Pol I and Pol III exonuclease confused

[hope_to_match]

Can someone please explain to me or give me a good link for Polymerase 1 and 3 exonuclease activity? I am not grasping the concept...

This is what it says in Feralis notes:

Pol 1 and 3 have 3'-->5' econuclease: breaks phosphodiester backbone on a single strand of DNA and removes a nucleotide. Exonuclease can also remove from (in this case of 3' end) of the chain


Pol 1 also has 5'--->3' exonuclease: to take off the primer and also proof with 3' to 5' when laying down the chain


Are these ways to correct mistakes? Can someone please help me understand this 😕

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[FeralisExtremum]

I think this is one of the areas I touched up for the second version of my notes:

o Every okazaki fragment has an RNA primer, these rna strips are later replaced with dna by DNA polymerase I
 DNA Pol 1 replaces BPs from the primer and does DNA repair; DNA pol 3 is pure replication [eukaryotes have different polymerases: alpha gamma etc – not important])
 Pol 1 and Pol 3 have 3'  5' exonuclease: breaks phosphodiester backbone on a single strand of DNA and removes a nucleotide. Exonuclease can only remove from (in this case of 3' end) of the chain
 Pol 3 can do some proofreading; if it makes a mistake it will go back and use this to replace it
 Pol 1 also has a 5'  3' exonuclease, to take off the primer; and can also proof with 3' to 5' when laying down new chain
 So in summary: Pol 3 mainly replicates the DNA 5' to 3' but can also proofread via 3' to 5' exonuclease. Pol 1 primary breaks down RNA primer via 5' to 3' exonuclease and replaces it with DNA (laid down between Okazaki fragments mainly) via 5' to 3' polymerase while proofreading as it goes, can proofread via 3' to 5' exonuclease as well.
 In prokaryotes the "good" strand is methylated after replication so it doesn't accidentally repair wrong strand
 In all cases of repair, ligase must come in to seal the backbone afterward

Hope that helps. They both can proofread, but Pol 3 acts mainly for replication.

 

[hope_to_match]

I think this is one of the areas I touched up for the second version of my notes:

o Every okazaki fragment has an RNA primer, these rna strips are later replaced with dna by DNA polymerase I
 DNA Pol 1 replaces BPs from the primer and does DNA repair; DNA pol 3 is pure replication [eukaryotes have different polymerases: alpha gamma etc – not important])
 Pol 1 and Pol 3 have 3’  5’ exonuclease: breaks phosphodiester backbone on a single strand of DNA and removes a nucleotide. Exonuclease can only remove from (in this case of 3’ end) of the chain
 Pol 3 can do some proofreading; if it makes a mistake it will go back and use this to replace it
 Pol 1 also has a 5’  3’ exonuclease, to take off the primer; and can also proof with 3’ to 5’ when laying down new chain
 So in summary: Pol 3 mainly replicates the DNA 5’ to 3’ but can also proofread via 3’ to 5’ exonuclease. Pol 1 primary breaks down RNA primer via 5’ to 3’ exonuclease and replaces it with DNA (laid down between Okazaki fragments mainly) via 5’ to 3’ polymerase while proofreading as it goes, can proofread via 3’ to 5’ exonuclease as well.
 In prokaryotes the “good” strand is methylated after replication so it doesn’t accidentally repair wrong strand
 In all cases of repair, ligase must come in to seal the backbone afterward

Hope that helps

yeah the sentence in bold is not in your early notes. makes a lot more sense now. the cliffs or ap bio doesnt talk about this so i was a little confused and definitely saw a question on this in qvault. thanks a lot !

 

[hope_to_match]

what about endonuclease ? is it the same thing only proof reading in the middle of the strand rather than starting at ends?

 

[aznnytezx]

I think this is one of the areas I touched up for the second version of my notes:

o Every okazaki fragment has an RNA primer, these rna strips are later replaced with dna by DNA polymerase I
 DNA Pol 1 replaces BPs from the primer and does DNA repair; DNA pol 3 is pure replication [eukaryotes have different polymerases: alpha gamma etc – not important])
 Pol 1 and Pol 3 have 3’  5’ exonuclease: breaks phosphodiester backbone on a single strand of DNA and removes a nucleotide. Exonuclease can only remove from (in this case of 3’ end) of the chain
 Pol 3 can do some proofreading; if it makes a mistake it will go back and use this to replace it
 Pol 1 also has a 5’  3’ exonuclease, to take off the primer; and can also proof with 3’ to 5’ when laying down new chain
 So in summary: Pol 3 mainly replicates the DNA 5’ to 3’ but can also proofread via 3’ to 5’ exonuclease. Pol 1 primary breaks down RNA primer via 5’ to 3’ exonuclease and replaces it with DNA (laid down between Okazaki fragments mainly) via 5’ to 3’ polymerase while proofreading as it goes, can proofread via 3’ to 5’ exonuclease as well.
 In prokaryotes the “good” strand is methylated after replication so it doesn’t accidentally repair wrong strand
 In all cases of repair, ligase must come in to seal the backbone afterward

Hope that helps. They both can proofread, but Pol 3 acts mainly for replication.

When are your next notes going be posted??

 

[FeralisExtremum]

what about endonuclease ? is it the same thing only proof reading in the middle of the strand rather than starting at ends?

The only thing I have on endonucleases is:
-Note: endonucleases cleave the phosphodiester backbone to chunk out NT’s, whereas exonucleases cut out just the NT’s

So difference seems to be whether or not they cut out the backbone to remove a nucleotide.

When are your next notes going be posted??

Good question. I've gotten through updating the first 1/3rd of it and added a lot of images. Depends on how quickly I move through the rest of bio. The middle 1/3 is slow for me because it's almost all plants and taxonomy which is stuff I haven't seen in years. I'm not sure if I plan on touching those in any way aside from editing some of the images to clearer ones. I don't know exactly how in depth taxonomy and plants goes on the DAT and whether or not it's worth my time changing those sections up or if the DAT is really basic questions on those subjects...hopefully someone that's taken the DAT can give me feedback and tell me if Cliff's is sufficient for plants and taxonomy.

Anyways, I'm guessing one week to finish updating at this point.

 

[Faux]

What does bp stand for again?

 

[hope_to_match]

What does bp stand for again?

base pair