Uracil

uracil is a pyrimidine, one of the four nitrogenous bases that make up RNA and is represented in the genetic code by the letter U. Its molecular formula is C₄H₄N₂O₂. Uracil replaces RNA in RNA. Thymine is one of the four nitrogenous bases that make up DNA. Like thymine, uracil always pairs with adenine via two hydrogen bonds, but it is missing the methyl group. It forms the uridine nucleoside (Urd) and the uridylate nucleotide (UMP). Uracil was originally discovered in the early 1900s. It was isolated by hydrolysis of yeast ribonucleic acid found in certain bovine organs: thymus and spleen, as well as herring sperm and wheat germ. Uracil is a molecule with a planar structure, unsaturated and that has the ability to absorb substances.

Properties

It is found in RNA, forming a base pair with adenine and being replaced by thymine in DNA. Uracil methylation produces thymine, which, being more stable, protects DNA and improves its replication efficiency. Uracil can form a base pair with either base depending on how the molecule is arranged in the double helix, but it forms a base pair more quickly with adenine due to its methyl group being repelled from a fixed position. Uracil pairs with adenosine through hydrogen bonding. Uracil is a hydrogen bond acceptor and can form two hydrogen bonds per molecule. Uracil can also bind to the hydrocarbon backbone sugar, ribose, to form a ribonucleoside, uridine. When a phosphate binds to uridine, uridine 5'-monophosphate is generated.

Tautomeric variants of uracil.

Tautomerism

Uracil (U) has a tautomeric variant in the form of amide-iminol that is produced thanks to its resonant structure in the nitrogen and oxygen substituents. Due to the instability of the molecule, it exhibits some property of aromaticity that is partly compensated by the stability of the cyclo-amide. The keto tautomer is usually the lactam structure, while the tautomer enol is referred to as the lactima structure. These tautomeric forms are predominant in an environment with a pH equal to 7. The lactam structure is the most common form of uracil.

Uracil recycles itself to form nucleotides by carrying out a series of phosphoribosyltransferase-type reactions. Uracil degradation produces substrates, aspartate, carbon dioxide, and ammonia.

Differences between uridine and pseudouridine structures

C₄H₄N₂O₂ → H₃NCH₂CH₂COO^- + NH₄ + CO₂

Pseudouracil

Pseudouracil does not really exist as a separate chemical entity, as it is chemically identical to uracil, but in some unusual nucleosides and nucleotides it binds to sugar through carbon 5 rather than nitrogen 1, in this situation it forms nucleosides commonly called pseudouridines and nucleotides commonly called pseudourilates.

Summary

There are many ways to make uracil in the laboratory. The first reaction described is the simplest of all, adding water to cytosine to produce uracil and ammonia. The most common way to produce uracil is by condensing maleic acid with urea in fuming sulfuric acid, as described you can see below. Uracil can be synthesized by a double decomposition of thiouracil to chloracetic acid in aqueous medium.

C₄H₅N₃O + H₂O → C₄H₄N₂O₂ + NH₃

C₄H₄O₄ + CH₄N₂O → C₄H₄N₂O₂ + 2 H₂O + CO

Photodehydrogenation of 5,6-diuracil, which causes it to be synthesized as beta-alanine, reacts with urea, producing uracil.