deoxyribose

D-Deoxyribose
IUPAC name	2-Deoxy-D-ribose
Other names	2-Deoxy-D-erythro-pentose Thyminose
Identifiers
CAS number	533-67-5 Y
PubChem	5460005
EC-number	208-573-0
SMILES	O=CC[C@H](O)[C@H](O)CO
InChI	1/C5H10O4/c6-2-1-4(8)5(9)3-7/h2,4-5,7-9H,1,3H2/t4-,5+/m0/s1
InChI key	ASJSAQIRZKANQN-CRCLSJGQBK
ChemSpider ID	4573703
Properties[1]
Molecular formula	C5H10O4
Molar mass	134.13 g/mol
Appearance	White solid
Melting point	91 °C, 364 K, 196 °F
Solubility in water	Very soluble
Y (what is this?)  (verify) Except where noted otherwise, data are given for materials in their standard state (at 25 °C, 100 kPa)
Infobox references

Deoxyribose, also known as D-Deoxyribose and 2-deoxyribose, is an aldopentose — a monosaccharide containing five carbon atoms, and including an aldehyde functional group in its linear structure. It is a deoxy sugar derived from the pentose sugar ribose by the replacement of the hydroxyl group at the 2 position with hydrogen, leading to the net loss of an oxygen atom. Replacement of the hydroxyl group also shifts the conformation of the ring from C3'-endo to C2'-endo. It was discovered in 1929 by Phoebus Levene and is an important part of the nucleic acid DNA.

Structure

Ribose forms a five-member ring composed of four carbon atoms and one oxygen. Hydroxyl groups are attached to three of the carbons. The other carbon and a hydroxyl group are attached to one of the carbon atoms adjacent to the oxygen. In deoxyribose, the carbon furthest from the attached carbon is stripped of the oxygen atom in what would be a hydroxyl group in ribose. Due to the common C3' and C4' stereochemistry of D-ribose and D-arabinose, D-2-deoxyribose is also D-2-deoxyarabinose.

In water, deoxyribose exists in three forms: as a straight-chain sugar, in the deoxyribofuranose five-membered ring and in the deoxyribopyranose six-membered ring.

Chemical equilibrium

Biological importance

Ribose and 2-deoxyribose 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 are also important diphosphate dimers called coenzymes that purines and pyrimidines form an important class of compounds with ribose and deoxyribose. When these purine and pyrimidine derivatives are coupled to a ribose sugar, they are called nucleosides. In these compounds, 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. The bases are attached to the 1′ ribose carbon in the common nucleosides. Phosphorylated nucleosides are called nucleotides. See Nucleic acid nomenclature for a diagram showing the numbered positions in a 5′-monophosphate nucleotide.

2-Deoxyribose and ribose nucleotides are often found in unbranched 5′-3′ polymers. In these 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.

In the nucleic acid DNA (deoxyribonucleic acid) each monomer is one of the nucleotides deoxy- adenine, thymine, guanine or cytosine. 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.

In contrast, very similar molecules, containing ribose instead of deoxyribose, and known generically as RNA, are known to form only relatively short double-helical complementary base paired structures. These are well known, for instance, in ribosomal RNA molecules and in transfer RNA (tRNA), where so-called hairpin structures from palindromic sequences within one molecule.

See also

• Arabinose
• Lyxose
• Ribose
• Ribulose
• Xylose
• Xylulose

References

1. ^ The Merck Index: An Encyclopedia of Chemicals, Drugs, and Biologicals (11th ed.), Merck, 1989, ISBN 091191028X , 2890.