The deoxyribose or D-2-deoxyribose It is a five-carbon sugar that makes up the nucleotides of deoxyribonucleic acid (DNA). This sugar works as a base for the union of the phosphate group and the nitrogenous base that make up the nucleotides.
Carbohydrates in general are essential molecules for living beings, they fulfill different essential functions, not only as molecules from which energy can be extracted for cells, but also to structure the DNA chains through which genetic information is transmitted.
All sugars or carbohydrates have the general formula CnH2nOn, in the case of deoxyribose its chemical formula is C5H10O4.
Deoxyribose is the sugar that structures DNA and it only differs from ribose (the sugar that makes up RNA) in that it has a hydrogen atom (-H) at carbon 3, while ribose has a hydroxyl functional group (- OH) in the same position.
Due to this structural similarity, ribose is the most important starting substrate for the cellular synthesis of deoxyribose sugars..
An average cell has an amount of RNA almost 10 times higher than DNA, and the fraction of RNA that is recycled, diverting itself towards the formation of deoxyribose has an important contribution to the survival of cells.
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Deoxyribose is a monosaccharide made up of five carbon atoms. It has an aldehyde group, therefore, it is classified within the group of aldopentoses (aldo, for aldehyde and pento for the five carbons).
By breaking down the chemical composition of deoxyribose we can say that:
This is composed of five carbon atoms, the aldehyde group is found on the carbon at position 1, on the carbon at position 2 it has two hydrogen atoms and on the carbon at position 3 it has two different substituents, namely: a hydroxyl group (-OH) and a hydrogen atom.
Carbon in position 4, as well as that in position 3, has an OH group and a hydrogen atom. It is through the oxygen atom of the hydroxyl group in this position that the molecule can acquire its cyclic conformation, since it binds to the carbon in position 1.
The fifth carbon atom is saturated with two hydrogen atoms and is located at the terminal end of the molecule, outside the ring.
In the aldehyde group of carbon atom 1 is where the nitrogenous bases are united that, together with the sugar, form the nucleosides (nucleotides without the phosphate group). In the oxygen attached to the carbon atom 5 is where the phosphate group that makes up the nucleotides joins.
In a DNA helix or strand, the phosphate group attached to carbon 5 of a nucleotide is the one that binds to the OH group of carbon at position 3 of another deoxyribose belonging to another nucleotide, and so on.
Among the five carbon atoms that make up the deoxyribose backbone are three carbons that have four different substituents on each side. Carbon in position 2 is asymmetric with respect to these, since it is not attached to any OH group.
Therefore, and according to this carbon atom, deoxyribose can be achieved in two "isoforms" or "optical isomers" which are known as L-deoxyribose and D-deoxyribose. Both forms can be defined from the carbonyl group at the top of the Fisher structure.
All deoxyribose are designated as "D-deoxyribose" in which the -OH group attached to carbon 2 is disposed to the right, while the "L-deoxyribose" forms have the -OH group to the left..
The “D” form of sugars, including deoxyribose, is the predominant one in the metabolism of organisms.
Deoxyribose is a sugar that functions as the building block of many important macromolecules such as DNA and high-energy nucleotides such as ATP, ADP, AMP, GTP, among others..
The difference between the cyclic structure of deoxyribose and ribose makes the former a much more stable molecule.
The absence of the oxygen atom at carbon 2 makes deoxyribose a less prone sugar to reduction, especially compared to ribose. This is of great importance, as it provides stability to the molecules of which it is part..
Deoxyribose, like ribose, can be synthesized in the body of an animal by routes that involve the breakdown of other carbohydrates (usually hexoses such as glucose) or by the condensation of smaller carbohydrates (trioses and other two-carbon compounds , for example).
In the first case, that is, the obtaining of deoxyribose from the degradation of "higher" carbohydrate compounds, this is possible thanks to the metabolic capacity of the cells to carry out the direct conversion of ribulose 5-phosphate obtained by the pathway of pentose phosphate in ribose 5-phosphate.
Ribose 5-phosphate can be further reduced to deoxyribose 5-phosphate, which can be used directly for the synthesis of energetic nucleotides.
The obtaining of ribose and deoxyribose from the condensation of smaller sugars has been demonstrated in bacterial extracts, where the formation of deoxyribose in the presence of glyceraldehyde phosphate and acetaldehyde has been verified..
Similar evidence has been obtained in studies using animal tissues, but incubating fructose-1-6-bisphosphate and acetaldehyde in the presence of iodoacetic acid..
Although small fractions of the carbon atoms destined for the nucleotide biosynthesis pathways are directed towards the biosynthesis of deoxynucleotides (the nucleotides of DNA that have deoxyribose as sugar), most of these are directed mainly towards the formation of ribonucleotides.
Consequently, deoxyribose is synthesized mainly from its oxidized derivative, ribose, and this is possible inside the cell thanks to the great difference in abundance between DNA and RNA, which is the main source of ribonucleotides (an important source of ribose sugar).
Thus, the first step in the synthesis of deoxynucleotides from ribonucleotides consists of the formation of deoxyribose from the ribose that makes up these nucleotides..
To do this, ribose is reduced, that is, the OH group at carbon 2 of ribose is removed and exchanged for a hydride ion (a hydrogen atom), preserving the same configuration..
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