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 monophosphate (UMP) is a pyrimidine nucleotide composed of uracil, ribose and a phosphate group, with a chemical formula: C9H13N2O9P
Uridine monophosphate (UMP) is a nucleoside phosphate in being comprised of a ribonucleoside and one phosphate group. This means that it has a ribose as its sugar constituent with one phosphate group 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. Its conjugate base form is uridylate, a nucleotide used as a monomer in RNA. RNA does not have thymine but instead is replaced by another pyrimdine, uracil. DNA, in turn, does not have uracil. Rather, it has thymine in place of the uracil. Both thymine and uracil complementary pairs with adenine.
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
Common biological reactions
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. In humans, the UMP synthase, a bifunctional enzyme that contains the activities of both orotate phosphoribosyltransferase and orotidine-5′-monophosphate decarboxylase, and a deficiency of this enzyme leads to orotic aciduria.
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.
Common biological reactions
Uridylylation (also called uridylation) is the process of attaching UMP by a covalent bond to a biomolecule, e.g. adenylyltransferase protein.
UMP is one of the monomer nucleotides in RNA, particularly when it is phosphorylated with one more phosphate group, thus producing UDP (uridine diphosphate), or with two more phosphate groups to form UTP (uridine triphosphate). UTP complementary base pairs with adenosine triphosphate (ATP).
UMP also serves as a precursor for the biosynthesis of other pyrimidine nucleotides. Apart from pyrimidine biosynthesis, UMP is also a metabolite of biological processes such as transcription/translation and lactose synthesis.1
- (2R,3S,4R,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-ylmethyl dihydrogen phosphate
- Human Metabolome Database: Showing metabocard for Uridine 5’-monophosphate (HMDB0000288). (2019). Retrieved from Hmdb.ca website: http://www.hmdb.ca/metabolites/HMDB0000288
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