Structural Biochemistry/Nucleic Acid/Sugars/Deoxyribose Sugar

Deoxyribose Sugar

Typically, deoxyribonucleic acid is depicted as the nucleic acid that serves as the template for the development of an organism or a double helix. DNA, unlike RNA, lacks a hydroxyl (-OH) group at the 2' carbon. Since there is no hydroxyl group, DNA can only form phosphodiester linkages with other nucleic acids at the 3' carbon to the 5' carbon of another nucleic acid.

Due to the lack of the hydroxyl group, DNA is more resistant to hydrolysis than RNA is. The lack of the partially negative hydroxyl group also favors DNA over RNA in stability. There is always a negative charge associated with the phosphodiester bridges that join two nucleotides which will repel the hydroxyl group in RNA, making it less stable than DNA.

The structure of ribose in RNA

The structure of deoxyribose in DNA

Deoxyribose is an aldopentose, meaning that it is a monosaccharide which contains five carbon atoms, and also contains an aldehyde functional group in its linear structure. Essentially, the deoxy sugar is just a pentose sugar ribose, with the hydroxyl group at position 2 replaced with a hydrogen instead. Another name for the deoxyribose is deoxyribofuranose, which is derived from the fact that it is a five membered ring with four carbon atoms and one oxygen atom.

Biological Importance of Deoxyribose

2-deoxyribose, as well as ribose, derivatives are important in biological processes. The most important of these derivatives involve a phosphate group attached at the 5-position of the ring. The mono-, di-, and triphosophate phosphates hold great imperance, as does the 3-5 cyclic monophosphate form purines and pyrimidines form an important class of compounds with ribose and deoxyribose through the formation of diphosphate dimers called coenzymes. Nucleosides are formed when purines and pyrimidines are coupled with a ribose sugar. Common nucleosides typically have a phosphate group attached at the 5-carbon and a base attached at the 1-carbon. Phosphorylated nucleosides are called nucleotides.

Nitrogenous bases can be added or react with the hemiacetal of the deoxyribose. Common bases added on are adenine and guanine (purine derivatives), and thymine, uracil, and cytosine (pyrimidine derivatives). When adenine is coupled with ribose, it is referred to as adenosine and when it is coupled with deoxyribose, it is referred to as deoxyadenosine. The 5'-triphosphate derivative of adenosine, also known as adenosine triphosphate (ATP), is vital for the transportation of energy molecules in the cell.

2-deoxyribose and ribose nucleotides are usually found as an unbranched 5'-3' polymer. The 3'-carbon of one monomer is attached to the 5'-carbon of another monomer, which is then attached to the 3'-carbon of another monomer, and can continue on for many millions of monomer units. These long polymer chains contain very different physical properties than those of small molecules, and so these polymers make up another division known as macromolecules. The backbone of the polymer is the sugar-phosphate-sugar chain that is created by the 3'-5'-3'-carbon bonds, which is independent of which base is attached to the sugars.

Chromosomes also contain the polymer chain of the 5'-3' of 2'-deoxyribose nucleotides. Each monomer is one of the aforementioned nucleotides, which are deoxy-adenine, thymine, guanine, or cytosine. These are often referred to as deoxyribonucleic acid, or DNA for short. In ribonucleic acid, or RNA, the thymine is replaced with uracil. DNA found in chromosomes form long helical structures which contain two molecules that run anti-parallel to each other with the backbones facing in and are held together by the hydrogen bonds formed between the complementary nucleotide bases (Adenine and Thymine, Guanine and Cytosine), which are lying between the helical backbones. The absence of the 2'-hydroxyl group in DNA allows the backbone to be more flexible and to assume the full conformation of the long double-helix structure, which in turn allows for coiling and, therefore, DNA is able to fit longer molecules into smaller volume spaces of a cell nucleus. RNA, on the other hand, are known to form relatively short double-helix structures.

References

http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/Phosphate

http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/Nitrogenous_Bases/Pyrimidines

http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/Nitrogenous_Bases/Purines/Adenine

http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/Nitrogenous_Bases/Purines/Guanine