Showing the arrangement of nucleotides within the structure of nucleic acids: At lower left, a monophosphate nucleotide; its nitrogenous base represents one side of a base-pair. At the upper right, four nucleotides form two base-pairs: thymine and adenine (connected bydouble hydrogen bonds) and guanine and cytosine (connected bytriple hydrogen bonds). The individual nucleotide monomers are chain-joined at their sugar and phosphate molecules, forming two 'backbones' (adouble helix) of nucleic acid, shown at upper left.
A nucleotide is composed of three distinctive chemical sub-units: a five-carbon sugar molecule, anucleobase (the two of which together are called anucleoside), and onephosphate group. With all three joined, a nucleotide is also termed a "nucleosidemonophosphate", "nucleosidediphosphate" or "nucleosidetriphosphate", depending on how many phosphates make up the phosphate group.[4]
Innucleic acids, nucleotides contain either apurine or apyrimidine base—i.e., the nucleobase molecule, also known as a nitrogenous base—and are termedribonucleotides if the sugar is ribose, ordeoxyribonucleotides if the sugar is deoxyribose. Individual phosphate molecules repetitively connect thesugar-ring molecules in two adjacent nucleotide monomers, thereby connecting the nucleotide monomers of a nucleic acid end-to-end into a long chain. These chain-joins of sugar and phosphate molecules create a 'backbone' strand for a single- ordouble helix. In any one strand, the chemical orientation (directionality) of the chain-joins runs from the5'-end to the3'-end (read: 5 prime-end to 3 prime-end)—referring to the five carbon sites on sugar molecules in adjacent nucleotides. In a double helix, the two strands are oriented in opposite directions, which permitsbase pairing andcomplementarity between the base-pairs, all which is essential forreplicating ortranscribing the encoded information found in DNA.[citation needed]
Nucleic acids then arepolymericmacromolecules assembled from nucleotides, themonomer-units of nucleic acids. The purine basesadenine andguanine and pyrimidine basecytosine occur in both DNA and RNA, while the pyrimidine basesthymine (in DNA) anduracil (in RNA) occur in just one. Adenine forms abase pair with thymine with two hydrogen bonds, while guanine pairs with cytosine with three hydrogen bonds.
In addition to being building blocks for the construction of nucleic acid polymers, singular nucleotides play roles in cellular energy storage and provision, cellular signaling, as a source of phosphate groups used to modulate the activity of proteins and other signaling molecules, and as enzymaticcofactors, often carrying outredox reactions. Signalingcyclic nucleotides are formed by binding the phosphate group twice to the same sugarmolecule, bridging the 5'- and 3'-hydroxyl groups of the sugar.[2] Some signaling nucleotides differ from the standard single-phosphate group configuration, in having multiple phosphate groups attached to different positions on the sugar.[5] Nucleotide cofactors include a wider range of chemical groups attached to the sugar via theglycosidic bond, includingnicotinamide andflavin, and in the latter case, the ribose sugar is linear rather than forming the ring seen in other nucleotides.
Structural elements of three nucleotides—where one-, two- or three-phosphates are attached to the nucleoside (in yellow, blue, green) at center: 1st, the nucleotide termed as anucleosidemonophosphate is formed by adding a phosphate (in red); 2nd, adding a second phosphate forms anucleosidediphosphate; 3rd, adding a third phosphate results in anucleosidetriphosphate. + The nitrogenous base (nucleobase) is indicated by"Base" and "glycosidic bond" (sugar bond). All fiveprimary, or canonical, bases—thepurines andpyrimidines—are sketched at right (in blue).
Examples of non-nucleic acid nucleotides
cAMP, a cyclic nucleotide signaling molecule with a single phosphate linked to both 5- and 3-positions.
pppGpp, a nucleotide signaling molecule with both 5'- and 3'-phosphates.
In vivo, nucleotides can be synthesizedde novo or recycled throughsalvage pathways.[1] The components used in de novo nucleotide synthesis are derived from biosynthetic precursors of carbohydrate andamino acid metabolism, and from ammonia and carbon dioxide. Recently it has been also demonstrated that cellular bicarbonate metabolism can be regulated by mTORC1 signaling.[6] 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 thepurine andpyrimidine nucleotides are carried out by several enzymes in thecytoplasm of the cell, not within a specificorganelle. Nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides.[citation needed]
Orotate is covalently linked with a phosphorylated ribosyl unit. The covalent linkage between the ribose and pyrimidine occurs at position C1[7] of theribose unit, which contains apyrophosphate, and N1 of the pyrimidine ring.Orotate phosphoribosyltransferase (PRPP transferase) catalyzes the net reaction yielding orotidine monophosphate (OMP):
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 ofCTP synthetase. Glutamine is the NH3 donor and the reaction is fueled by ATP hydrolysis, too:
UTP + Glutamine + ATP + H2O → CTP + ADP + Pi
Cytidine monophosphate (CMP) is derived from cytidine triphosphate (CTP) with subsequent loss of two phosphates.[8][9]
N1 arises from the amine group ofAsp C2 and C8 originate fromformate N3 and N9 are contributed by the amide group ofGln C4, C5 and N7 are derived fromGly C6 comes from HCO3− (CO2)Diagram of the synthesis of IMP.
enzymes
coenzymes
substrate names
metal ions
inorganic molecules
Thede novo synthesis ofpurine nucleotides by which these precursors are incorporated into the purine ring proceeds by a 10-step pathway to the branch-point intermediateIMP, the nucleotide of the basehypoxanthine.AMP andGMP are subsequently synthesized from this intermediate via separate, two-step pathways. Thus, purinemoieties are initially formed as part of theribonucleotides rather than asfree bases.
Six enzymes take part in IMP synthesis. Three of them are multifunctional:
The pathway starts with the formation ofPRPP.PRPS1 is theenzyme that activatesR5P, which is formed primarily by thepentose phosphate pathway, to PRPP by reacting it withATP. The reaction is unusual in that a pyrophosphoryl group is directly transferred from ATP to C1 of R5P and that the product has theα configuration about C1. This reaction is also shared with the pathways for the synthesis ofTrp,His, and thepyrimidine 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'spyrophosphate group (PPi) by an amide nitrogen donated from eitherglutamine (N),glycine (N&C),aspartate (N),folic acid (C1), or CO2. This is the committed step in purine synthesis. The reaction occurs with the inversion of configuration about ribose C1, thereby formingβ-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 NH2 previously introduced. A one-carbon unit from folic acid coenzyme N10-formyl-THF is then added to the amino group of the substituted glycine followed by the closure of the imidazole ring. Next, a second NH2 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 NH2 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 C2. NAD+ is the electron acceptor in the oxidation reaction. The amide group transfer from glutamine is fueled by ATP hydrolysis.
In humans, pyrimidine rings (C, T, U) can be degraded completely to CO2 and NH3 (urea excretion). That having been said, purine rings (G, A) cannot. Instead, they are degraded to the metabolically inerturic 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 (NH3 donor).[citation needed]
Theories about theorigin of life require knowledge of chemical pathways that permit formation of life's key building blocks under plausible prebiotic conditions. TheRNA world hypothesis holds that in theprimordial soup there existed free-floatingribonucleotides, the fundamental molecules that combine in series to formRNA. Complex molecules like RNA must have arisen from small molecules whose reactivity was governed by physico-chemical processes. RNA is composed ofpurine andpyrimidine nucleotides, both of which are necessary for reliable information transfer, and thus Darwinianevolution. Becker et al. showed how pyrimidinenucleosides can be synthesized from small molecules andribose, driven solely by wet-dry cycles.[10] Purine nucleosides can be synthesized by a similar pathway. 5'-mono- and di-phosphates also form selectively from phosphate-containing minerals, allowing concurrent formation ofpolyribonucleotides with both the purine and pyrimidine bases. Thus a reaction network towards the purine and pyrimidine RNA building blocks can be established starting from simple atmospheric or volcanic molecules.[10]
An unnatural base pair (UBP) is a designed subunit (ornucleobase) ofDNA which is created in a laboratory and does not occur in nature.[11] Examples included5SICS anddNaM. These artificial nucleotides bearing hydrophobicnucleobases, feature two fusedaromatic rings that form a (d5SICS–dNaM) complex or base pair in DNA.[12][13]E. coli have been induced to replicate a plasmid containing UBPs through multiple generations.[14] This is the first known example of a living organism passing along an expanded genetic code to subsequent generations.[12][15]
Synthetic guide RNA (gRNA): synthetic nucleotides can be used to designgRNA which are essential for the proper function of gene-editing technologies such asCRISPR-Cas9.
Nucleotide (abbreviated "nt") is a common unit of length for single-stranded nucleic acids, similar to howbase pair is a unit of length for double-stranded nucleic acids.[19]
TheIUPAC has designated the symbols for nucleotides.[20] Apart from the five (A, G, C, T/U) bases, often degenerate bases are used especially for designingPCR primers. These nucleotide codes are listed here. Some primer sequences may also include the character "I", which codes for the non-standard nucleotideinosine. Inosine occurs intRNAs and will pair with adenine, cytosine, or thymine. This character does not appear in the following table, however, because it does not represent a degeneracy. While inosine can serve a similar function as the degeneracy "H", it is an actual nucleotide, rather than a representation of a mix of nucleotides that covers each possible pairing needed.
^abAlberts B, Johnson A, Lewis J, Raff M, Roberts K & Walter P (2002).Molecular Biology of the Cell (4th ed.). Garland Science.ISBN0-8153-3218-1. pp. 120–121.
^Jones ME (1980). "Pyrimidine nucleotide biosynthesis in animals: genes, enzymes, and regulation of UMP biosynthesis".Annual Review of Biochemistry.49 (1):253–79.doi:10.1146/annurev.bi.49.070180.001345.PMID6105839.
^McMurry JE, Begley TP (2005).The organic chemistry of biological pathways. Roberts & Company.ISBN978-0-9747077-1-6.
^Ramesh D, Vijayakumar BG, Kannan T (December 2020). "Therapeutic potential of uracil and its derivatives in countering pathogenic and physiological disorders".European Journal of Medicinal Chemistry.207: 112801.doi:10.1016/j.ejmech.2020.112801.PMID32927231.S2CID221724578.
Sigel A, Operschall BP, Sigel H (2017). "Chapter 11. Complex Formation of Lead(II) with Nucleotides and Their Constituents". In Astrid S, Helmut S, Sigel RK (eds.).Lead: Its Effects on Environment and Health. Metal Ions in Life Sciences. Vol. 17. de Gruyter. pp. 319–402.doi:10.1515/9783110434330-011.ISBN9783110434330.PMID28731304.
IUPAC-IUB Commission on Biochemical Nomenclature (CBN) (14 February 1971). "Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents".Journal of Molecular Biology.55 (3):299–310.doi:10.1016/0022-2836(71)90319-6.PMID5551389.
