Editing Ribonucleotide

{{Short description|Nucleotide containing ribose as its pentose component}}
In biochemistry, a '''ribonucleotide''' is a [[nucleotide]] containing [[ribose]] as its [[pentose]] component. It is considered a molecular precursor of [[nucleic acids]]. Nucleotides are the basic building blocks of [[DNA]] and [[RNA]]. Ribonucleotides themselves are basic monomeric building blocks for RNA. [[Deoxyribonucleotide]]s, formed by reducing ribonucleotides with the enzyme [[ribonucleotide reductase]] (RNR), are essential building blocks for DNA.<ref name=Nelson08>{{cite book|last1=Nelson|first1=David L. |first2=Albert L. |last2=Lehninger |first3=Michael M. |last3=Cox |title=Lehninger Principles of Biochemistry|year=2008|publisher=W H Freeman |pages=272–3 |edition=5th |isbn=978-0-7167-7108-1}}</ref> There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides. Successive nucleotides are linked together via phosphodiester bonds.

Ribonucleotides are also utilized in other cellular functions. These special monomers are utilized in both cell regulation and [[cell signaling]] as seen in adenosine-monophosphate ([[Adenosine monophosphate|AMP]]). Furthermore, ribonucleotides can be converted to adenosine triphosphate ([[Adenosine triphosphate|ATP]]), the energy currency in organisms. Ribonucleotides can be converted to cyclic adenosine monophosphate ([[cyclic AMP]]) to regulate hormones in organisms as well.<ref name=Nelson08 /> In living organisms, the most common bases for ribonucleotides are [[adenine]] (A), [[guanine]] (G), [[cytosine]] (C), or [[uracil]] (U). The nitrogenous bases are classified into two parent compounds, [[purine]] and [[pyrimidine]].

[[File:Ribonucleotide General.png|320px|thumb|class=skin-invert|General Ribonucleotide Structure: phosphate group, Ribose, Nucleobase.]]

==Structure==

===General structure===

[[File:AMP structure.svg|200px|thumbnail|class=skin-invert|Structure of adenosine 5'-monophosphate (AMP)]]
[[File:GMP chemical structure.png|200px|thumbnail|class=skin-invert|Structure of guanosine 5'-monophosphate (GMP)]]
[[File:Uridinmonophosphat protoniert.svg|200px|thumbnail|class=skin-invert|Structure of uridine 5'-monophosphate (UMP)]]
[[File:CMP chemical structure.png|200px|thumbnail|class=skin-invert|Structure of cytidine 5'-monophosphate (CMP)]]

The general structure of a ribonucleotide consists of a phosphate group, a ribose sugar group, and a nucleobase, in which the nucleobase can either be adenine, guanine, cytosine, or uracil. Without the phosphate group, the composition of the nucleobase and sugar is known as a nucleoside. The interchangeable nitrogenous nucleobases are derived from two parent compounds, purine and pyrimidine. Nucleotides are [[heterocyclic compounds]], that is, they contain at least two different chemical elements as members of its rings.{{citation needed|date=July 2024}}

Both RNA and DNA contain two major purine bases, adenine (A) and guanine (G), and two major pyrimidines. In both DNA and RNA, one of the pyrimidines is cytosine (C). However, DNA and RNA differ in the second major pyrimidine. DNA contains thymine (T) while RNA contains uracil (U). There are some rare cases where thymine does occur in RNA and uracil in DNA.<ref name=Nelson08 />

Here are the 4 major ribonucleotides (ribonucleoside 5'-monophosphate) which are the structural units of RNAs.
{| class="wikitable"
|-
! Nucleotide !! Symbols !! Nucleoside
|-
| Adenylate (adenosine 5'-monophosphate)  || A, AMP || Adenosine
|-
| Guanylate (guanosine 5'-monophosphate) || G, GMP || Guanosine
|-
| Uridylate (uridine 5'-monophosphate)  || U, UMP || Uridine
|-
| Cytidylate (cytidine 5'-monophosphate) || C, CMP || Cytidine
|}

===DNA deoxyribonucleotides versus RNA ribonucleotides===

In ribonucleotides, the sugar component is ribose while in deoxyribonucleotides, the sugar component is deoxyribose. Instead of a hydroxyl group at the second carbon in the ribose ring, it is replaced by a hydrogen atom.<ref>{{cite book |last1=Newsholme |first1=Eric A. |last2=Leech |first2=Anthony R. |last3=Board |first3=Mary |title=Functional biochemistry in health & disease: metabolic regulation in health and disease |year=2008 |publisher=Wiley |location=Hoboken, N.J. |isbn=978-0-471-98820-5 |edition=2nd}}</ref>

Both types of pentoses in DNA and RNA are in their β-furanose (closed five-membered ring) form and they define the identity of a nucleic acid. DNA is defined by containing 2'-deoxy-ribose nucleic acid while RNA is defined by containing ribose nucleic acid.<ref name=Nelson08 />

In some occasions, DNA and RNA may contain some minor bases. Methylated forms of the major bases are most common in DNA. In viral DNA, some bases may be hydroxymethylated or glucosylated. In RNA, minor or modified bases occur more frequently. Some examples include hypoxanthine, dihydrouracil, methylated forms of uracil, cytosine, and guanine, as well as modified nucleoside pseudouridine.<ref>{{cite book|last=Das|first=Debajyoti|title=Biochemistry|year=2010|publisher=Bimal Kumar Dhur of Academic Publishers}}</ref> Nucleotides with phosphate groups in positions other than on the 5' carbon have also been observed. Examples include ribonucleoside 2',3'-cyclic monophosphates which are isolatable intermediates, and ribonucleoside 3'-monophosphates which are end products of the hydrolysis of RNA by certain ribonucleases. Other variations include adenosine 3',5'-cyclic monophosphate (cAMP) and guanosine 3',5'-cyclic monophosphate (cGMP).<ref>{{cite book |last1=Cox |first1=Michael M. |last2=Nelson |first2=David L. |title=Principles of Biochemistry |year=2008 |publisher=W H Freeman |isbn=978-1-4292-2263-1 |oclc=216940502}}</ref>

===Linking successive nucleotides===

Ribonucleotides are linked together to form RNA strands via [[phosphodiester bonds]]. The 5'-phosphate group of one nucleotide is linked to the 3'-hydroxyl group of the next nucleotide, creating a backbone of alternating phosphate and pentose residues. There is no phosphodiester bond at each end of the polynucleotide.<ref>{{cite book |last=Raymond |first=Kenneth W. |title=General, organic, and biological chemistry: an integrated approach |year=2010 |publisher=Wiley |isbn=978-0-470-55124-0 |edition=3rd |oclc=699600111}}</ref> Phosphodiester bonds are formed between ribonucleotides by the enzyme [[RNA polymerase]]. The RNA chain is synthesized from the 5' end to the 3' end as the 3'-hydroxyl group of the last ribonucleotide in the chain acts as a nucleophile and launches a hydrophilic attack on the 5'-triphosphate of the incoming ribonucleotide, releasing pyrophosphate as a by-<ref>{{cite book |editor1-first=Moselio |editor1-last=Schaechter |editor2-first=Joshua |editor2-last=Lederberg |title=The Desk Encyclopedia of Microbiology |year=2004 |publisher=Elsevier |location=Amsterdam |isbn=0-12-621361-5 |edition=1st |oclc=1055874153}}</ref> product. Due to the physical properties of the nucleotides, the backbone of RNA is very hydrophilic and polar. At neutral pH, nucleic acids are highly charged as each phosphate group carries a negative charge.<ref>{{cite book |last1=Turner |first1=Phil |last2=McLennan |first2=Alexander |last3=Bates |first3=Andy |last4=White |first4=Mike |display-authors=1 |title=Molecular Biology |series=Instant Notes |year=2005 |publisher=CRC, Taylor & Francis |isbn=0-415-35167-7 |edition=3rd |oclc=61745541}}</ref>

Both DNA and RNA are built from nucleoside phosphates, also known as mononucleotide monomers, which are thermodynamically less likely to combine than amino acids. Phosphodiester bonds, when hydrolyzed, release a considerable amount of free energy. Therefore, nucleic acids tend to spontaneously hydrolyze into mononucleotides. The precursors for RNA are GTP, CTP, UTP and ATP, which is a major source of energy in group-transfer reactions.<ref>{{cite book|last=Nelson|first=David|title=Lehninger Principles of Biochemistry|year=2008|publisher=W H Freeman and Co|pages=274–275}}</ref>

==Function==

===Precursors of deoxyribonucleotides===
Scientists believe that RNA was developed before DNA.<ref>{{cite book |editor1-last=Chauhan |editor1-first=Ashok K. |editor2-last=Varma |editor2-first=Ajit |title=A textbook of molecular biotechnology |year=2009 |publisher=I.K. International Pub. House |location=New Delhi |isbn=978-93-80026-37-4}}</ref>

The reduction of ribonucleotides to deoxyribonucleotides is catalyzed by [[ribonucleotide reductase]]. Ribonucleotide reductase (RNR) is an essential enzyme for all living organisms since it is responsible for the last step in the synthesis of the four deoxyribonucleotides (dNTPs) necessary for DNA replication and repair.<ref>{{cite journal|last=Cendra Mdel|first=M|author2=Juárez, A |author3=Torrents, E |title=Biofilm modifies expression of ribonucleotide reductase genes in Escherichia coli.|journal=PLOS ONE|year=2012|volume=7|issue=9|pages=e46350|pmid=23050019|doi=10.1371/journal.pone.0046350|pmc=3458845|bibcode=2012PLoSO...746350C|doi-access=free}}</ref> The reaction also requires two other proteins: [[thioredoxin]] and [[thioredoxin reductase]]. Ribonucleoside diphosphate (NDP) is reduced by thioredoxin to a deoxyribonucleoside diphosphate (dNTP).

The general reaction is:<br/>
Ribonucleoside diphosphate + NADPH + {{chem2|H+ ->}} Deoxyribonucleoside diphosphate + {{chem2|NADP+}} + {{H2O}}
<ref>{{cite book |last1=Campbell |first1=Mary K. |last2=Farrell |first2=Shawn O. |title=Biochemistry |year=2009 |publisher=Brooks/Cole Cengage Learning |location=Belmont, CA |isbn=978-0-8400-6858-3 |edition=7th}}</ref>

To illustrate this equation, dATP and dGTP are synthesized from ADP and GDP, respectively. They are first reduced by RNR and then phosphorylated by nucleoside diphosphate kinases to dATP and dGTP. Ribonucleotide reductase is controlled by allosteric interactions. Once dATP binds to ribonucleotide reductase, the overall catalytic activity of the enzyme decreases, as it signifies an abundance of deoxyribonucleotides. This feedback inhibition is reversed once ATP binds.<ref name=Berg07/>

===Ribonucleotide discrimination===
During DNA synthesis, DNA polymerases must select against ribonucleotides, present at much higher levels compared with deoxyribonucleotides. It is crucial that there is selectivity as DNA replication has to be accurate to maintain the organism's genome. It has been shown that the active sites of Y-family DNA polymerases are responsible for maintaining a high selectivity against ribonucleotides.<ref>{{cite journal |last1=Kirouac |title=Structural Mechanism of Ribonucleotide Discrimination by a Y-Family DNA Polymerase|journal=Journal of Molecular Biology|date=1 April 2011|volume=407|issue=3|pages=382–390|doi=10.1016/j.jmb.2011.01.037|pmid=21295588|first1=Kevin N.|last2=Suo|first2=Zucai|last3=Ling|first3=Hong}}</ref> Most DNA polymerases are also equipped to exclude ribonucleotides from their active site through a bulky side chain residue that can sterically block the 2'-hydroxyl group of the ribose ring. However, many nuclear replicative and repair DNA polymerases incorporate ribonucleotides into DNA,<ref>{{cite journal |last1=Nick McElhinny |first1=SA |last2=Kumar |first2=D |last3=Clark |first3=AB |last4=Watt |first4=DL |last5=Watts |first5=BE |last6=Lundström |first6=EB |last7=Johansson |first7=E |last8=Chabes |first8=A |last9=Kunkel |first9=TA |title=Genome instability due to ribonucleotide incorporation into DNA. |journal=Nature Chemical Biology |date=October 2010 |volume=6 |issue=10 |pages=774–81 |doi=10.1038/nchembio.424 |pmid=20729855|pmc=2942972 }}</ref><ref>{{cite journal |last1=Nick McElhinny |first1=SA |last2=Watts |first2=BE |last3=Kumar |first3=D |last4=Watt |first4=DL |last5=Lundström |first5=EB |last6=Burgers |first6=PM |last7=Johansson |first7=E |last8=Chabes |first8=A |last9=Kunkel |first9=TA |title=Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=16 March 2010 |volume=107 |issue=11 |pages=4949–54 |doi=10.1073/pnas.0914857107 |pmid=20194773|pmc=2841928 |bibcode=2010PNAS..107.4949N |doi-access=free }}</ref> suggesting that the exclusion mechanism is not perfect.<ref>{{cite journal|last=Kasiviswanathan|first=R|author2=Copeland, WC |title=Ribonucleotide discrimination and reverse transcription by the human mitochondrial DNA polymerase.|journal=The Journal of Biological Chemistry|date=Sep 9, 2011|volume=286|issue=36|pages=31490–500|pmid=21778232|doi=10.1074/jbc.M111.252460|pmc=3173122|doi-access=free}}</ref>

==Synthesis==

===Ribonucleotide synthesis===

Ribonucleotides can be synthesized in organisms from smaller molecules through the de novo pathway or recycled through the salvage pathway. In the case of the de novo pathway, both purines and pyrimidines are synthesized from components derived from precursors of amino acids, ribose-5-phosphates, {{CO2}}, and {{chem2|NH3}}.<ref>{{harvnb|Nelson|Lehninger|Cox|2008|pp=881–894}}</ref><ref name=Berg07>{{cite book|last1=Berg|first1=J.M. |first2=J.L. |last2=Tymoczko |first3=L. |last3=Stryer|title=Biochemistry |chapter=§25.2 Purine Bases can be Synthesized by de Novo or Recycled by Salvage Pathways|year=2002 |publisher=W.H. Freeman |isbn=9780716730514 |oclc=48055706 <!-- NBK22385 nolonger at NLM -->}}</ref>
[[File:Nucleotides syn1.svg|thumb|200x200px|The synthesis of IMP.
{{legend|blue|enzymes}}
{{legend|rgb(219,155,36)|coenzymes}}
{{legend|rgb(151,149,45)|substrate names}}
{{legend|rgb(227,13,196)|metal ions}}
{{legend|rgb(128,0,0)|inorganic molecules}}]]
{| class="wikitable" style="margin: 1em auto 1em auto"

| [[File:Nucleotide synthesis.svg|230px]] || '''The [[biosynthetic]] origins of purine ring [[atoms]]'''<br><br>{{chem2|N1}} arises from the amine group of [[Aspartic acid|Asp]]<br>{{chem2|C2}} and {{chem2|C8}} originate from [[formate]]<br>{{chem2|N3}} and {{chem2|N9}} are contributed by the amide group of [[Glutamine|Gln]]<br>{{chem2|C4}}, {{chem2|C5}} and {{chem2|N7}} are derived from [[Glycine|Gly]] <br>{{chem2|C6}} comes from {{chem2|HCO3−(CO2)}}
|}

De novo biosynthesis of purine nucleotides is fairly complex, consisting of several enzymatic reactions. Utilizing the five-ring sugar structure as a base, the purine ring is built a few atoms at a time in an eleven-step process that leads to the formation of inosinate (IMP). Essentially, IMP is converted into the purine nucleotides required for nucleic acid synthesis.<ref name=Nelson08 />

The pathway begins with the conversion of Ribose-5-Phosphate(R5P) to phosphoribosyl pyrophosphate (PRPP) by enzyme ribose-phosphate diphosphokinase (PRPS1). PRPP is then converted to 5-phosphoribosylamine (5-PRA) as glutamine donates an amino group to the C-1 of PRPP. In a condensation reaction, enzyme GAR synthetase, along with glycine and ATP, activates the glycine carboxylase group of 5-PRA to form Glycinamide ribonucleotide (GAR). Co-enzyme N10-formyl-THF, along with enzyme GAR transformylase, then donates a one-carbon unit to the amino group onto the glycine of GAR, followed by glutamine addition by enzyme FGAR amidotransferase, leading to the formation of formylglycinamidine ribonucleotide (FGAM). Dehydration of FGAM by enzyme FGAM cyclase results in the closure of the imidazole ring, as 5-aminoimidazole ribonucleotide (AIR). A carboxyl group is attached to AIR by N5-CAIR synthetase to form N5-Carboxyaminoimidazole ribonucleotide (N5-CAIR), which is then converted to Carboxyamino-imidazole ribonucleotide (CAIR) with enzyme N5-CAIR mutase. Enzyme SAICAR synthetase, along with amino group from aspartate forms an amide bond to create N-succinyl-5-aminoimidazole-4-carboxamide ribonucleotide (SAICAR). Continuing down the pathway, the removal of the carbon skeleton of aspartate by SAICAR lyase results in 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR). Enzyme AICAR transformylase assists in the final carbon transfer from N10-formyltetrahydrofolate, forming N-formylaminoimidazole-4-carboxamide ribonucleotide (FAICAR). Lastly, closure of the second ring structure is carried out by IMP synthase to form IMP, where IMP fate would lead to the formation of a purine nucleotide.<ref name=Nelson08 />

[[File:Nucleotides syn2.png|220px|thumbnail|Pyrimidine de Novo pathway]]

Synthesis of pyrimidine nucleotides is a much simpler process. The formation of the pyrimidine ring begins with the conversion of Aspartate to N-Carbamoylaspartate by undergoing a condensation reaction with carbamoyl phosphate. Dihydroorotase and dihydroorotase dehydrogenase then converts N-Carbamoylaspartate to orotate. Orotate is covalently linked with phosphoribosyl pyrophosphate (PRPP) by orotate phosphoribysol-transferase yielding orotidine monophosphate (OMP). OMP follows with the decarboxylation by orotidylate decarboxylase to form the Uridylate (UMP) ribonucleotide structure. UMP can then be converted to Uridine-5'-trisphosphate (UTP) by two kinases reaction. Formation of Cytidine-5'-trisphosphate (CTP) from UTP can be achieved by cytidylate synthetase by an acyl phosphate intermediate.<ref name=Nelson08 />

==Prebiotic synthesis of ribonucleotides==

In order to understand how [[life]] arose, knowledge is required of the chemical pathways that permit formation of the key building blocks of life under plausible [[abiogenesis|prebiotic conditions]].  According to the [[RNA world]] hypothesis free-floating ribonucleotides were present in the primitive soup.  These were the fundamental molecules that combined in series to form [[RNA]].  Molecules as complex as RNA must have arisen from small molecules whose reactivity was governed by physico-chemical processes.  RNA is composed of [[purine]] and [[pyrimidine]] nucleotides, both of which are necessary for reliable information transfer, and thus Darwinian natural selection and [[evolution]]. The synthesis of activated [[pyrimidine]] ribonucleotides was demonstrated under plausible prebiotic conditions.<ref name = Powner2009>{{cite journal |vauthors=Powner MW, Gerland B, Sutherland JD |title=Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions |journal=Nature |volume=459 |issue=7244 |pages=239–42 |date=May 2009 |pmid=19444213 |doi=10.1038/nature08013 |bibcode=2009Natur.459..239P }}</ref> The starting materials for the synthesis ([[cyanamide]], [[cyanoacetylene]], [[glycolaldehyde]], [[glyceraldehyde]] and inorganic [[phosphate]]) were considered to be plausible prebiotic feedstock molecules.<ref name = Powner2009/> Nam et al. demonstrated the direct condensation of nucleobases with ribose to give ribonucleosides in aqueous microdroplets, a key step leading to RNA formation.<ref>{{cite journal |vauthors=Nam I, Nam HG, Zare RN |title=Abiotic synthesis of purine and pyrimidine ribonucleosides in aqueous microdroplets |journal=Proc Natl Acad Sci U S A |volume=115 |issue=1 |pages=36–40 |date=January 2018 |pmid=29255025 |pmc=5776833 |doi=10.1073/pnas.1718559115 |doi-access=free |bibcode=2018PNAS..115...36N }}</ref> Also, a plausible prebiotic process for synthesizing pyrimidine and purine ribonucleotides using wet-dry cycles was presented by Becker et al.<ref>{{cite journal |vauthors=Becker S, Feldmann J, Wiedemann S, Okamura H, Schneider C, Iwan K, Crisp A, Rossa M, Amatov T, Carell T |title=Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides |journal=Science |volume=366 |issue=6461 |pages=76–82 |date=October 2019 |pmid=31604305 |doi=10.1126/science.aax2747 |bibcode=2019Sci...366...76B }}</ref>

==History==
[[File:Levene.jpg|200px|thumbnail|Phoebus Levene]]

Prior to [[James Watson]] and [[Francis Crick|Francis Crick']]s landmark paper that detailed the structure of [[DNA]] from [[Rosalind Franklin]]'s [[X-ray crystallography]] image, there were several historical scientists that also contributed to its discovery.<ref name="Watson Crick">{{cite journal|last=Watson|first=JD|author2=Crick, FH |title=Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.|journal=Nature|date=Apr 25, 1953|volume=171|issue=4356|pages=737–8|pmid=13054692|doi=10.1038/171737a0|bibcode=1953Natur.171..737W|s2cid=4253007}}</ref> [[Friedrich Miescher]], a Swiss physician, who, in 1869, was first to isolate and identify nucleic substance from the nuclei of white blood cells he later called "nuclein", paving the way for the discovery of DNA.<ref name="Friedrich Miescher">{{cite journal|last=Dahm|first=R|title=Discovering DNA: Friedrich Miescher and the early years of nucleic acid research.|journal=Human Genetics|date=January 2008|volume=122|issue=6|pages=565–81|pmid=17901982|doi=10.1007/s00439-007-0433-0|s2cid=915930}}</ref> Following Mieschers work, was the German biochemist, [[Albrecht Kossel]], who, in 1878, isolated the non-protein components of  "nuclein", and discovered the five nucleobases present in nucleic acids: adenine, cytosine, guanine, thymine and uracil.<ref name="Albrecht Kossel">{{cite journal|last=Jones|first=ME|title=Albrecht Kossel, a biographical sketch.|journal=The Yale Journal of Biology and Medicine|date=September 1953|volume=26|issue=1|pages=80–97|pmid=13103145|pmc=2599350}}</ref> Although some fundamental facts were known about nucleic acids due to these early discoveries, its structure and function remained a mystery.

It wasn't until the discovery of nucleotides in 1919 by [[Phoebus Levene]], a Russian-Lithuanian biochemist that re-opened the gates of the DNA discovery. Levene first identified the carbohydrate component present in yeast [[RNA]] was in fact [[ribose]]. However, it was not until his discovery that the carbohydrate component in thymus nucleic acid was also a sugar but lacked one oxygen atom, termed [[deoxyribose]], that his discovery was widely appreciated by the scientific community. Eventually, Levene was able to identify the correct order of which the components of RNA and DNA are put together, a phosphate-sugar-base unit, in which he later called a [[nucleotide]]. Although the order of nucleotide components were well understood by Levene, the structure of nucleotide arrangement in space and its genetic code still remained a mystery during the early years of his career.<ref name="Phoebus Leven">{{cite journal|last=Levene|first=Phoebus|title=The structure of yeast nucleic acid IV. Ammonia Hydrolysis |year=1919|journal=Journal of Biological Chemistry |volume=40 |issue=2 |pages=415–424 |doi=10.1016/S0021-9258(18)87254-4|doi-access=free }}</ref>

==See also==
* [[Ribonucleosides]] or ribosides

==References==
{{reflist}}

{{Nucleobases, nucleosides, and nucleotides}}

[[Category:RNA]]
[[Category:Ribosides]]