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Nucleotide

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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.

Nucleotides 1

The structure elements of the most common nucleotides

Nucleotides Edit

AMP structure
Adenosine monophosphate
AMP
ADP structure
Adenosine diphosphate
ADP
ATP structure
Adenosine triphosphate
ATP
GMP chemical structure
Guanosine monophosphate
GMP
GDP chemical structure
Guanosine diphosphate
GDP
GTP chemical structure
Guanosine triphosphate
GTP
TMP chemical structure
Thymidine monophosphate
TMP
TDP chemical structure
Thymidine diphosphate
TDP
TTP chemical structure
Thymidine triphosphate
TTP
UMP chemical structure
Uridine monophosphate
UMP
UDP chemical structure
Uridine diphosphate
UDP
UTP chemical structure
Uridine triphosphate
UTP
CMP chemical structure
Cytidine monophosphate
CMP
CDP chemical structure
Cytidine diphosphate
CDP
CTP chemical structure
Cytidine triphosphate
CTP

Deoxynucleotides Edit

DAMP chemical structure
Deoxyadenosine monophosphate
dAMP
DADP chemical structure
Deoxyadenosine diphosphate
dADP
DATP chemical structure
Deoxyadenosine triphosphate
dATP
DGMP chemical structure
Deoxyguanosine monophosphate
dGMP
DGDP chemical structure
Deoxyguanosine diphosphate
dGDP
DGTP chemical structure
Deoxyguanosine triphosphate
dGTP
TMP chemical structure
thymidine monophosphate
TMP
TDP chemical structure
thymidine diphosphate
TDP
TTP chemical structure
thymidine triphosphate
TTP
DUMP chemical structure
Deoxyuridine monophosphate
dUMP
DUDP chemical structure
Deoxyuridine diphosphate
dUDP
DUTP chemical structure
Deoxyuridine triphosphate
dUTP
DCMP chemical structure
Deoxycytidine monophosphate
dCMP
DCDP chemical structure
Deoxycytidine diphosphate
dCDP
DCTP chemical structure
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 Edit

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 Edit

Purine ribonucleotides Edit

By using a variety of isotopically labeled compounds it was demonstrated that the sources of the atoms in purines are as follows:

Nucleotides syn3 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)
Nucleotides syn1

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 Edit

Nucleotides syn2

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


Protection Chemistry Edit

Nucleic acids can be synthetised in the lab using protecting groups, typically this is acchived 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 oligonulceotide.

Nucleotide Frequencies Edit

A connection has been proposed between the Fibonacci numbers and Chargaff's second rule concerning the proportions of nucleotides in the human genome.[1]

ReferencesEdit

  1. ^ Yamagishi M. E. B. and Shimabukuro A. I. (2007) Nucleotide Frequencies in Human Genome and Fibonacci Numbers. Bulletin of Mathematical Biology (http://www.springerlink.com/content/p140352473151957/?p=d5b18a2dfee949858e2062449e9ccfad&pi=0)


See also Edit

External links Edit


This page uses content from the English language Wikipedia. The original content was at Nucleotide. The list of authors can be seen in the page history. As with this Familypedia wiki, the content of Wikipedia is available under the Creative Commons License.

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