Structural Biochemistry/Organic Chemistry/Important Organic Reactions in Biochemistry

Organic Reactions in Biochemistry
Biochemistry has a very close relation with organic chemistry, as a good amount of reactions within the body occur through organic reactions. Thus, it is important to look at some of the important Biochemical molecules and the reactions surrounding them through the perspective of organic chemistry. Through the formation of peptide Bonds, long polypeptide chains form which then can fold into proteins.

Phosphodiester Bonds
A phosphodiester bond is a bond between a two pentoses and a phosphate group through esterification. It is formed by strong covalent bonds, in which the phosphate groups that are bonded together are negatively charged, so that they repel nucleophilic species like they hydroxide ion. This protects the phosphodiester bonds from hydrolytic attack, unlike with most other esters. These bonds are an important part of all life and make up the backbone of nucleic acids(including DNA and RNA). The phosphodiester bond links the 3’ end of a strand of DNA to the 5’ end of another strand by bonding the hydroxyl group of the 3’ end of the sugar to the hydroxyl group of the 5’ end of the other sugar. Because of the free 2’ hydroxyl group in the sugar groups, the phosphodiester bonds between two ribonucleotides can be broken through the process of alkaline hydrolysis.

Phosphodiesterases
Phosphodiesterases are enzymes that catalyze the hydrolysis of phosphodiester bonds and repair DNA sequences.

DNA Polymerase
DNA polymerases are enzymes that help to catalyze the formation of phosphodiester bonds through the reaction:

(DNA)n + dNTP <=> (DNA)n+1 + PPi

In this formula, dNTP is deoxyribonucleotide and PPi is pyrophosphate ion.