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 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.
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[edit] 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.
[edit] Nucleotide structural diagrams
[edit] Deoxynucleotide structural diagrams
[edit] 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.
[edit] 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.
[edit] Pyrimidine ribonucleotides
The synthesis of a single pyrimidine is complex; the diagram to the left demonstrates the synthesis of a single pyrimidine.
[edit] Purine ribonucleotides
The atoms which are used to build the purine nucleotides come from a variety of sources:
| Image: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 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 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.
[edit] See also
[edit] External links
- Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents (IUPAC)
- Provisional Recommendations 2004 (IUPAC)
- Chemistry explanation of nucleotide structure
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