Deoxyribose

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Deoxyribose

Deoxyribose, also known as D-Deoxyribose and 2-deoxyribose, is a pentose sugar (monosaccharide containing five carbon atoms) that is a key component of the nucleic acid deoxyribonucleic acid (DNA). It is derived from the pentose sugar ribose. Deoxyribose has the chemical formula C5H10O4.

Deoxyribose is the sugar component of DNA, just as ribose serves that role in RNA (ribonucleic acid). Alternating with phosphate bases, deoxyribose forms the backbone of the DNA, binding to the nitrogenous bases adenine, thymine, guanine, and cytosine. In RNA, uracil is the base rather than thymine.

As a component of DNA, which represents the genetic information in all living cells, deoxyribose is critical to life. This ubiquitous sugar reflects a commonality among all living organisms.

Contents

Structure

Ribose in acyclic form. The hydroxyl group at the 2 position is replaced with hydrogen in forming deoxyribose.
A conventional skeletal formula of ribose.

Deoxyribose is an aldopentose, which means a pentose sugar with an aldehyde functional group in position 1. An aldehyde group consists of a carbon atom that is bonded to a hydrogen atom and double-bonded to an oxygen atom (chemical formula O=CH-).

Deoxyribose is derived from ribose. Ribose forms a five-member ring composed of four carbon atoms and one oxygen atom. Hydroxyl (-OH) groups are attached to three of the carbons. The fourth carbon in the ring (one of the carbon atoms adjacent to the oxygen) is attached to the fifth carbon atom and a hydroxyl group. Deoxyribose is formed by the replacement of the hydroxyl group at the 2 position (the carbon furthest from the attached carbon) with hydrogen, leading to the net loss of an oxygen atom. Ribose has the chemical formula C5H10O5. Thus, deoxyribose has the chemical formula C5H10O4.

Due to the common C3 and C4 stereochemistry of D-ribose and D-arabinose, D-2-deoxyribose is also D-2-deoxyarabinose.

Deoxyribofuranose is an alternative name for the ring structure of deoxyribose. This alternative name merely refers to the fact that deoxyribose has a five membered ring consisting of four carbons and an oxygen and is more a structural description than a name.

Deoxyribose was discovered in 1929 by Phoebus Levene, who also discovered DNA that year, and found that DNA contained adenine, guanine, thymine, cytosine, deoxyribose, and a phosphate group. Levene had discovered ribose in 1909.

Biological Importance of Deoxyribose

Deoxyribose and ribose derivatives have an important role in biology. Among the most important derivatives are those with phosphate groups attached at the 5 position. Mono-, di-, and triphosphate forms are important, as well as 3-5 cyclic monophosphates. There also are diphosphate dimers called coenzymes that purines and pyrimidines form an important class of compounds with deoxyribose and ribose.

Chemical structure of adenosine, a nucleoside.
Chemical structure of deoxyadenosine, a nucleoside.
Chemical structure of adenosine monophosphate, a nucleotide.

Nucleosides are structural subunits of nucleic acids, the macromolecules that convey genetic information in living cells. Nucleosides consist of a nitrogen-containing base bonded to a five-carbon (pentose) sugar. The sugar component is either deoxyribose or ribose. (“Deoxy” simply indicates that the sugar lacks an oxygen atom present in ribose, the parent compound.)

The nitrogen-containing base is typically a derivative of either purine or pyrimidine. The most common bases in nucleosides are:

One of the common bases is adenine (a purine derivative); coupled to ribose it is called adenosine; coupled to deoxyribose it is called deoxyadenosine.

A nucleotide is a chemical compound with three components: a nitrogen-containing base, a pentose (five-carbon) sugar (relatively simple carbohydrates), and one or more phosphate groups. Depending on their base sugar, nucleotides are therefore known as “deoxyribonucleotides” or “ribonucleotides.” Adenosine triphosphate, known as ATP, is the energy currency in the cell.

The nucleic acid DNA (which stands for deoxyribonucleic acid) is built of nucleotides with a deoxyribose sugar, whereas RNA (or ribonucleic acid) contains nucleotides composed of ribose sugars. As noted above, adenine, guanine, cytosine, and thymine are the purines and pyrmidines used in forming DNA, and uracil replaces thymine in RNA.

DNA in chromosomes forms very long helical structures containing two molecules with the backbones running in opposite directions on the outside of the helix and held together by hydrogen bonds between complementary nucleotide bases lying between the helical backbones. The lack of the 2′ hydroxyl group in DNA appears to allow the backbone the flexibility to assume the full conformation of the long double-helix, which involves not only the basic helix, but additional coiling necessary to fit these very long molecules into the very small volume of a cell nucleus.

2-Deoxyribose and ribose nucleotides are often found in unbranched 5′-3′polymers. (The convention is to put a ′, pronounced "prime," after the carbon numbers of the sugar, so that in nucleoside derivatives a name might include, for instance, the term "5′-monophosphate," meaning that the phosphate group is attached to the fifth carbon of the sugar, and not to the base.) In these 5′-3′ structures, the 3′carbon of one monomer unit is linked to a phosphate that is attached to the 5′ carbon of the next unit, and so on. These polymer chains often contain many millions of monomer units. Since long polymers have physical properties distinctly different from those of small molecules, they are called macromolecules. The sugar-phosphate-sugar chain is called the backbone of the polymer. One end of the backbone has a free 5′ phosphate, and the other end has a free 3′ OH group. The backbone structure is independent of which particular bases are attached to the individual sugars.

References

  • Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., and Watson, J.D. Molecular Biology of the Cell. New York: Garland Publishing. 1989. ISBN 0824036956
  • Doonan, S. Nucleic Acids. Great Britain: Royal Society of Chemistry. 2004. ISBN 0854044817
  • Stryer, L. Biochemistry. New York: W.H. Freeman. 1988. ISBN 071671843X

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