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A
nucleotide is a
chemical compound that consists of 3 portions: a
Basic aromatic ring, a sugar, and one or more phosphate
Functional groups. In the most common nucleotides the base is a derivative of
purine or pyrimidine, and the sugar is the
pentose (five-carbon sugar)
deoxyribose or ribose. Nucleotides are the
monomers of nucleic acids, with three or more bonding together in order to form a nucleic acid.
Nucleotides are the structural units of
RNA,
DNA, and several cofactors -
coenzyme A,
FAD, flavin mononucleotide,
adenosine triphosphate and
nicotinamide adenine dinucleotide phosphate. In the
cell (biology) they have important roles in metabolism and signaling.
Nucleotides
{||- align="center" valign="bottom"|
Adenosine monophosphateAMP]ADP|
Adenosine triphosphateATP]GMP| Guanosine diphosphateGDP]GTP|- align="center" valign="bottom"|
Thymidine monophosphateTMP]TDP| Thymidine triphosphateTTP]UMP|
Uridine diphosphateUDP]UTP|- align="center" valign="bottom"|
Cytidine monophosphateCMP]CDP| Cytidine triphosphateCTP|-|}
Deoxynucleotides
{||- align="center" valign="bottom"|
Deoxyadenosine monophosphatedAMP]dADP| Deoxyadenosine triphosphatedATP]dGMP|
Deoxyguanosine diphosphatedGDP]dGTP|- align="center" valign="bottom"| Deoxythymidine monophosphatedTMP]dTDP| Deoxythymidine triphosphatedTTP]dUMP|
Deoxyuridine diphosphatedUDP]dUTP|- align="center" valign="bottom"| Deoxycytidine monophosphatedCMP]dCDP| Deoxycytidine triphosphatedCTP|-|}
Synthesis
Salvage synthesis refers to the reuse of parts of
nucleotides in resynthesizing new nucleotides. Salvage synthesis requires both breakdown and synthesis reactions in order to exchange the useful parts.
Natural
Purine ribonucleotides
By using a variety of isotopically labeled compounds it was demonstrated that the sources of the atoms in purines are as follows:
{| class="wikitable" style="margin: 1em auto 1em auto"| ||
The biosynthetic origins of purine ring atomsN1 arises from the amine group of Aspartic acid
C2 and C8 originate from
formateN3 and N9 are contributed by the amide group of Glutamine
C4, C5 and N7 are derived from Glycine
C6 comes from HCO3- (CO2)|}
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:
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. 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, and
Histidine. 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 (PPi) 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 PPi, is the pathway's flux generating step and is therefore regulated too.
Reaction 3.
Pyrimidine ribonucleotides
See also
External links
- Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents (IUPAC)
- Provisional Recommendations 2004 (IUPAC)
- Chemistry explanation of nucleotide structure
A
nucleotide is a chemical compound that consists of 3 portions: a
Basic aromatic ring, a sugar, and one or more
phosphate Functional groups. In the most common nucleotides the base is a derivative of
purine or pyrimidine, and the sugar is the
pentose (five-carbon sugar) deoxyribose or
ribose. Nucleotides are the
monomers of
nucleic acids, with three or more bonding together in order to form a nucleic acid.
Nucleotides are the structural units of RNA, DNA, and several cofactors - coenzyme A, FAD,
flavin mononucleotide,
adenosine triphosphate and
nicotinamide adenine dinucleotide phosphate. In the cell (biology) they have important roles in metabolism and signaling.
Nucleotides
{||- align="center" valign="bottom"| Adenosine monophosphateAMP]ADP|
Adenosine triphosphateATP]GMP|
Guanosine diphosphateGDP]GTP|- align="center" valign="bottom"|
Thymidine monophosphateTMP]TDP| Thymidine triphosphateTTP]UMP|
Uridine diphosphateUDP]UTP|- align="center" valign="bottom"|
Cytidine monophosphateCMP]CDP| Cytidine triphosphateCTP|-|}
Deoxynucleotides
{||- align="center" valign="bottom"| Deoxyadenosine monophosphatedAMP]dADP|
Deoxyadenosine triphosphatedATP]dGMP|
Deoxyguanosine diphosphatedGDP]dGTP|- align="center" valign="bottom"|
Deoxythymidine monophosphatedTMP]dTDP|
Deoxythymidine triphosphatedTTP]dUMP| Deoxyuridine diphosphatedUDP]dUTP|- align="center" valign="bottom"| Deoxycytidine monophosphatedCMP]dCDP| Deoxycytidine triphosphatedCTP|-|}
Synthesis
Salvage synthesis refers to the reuse of parts of nucleotides in resynthesizing new nucleotides. Salvage synthesis requires both breakdown and synthesis reactions in order to exchange the useful parts.
Natural
Purine ribonucleotides
By using a variety of isotopically labeled compounds it was demonstrated that the sources of the atoms in purines are as follows:
{| class="wikitable" style="margin: 1em auto 1em auto"| ||
The biosynthetic origins of purine ring atomsN1 arises from the amine group of
Aspartic acidC2 and C8 originate from formate
N3 and N9 are contributed by the amide group of Glutamine
C4, C5 and N7 are derived from
Glycine C6 comes from HCO3- (CO2)|}
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:
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. 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, and
Histidine. 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 (PPi) 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 PPi, is the pathway's flux generating step and is therefore regulated too.
Reaction 3.
Pyrimidine ribonucleotides
See also
External links
- Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents (IUPAC)
- Provisional Recommendations 2004 (IUPAC)
- Chemistry explanation of nucleotide structure
Nucleotide - Wikipedia, the free encyclopedia
Nucleotides are organic compounds that consist of three joined structures: a nitrogenous base, a sugar, and a phosphate group. The most common nucleotides can be divided into two ...
Definition: nucleotide from Online Medical Dictionary
The Online Medical Dictionary is a searchable dictionary of definitions from medicine, science and technology.
nucleotide - definition of nucleotide by the Free Online Dictionary ...
nu·cle·o·tide (n kl--t d, ny-) n. Any of various compounds consisting of a nucleoside combined with a phosphate group and forming the basic constituent of DNA and RNA.
EBI Databases: Nucleotide Databases
nucleotide Databases, ASD, ATD, EMBL-Align, EMBL-Bank, EMBL-CDS, Ensembl, Genome Reviews, Genomes Server, Karyns Genomes, IMGT/HLA, IMGT/LIGM, IPD, LGICdb, Mutations, Parasites
Nucleotide
Encyclopedia information on Nucleotide ... Nucleotide. Nucleotides are the single units that make up nucleic acid s like RNA and DNA – literally the building blocks of life.
nucleotide - Hutchinson encyclopedia article about nucleotide
Organic compound consisting of a purine (adenine or guanine) or a pyrimidine (thymine, uracil, or cytosine) base linked to a sugar (deoxyribose or ribose) and a phosphate group ...
2Can Support Portal: Nucleotide Analysis - BLAST homology & similarity ...
BLAST similarity search - Introduction WU-BLAST2 stands for W ashington U niversity B asic L ocal A lignment S earch T ool Version 2.0. It is used to compare a query sequence with ...
INSDC :: About INSDC
International Nucleotide Sequence Database Collaboration . The International Nucleotide Sequence Databases (INSD) have been developed and ...
Entrez Nucleotide
Nucleic Acid Symbols
... of the chemistry of the nucleosides or nucleotides, the more systematic three-letter symbols (N-2) should be used, e.g., Ado-5' PPP or Urd-5' PP-Glc (N-2.4.3). N-1.2. Nucleotide ...
