(1) Which RNA primer would be the first to be removed by DNA polymerase I? For t
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Question
(1) Which RNA primer would be the first to be removed by DNA polymerase I? For the resulting gap to be filled in by new DNA, is it necessary for the Okazaki fragment in the middle to have already been synthesized? Explain.
(2) Let?s consider how DNA ligase connects the left Okazaki fragment to the middle Okazaki fragment. After DNA polymerase I removes the middle RNA primer and fills in the gap with DNA, where does the DNA ligase work: is ligase needed at the left arrow or the right arrow or both?
In the following diagram, the top strand is the template DNA and the bottom strand shows the lagging strand prior to the action of DNA polymerase I. The lagging strand contains Okazaki fragments. The RÑA primers have not yet been removed The lagging strand contains Okazaki fragments. The RNA primers 3' 5' 5 3 RNA primer RNA primer RNA primer Middle Okazaki Right Okazaki Left Okazaki fragment fragment fragmentExplanation / Answer
(1) RNA primer present at the left Okazaki fragment would be the first to be removed by DNA polymerase. Yes, in order to fill the gap the Okazaki fragment in the middle should be synthesized, because this fragment would provide free 3-OH group to which new nucleotides are attached.
(2) The ligase should work at the right arrow, because DNA ligases catalyze the formation of a phosphodiester bond between the 3' hydroxyl and 5' phosphate of adjacent DNA residues.
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