helm M, Eyers CE | title = Attempting to rewrite History: challenges with the analysis of histidine-phosphorylated peptides | journal = Biochemical Society Transactions | volume = 41 | issue = 4 | pages = 1089–1095 | date = August 2013 | pmid = 23863184 | doi = 10.1042/bst20130072 }}</ref> and special procedures and separation techniques are required for their preservation alongside classical Ser, Thr and Tyr phosphorylation.<ref>{{cite bioRxiv|vauthors=Hardman G, Perkins S, Ruan Z, Kannan N, Brownridge P, Byrne DP, Eyers PA, Jones AR, Eyers CE |title=Extensive non-canonical phosphorylation in human cells revealed using strong-anion exchange-mediated phosphoproteomics|year=2017|biorxiv=10.1101/202820}}</ref>

The prominent role of protein phosphorylation in [[biochemistry]] is illustrated by the huge body of studies published on the subject (as of March 2015, the [[MEDLINE]] database returns over 240,000 articles, mostly on ''protein'' phosphorylation).

==Further reading==
<ref>{{cite journal |doi=10.1021/cr000225s |title=Structural Basis for Control by Phosphorylation |date=2001 |last1=Johnson |first1=Louise N. |last2=Lewis |first2=Richard J. |journal=Chemical Reviews |volume=101 |issue=8 |pages=2209–2242 |pmid=11749371 }}</ref>
<ref>{{cite journal |doi=10.1021/cr000243+ |title=Histidine Phosphorylation and Two-Component Signaling in Eukaryotic Cells |date=2001 |last1=Saito |first1=Haruo |journal=Chemical Reviews |volume=101 |issue=8 |pages=2497–2510 |pmid=11749385 }}</ref>
<ref>{{cite journal |doi=10.1021/cr010144b |title=Introduction: Protein Phosphorylation and Signaling |date=2001 |last1=Ahn |first1=Natalie |journal=Chemical Reviews |volume=101 |issue=8 |pages=2207–2208 |doi-access=free }}</ref>
<ref>{{cite journal |doi=10.1021/acs.chemrev.8b00442 |title=Site-Selective Functionalization of Hydroxyl Groups in Carbohydrate Derivatives |date=2018 |last1=Dimakos |first1=Victoria |last2=Taylor |first2=Mark S. |journal=Chemical Reviews |volume=118 |issue=23 |pages=11457–11517 |pmid=30507165 }}</ref>

== See also ==
* [[Moiety conservation]]
* [[Phosida]]
* [[Phosphoamino acid analysis]]
* [[Phospho3D]]
{{-}}

== References ==
{{Reflist|colwidth=28em}}

== External links ==
*[https://web.archive.org/web/20090416125554/http://natureprotocols.com/2007/01/10/functional_analyses_for_sitesp.php Functional analyses for site-specific phosphorylation of a target protein in cells (A Protocol)]

{{Protein posttranslational modification}}
{{Authority control}}

[[Category:Cell biology]]
[[Category:Cell signaling]]
[[Category:Phosphorus]]
[[Category:Post-translational modification]]