You are too good with your content. Respect for your hard word. What are your resources for making content? Most of the book do not have clarity on many topics.
RNase H does remove RNA primers in eukaryotes too. However, it seems like in the absence of RNase H, eukaryotes (at least yeast) is still able to process okazaki fragments. So it seems like RNase H (specifically, RNase H2) is a redundant and maybe not so dominant pathway to remove RNA primers in eukaryotes. This makes logical sense if the DNA polymerase can do the same, in which why would a cell spend time recruiting a different enzyme to do the same task. But encoding redundancy is good to make a system robust. Short answer: RNase H and DNA Pol both remove RNA primers in eukaryotes. If you need more info, check out the paper -> PMC5377794 For prokaryotes, please refer to ruclips.net/video/fK4ZB0LGYks/видео.html
@theCrux Thanks a lot for the detailed answer! Yes, I just checked the video on prokaryotes. Was struggling really hard to under the Trombone Loop Model but finally understood it! It was so helpful! Thanks again!!
Connection to replisome is not a pre-requisite for DNA polymerase d activity. Replisome is just a starting point since you need PCNA to be loaded (by RFC at replisome). Once PCNA is loaded, the polymerase delta and PCNA don't require proximity to the replisome for continued DNA synthesis/polymerization.
Who adds DNA nucleotides after primers removal during okazaki fragments maturation phase? In prokaryotes there is dna pol 1 that removes primer and adds nucleotides at the same but here it seems that there won't be any adding nucleotide, just removing primers....how is it, do i understand correctly? Thank you for your videos!
Pol delta and epsilon both have the capacity to add dNTPs following primer removal (during or following the flap removal). Okazaki fragments predominantly have pol delta associated with the maturation.
hello i have some questions if you can help please, in eukaryotes when delta gets to the 5' of the next primer and displaces it does it stay on the 3' of the newly synthesized Okazaki fragment and pause then the flap is cleaved and nick ligated so there is no free 5' end then delta can continue extending the next primer? or does fen1 cleavage cause delta to dissociate and then delta is recruited to the 3' of the new primer closest to the fork then it reaches the 5' RNA portion of the primer on the Okazaki fragment and cycle repeats like that?
Pol Delta (or any polymerase) has limited processivity to displace strands. So it exits, then flap gets nicked by FEN1, and then ligase can come to join the strands. It seems like your questions are related to some form of homework. Unless it is high-level discussion, I will not be replying to such questions. If you want consulation and extended explanations, you can find me on Patreon (link is in the description).
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best molecular biology RUclips channel ever been
Finally... Everything makes sense!!! Thank you so much! You explained all the passages very thoroughly!
such a perfect explanation
thank you sir for your efforts 🤌
continue
You are too good with your content. Respect for your hard word. What are your resources for making content? Most of the book do not have clarity on many topics.
I used published research articles as my resource :)
Thank you so much 😊👍
Hi, thanks for the informative video!
A quick doubt: Does RNase H have no role in removing the primers?
RNase H does remove RNA primers in eukaryotes too. However, it seems like in the absence of RNase H, eukaryotes (at least yeast) is still able to process okazaki fragments. So it seems like RNase H (specifically, RNase H2) is a redundant and maybe not so dominant pathway to remove RNA primers in eukaryotes. This makes logical sense if the DNA polymerase can do the same, in which why would a cell spend time recruiting a different enzyme to do the same task. But encoding redundancy is good to make a system robust.
Short answer: RNase H and DNA Pol both remove RNA primers in eukaryotes.
If you need more info, check out the paper -> PMC5377794
For prokaryotes, please refer to ruclips.net/video/fK4ZB0LGYks/видео.html
@theCrux Thanks a lot for the detailed answer!
Yes, I just checked the video on prokaryotes.
Was struggling really hard to under the Trombone Loop Model but finally understood it! It was so helpful! Thanks again!!
Hello do you know why Okazaki fragments are formed if DNA polymerase-δ is not connected to the replisome? thanks
Connection to replisome is not a pre-requisite for DNA polymerase d activity. Replisome is just a starting point since you need PCNA to be loaded (by RFC at replisome). Once PCNA is loaded, the polymerase delta and PCNA don't require proximity to the replisome for continued DNA synthesis/polymerization.
Who adds DNA nucleotides after primers removal during okazaki fragments maturation phase? In prokaryotes there is dna pol 1 that removes primer and adds nucleotides at the same but here it seems that there won't be any adding nucleotide, just removing primers....how is it, do i understand correctly? Thank you for your videos!
Pol delta and epsilon both have the capacity to add dNTPs following primer removal (during or following the flap removal). Okazaki fragments predominantly have pol delta associated with the maturation.
also do you know why doesn't DNA polymerase-ε displace the RNA primer to cause a flap?
Pol E can also displace the RNA primer (happens during Termination). See: ruclips.net/video/qu9-Dj-byCI/видео.html
I wish I found this before 😭
hello i have some questions if you can help please, in eukaryotes when delta gets to the 5' of the next primer and displaces it does it stay on the 3' of the newly synthesized Okazaki fragment and pause then the flap is cleaved and nick ligated so there is no free 5' end then delta can continue extending the next primer?
or does fen1 cleavage cause delta to dissociate and then delta is recruited to the 3' of the new primer closest to the fork then it reaches the 5' RNA portion of the primer on the Okazaki fragment and cycle repeats like that?
Pol Delta (or any polymerase) has limited processivity to displace strands. So it exits, then flap gets nicked by FEN1, and then ligase can come to join the strands. It seems like your questions are related to some form of homework. Unless it is high-level discussion, I will not be replying to such questions. If you want consulation and extended explanations, you can find me on Patreon (link is in the description).
@@theCrux just trying to figure out step by step but no worries, thanks