Question

in a nucleic acid, a phosphodiester bond links the sugar and phosphate group while a glycosidic bond links the sugar with the nitrogenous base. why is the phosphodiester bond also not a glycosidic bond in this case? A glycosidic bond links any carbohydrate to another group; can't the bond between the sugar and phosphate group be both a phosphodiester bond and a glycosidic bond?

Answer 1

A glycosidic bond is a covalent chemical bond formed by the hemiacetal or hemiketal group in a saccharide and the hydroxyl group of some compound in a condensation reaction. This reaction involves the anomeric carbon of the sugar molecule. There can be many types pf glycosidic linkage. In the case of the sugar and nitrogenous base the bond oxygen is replaced with nitrogen and is thus called N-glycosidic bond.

The phosphodiester bond is formed between 3' of one sugar molecule and 5' of another and involves the reaction of two hydroxyl groups of the phosphoric acid with two hydroxyl of the sugar molecules.

So the mechanism of formation of the phosphodiester bond and the involvement of the carbons in case of phosphodiester bond and glycosidic bond are different.

So although a glycosidic bond means formation of a bond between a sugar and any other molecule, the phosphodiester bond is not formed via the same mechanism and is thus not a glycosidic bond in this case.