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During the process of Conversion to Ribonucleoside Monophosphates the various ribonucleoside triphosphates break off their high energy bonds after linkage to the DNA.But the first ribonucleotide triphosphate retains all the phosphates thus chemically distinct from the rest.

Now my question is: Why does it retain the phosphates?

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You've tagged this DNA, but really it is about RNA (although the same principles apply). – Alan Boyd Jan 18 '14 at 13:02
up vote 2 down vote accepted

There is a useful diagram at this site.

During RNA synthesis in vivo the 3'-OH oxygen atom of the growing chain reacts with the α 5'-phosphate of the incoming ribonucleotide (nucleophilic attack), displacing the β + γ phosphates as a pyrophosphate group. This results in a 3'-5' bond between the prexisting oligoribonucleotide and the incoming ribonucleotide. In other words the loss of the pyrophosphate group is an inevitable consequence of the elongation reaction.

At initiation, however, the first ribonucleotide has not been the subject of a nucleophilic attack, because it is first in the chain. Its 3'-OH will carry out the nucleophilic attack descibed above when the next ribonucleotide is added to the chain.

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