Structural Biochemistry/Nucleic Acid/Phosphate

In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry.

General Phosphate structure

The backbone of the DNA strand is made from alternating phosphate and sugar residues. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings.

As you noticed in the deoxyribose sugar, it does not contain a hydroxyl group on the 2' carbon. This absence of the hydroxyl group allows greater stability because the absence of hydroxyl group allows the 2' carbon to resist hydrolysis. This is one of the reasons why the hereditary material is stored in the DNA and not RNA. However, the net negative charge of the phosphate group must be stabilized by metal ions, such as magnesium or manganese.

Phosphodiester bond

In the molecular bonding of the deoxyribonucleotide (DNA) and ribonucleotide(RNA), phosphodiester bond is a strong covalent bond between a phosphate group and two 5-carbon ring. The phosphate group contains a negative charge as it bonds to a 3' carbon in one ring and a 5' carbon in another ring.

Phosphodiester linkage

The phosphodiester is formed when a single phosphate or two phosphates break away and catalyze the reaction by DNA polymerase. dATP would dissociate one phosphates in order to form a phosphodiester bond with a deoxyribose sugar from a nucleotide during the process of DNA elongation.

(DNA)n + dATP <------> (DNA) n+1 + Ppi

Phosphodiesterase is an enzyme that breaks a cyclic nucleotide phosphate due to incorrect hydrolysis of phosphodiester bonds. Phosphodiesterase will be an important clinical significance in repairing DNA sequences.