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Thymine

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Definition

noun

plural: thymines

thy·mine, [ˈθaɪmɪn]


(biochemistry) A pyrimidine nucleobase in the DNA molecule that complementary pairs with adenine, and has a chemical formula of C5H6N2O2

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. Thymine is a pyrimdine nucleobase.


Properties

Thymine is a pyrimidine nucleobase with a chemical formula of C5H6N2O2. Pyrimidine is a heterocyclic aromatic organic compound with a single ring (called a pyrimidine ring) with alternating carbon and nitrogen atoms. Thymine has a molar mass of 126.115 g/mol and a melting point of 316 to 317 °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 one of the five primary (canonical) nucleobases in nucleic acids. In RNA though, thymine is replaced by uracil. Both thymine and uracil complementary pairs with adenine.



Thymine vs. Uracil vs. Cytosine

Thymine, cytosine, and uracil are pyrimidine nucleobases. Thymine has two keto groups at positions 2 and 4, and a methyl group at position 5 in its heterocyclic aromatic ring. Thymine complementary base pairs with adenine by two hydrogen bonds. However, unlike cytosine that is present in both DNA and RNA, thymine is 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 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 complementary pairs with guanine in both DNA and RNA as opposed to thymine and uracil that pairs up with adenine in DNA and RNA, respectively.


Common biological reactions

Thymine biosynthesis

Thymine, 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.[1] 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.


Thymine nucleosides

Thymine that is attached to a deoxyribose (a pentose sugar) is referred to as deoxythymidine (or thymidine). When phosphorylated with three phosphoric acid groups, the deoxythymidine becomes deoxythymidine triphosphate (dTTP), which is one of the nucleotide monomeric units that build up DNA.


Thymine degradation and salvage

Thymine may be degraded as follows: thymine » β-aminoisobutyrate » » Citric acid cycle. Thymine may be recycled by a salvage pathway. In brief, thymine is converted into thymidine by reacting with deoxyribose-1-phosphate and by the enzyme thymidine phosphorylase. Thymidine is then converted into thymidine monophosphate by the enzyme nucleoside kinase.


Mutation

Mutation is a change in the nucleotide sequence of a gene or a chromosome. Mutations in the DNA often involve two adjacent thymines. In the presence of UV light, thymine dimers form. This causes kinks in the DNA molecule. As a result, the normal function of the affected DNA may be hindered. When mutation occurs, repair mechanisms rectify the DNA sequence. One of the ways to correct a mutation involving only a single strand of the DNA is base excision repair. This repair mechanism works by removing the damaged region and then replacing it using the other strand (i.e. the complementary strand) as the template.


Biological functions

Thymine is one of the five primary (or canonical) nucleobases; the others are cytosine, uracil, 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.


Trivia

The isolation and naming of the five nucleobases, including cytosine, is attributed to Albrecht Kossel (a German biochemist). From 1885 to 1901 he and his students discovered them through chemical analyses of the nucleic acids.[2]


Supplementary

Etymology

  • thymic +‎ -ine

IUPAC name

  • 5-Methylpyrimidine-2,4(1H,3H)-dione

Chemical formula

  • C5H6N2O2

Abbreviation

  • T
  • Thy

Also called

  • 5-methyluracil

Derived term(s)


Further reading

See also


Reference

  1. Charma, K. & Somani, D. (2015). Pyrimidine Biosynthesis. Retrieved from Slideshare.net website: [Link]
  2. The Editors of Encyclopedia Britannica. (2018). Albrecht Kossel | German biochemist. In Encyclopædia Britannica. Retrieved from https://www.britannica.com/biography/Albrecht-Kossel



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