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:
And here are the pyrimidine-based structures:
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:
In order for base-pairing to occur in a nucleic acid, the anti- conformation is required. But how about for the nucleotide itself?
The structures above were produced by low-level ab initio MO calculations, and these find the syn- isomer to be more stable by a couple of kcal/mol, largely on the basis of a hydrogen bond between the 5' OH and a ring nitrogen.
Textbooks say that for purine bases, the syn- and anti- are in equilibrium, but pyrimidines exist entirely in the anti- conformation. This seems counter-intuitive.
The puckering of the sugar ring usually involves having either C2' or C3' out of the plane formed by C1', O, and C4'.
If C2' or C3' is on the same side of the ring as the glycosidic bond, the conformation is described as endo-; if on the other side, it is exo-.
Numerous papers discuss the factors involved in one preference or the other, but in general, the two conformations are in equilibrium in solution.
Nucleotides are phosphate esters of nucleosides.
Most commonly, the phosphoryl group is attached to the oxygen of the 5'-hydroxyl
Nucleotides are typically assumed to be 5'- unless otherwise stated.
Monophospates can be further phosphorylated to produce di- and tri- phosphates, as illustrated below for adenosine:
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.