Nucleotide

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Editor-In-Chief: C. Michael Gibson, M.S., M.D. [1]



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 (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 - CoA, flavin adenine dinucleotide, flavin mononucleotide, adenosine triphosphate and nicotinamide adenine dinucleotide phosphate. In the cell they have important roles in metabolism and signaling.

The structure elements of the most common nucleotides

Nucleotides

File:AMP structure.svg
Adenosine monophosphate
AMP
Chemical structure of adenosine diphosphate
Adenosine diphosphate
ADP
File:ATP structure.svg
Adenosine triphosphate
ATP
Chemical structure of guanosine monophosphate
Guanosine monophosphate
GMP
Chemical structure of guanosine diphosphate
Guanosine diphosphate
GDP
Chemical structure of guanosine triphosphate
Guanosine triphosphate
GTP
Chemical structure of uridine monophosphate
Uridine monophosphate
UMP
Chemical structure of uridine diphosphate
Uridine diphosphate
UDP
Chemical structure of uridine triphosphate
Uridine triphosphate
UTP
Chemical structure of cytidine monophosphate
Cytidine monophosphate
CMP
Chemical structure of cytidine diphosphate
Cytidine diphosphate
CDP
Chemical structure of cytidine triphosphate
Cytidine triphosphate
CTP

Deoxynucleotides

Chemical structure of deoxyadenosine monophosphate
Deoxyadenosine monophosphate
dAMP
Chemical structure of deoxyadenosine diphosphate
Deoxyadenosine diphosphate
dADP
Chemical structure of deoxyadenosine triphosphate
Deoxyadenosine triphosphate
dATP
Chemical structure of deoxyguanosine monophosphate
Deoxyguanosine monophosphate
dGMP
Chemical structure of deoxyguanosine diphosphate
Deoxyguanosine diphosphate
dGDP
Chemical structure of deoxyguanosine triphosphate
Deoxyguanosine triphosphate
dGTP
Chemical structure of thymidine monophosphate
Thymidine monophosphate
TMP
Chemical structure of thymidine diphosphate
Thymidine diphosphate
TDP
Chemical structure of thymidine triphosphate
Thymidine triphosphate
TTP
Chemical structure of deoxycytidine monophosphate
Deoxycytidine monophosphate
dCMP
Chemical structure of deoxycytidine diphosphate
Deoxycytidine diphosphate
dCDP
Chemical structure of deoxycytidine triphosphate
Deoxycytidine triphosphate
dCTP

NOTE: If in place of ribose , the sugar deoxyribose is present the prefix `deoxy` may be added before the name of the nucleoside in all cases except thymidine.

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 labelled compounds it was demonstrated that the sources of the atoms in purines are as follows:

Nucleotides syn3.png 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 synthesis of IMP.
The color scheme is as follows: enzymes, coenzymes, substrate names, metal ions, inorganic molecules

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.

Reaction 3.

Pyrimidine ribonucleotides

The synthesis of UMP.
The color scheme is as follows: enzymes, coenzymes, substrate names, inorganic molecules

Protection Chemistry

Nucleic acids can be synthesised in the lab. using protecting groups, typically this is achieved by protecting a purified nucleoside or nucleobase, a protected base is called a phosphoramidite. these can be used to obtain analogues not present in nature and/or to create an oligonucleotide.

References


See also

External links



<tr bgcolor="#ccccff"><td colspan="3" align="center">
v  d  e
Major families of biochemicals</td></tr><tr><td colspan="3" style="text-align: center;">Peptides | Amino acids | Nucleic acids | Carbohydrates | Nucleotide sugars | Lipids | Terpenes | Carotenoids | Tetrapyrroles | Enzyme cofactors | Steroids | Flavonoids | Alkaloids | Polyketides | Glycosides</td></tr><tr bgcolor="pink"><td style="white-space: nowrap; width: 10%; color: pink;">Analogues of nucleic acids:</td><td align="center">Types of Nucleic Acids</td><td style="white-space: nowrap; width: 10%; color: pink;">Analogues of nucleic acids:</td></tr>
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 | tRNA | rRNA | gRNA | miRNA | ncRNA | piRNA | shRNA | siRNA | snRNA | snoRNA
Deoxyribonucleic acids: DNA | mtDNA | cDNA
Nucleic acid analogues: GNA | LNA | PNA | TNA | morpholino
Cloning vectors: plasmid | cosmid | fosmid | phagemid | BAC | YAC | HAC
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