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Nucleotide



A nucleotide is a chemical compound that consists of 3 portions: a heterocyclic base, a sugar, and one or more phosphate groups. In the most common nucleotides the base is a derivative of purine or pyrimidine, and the sugar is the pentose 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 - CoA, flavin adenine dinucleotide, flavin mononucleotide, adenosine triphosphate and nicotinamide adenine dinucleotide phosphate. In the cell they have important roles in metabolism and signaling.

Additional recommended knowledge

Contents

Nucleotide structure

  A nucleotide is comprised of a ring of nitrogen, carbon and oxygen atoms, a five carbon sugar (together referred to as a nucleoside) and one or more phosphate groups. 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 thymidine. The nucleoside may bond to one, two or three functional group(s) of phosphate(s), forming respectively a monophosphate, diphosphate or triphosphate nucleotide. There are a wide variety of nucleotide and deoxynucleotide structures, as illustrated in the diagrams below.

Nucleotide structural diagrams


Adenosine monophosphate
AMP

Adenosine diphosphate
ADP

Adenosine triphosphate
ATP

Guanosine monophosphate
GMP

Guanosine diphosphate
GDP

Guanosine triphosphate
GTP

Ribothymidine monophosphate
rTMP

Ribothymidine diphosphate
rTDP

Ribothymidine triphosphate
rTTP

Uridine monophosphate
UMP

Uridine diphosphate
UDP

Uridine triphosphate
UTP

Cytidine monophosphate
CMP

Cytidine diphosphate
CDP

Cytidine triphosphate
CTP

Deoxynucleotide structural diagrams


Deoxyadenosine monophosphate
dAMP

Deoxyadenosine diphosphate
dADP

Deoxyadenosine triphosphate
dATP

Deoxyguanosine monophosphate
dGMP

Deoxyguanosine diphosphate
dGDP

Deoxyguanosine triphosphate
dGTP

Thymidine monophosphate
TMP

Thymidine diphosphate
TDP

Thymidine triphosphate
TTP

Deoxyuridine monophosphate
dUMP

Deoxyuridine diphosphate
dUDP

Deoxyuridine triphosphate
dUTP

Deoxycytidine monophosphate
dCMP

Deoxycytidine diphosphate
dCDP

Deoxycytidine triphosphate
dCTP

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 groups 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.

Types of bases

Nucleotides can be synthesized with both purine and pyrimidine as bases. The nucleotide passes through numerous biochemical steps while being processed, adding and removing atoms through the use of numerous enzymes.

Pyrimidine ribonucleotides

  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:

The biosynthetic origins of purine ring atoms

N1 arises from the amine group of Asp
C2 and C8 originate from formate
N3 and N9 are contributed by the amide group of Gln
C4, C5 and N7 are derived from Gly
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:

  • GART (reactions 2, 3, and 5)
  • PAICS (reactions 6, and 7)
  • 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 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, Trp, and 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 (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.

See also


Nucleobases: Purine (Adenine, Guanine) | Pyrimidine (Uracil, Thymine, Cytosine)
Nucleosides: Adenosine/Deoxyadenosine | Guanosine/Deoxyguanosine | Uridine | Thymidine | Cytidine/Deoxycytidine
Nucleotides: monophosphates (AMP, GMP, UMP, CMP) | diphosphates (ADP, GDP, UDP, CDP) | triphosphates (ATP, GTP, UTP, CTP) | cyclic (cAMP, cGMP, cADPR)
Deoxynucleotides: monophosphates (dAMP, dGMP, TMP, dCMP) | diphosphates (dADP, dGDP, TDP, dCDP) | triphosphates (dATP, dGTP, TTP, dCTP)
Ribonucleic acids: RNA | mRNA (pre-mRNA/hnRNA) | tRNA | rRNA | gRNA | miRNA | ncRNA | piRNA | shRNA | siRNA | snRNA | snoRNA
Deoxyribonucleic acids: DNA | cDNA | gDNA | msDNA | mtDNA
Nucleic acid analogues: GNA | LNA | PNA | TNA | morpholino
Cloning vectors: phagemid | plasmid | lambda phage | cosmid | P1 phage | fosmid | BAC | YAC | HAC
 
This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Nucleotide". A list of authors is available in Wikipedia.
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