Nucleotide 21505 220465433 2008-06-20T00:11:58Z ToePeu.bot 4082686 robot Adding: [[no:Nukleotid]] {{Nofootnotes|date=February 2008}} '''Nucleotides''' are [[organic compound]]s that consist of three joined structures: a nitrogenous base, a [[sugar]], and a [[phosphate]] group. The most common nucleotides can be divided into two groups ([[purine]]s and [[pyrimidine]]s) based on the structure of the nitrogenous base. The joined sugar is either [[ribose]] or [[deoxyribose]]. Nucleotides are the structural units of [[RNA]] and [[DNA]]. They also serve as important cofactors in [[cell (biology)|cellular]] signaling and [[metabolism]]. These cofactors include [[coenzyme A|CoA]], [[FAD|flavin adenine dinucleotide]], [[flavin mononucleotide]], [[adenosine triphosphate]] and [[nicotinamide adenine dinucleotide phosphate]]. == Nucleotide synthesis and structure == [[Image:Nucleotides v2.png|thumb|500px|The structure elements of the most common nucleotides]] A nucleotide is composed of a [[Basic aromatic ring|ring of nitrogen, carbon and oxygen]] atoms, a [[Pentose|five carbon sugar]] (together referred to as a [[nucleoside]]) and one [[phosphate]] group. Nucleotides can be synthesized through a variety of methods both [[in vitro]] and [[in vivo]]. This can involve ''salvage synthesis'' (the re-use of parts of nucleotides in resynthesizing new nucleotides through breakdown and synthesis reactions in order to exchange useful parts), or the use of [[protecting group]]s in a laboratory. In the latter case, a purified [[nucleoside]] or [[nucleobase]] is protected to create a [[phosphoramidite]], and can be used to obtain analogues not present in nature and/or to create an [[oligonucleotide synthesis|oligonucleotide]]. The first step of nucleotide synthesis is the formation of a ''nucleoside'' (the nitrogenous base joined to a sugar). The sugar involved in the synthesis and structure of a nucleotide may be either [[ribose]] or [[deoxyribose]]; in the latter case, the prefix 'deoxy' may be added before the name of the nucleoside in all cases except [[Uracil]]. A [[functional group]] of phosphate is then [[esterified]] to the sugar, creating a nucleotide. The phosphate group may consist of one, two, or three phosphates, forming monophosphates, diphosphates, or triphosphates, respectively. ==Synthesis== Nucleotides can be synthesized through a variety of methods both [[in vitro]] and [[in vivo]]. This can involve ''salvage synthesis'' (the re-use of parts of nucleotides in resynthesizing new nucleotides through breakdown and synthesis reactions in order to exchange useful parts), or the use of [[protecting group]]s in a laboratory. In the latter case, a purified [[nucleoside]] or [[nucleobase]] is protected to create a [[phosphoramidite]], and can be used to obtain analogues not present in nature and/or to create an [[oligonucleotide synthesis|oligonucleotide]]. ==Types of bases== Nucleotides can be [[Biosynthesis|synthesized]] with both [[purine]] and [[pyrimidine]] as bases. In [[DNA]], the purine bases are [[adenine]] and [[guanine]], while the pyrimidines are [[thymine]] and [[cytosine]]. [[RNA]] uses [[uracil]] rather than thymine (thymine is produced by adding a methyl to uracil). The nucleotide passes through numerous biochemical steps while being processed, adding and removing [[atom]]s through the use of numerous [[enzyme]]s. ===Pyrimidine ribonucleotides=== [[Image:Nucleotides syn2.png|thumb|right|300px|<div style="border-width: 0px; border-bottom: 1px solid black; text-align: left;">'''The synthesis of [[Uridine monophosphate|UMP]]'''.</div>The color scheme is as follows: <span style="font-weight: bold;"><span style="color: blue;">enzymes</span>, <span style="color: rgb(219,155,36);">coenzymes</span>, <span style="color: rgb(151,149,45);">substrate names</span>, <span style="color: rgb(128,0,0);">inorganic molecules</span> </span>]] The synthesis of a single pyrimidine is complex; the diagram to the left demonstrates the synthesis of a single pyrimidine. ===Purine ribonucleotides=== The atoms which are used to build the purine nucleotides come from a variety of sources: {| class="wikitable" style="margin: 1em auto 1em auto" | [[Image:Nucleotides syn3.png]] || '''The biosynthetic origins of purine ring atoms'''<BR><BR>N1 arises from the amine group of [[Aspartic acid|Asp]]<BR>C2 and C8 originate from [[formate]]<BR>N3 and N9 are contributed by the amide group of [[Glutamine|Gln]]<BR>C4, C5 and N7 are derived from [[Glycine|Gly]] <BR>C6 comes from HCO<sub>3</sub><sup>-</sup> (CO<sub>2</sub>) |} [[Image:Nucleotides syn1.png|thumb|right|300px|<div style="border-width: 0px; border-bottom: 1px solid black; text-align: left;">'''The synthesis of IMP'''.</div>The color scheme is as follows: <span style="font-weight: bold;"><span style="color: blue;">enzymes</span>, <span style="color: rgb(219,155,36);">coenzymes</span>, <span style="color: rgb(151,149,45);">substrate names</span>, <span style="color: rgb(227,13,196);">metal ions</span>, <span style="color: rgb(128,0,0);">inorganic molecules</span> </span>]] 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 IMP, the nucleotide of the base [[hypoxanthine]]. AMP and GMP are subsequently synthesized from this intermediate via separate, two step each, pathways. Thus purine [[moieties]] are initially formed as part of the ribonucleotides rather than as [[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) '''Reaction 1'''. The pathway starts with the formation of [[PRPP]]. [[PRPS1]] is the enzyme that activates [[R5P]], which is primarily formed 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 C1 of R5P and that the product has the '''α''' configuration about C1. This reaction is also shared with the pathways for the synthesis of the pyrimidine nucleotides, [[Tryptophan|Trp]], and [[Histidine|His]]. As a result of being on (a) such (a) major metabolic crossroad and the use of energy, this reaction is highly regulated. '''Reaction 2'''. In the first reaction unique to purine nucleotide biosynthesis, [[PPAT]] catalyzes the displacement of PRPP's pyrophosphate group (PP<sub>i</sub>) by Gln's amide nitrogen. The reaction occurs with the inversion of configuration about ribose C1, thereby forming '''β'''-[[5-phosphorybosylamine]] (5-PRA) and establishing the anomeric form of the future nucleotide. This reaction which is driven to completion by the subsequent hydrolysis of the released PP<sub>i</sub>, is the pathway's flux generating step and is therefore regulated too. == See also == * [[Chromosome]] * [[Gene]] * [[Genetics]] * [[Nucleic acid analogues]] == External links == * [http://www.chem.qmul.ac.uk/iupac/misc/naabb.html Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents] ([[IUPAC]]) * [http://www.iupac.org/reports/provisional/abstract04/BB-prs310305/Chapter10.pdf Provisional Recommendations 2004] (IUPAC) * [http://dl.clackamas.cc.or.us/ch106-09/nucleoti.htm Chemistry explanation of nucleotide structure] {{Nucleobases, nucleosides, and nucleotides}} [[Category:Nucleic acids]] [[Category:Nucleotides]] [[Category:Genetics]] [[ar:نيوكليوتايد]] [[zh-min-nan:He̍k-kam-sng]] [[bs:Nukleotidi]] [[bg:Нуклеотид]] [[ca:Nucleòtid]] [[cs:Nukleotid]] [[da:Nukleotid]] [[de:Nukleotid]] [[el:Νουκλεοτίδιο]] [[es:Nucleótido]] [[eo:Nukleotido]] [[fa:نوکلئوتید]] [[fr:Nucléotide]] [[gl:Nucleótido]] [[ko:뉴클레오티드]] [[id:Nukleotida]] [[it:Nucleotide]] [[he:נוקלאוטיד]] [[ka:ნუკლეოტიდი]] [[lb:Nukleotid]] [[lt:Nukleotidas]] [[hu:Nukleotid]] [[mk:Нуклеотид]] [[ms:Nukleotida]] [[nl:Nucleotide]] [[ja:ヌクレオチド]] [[no:Nukleotid]] [[oc:Nucleotid]] [[pl:Nukleotydy]] [[pt:Nucleótido]] [[ro:Nucleotidă]] [[ru:Нуклеотид]] [[sq:Nukleotidi]] [[simple:Nucleotide]] [[sk:Nukleotid]] [[sl:Nukleotid]] [[sr:Нуклеотид]] [[fi:Nukleotidi]] [[sv:Nukleotid]] [[th:นิวคลีโอไทด์]] [[vi:Nucleotide]] [[tr:Nükleotit]] [[uk:Нуклеотиди]] [[ur:مرثالثہ]] [[zh:核苷酸]]