8 julio, 2024

Thymine: what it is, chemical structure, functions

What is thymine?

The thymine It is an organic compound consisting of a heterocyclic ring derived from that of pyrimidine, a benzene ring with two carbon atoms substituted by two nitrogen atoms. Its condensed formula is C5H6N2O2, being a cyclic amide and one of the nitrogenous bases that make up DNA.

Specifically, thymine is a pyrimidine nitrogenous base, along with cytosine and uracil. The difference between thymine and uracil is that the former is present in the DNA structure while the latter is in the RNA structure.

Deoxyribonucleic acid (DNA) is made up of two helices or bands wound around each other. The outside of the bands is formed by a chain of deoxyribose sugar, whose molecules are linked through a phosphodiester bond between the 3′ and 5′ positions of neighboring deoxyribose molecules.

One of the nitrogenous bases: adenine, guanine, cytosine, and thymine, binds to the 1′ position of deoxyribose. The adenine purine base of one helix couples or binds to the thymine pyrimidine base of the other helix through two hydrogen bonds.

chemical structure

The upper image represents the chemical structure of thymine, in which two carbonyl groups (C=O) and the two nitrogen atoms that complete the heterocyclic amide can be seen, and in the upper left corner is the methyl group ( –CH3).

The ring derives from that of pyrimidine (pyrimidine ring), it is flat but not aromatic. The respective number of atoms in the thymine molecule is assigned starting with the bottom nitrogen.

Thus, C-5 is linked to the –CH3 group, C-6 is the left adjacent carbon atom of N-1, and C-4 and C-2 correspond to carbonyl groups.

What is this numbering for? The thymine molecule has two hydrogen bond accepting groups, C-4 and C-2, and two hydrogen bond donor atoms, N-1 and N-3.

Accordingly, carbonyl groups can accept C=O—H- type bonds, while nitrogens provide NH—X type bonds, where X is equal to O, N, or F.

Thanks to the groups of C-4 and N-3 atoms, thymine pairs with adenine forming a pair of nitrogenous bases, which is one of the determining factors in the perfect and harmonious structure of DNA:

Thymine tautomers

The top image lists the six possible tautomers of thymine. What are they? They consist of the same chemical structure but with different relative positions of their atoms; specifically, of the H bonded to the two nitrogens.

Maintaining the same numbering of the atoms, from the first to the second it is observed how the H of the N-3 atom migrates to the oxygen of C-2.

The third also derives from the first, but this time the H migrates to the oxygen of C-3. The second and the fourth are similar but not equivalent, because in the fourth the H comes out of N-1 and not N-3.

On the other hand, the sixth is similar to the third, and as occurs with the pair formed by the fourth and the second, the H migrates from N-1 and not from N-3.

Finally, the fifth is the pure enolic form (lactima), in which both carbonyl groups are hydrogenated into hydroxyl groups (–OH); this is contrary to the first, the pure ketone form and the one that predominates in physiological conditions.

Because? Probably due to the great energetic stability that it acquires when pairing with adenine by hydrogen bonds and belonging to the DNA structure.

Otherwise, the enolic form number 5 should be more abundant and stable, due to its marked aromatic character, unlike the other tautomers.

thymine functions

The main function of thymine is the same as that of the other nitrogenous bases in DNA: to participate in the necessary coding in DNA for the synthesis of polypeptides and proteins.

One of the DNA helices serves as a template for the synthesis of an mRNA molecule in a process known as transcription and catalyzed by the enzyme RNA polymerase. In the transcription, the DNA bands are separated, as well as their unwinding.

Transcription

Transcription begins when RNA polymerase binds to a region of DNA known as the promoter, initiating mRNA synthesis.

Subsequently, RNA polymerase moves along the DNA molecule, producing an elongation of the nascent mRNA until it reaches a region of DNA with the information for the termination of transcription.

There is an anti-parallelism in the transcription: while the reading of the template DNA is done in the 3′ to 5′ orientation, the synthesized mRNA has the 5′ to 3′ orientation.

During transcription there is complementary base coupling between the template DNA strand and the mRNA molecule. Once transcription is complete, the DNA strands and their original coil are reunited.

mRNA is moved from the cell nucleus to the rough endoplasmic reticulum to initiate protein synthesis in the process known as translation. In this, thymine does not intervene directly, since the mRNA lacks it, taking instead the pyrimidine uracil base.

Genetic code

Indirectly, thymine does intervene, since the sequence of mRNA bases is a reflection of that of nuclear DNA.

The sequence of bases can be grouped into triplets of bases known as codons. The codons have the information for the incorporation of the different amino acids to the protein chain being synthesized; this constitutes the genetic code.

The genetic code is made up of 64 base triplets constituting the codons; there is at least one codon for each of the amino acids in proteins. Likewise, there are initiation codons (AUG) of translation and codons for its termination (UAA, UAG).

In summary, thymine plays a determining role in the process that concludes with protein synthesis.

health implications

Thymine is the target for the action of 5-fluorouracil, a structural analogue of this compound. The drug used in the treatment of cancer is incorporated instead of thymine into cancer cells, blocking their proliferation.

Ultraviolet light acts on the regions of the DNA bands that contain thymine at neighboring sites, forming thymine dimers. These dimers create «knots» that block the functioning of the nucleic acid.

Initially it is not a problem due to the existence of repair mechanisms, but if these fail they can cause serious disorders. This seems to be the case with xeroderma pigmentosa, a rare autosomal recessive disease.

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