DEOXYRIBOSE: STRUCTURE, FUNCTIONS AND BIOSYNTHESIS - CHEMISTRY - 2025

The deoxyribose or D-2-deoxyribose is a five - carbon sugar that comprises nucleotides 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.

Chemical structure of deoxyribose (Source: Edgar181 via Wikimedia Commons)

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 only differs from ribose (the sugar that makes up RNA) in that it has a hydrogen atom (-H) at carbon 3, meanwhile 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 greater than that of DNA, and the fraction of RNA that is recycled, being diverted towards the formation of deoxyribose has an important contribution to the survival of cells.

Structure

Deoxyribose is a monosaccharide composed 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:

It is made up 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, as 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.

It is in the aldehyde group of carbon 1 that the nitrogenous bases are joined, together with the sugar, they form the nucleosides (nucleotides without the phosphate group). The oxygen attached to the carbon 5 atom is where the phosphate group that makes up the nucleotides is attached.

In a DNA helix or strand, the phosphate group attached to carbon 5 of a nucleotide is the one that attaches to the OH group of carbon at position 3 of another deoxyribose belonging to another nucleotide, and so on.

Optical isomers

Among the five carbon atoms that make up the main backbone of deoxyribose are three carbons that have four different substituents on each side. The 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 obtained 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" where 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.

Features

Deoxyribose is a sugar that functions as a building block for many important macromolecules such as DNA and high-energy nucleotides such as ATP, ADP, AMP, and GTP, among others.

The difference that the cyclic structure of deoxyribose presents with respect to 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 very important, as it provides stability to the molecules of which it is a part.

Biosynthesis

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 via of pentose phosphate into ribose 5-phosphate.

Structural comparison between ribose and deoxyribose (Source: Genomics Education Program via Wikimedia Commons)

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 has been verified in the presence of glyceraldehyde phosphate and acetaldehyde.

Similar evidence has been obtained in studies using animal tissues, but incubating fructose-1-6-bisphosphate and acetaldehyde in the presence of iodoacetic acid.

Conversion of ribonucleotides to deoxyribonucleotides

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 within 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.

For this, ribose is reduced, that is, the OH group at carbon 2 of the ribose is removed and exchanged for a hydride ion (a hydrogen atom), keeping the same configuration.

References

1. Bernstein, IA, & Sweet, D. (1958). Biosynthesis of deoxyribose in intact Escherichia coli. Journal of Biological Chemistry, 233 (5), 1194-1198.
2. Griffiths, AJ, Wessler, SR, Lewontin, RC, Gelbart, WM, Suzuki, DT, & Miller, JH (2005). An introduction to genetic analysis. Macmillan.
3. Mathews, CK, Van Holde, KE, & Ahern, KG (2000). Biochemistry. 2000. San Francisco: Benjamin Cummings.
4. McGEOWN, MG, & Malpress, FH (1952). Synthesis of deoxyribose in animal tissues. Nature, 170 (4327), 575-576.
5. Watson, JD, & Crick, F. (1953). A structure for deoxyribose nucleic acid.