Editing Nucleotide (section)

==Synthesis==
Nucleotides can be [[Nucleic acid metabolism|synthesized]] by a variety of means, both [[in vitro]] and [[in vivo]].{{cn|date=February 2024}}

In vitro, [[protecting group]]s may be used during laboratory production of nucleotides. A purified [[nucleoside]] is protected to create a [[phosphoramidite]], which can then be used to obtain analogues not found in nature and/or to [[oligonucleotide synthesis|synthesize an oligonucleotide]].{{cn|date=February 2024}}

In vivo, nucleotides can be synthesized [[de novo synthesis|de novo]] or recycled through [[nucleotide salvage|salvage pathways]].<ref name = "easy-peasy" >{{cite journal | vauthors = Zaharevitz DW, Anderson LW, Malinowski NM, Hyman R, Strong JM, Cysyk RL | title = Contribution of de-novo and salvage synthesis to the uracil nucleotide pool in mouse tissues and tumors in vivo | journal = European Journal of Biochemistry | volume = 210 | issue = 1 | pages = 293–6 | date = November 1992 | pmid = 1446677 | doi=10.1111/j.1432-1033.1992.tb17420.x| doi-access = free }}</ref> The components used in de novo nucleotide synthesis are derived from biosynthetic precursors of carbohydrate and [[amino acid]] metabolism, and from ammonia and carbon dioxide. Recently it has been also demonstrated that cellular bicarbonate metabolism can be regulated by mTORC1 signaling.<ref>{{cite journal | vauthors = Ali E, Liponska A, O'Hara B, Amici D, Torno M, Gao P, Asara J, Yap M-N F, Mendillo M, Ben-Sahra I | title = The mTORC1-SLC4A7 axis stimulates bicarbonate import to enhance de novo nucleotide synthesis | journal = Molecular Cell | volume = 82 | issue = 1 | pages = 3284–3298.e7 | date = June 2022 | doi = 10.1016/j.molcel.2022.06.008 | pmid = 35772404 | pmc = 9444906 }}</ref> The liver is the major organ of de novo synthesis of all four nucleotides. De novo synthesis of pyrimidines and purines follows two different pathways. Pyrimidines are synthesized first from aspartate and carbamoyl-phosphate in the cytoplasm to the common precursor ring structure orotic acid, onto which a phosphorylated ribosyl unit is covalently linked. Purines, however, are first synthesized from the sugar template onto which the ring synthesis occurs. For reference, the syntheses of the [[purine]] and [[pyrimidine]] nucleotides are carried out by several enzymes in the [[cytoplasm]] of the cell, not within a specific [[organelle]]. Nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides.{{cn|date=February 2024}}

===Pyrimidine ribonucleotide synthesis===
[[File:Nucleotides syn2.png|thumb|right|400px|The synthesis of [[Uridine monophosphate|UMP]].
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{{main|Pyrimidine metabolism}}
The synthesis of the pyrimidines CTP and UTP occurs in the cytoplasm and starts with the formation of carbamoyl phosphate from [[glutamine]] and CO<sub>2</sub>. Next, [[aspartate carbamoyltransferase]] catalyzes a condensation reaction between [[aspartate]] and [[carbamoyl phosphate]] to form [[carbamoyl aspartic acid]], which is cyclized into [[4,5-dihydroorotic acid]] by [[dihydroorotase]]. The latter is converted to [[orotate]] by [[dihydroorotate oxidase]]. The net reaction is:

:(''S'')-Dihydroorotate + O<sub>2</sub> → Orotate + H<sub>2</sub>O<sub>2</sub>

Orotate is covalently linked with a phosphorylated ribosyl unit. The covalent linkage between the ribose and pyrimidine occurs at position C<sub>1</sub><ref>See [[IUPAC nomenclature of organic chemistry]] for details on carbon residue numbering</ref> of the [[ribose]] unit, which contains a [[pyrophosphate]], and N<sub>1</sub> of the pyrimidine ring. [[Orotate phosphoribosyltransferase]] (PRPP transferase) catalyzes the net reaction yielding orotidine monophosphate (OMP):

:Orotate + [[Phosphoribosyl pyrophosphate|5-Phospho-α-D-ribose 1-diphosphate (PRPP)]]  →  Orotidine 5'-phosphate + Pyrophosphate

[[Orotidine 5'-monophosphate]] is decarboxylated by orotidine-5'-phosphate decarboxylase to form uridine monophosphate (UMP). PRPP transferase catalyzes both the ribosylation and decarboxylation reactions, forming UMP from orotic acid in the presence of PRPP. It is from UMP that other pyrimidine nucleotides are derived.  UMP is phosphorylated by two kinases to uridine triphosphate (UTP) via two sequential reactions with ATP.  First, the diphosphate from UDP is produced, which in turn is phosphorylated to UTP. Both steps are fueled by ATP hydrolysis:

:ATP + UMP → ADP + UDP

:UDP + ATP → UTP + ADP

CTP is subsequently formed by the amination of UTP by the catalytic activity of [[CTP synthetase]]. Glutamine is the NH<sub>3</sub> donor and the reaction is fueled by ATP hydrolysis, too:

:UTP + Glutamine + ATP + H<sub>2</sub>O → CTP + ADP + P<sub>i</sub>

Cytidine monophosphate (CMP) is derived from cytidine triphosphate (CTP) with subsequent loss of two phosphates.<ref>{{cite journal | vauthors = Jones ME | title = Pyrimidine nucleotide biosynthesis in animals: genes, enzymes, and regulation of UMP biosynthesis | journal = Annual Review of Biochemistry | volume = 49 | issue = 1 | pages = 253–79 | date = 1980 | pmid = 6105839 | doi = 10.1146/annurev.bi.49.070180.001345 }}</ref><ref>{{cite book |title=The organic chemistry of biological pathways |vauthors=McMurry JE, Begley TP |date=2005 |publisher=Roberts & Company |isbn=978-0-9747077-1-6}}
</ref>

===Purine ribonucleotide synthesis===

{{main|Purine metabolism}}

The atoms that are used to build the [[purine nucleotides]] come from a variety of sources:
[[File:Nucleotide synthesis.svg|thumb|250px|class=skin-invert-image|'''The [[biosynthetic]] origins of purine ring [[atoms]]'''<br /><br />N<sub>1</sub> arises from the amine group of [[Aspartic acid|Asp]]<br />C<sub>2</sub> and C<sub>8</sub> originate from [[formate]]<br />N<sub>3</sub> and N<sub>9</sub> are contributed by the amide group of [[Glutamine|Gln]]<br />C<sub>4</sub>, C<sub>5</sub> and N<sub>7</sub> are derived from [[Glycine|Gly]] <br />C<sub>6</sub> comes from HCO<sub>3</sub><sup>−</sup> (CO<sub>2</sub>)]]
[[File:Nucleotides syn1.svg|class=skin-invert-image|thumb|600px|Diagram of the synthesis of IMP.
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The [[de novo synthesis]] of [[purine nucleotides]] by which these precursors are incorporated into the purine ring proceeds by a 10-step pathway to the branch-point intermediate [[Inosine monophosphate|IMP]], the nucleotide of the base [[hypoxanthine]]. [[Adenosine monophosphate|AMP]] and [[Guanosine monophosphate|GMP]] are subsequently synthesized from this intermediate via separate, two-step pathways. Thus, purine [[Moiety (chemistry)|moieties]] are initially formed as part of the [[ribonucleotides]] rather than as [[Freebase (chemistry)|free bases]].

Six enzymes take part in IMP synthesis. Three of them are multifunctional:
* [[Phosphoribosylglycinamide formyltransferase|GART]] (reactions 2, 3, and 5)
* [[Phosphoribosylaminoimidazole carboxylase|PAICS]] (reactions 6, and 7)
* [[Inosine monophosphate synthase|ATIC]] (reactions 9, and 10)

The pathway starts with the formation of [[PRPP]]. [[PRPS1]] is the [[enzyme]] that activates [[R5P]], which is formed primarily by the [[pentose phosphate pathway]], to PRPP by reacting it with [[Adenosine triphosphate|ATP]]. The reaction is unusual in that a pyrophosphoryl group is directly transferred from ATP to C<sub>1</sub> of R5P and that the product has the '''α''' configuration about C1. This reaction is also shared with the pathways for the synthesis of [[Tryptophan|Trp]], [[Histidine|His]], and the [[pyrimidine nucleotides]]. Being on a major metabolic crossroad and requiring much energy, this reaction is highly regulated.

In the first reaction unique to purine nucleotide biosynthesis, [[PPAT]] catalyzes the displacement of PRPP's [[pyrophosphate]] group (PP<sub>i</sub>) by an amide nitrogen donated from either [[glutamine]] (N), [[glycine]] (N&C), [[aspartate]] (N), [[folic acid]] (C<sub>1</sub>), or CO<sub>2</sub>. This is the committed step in purine synthesis. The reaction occurs with the inversion of configuration about ribose C<sub>1</sub>, thereby forming '''β'''-[[5-phosphorybosylamine]] (5-PRA) and establishing the anomeric form of the future nucleotide.

Next, a glycine is incorporated fueled by ATP hydrolysis, and the carboxyl group forms an amine bond to the NH<sub>2</sub> previously introduced. A one-carbon unit from folic acid coenzyme N<sub>10</sub>-formyl-THF is then added to the amino group of the substituted glycine followed by the closure of the imidazole ring. Next, a second NH<sub>2</sub> group is transferred from glutamine to the first carbon of the glycine unit. A carboxylation of the second carbon of the glycin unit is concomitantly added. This new carbon is modified by the addition of a third NH<sub>2</sub> unit, this time transferred from an aspartate residue. Finally, a second one-carbon unit from formyl-THF is added to the nitrogen group and the ring is covalently closed to form the common purine precursor inosine monophosphate (IMP).

Inosine monophosphate is converted to adenosine monophosphate in two steps. First, GTP hydrolysis fuels the addition of aspartate to IMP by adenylosuccinate synthase, substituting the carbonyl oxygen for a nitrogen and forming the intermediate adenylosuccinate. Fumarate is then cleaved off forming adenosine monophosphate. This step is catalyzed by adenylosuccinate lyase.

Inosine monophosphate is converted to guanosine monophosphate by the oxidation of IMP forming xanthylate, followed by the insertion of an amino group at C<sub>2</sub>.  NAD<sup>+</sup> is the electron acceptor in the oxidation reaction. The amide group transfer from glutamine is fueled by ATP hydrolysis.

===Pyrimidine and purine degradation===
In humans, pyrimidine rings (C, T, U) can be degraded completely to CO<sub>2</sub> and NH<sub>3</sub> (urea excretion). That having been said, purine rings (G, A) cannot. Instead, they are degraded to the metabolically inert [[uric acid]] which is then excreted from the body. Uric acid is formed when GMP is split into the base guanine and ribose. Guanine is deaminated to xanthine which in turn is oxidized to uric acid. This last reaction is irreversible. Similarly, uric acid can be formed when AMP is deaminated to IMP from which the ribose unit is removed to form hypoxanthine. Hypoxanthine is oxidized to xanthine and finally to uric acid. Instead of uric acid secretion, guanine and IMP can be used for recycling purposes and nucleic acid synthesis in the presence of PRPP and aspartate (NH<sub>3</sub> donor).{{cn|date=February 2024}}