Thymine

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Thymine
Thymin.svg
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Names
IUPAC name
5-Methylpyrimidine-2,4(1H,3H)-dione
Other names
5-methyluracil
Identifiers
3D model (JSmol)
ChEBI
ChEMBL
ChemSpider
ECHA InfoCard 100.000.560
MeSH Thymine
PubChem CID
UNII
Properties
C5H6N2O2
Molar mass 126.115 g·mol−1
Density 1.223 g cm−3 (calculated)
Melting point 316 to 317 °C (601 to 603 °F; 589 to 590 K)
Boiling point 335 °C (635 °F; 608 K)(decomposes)
Acidity (pKa)9.7
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
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Infobox references

Thymine /ˈθmɪn/ (T, Thy) is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. In RNA, thymine is replaced by the nucleobase uracil. Thymine was first isolated in 1893 by Albrecht Kossel and Albert Neumann from calves' thymus glands, hence its name. [1]

Contents

Derivation

As its alternate name (5-methyluracil) suggests, thymine may be derived by methylation of uracil at the 5th carbon. In RNA, thymine is replaced with uracil in most cases. In DNA, thymine (T) binds to adenine (A) via two hydrogen bonds, thereby stabilizing the nucleic acid structures.

Thymine combined with deoxyribose creates the nucleoside deoxythymidine, which is synonymous with the term thymidine. Thymidine can be phosphorylated with up to three phosphoric acid groups, producing dTMP (deoxythymidine monophosphate), dTDP, or dTTP (for the di- and tri- phosphates, respectively).

One of the common mutations of DNA involves two adjacent thymines or cytosine, which, in presence of ultraviolet light, may form thymine dimers, causing "kinks" in the DNA molecule that inhibit normal function.

Thymine could also be a target for actions of 5-fluorouracil (5-FU) in cancer treatment. 5-FU can be a metabolic analog of thymine (in DNA synthesis) or uracil (in RNA synthesis). Substitution of this analog inhibits DNA synthesis in actively dividing cells.

Thymine bases are frequently oxidized to hydantoins over time after the death of an organism. [2]

Theoretical aspects

In March 2015, NASA scientists reported that, for the first time, complex DNA and RNA organic compounds of life, including uracil, cytosine and thymine, have been formed in the laboratory under outer space conditions, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), the most carbon-rich chemical found in the Universe, may have been formed in red giants or in interstellar dust and gas clouds, according to the scientists. [3] Thymine has not been found in meteorites, which suggests the first strands of DNA had to look elsewhere to obtain this building block. Thymine likely formed within some meteorite parent bodies, however may not have persisted within these bodies due to an oxidation reaction with hydrogen peroxide. [4]

See also

Related Research Articles

Base pair Unit consisting of two nucleobases bound to each other by hydrogen bonds

A base pair (bp) is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson–Crick base pairs allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes.

Cytosine Chemical compound in nucleic acids

Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine. It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached. The nucleoside of cytosine is cytidine. In Watson-Crick base pairing, it forms three hydrogen bonds with guanine.

Guanine Chemical compound of DNA and RNA

Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine. In DNA, guanine is paired with cytosine. The guanine nucleoside is called guanosine.

Nucleic acid polymeric macromolecules

Nucleic acids are the biopolymers, or large biomolecules, essential to all known forms of life. The term nucleic acid is the overall name for DNA and RNA. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a compound ribose, the polymer is RNA ; if the sugar is derived from ribose as deoxyribose, the polymer is DNA.

Nucleotide biological molecules that form the building blocks of nucleic acids

Nucleotides are molecules consisting of a nucleoside and a phosphate group. They are the basic building blocks of DNA and RNA.

Pyrimidine is an aromatic heterocyclic organic compound similar to pyridine. One of the three diazines, it has the nitrogen atoms at positions 1 and 3 in the ring. The other diazines are pyrazine and pyridazine. In nucleic acids, three types of nucleobases are pyrimidine derivatives: cytosine (C), thymine (T), and uracil (U).

Adenine Chemical compound in DNA and RNA

Adenine is a nucleobase. It is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The three others are guanine, cytosine and thymine. Its derivatives have a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD). It also has functions in protein synthesis and as a chemical component of DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA.

Uracil Chemical compound of RNA

Uracil is one of the four nucleobases in the nucleic acid RNA that are represented by the letters A, G, C and U. The others are adenine (A), cytosine (C), and guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine. Uracil is a demethylated form of thymine.

Nucleobase nitrogen-containing biological compounds that form nucleosides

Nucleobases, also known as nitrogenous bases or often simply bases, are nitrogen-containing biological compounds that form nucleosides, which in turn are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).

Thymidine Chemical compound

Thymidine is a pyrimidine deoxynucleoside. Deoxythymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. In cell biology it is used to synchronize the cells in G1/early S phase.

Albrecht Kossel German biochemist and pioneer in the study of genetics

Ludwig Karl Martin Leonhard Albrecht Kossel was a German biochemist and pioneer in the study of genetics. He was awarded the Nobel Prize for Physiology or Medicine in 1910 for his work in determining the chemical composition of nucleic acids, the genetic substance of biological cells.

Ribonucleotide chemical compound

In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. The monomer itself from ribonucleotides forms the basic building blocks for RNA. However, the reduction of ribonucleotide, by enzyme ribonucleotide reductase (RNR), forms deoxyribonucleotide, which is the essential building block for DNA. There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides. Successive nucleotides are linked together via phosphodiester bonds by 3'-5'.

A nucleoside triphosphate is a molecule containing a nitrogenous base bound to a 5-carbon sugar, with three phosphate groups bound to the sugar. It is an example of a nucleotide. They are the building blocks of both DNA and RNA, which are chains of nucleotides made through the processes of DNA replication and transcription. Nucleoside triphosphates also serve as a source of energy for cellular reactions and are involved in signalling pathways.

A nitrogenous base, or nitrogen-containing base, is an organic molecule with a nitrogen atom that has the chemical properties of a base. The main biological function of a nitrogenous base is to bond nucleic acids together. A nitrogenous base owes its basic properties to the lone pair of electrons of a nitrogen atom.

Nucleic acid metabolism

Nucleic acid metabolism is the process by which nucleic acids are synthesized and degraded. Nucleic acids are polymers of nucleotides. Nucleotide synthesis is an anabolic mechanism generally involving the chemical reaction of phosphate, pentose sugar, and a nitrogenous base. Destruction of nucleic acid is a catabolic reaction. Additionally, parts of the nucleotides or nucleobases can be salvaged to recreate new nucleotides. Both synthesis and degradation reactions require enzymes to facilitate the event. Defects or deficiencies in these enzymes can lead to a variety of diseases.

Nucleic acid analogue compound which is analogous (structurally similar) to naturally occurring RNA and DNA, used in medicine and in molecular biology research

Nucleic acid analogues are compounds which are analogous to naturally occurring RNA and DNA, used in medicine and in molecular biology research. Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases. An analogue may have any of these altered. Typically the analogue nucleobases confer, among other things, different base pairing and base stacking properties. Examples include universal bases, which can pair with all four canonical bases, and phosphate-sugar backbone analogues such as PNA, which affect the properties of the chain . Nucleic acid analogues are also called Xeno Nucleic Acid and represent one of the main pillars of xenobiology, the design of new-to-nature forms of life based on alternative biochemistries.

Thymidine phosphorylase class of enzymes

Thymidine phosphorylase is an enzyme that is encoded by the TYMP gene and catalyzes the reaction:

Nucleic acid structure organization of DNA and RNA molecules at different scales

Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary.

Complementarity (molecular biology) describes a relationship between two structures each following the lock-and-key principle

In molecular biology, complementarity describes a relationship between two structures each following the lock-and-key principle. In nature complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the reverse of things. This complementary base pairing allows cells to copy information from one generation to another and even find and repair damage to the information stored in the sequences.

Non-canonical base pairing occurs when nucleobases hydrogen bond, or base pair, to one another in schemes other than the standard Watson-Crick base pairs. There are three main types of non-canonical base pairs: those stabilized by polar hydrogen bonds, those having interactions among C−H and O/N groups, and those that have hydrogen bonds between the bases themselves. The first discovered non-canonical base pairs are Hoogsteen base pairs, which were first described by American biochemist Karst Hoogsteen.

References

  1. Albrecht Kossel and Albert Neumann (1893) "Ueber das Thymin, ein Spaltungsproduct der Nucleïnsäure" (On thymine, a cleavage product of nucleic acid), Berichte der Deutschen Chemischen Gesellschaft zu Berlin, 26 : 2753-2756. From p. 2754: "Wir bezeichnen diese Substanz als Thymin." (We designate this substance as "thymine" [because it was initially obtained from the thymus glands of calves].)
  2. Hofreiter M., Serre D., Poinar H.N., Kuch M., and Paabo S. Nature Reviews Genetics (2001) 2:353.
  3. Marlaire, Ruth (3 March 2015). "NASA Ames Reproduces the Building Blocks of Life in Laboratory". NASA . Retrieved 5 March 2015.
  4. Tasker, Elizabeth. "Did the Seeds of Life Come from Space?". Scientific American Blog Network. Retrieved 2016-11-24.