Question

Describe the nature of the phosphodiester bridge and how it gives polarity to polynucleotides and the labile nature of this bond in RNA relative to DNA in detail. 15 mks

Answer 1

Deoxy ribonucleic acid and ribose nucleic acid contains nucleosides that consist of the nucleic acids and ribose sugar in RNA and deoxy ribose sugar in DNA. Two nucleosides are connected via phophodiester bond. This phosphodiester bond connects 3’ –OH group of one sugar to next 5’ –OH group of the sugar of second nucleoside. This bond is formed between the two –OH group that’s why it called di-ester bond that contain one phosphate group. This bond gave the negative charge to DNA and RNA because the pKa value of phosphate group is zero hence at pH 7 it is negatively charged. See the figure of phosphate bond in DNA and RNA.

RNA contains 2’-OH group and due to presence of oxygen atom that contain one lone pair of electron can attack on phophodiester boond. In this mechanism 2’ –OH group is depronated and become a potent nucleophile. This nucleophile attacks on phosphdiester bond and make intermediate pentavalent structure that structure cleave one –OH group. In this cleavage it makes a 2’-3’ cyclic nucleotide. That is leads to self cleavage of the RNA. Therefore RNA is unstable.

See the fig