Nucleoside triphosphate

The term nucleoside refers to a nitrogenous base linked to a 5-carbon sugar (either ribose or deoxyribose). Nucleotides are nucleosides covalently linked to one or more phosphate groups.{{cite book| vauthors = Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J |date=2000|title=Structure of Nucleic Acids|url=https://www.ncbi.nlm.nih.gov/books/NBK21514/}} To provide information about the number of phosphates, nucleotides may instead be referred to as nucleoside (mono, di, or tri) phosphates.{{cite journal | vauthors = Secrist JA | title = Nucleoside and nucleotide nomenclature | journal = Current Protocols in Nucleic Acid Chemistry | volume = Appendix 1 | pages = A.1D.1–A.1D.3 | date = May 2001 | pmid = 18428808 | doi = 10.1002/0471142700.nca01ds00 | hdl = 2027.42/143595 | s2cid = 205152902 | url = https://deepblue.lib.umich.edu/bitstream/2027.42/143595/1/cpnca01d.pdf | hdl-access = free }} Thus, nucleoside triphosphates are a type of nucleotide.

Nucleotides are commonly abbreviated with 3 letters (4 or 5 in case of deoxy- or dideoxy-nucleotides). The first letter indicates the identity of the nitrogenous base (e.g., A for adenine, G for guanine), the second letter indicates the number of phosphates (mono, di, tri), and the third letter is P, standing for phosphate.{{Cite web|url=http://www.biochem.uthscsa.edu/med/02-Nucleotide-Metab/PrereqNucleotideMetab3.html|title=Nomenclature of Nucleosides|website=www.biochem.uthscsa.edu|access-date=2017-11-11}} Nucleoside triphosphates that contain ribose as the sugar are conventionally abbreviated as NTPs, while nucleoside triphosphates containing deoxyribose as the sugar are abbreviated as dNTPs. For example, dATP stands for deoxyribose adenosine triphosphate. NTPs are the building blocks of RNA, and dNTPs are the building blocks of DNA.{{Cite news|url=https://science-explained.com/theory/dna-rna-and-protein/|title=From DNA to RNA to protein, how does it work?|work=Science Explained|access-date=11 November 2017}}

The carbons of the sugar in a nucleoside triphosphate are numbered around the carbon ring starting from the original carbonyl of the sugar. Conventionally, the carbon numbers in a sugar are followed by the prime symbol (‘) to distinguish them from the carbons of the nitrogenous base. The nitrogenous base is linked to the 1’ carbon through a glycosidic bond, and the phosphate groups are covalently linked to the 5’ carbon.{{Cite web|url=http://www.biosyn.com/tew/numbering-convention-for-nucleotides.aspx|title=Numbering convention for nucleotides |website=www.biosyn.com|access-date=2017-11-11}} The first phosphate group linked to the sugar is termed the α-phosphate, the second is the β-phosphate, and the third is the γ-phosphate; these are linked to one another by two phosphoanhydride bonds.{{cite web | url = http://www.sparknotes.com/biology/molecular/dnareplicationandrepair/section2.rhtml|title=SparkNotes: DNA Replication and Repair: The Chemistry of the Addition of Substrates of DNA Replication|website=www.sparknotes.com|access-date=2017-11-11}}File:Nucleotides 1.svg

File:DNA synthesis EN.pngThe cellular processes of DNA replication and transcription involve DNA and RNA synthesis, respectively. DNA synthesis uses dNTPs as substrates, while RNA synthesis uses rNTPs as substrates. NTPs cannot be converted directly to dNTPs. DNA contains four different nitrogenous bases: adenine, guanine, cytosine and thymine. RNA also contains adenine, guanine, and cytosine, but replaces thymine with uracil.{{Cite news|url=https://www.thoughtco.com/dna-versus-rna-608191|title=Do You Know the Differences Between DNA and RNA?|work=ThoughtCo|access-date=2017-11-11}} Thus, DNA synthesis requires dATP, dGTP, dCTP, and dTTP as substrates, while RNA synthesis requires ATP, GTP, CTP, and UTP.

Nucleic acid synthesis is catalyzed by either DNA polymerase or RNA polymerase for DNA and RNA synthesis respectively.{{Cite web|url=http://www.differencebetween.com/difference-between-dna-polymerase-and-vs-rna-polymerase/|title=Difference Between DNA Polymerase and RNA Polymerase|access-date=2017-11-11|date=2011-12-24}} These enzymes covalently link the free -OH group on the 3’ carbon of a growing chain of nucleotides to the α-phosphate on the 5’ carbon of the next (d)NTP, releasing the β- and γ-phosphate groups as pyrophosphate (PP_i).{{cite book | vauthors = Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J |date=2000|title=Nucleic Acid Synthesis|url=https://www.ncbi.nlm.nih.gov/books/NBK21644/}} This results in a phosphodiester linkage between the two (d)NTPs. The release of PP_i provides the energy necessary for the reaction to occur. Nucleic acid synthesis occurs exclusively in the 5’ to 3’ direction.

Given their importance in the cell, the synthesis and degradation of nucleoside triphosphates is under tight control. This section focuses on nucleoside triphosphate metabolism in humans, but the process is fairly conserved among species.{{cite journal | vauthors = Samant S, Lee H, Ghassemi M, Chen J, Cook JL, Mankin AS, Neyfakh AA | title = Nucleotide biosynthesis is critical for growth of bacteria in human blood | journal = PLOS Pathogens | volume = 4 | issue = 2 | pages = e37 | date = February 2008 | pmid = 18282099 | doi = 10.1371/journal.ppat.0040037 | pmc=2242838 | doi-access = free }} Nucleoside triphosphates cannot be absorbed well, so all nucleoside triphosphates are typically made de novo.{{cite book | vauthors = Berg JM, Tymoczko JL, Stryer L |date=2002|title=Nucleotide Biosynthesis|url=https://www.ncbi.nlm.nih.gov/books/NBK21216/}} The synthesis of ATP and GTP (purines) differs from the synthesis of CTP, TTP, and UTP (pyrimidines). Both purine and pyrimidine synthesis use phosphoribosyl pyrophosphate (PRPP) as a starting molecule.{{cite web | url = https://themedicalbiochemistrypage.org/nucleotide-metabolism.php|title=Nucleotide Metabolism: Nucleic Acid Synthesis|website=themedicalbiochemistrypage.org|access-date=2017-11-15}}

The conversion of NTPs to dNTPs can only be done in the diphosphate form. Typically a NTP has one phosphate removed to become a NDP, then is converted to a dNDP by an enzyme called ribonucleotide reductase, then a phosphate is added back to give a dNTP.{{cite journal | vauthors = Stubbe J | title = Ribonucleotide reductases: amazing and confusing | journal = The Journal of Biological Chemistry | volume = 265 | issue = 10 | pages = 5329–32 | year = 1990 | doi = 10.1016/S0021-9258(19)39357-3 | pmid = 2180924 | url = http://www.jbc.org/content/265/10/5329.full.pdf | doi-access = free }}

A nitrogenous base called hypoxanthine is assembled directly onto PRPP.{{cite book| vauthors = Berg J, Tymoczko JL, Stryer L |date=2002 |title=Purine Bases Can Be Synthesized de Novo or Recycled by Salvage Pathways|url=https://www.ncbi.nlm.nih.gov/books/NBK22385/}} This results in a nucleotide called inosine monophosphate (IMP). IMP is then converted to either a precursor to AMP or GMP. Once AMP or GMP are formed, they can be phosphorylated by ATP to their diphosphate and triphosphate forms.{{Cite news|url=http://www.biochemden.com/purine-synthesis/|title=Purine Synthesis : Synthesis of Purine RiboNucleotides|date=2016-03-16|work=BiochemDen.com|access-date= 15 November 2017 }}

Purine synthesis is regulated by the allosteric inhibition of IMP formation by the adenine or guanine nucleotides.{{cite book | vauthors = Berg JM, Tymoczko JL, Stryer L |date=2002|title=Key Steps in Nucleotide Biosynthesis Are Regulated by Feedback Inhibition|url=https://www.ncbi.nlm.nih.gov/books/NBK22428/}} AMP and GMP also competitively inhibit the formation of their precursors from IMP.{{cite journal | vauthors = Nierlich DP, Magasanik B | title = Regulation of purine ribonucleotide synthesis by end product inhibition. the effect of adenine and guanine ribonucleotides on the 5'-phosphoribosyl-pyrophosphate amidotransferase of aerobacter aerogenes | journal = The Journal of Biological Chemistry | volume = 240 | pages = 358–65 | year = 1965 | doi = 10.1016/S0021-9258(18)97657-X | pmid = 14253438 | doi-access = free }}

A nitrogenous base called orotate is synthesized independently of PRPP. After orotate is made it is covalently attached to PRPP. This results in a nucleotide called orotate monophosphate (OMP).{{cite journal | vauthors = Moffatt BA, Ashihara H | title = Purine and pyrimidine nucleotide synthesis and metabolism | journal = The Arabidopsis Book | volume = 1 | pages = e0018 | date = April 2002 | pmid = 22303196 | pmc = 3243375 | doi = 10.1199/tab.0018 }} OMP is converted to UMP, which can then be phosphorylated by ATP to UDP and UTP. UTP can then be converted to CTP by a deamination reaction.{{cite web|url=https://www.cliffsnotes.com/study-guides/biology/biochemistry-ii/purines-and-pyrimidines/pyrimidine-metabolism|title=Pyrimidine Metabolism|website=www.cliffsnotes.com|access-date=2017-11-15}} TTP is not a substrate for nucleic acid synthesis, so it is not synthesized in the cell. Instead, dTTP is made indirectly from either dUDP or dCDP after conversion to their respective deoxyribose forms.

Pyrimidine synthesis is regulated by the allosteric inhibition of orotate synthesis by UDP and UTP. PRPP and ATP are also allosteric activators of orotate synthesis.{{cite journal | vauthors = Lane AN, Fan TW | title = Regulation of mammalian nucleotide metabolism and biosynthesis | journal = Nucleic Acids Research | volume = 43 | issue = 4 | pages = 2466–85 | date = February 2015 | pmid = 25628363 | doi = 10.1093/nar/gkv047 | pmc=4344498}}

Ribonucleotide reductase (RNR) is the enzyme responsible for converting NTPs to dNTPs. Given that dNTPs are used in DNA replication, the activity of RNR is tightly regulated. RNR can only process NDPs, so NTPs are first dephosphorylated to NDPs before conversion to dNDPs.{{cite journal | vauthors = Kolberg M, Strand KR, Graff P, Andersson KK | title = Structure, function, and mechanism of ribonucleotide reductases | journal = Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics | volume = 1699 | issue = 1–2 | pages = 1–34 | date = June 2004 | pmid = 15158709 | doi = 10.1016/j.bbapap.2004.02.007 }} dNDPs are then typically re-phosphorylated. RNR has 2 subunits and 3 sites: the catalytic site, activity (A) site, and specificity (S) site. The catalytic site is where the NDP to dNDP reaction takes place, the activity site determines whether or not the enzyme is active, and the specificity site determines which reaction takes place in the catalytic site.

The activity site can bind either ATP or dATP.{{cite book |doi=10.1016/B978-0-12-386931-9.00014-3 |chapter=The Structural Basis for the Allosteric Regulation of Ribonucleotide Reductase |title=Oligomerization in Health and Disease |series=Progress in Molecular Biology and Translational Science |year=2013 | vauthors = Ahmad MF, Dealwis CG |volume=117 |pages=389–410 |pmid=23663976 |pmc=4059395 |isbn=9780123869319 }} When bound to ATP, RNR is active. When ATP or dATP is bound to the S site, RNR will catalyze synthesis of dCDP and dUDP from CDP and UDP. dCDP and dUDP can go on to indirectly make dTTP. dTTP bound to the S site will catalyze synthesis of dGDP from GDP, and binding of dGDP to the S site will promote synthesis of dADP from ADP.{{cite journal | vauthors = Fairman JW, Wijerathna SR, Ahmad MF, Xu H, Nakano R, Jha S, Prendergast J, Welin RM, Flodin S, Roos A, Nordlund P, Li Z, Walz T, Dealwis CG | title = Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization | journal = Nature Structural & Molecular Biology | volume = 18 | issue = 3 | pages = 316–22 | date = March 2011 | pmid = 21336276 | doi = 10.1038/nsmb.2007 | pmc=3101628}} dADP is then phosphorylated to give dATP, which can bind to the A site and turn RNR off.

File:Adenosintriphosphat protoniert.svg

ATP is the primary energy currency of the cell.{{cite web |title=ATP |url=https://www.nature.com/scitable/definition/atp-318/ |website=Scitable }} Despite being synthesized through the metabolic pathway described above, it is primarily synthesized during both cellular respiration{{cite web |title=Mitochondria, Cell Energy, ATP Synthase |url=https://www.nature.com/scitable/topicpage/mitochondria-14053590/ |website=Scitable }} and photosynthesis{{Cite web|url=http://plantsinaction.science.uq.edu.au/content/124-atp-synthesis|title=ATP Synthesis|website=Plants in Action|access-date=2017-11-12}} by ATP synthase. ATP synthase couples the synthesis of ATP from ADP and phosphate with an electrochemical gradient generated by the pumping of protons through either the inner mitochondrial membrane (cellular respiration) or the thylakoid membrane (photosynthesis).{{cite journal | vauthors = Jonckheere AI, Smeitink JA, Rodenburg RJ | title = Mitochondrial ATP synthase: architecture, function and pathology | journal = Journal of Inherited Metabolic Disease | volume = 35 | issue = 2 | pages = 211–25 | date = March 2012 | pmid = 21874297 | pmc = 3278611 | doi = 10.1007/s10545-011-9382-9 }} This electrochemical gradient is necessary because the formation of ATP is energetically unfavourable.

The hydrolysis of ATP to ADP and P_i proceeds as follows:{{cite journal | vauthors = Dittrich M, Hayashi S, Schulten K | title = On the mechanism of ATP hydrolysis in F1-ATPase | journal = Biophysical Journal | volume = 85 | issue = 4 | pages = 2253–66 | date = October 2003 | pmid = 14507690 | pmc = 1303451 | doi = 10.1016/S0006-3495(03)74650-5 | bibcode = 2003BpJ....85.2253D }}

:ATP + H2O -> ADP + P_{i}

This reaction is energetically favourable and releases 30.5 kJ/mol of energy. In the cell, this reaction is often coupled with unfavourable reactions to provide the energy for them to proceed.{{Cite web|url=https://courses.lumenlearning.com/boundless-biology/chapter/atp-adenosine-triphosphate/|title=ATP: Adenosine Triphosphate {{!}} Boundless Biology|website=courses.lumenlearning.com-US|access-date=2017-11-12}} GTP is occasionally used for energy-coupling in a similar manner.{{cite journal | vauthors = Carvalho AT, Szeler K, Vavitsas K, Åqvist J, Kamerlin SC | title = Modeling the mechanisms of biological GTP hydrolysis | journal = Archives of Biochemistry and Biophysics | volume = 582 | issue = Supplement C | pages = 80–90 | date = September 2015 | pmid = 25731854 | doi = 10.1016/j.abb.2015.02.027 | series = Special issue in computational modeling on biological systems | url = http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-264885 | doi-access = free }} File:Activatoin-Adenylate cyclase-outlined.svg

GTP is essential for signal transduction, especially with G proteins. G proteins are coupled with a cell membrane bound receptor. This whole complex is called a G protein-coupled receptor (GPCR). G proteins can bind either GDP or GTP. When bound to GDP, G proteins are inactive. When a ligand binds a GPCR, an allosteric change in the G protein is triggered, causing GDP to leave and be replaced by GTP.{{Cite encyclopedia|url=https://www.britannica.com/science/G-protein-coupled-receptor|title=G protein-coupled receptor (GPCR) {{!}} biochemistry|encyclopedia=Encyclopedia Britannica|access-date=2017-11-12}} GTP activates the alpha subunit of the G protein, causing it to dissociate from the G protein and act as a downstream effector.

Nucleoside analogues can be used to treat viral infections.{{Cite web|url=http://www.mdpi.com/journal/molecules/special_issues/nucleoside_analogues|title=Nucleoside Analogues|website=Molecules|access-date=2017-11-13}} Nucleoside analogues are nucleosides that are structurally similar (analogous) to the nucleosides used in DNA and RNA synthesis.{{cite journal | vauthors = Jordheim LP, Durantel D, Zoulim F, Dumontet C | title = Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases | journal = Nature Reviews. Drug Discovery | volume = 12 | issue = 6 | pages = 447–64 | date = June 2013 | pmid = 23722347 | doi = 10.1038/nrd4010 | s2cid = 39842610 }} Once these nucleoside analogues enter a cell, they can become phosphorylated by a viral enzyme. The resulting nucleotides are similar enough to the nucleotides used in DNA or RNA synthesis to be incorporated into growing DNA or RNA strands, but they do not have an available 3' OH group to attach the next nucleotide, causing chain termination.{{cite journal | vauthors = Ewald B, Sampath D, Plunkett W | title = Nucleoside analogs: molecular mechanisms signaling cell death | journal = Oncogene | volume = 27 | issue = 50 | pages = 6522–37 | date = October 2008 | pmid = 18955977 | doi = 10.1038/onc.2008.316 | s2cid = 23817516 | doi-access = }} This can be exploited for therapeutic uses in viral infections because viral DNA polymerase recognizes certain nucleotide analogues more readily than eukaryotic DNA polymerase. For example, azidothymidine is used in the treatment of HIV/AIDS. Some less selective nucleoside analogues can be used as chemotherapy agents to treat cancer,{{cite journal | vauthors = Galmarini CM, Mackey JR, Dumontet C | title = Nucleoside analogues and nucleobases in cancer treatment | journal = The Lancet. Oncology | volume = 3 | issue = 7 | pages = 415–24 | date = July 2002 | pmid = 12142171 | doi=10.1016/s1470-2045(02)00788-x}} such as cytosine arabinose (ara-C) in the treatment of certain forms of leukemia.

Resistance to nucleoside analogues is common, and is frequently due to a mutation in the enzyme that phosphorylates the nucleoside after entry into the cell.{{cite journal | vauthors = Galmarini CM, Mackey JR, Dumontet C | title = Nucleoside analogues: mechanisms of drug resistance and reversal strategies | journal = Leukemia | volume = 15 | issue = 6 | pages = 875–90 | year = 2001 | pmid = 11417472 | doi = 10.1038/sj.leu.2402114 | s2cid = 760764 | doi-access = }} This is common in nucleoside analogues used to treat HIV/AIDS.{{cite journal | vauthors = Menéndez-Arias L | title = Mechanisms of resistance to nucleoside analogue inhibitors of HIV-1 reverse transcriptase | journal = Virus Research | volume = 134 | issue = 1–2 | pages = 124–46 | date = June 2008 | pmid = 18272247 | doi = 10.1016/j.virusres.2007.12.015 }}

• Biology
• Chromosome
• Gene
• Genetics
• Nucleic acid sequence
• Nucleobase

{{Reflist}}

{{Nucleobases, nucleosides, and nucleotides}}

Category:Nucleic acids

Category:Nucleotides

Category:Phosphate esters