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Why does RNA Polymerase always move toward the 5' end of the

  1. Oct 11, 2008 #1
    DNA strand (template strand) it is transcribing? Why couldnt it move toward the 3' end? Please explain with as much clarification as possible.
    I understand the 5' end is the phosphate group end of a nucleotide, and 3' end is the hydroxyl (-OH) end.
    I also know that nucleotides are only added to the 3' end of the growing mRNA, but I am confused about why this is, at the molecular level (that the only way to totally understand, isnt it?)
    please explain with as much clarification/detail possible, i really need to get this.
    thanks alot
  2. jcsd
  3. Oct 12, 2008 #2


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    My guess is that, if growth were to occur from the 5' end of the primer (i.e. toward the 3' end of the template), the cell would have problems with loss of the 5' phosphate groups. The 5' phosphate is important because the loss of pyrophosphate is the thermodynamic driving force behind DNA/RNA synthesis. The bond is fairly weak, so replacing the pyrophosphate group with the 3'OH of a nucleic acid strand forms a stronger bond and is energetically favorable.

    Because the pyrophosphate group is weakly bound, it can sometimes come off due to the thermal energy in the cell. Thus, in an RNA that is transcribed by adding nucleotides to the 5' end, loss of the 5' phosphate would halt synthesis until a repair enzyme could phosphorylate the 5' end again. In contrast, in normal transcription, the transcribed RNA does not have this problem. The pyrophosphate groups are on the nucleotides and loss of these pyrophosphate groups is not a problem because the cell has a large pool of nucleotides that is constantly being replenished.
  4. Oct 21, 2008 #3
    I like this explanation.
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