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Uridine diphosphate

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Definition

noun

plural: uridine diphosphates

(biochemistry) A nucleotide composed of uracil, ribose and two phosphate groups; chemical formula of C9H14N2O12P2


Details

Overview

A nucleotide is an organic compound made up of three subunits: a nucleobase, a five-carbon sugar, and a phosphate group. The sugar component may either be ribose or deoxyribose. The ribose is the sugar component of the nucleotides that make up RNA. The deoxyribose is the sugar component of DNA. Nucleotides are the monomeric units of nucleic acids. Each phosphate group connects the sugar rings of two adjacent nucleotide monomers. The phosphate groups and the sugar moieties form the backbone of a nucleic acid. The directionality of the chain runs from 5'-end to 3'-end. In DNA, the orientation of the two strands is in opposite directions. This is to allow complementary base pairing between nucleobase constituents. A nucleotide is, thus, a nucleoside with a phosphate group. Depending on the number of phosphate groups attached to the sugar moiety, it may be called nucleoside monophosphate (if with only one phosphate group), nucleoside diphosphate (with two phosphate groups), or nucleoside triphosphate (when with three phosphate groups). Depending on the pentose sugar component, a nucleoside may be a ribonucleoside or a deoxyribonucleoside. A ribonucleoside is a nucleoside with a ribose sugar component. (Depending on the nucleobase component, the ribonucleoside may be adenosine, guanosine, cytidine, uridine, or 5-methyluridine). A deoxyribonucleoside is a nucleoside with a deoxyribose sugar. Depending on the nucleobase component, a deoxyribonucleoside may be deoxyadenosine, deoxyguanosine, deoxycytidine, thymidine, or deoxyuridine. Also, depending on the nucleobase component, the nucleosides may be grouped into either the "double-ringed" purine or the "single-ringed" pyrimidine.


Uridine diphosphate (UDP) is a pyrimidine nucleotide composed of uracil, ribose and two phosphate groups. Its chemical formula: C9H14N2O12P2


Characteristics

Uridine diphosphate (UDP) is a nucleoside phosphate in being comprised of a ribonucleoside and two phosphate groups. This means that it has a ribose as its sugar constituent with two phosphate groups attached. Its nucleoside contains a pyrimidine base, i.e. uracil attached to the ribose sugar. It has only one phosphate group attached to the nucleoside.


Uracil is similar to thymine in terms of structure except for the methyl group at position 5 in the heterocyclic aromatic ring present in thymine. One of the possible explanations why DNA has thymine instead of uracil is associated with the conversion of cytosine into uracil by spontaneous deamination. Cytosine can turn into uracil when it loses its amine group. This deamination of cytosine is a common occurrence. Nevertheless, the error is corrected through an inherent DNA repair systems. If not repaired though, it could lead to a point mutation. Had uracil been present in the DNA, the repair systems might not be able to distinguish the original uracil from the cytosine-turned-uracil and therefore may fail to discern which uracil to correct. The presence of methyl group in thymine (which is absent in uracil) helps avert this from happening, thereby, preserving the integrity and stability of the genetic code.


Common biological reactions

Biosynthesis of uracil for uracil nucleotides

Uracil, similar to other pyrimidines, is formed from a series of steps, beginning with the formation of carbamoyl phosphate. Carbamoyl phosphate forms from a reaction involving bicarbonate, glutamine, ATP, and water molecule. This process is catalyzed by the enzyme carbamoyl phosphate synthetase. The carbamoyl phosphate is then converted into carbamoyl aspartate through the catalytic activity of aspartate transcarbamylase. Carbamoyl aspartate is next converted into dihydroorotate, which is then oxidized to produce orotate. 5-phospho-α-D-ribosyl 1-pyrophosphate (PRPP), a ribose phosphate, reacts to orotate to form orotidine-5-monophosphate (OMP). OMP is decarboxylated by the enzyme OMP decarboxylase to yield uridine monophosphate (UMP). Eventually, uridine diphosphate (UDP) and uridine triphosphate (UTP) are produced down the biosynthetic pathway by kinases and dephosphorylation of ATPs. Uridine may also be a source of thymidine (which is a nucleoside of thymine). In order to synthesize thymidine, uridine is reduced first to deoxyuridine (by the enzyme ribonucleotide reductase). After which, it is methylated by the enzyme thymidylate synthase to form thymidine.


Glycogenesis

UDP is an important metabolite in glycogenesis. Glycogenesis is a metabolic process of producing glycogen from glucose for storage mainly in liver and muscle cells in response to high glucose level in the bloodstream. Before glucose can be stored as glycogen, glucose 1-phosphate is combined with uridine triphosphate (UTP) via the catalytic action of the enzyme UDP-glucose pyrophosphorylase. UTP loses one pyrophosphate ion in the process resulting in the formation of UDP-glucose unit. The enzyme glycogen synthase next adds the UDP-glucose unit to the growing glycogen chain, and then the UDP molecule detaches from the complex. The detached UDP may be utilized again by the UDP-glucose pyrophosphorylase.


Biological functions

UDP is a metabolite of many biological processes such as pyrimidine biosynthesis, lactose synthesis, amino sugar metabolism, androgen and estrogen metabolism, androstenedione metabolism, androstenedione metabolism, estrone metabolism, galactose metabolism, porphyrin metabolism, sphingolipid metabolism, etc.[1]


Supplementary

Abbreviation(s)

  • UDP

Chemical formula

  • C9H14N2O12P2

IUPAC name

  • [({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Synonyms

  • Uridine 5'-(trihydrogen diphosphate)
  • Uridine diphosphoric acid
  • Uridine pyrophosphate
  • Uridine 5'-pyrophosphorate
  • Uridine 5'-pyrophosphoric acid


Further reading

See also


Reference

  1. Human Metabolome Database: Showing metabocard for Uridine 5’-diphosphate (HMDB0000295). (2019). Retrieved from Hmdb.ca website: http://www.hmdb.ca/metabolites/HMDB0000295



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