Structure and Properties of Nucleosides and Nucleotides

Nucleosides are N-glycosides of ribose and deoxyribose; the N comes from the purines and pyrimidines we examined on another page.

Nucleosides are the basic building blocks of nucleic acids: ribonucleic acid (RNA) and deoxyriboneculeic acid (DNA).

Net, they are formed by the loss of water from a sugar plus a purine or pyrimidine, OH from the anomeric position of the sugar, and H from a nitrogen of the base.

Here are the structures of those based on purines:

Adenosine Guanosine
Deoxyadenosine Deoxyguanosine

And here are the pyrimidine-based structures:

Cytidine Uridine
Deoxycytidine Thymidine (Deoxythymidine)

One exception to the glycosidic structure of nucleosides is pseudouridine (found in tRNA):

in which C5 of the pyrimidine ring is attached directly to C1' of the sugar.

Structural issues: two conformational variations are possible: rotation around the base-to-sugar bond, and puckering of the sugar ring. Consider the two structures below for adenosine:

Anti-conformation Syn-conformation

In order for base-pairing to occur in a nucleic acid, the anti- conformation is required. But how about for the nucleotide itself?

The puckering of the sugar ring usually involves having either C2' or C3' out of the plane formed by C1', O, and C4'.

Nucleotides are phosphate esters of nucleosides.

At physiological pH, the phospates are ionized, as depicted in the picture.

In nucleic acids, the 5' phosporyl is esterified to the 3' OH of the next sugar, forming a sugar phosphate backbone, from which the purine and pyrimidine bases extend.

The ionization of the phospates means that RNA and DNA bear multiple negative charges - they are polyelectrolytes. This in turn means that cations of various kinds, especially Mg++, tend to cluster near the phosphates.

This page last modified 2:16 PM on Thursday December 18th, 2008.
Webmaster, Department of Chemistry, University of Maine, Orono, ME 04469