Uracil( C4H4N2O2) is one of four nitrogenous bases in the nucleic acid of RNA that are represented by the letters A, G, C and U. The others are adenine, cytosine, and guanine. A nucleotide is made up of a five carbon sugar, pentose sugar, with a phosphate group and base attached. Nucleotides are the building blocks for two important nucleic acids – deoxyribonucleic acid, DNA, and ribonucleic acid.
Within the cell, the bases are paired to make DNA molecules and also during certain processes, such as DNA replication and protein synthesis. Pairing of the bases is very specific and each base only pairs with one other. Adenine pairs with thymine or uracil and cytosine pairs with guanine. The complementary base pairs are always made up of a purine base and pyrimidine base to ensure the distance between the paired strands is uniform and stable.
When DNA is synthesised, the DNA polymerase enzymes (which catalyse the synthesis) cannot discriminate between thymine and uracil. They only check whether the hydrogen bonds form correctly, i.e. whether the base pairs are matched properly. To these enzymes, it does not matter whether thymine or uracil binds to adenine. Normally, the amounts of deoxyuridine triphosphate (dUTP) in the cell are kept very low compared to levels of deoxythymidine triphosphate (dTTP), preventing its incorporation during DNA synthesis.
Although most cells use the acid for RNA and thymine for DNA, there are exceptions. Some organisms have uracil instead of thymine in all their DNA, and other organisms have it in only some of their DNA. What could be the evolutionary advantage of that?
Two species of phage (viruses that infect bacteria) are known to have DNA genomes with only uracil and no thymine. We do not yet know whether these phages are representatives of an ancient life form that never evolved thymine DNA, or whether their uracil-substituted genomes are a newly evolved strategy. Nor do we know why these phages use it instead of thymine, but it may play an essential role in the life cycle of these viruses. If that is the case, it would make sense for the viruses to ensure that the acid in their DNA is not
replaced with thymine. And one of these phages has in fact been shown to have a gene that encodes a specific protein to inhibit the host’s glycosylase, thus preventing the
viral genome from having its uracil “repaired” by the host enzymes.
The structure of uracil(CAS number 66-22-8) and thymine differs very slightly also. The only difference is that the former lacks a methyl group, a carbon atom with three hydrogen atoms attached, which thymine has. This slight difference is enough to allow enzymes to distinguish between DNA and RNA molecules. Enzymes have a very specific shape at the active site where they attach to other molecules. The methyl group gives thymine a different shape to uracil, which ensures the correct enzymes interact with the correct molecules.
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