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11.5: N-glycosidic bonds

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We have seen that when a second alcohol attacks a hemiacetal or hemiketal, the result is an acetal or ketal, with the glycosidic bonds in carbohydrates provided as an important example.  But what if a hemiacetal is attacked not by a second alcohol, but by an amine? 


What results in this case is a kind of ‘mixed acetal’ in which the carbon that was originally part of the aldehyde is bonded to one oxygen and one nitrogen.  These are referred to by biochemists as N-glycosidic bonds.  You may recognize them as the bonds that link DNA and RNA bases to the sugar-phosphate backbone:


The starting point for the synthesis of purine nucleotide triphosphates (ATP and GTP) is a phosphorylated derivative of the ribofuranose called phosphoribosylprophosphate (PRPP). In the first step of purine base synthesis, a molecule of ammonia attacks the anomeric carbon of PRPP, displacing the diphosphate group in a two-step (SN1) mechanism with an oxonium ion intermediate. 


As you can see, the reaction proceeds with inversion of configuration.  With the N-glycosidic bond in place, the rest of the DNA base is then built piece by piece.

In the breakdown of the RNA base uridine, the N-glycosidic bond is broken by an attacking phosphate nucleophile:


This reaction also takes place with inversion of configuration, and although it would seem reasonable to assume that it proceeds via an SN1-like mechanism, recent evidence (Biochemistry 2011, 50, 9158) suggests that the mechanism is actually SN2.