Nucleoside (N-glycosidic bond): mechanism and explanation
A nucleobase (here adenine) is bonded through a ring N to the anomeric C1′ of ribose. This N-glycosidic bond is β-configured: the base is on the same side as the CH₂OH group.
Example
Formally an N–H of the base replaces the anomeric OH of ribose (as in glycoside formation with an alcohol). In the cell this goes via activated sugar phosphates. With 2-deoxyribose (no 2′-OH) the DNA building blocks form.
Mechanism step by step
- 1
At the anomeric C1′ of ribose an oxocarbenium-like electrophile forms (enzymatically, with a phosphate as leaving group).
- 2
N9 of the purine (or N1 of a pyrimidine) attacks C1′ from above.
- 3
The β-nucleoside forms; the base is linked to the sugar by a C–N bond.
To read
This topic is part of the syllabus but not in the training: polymers consist of repeating units and biomolecules react through enzymes in the cell. There is no clear-cut task with exactly one product for it.
Go to the trainer with 157 reactions to practiseBackground
Nucleoside and nucleotide
A nucleoside is a base and a sugar joined by the N-glycosidic bond. Add one or more phosphate groups at the 5′-OH and it becomes a nucleotide (for example AMP, ATP). Nucleotides are the building blocks of DNA and RNA.
Which nitrogen is bonded
Purines (adenine, guanine) are bonded through N9 to C1′, pyrimidines (cytosine, thymine, uracil) through N1. The bond is β, on the same side as the sugar’s CH₂OH group.
Stability
In acidic solution the N-glycosidic bond can be hydrolysed, much more easily for purines than for pyrimidines (depurination). In cells this happens spontaneously thousands of times a day and is fixed by repair enzymes.
Frequently asked questions
Which bases are there?
Purines: adenine, guanine. Pyrimidines: cytosine, thymine (DNA only), uracil (RNA only).
Nucleoside or nucleotide?
Nucleoside = base + sugar. Nucleotide = nucleoside + phosphate (usually at C5′).
What is an N-glycosidic bond?
The bond between the anomeric carbon (C1′) of a sugar and a nitrogen atom, in nucleosides the N of the base. It is the counterpart of the O-glycosidic bond in carbohydrates, with N instead of O.