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Uracil

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Definition

noun

plural: uracils

u·ra·cil, [ˈjʊərəsɪl]

(biochemistry) A pyrimidine nucleobase in RNA that complementary pairs with adenine, and has a chemical formula of C4H4N2O2



Details

Overview

Nucleic acids such as DNA and RNA are polymers of monomeric nucleotides. Each nucleotide is made up of phosphoric acid, sugar (5-carbon), and nitrogenous base (or nucleobase). There are five nucleobases that serve as fundamental units of the genetic code: (1) adenine, (2) guanine, (3) cytosine, (4) thymine, and (5) uracil. These nitrogenous bases may be classified into purines and pyrimidines. Uracil is a pyrimdine nucleobase.


Properties

Uracil is a pyrimidine nucleobase with a chemical formula of C4H4N2O2. Pyrimidine is a heterocyclic aromatic organic compound with a single ring (called a pyrimidine ring) with alternating carbon and nitrogen atoms. Uracil has a molar mass of 112.08676 g/mol and a melting point of 335 °C. It may occur as a component of a nucleoside (nucleobase + sugar deoxyribose or ribose) or of a nucleotide (nucleoside with phosphate groups). It is also one of the five primary (canonical) nucleobases in nucleic acids. It replaces thymine in RNA and does not normally occur in DNA. Both uracil and thymine complementary pairs with adenine.


Uracl vs. Thymine vs. Cytosine

Uracil, thymine, and cytosine are pyrimidine nucleobases. Uracil is similar to thymine in terms of structure except for the methyl group at position 5 in the heterocyclic aromatic ring that present in thymine. It has a chemical formula of C4H4N2O2. In complementary base pairing, uracil pairs with adenine by two hydrogen bonds.


Thymine has two keto groups at positions 2 and 4, and a methyl group at position 5 in its heterocyclic aromatic ring. Similar to uracil, thymine complementary base pairs with adenine by two hydrogen bonds. However, thymine is normally present only in the DNA molecule because uracil takes its place in RNA. 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.


Cytosine can be differed structurally from thymine and uracil by having a keto group at position 2 and an amine group at position 4 in its heterocyclic aromatic ring. It has a chemical formula of C4H5N3O. Cytosine occurs in both DNA and RNA. It pairs up with guanine.


Common biological reactions

Uracil biosynthesis

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. Eventually, uridine diphosphate (UDP) and uridine triphosphate (UTP) are produced down the biosynthetic pathway by kinases and dephosphorylation of ATPs. UTP can be converted into cytidine triphosphate (CTP) by amination of UTP via the enzyme CTP synthetase.[1]


Uracil nucleosides

Uracil that is attached to a deoxyribose (a pentose sugar) is referred to as uridine. When phosphorylated with three phosphoric acid groups, uridine becomes uridine triphosphate (UTP), which is one of the nucleotide monomeric units that build up RNA.


Uracil degradation and salvage

Uracil may be degraded as follows: uracil » β-alanine » » malonyl-CoA. The malonyl-CoA may be used in fatty acid synthesis. Otherwise, further degradation ends in the formation of ammonium, water, and CO2. The resulting ammonium may proceed to the urea cycle.


Uracil may be recycled by a salvage pathway. For instance, uracil can combine with ribose-1-phosphate by uridine phosphorylase to form UMP.


Biological functions

Uracil is one of the five primary (or canonical) nucleobases; the others are cytosine, thymine, guanine, and adenine. They are the fundamental nucleobases that make up the genetic code. Nucleic acids such as DNA and RNA molecules contain the genetic code for a particular protein based on the sequence of nucleobases. Nucleic acids hold an important role in cellular functions, heredity, and survival of an organism.


Uracil is also a constituent of nucleotides UMP, UDP, and UTP. The name of the nucleotides are based on the number of phosphate groups attached, i.e. one, two, or three, respectively. UDP plays an important role in glycogenesis. UDP forms from the combining of glucose-1-phosphate and UTP. The enzyme glycogen synthase forms glycogen chain by combining units of UDP-glucose. As UDP-glucose is added to the growing chain of glycogen, UDP is cleaved from the UDP-glucose. Thus, UDP helps convert glucose to glycogen especially in the liver and muscle cells. UTP, in turn, is essential as it is a direct precursor of RNA during transcription.


Supplementary

IUPAC name

  • Pyrimidine-2,4(1H,3H-dione

Chemical formula

  • C4H4N2O2

Abbreviation

  • U

Also called

  • 2-oxy-4-oxy pyrimidine
  • 2,4(1H,3H)-pyrimidinedione
  • 2,4-dihydroxypyrimidine
  • 2,4-pyrimidinediol


Further reading

See also


Reference

  1. Charma, K. & Somani, D. (2015). Pyrimidine Biosynthesis. Retrieved from Slideshare.net website: [Link]



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