Polymerases

[Phloston]

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I just want to make a brief list comparing prokaryotic vs their analogous eukaryotic polymerases.

Prokaryotic : Eukaryotic

DNA primase : DNA polymerase ALPHA
DNA polymerase I : DNA polymerase BETA
DNA polymerase III : DNA polymerase DELTA

Would you say those comparisons are correct??

I'm also aware that in base-excision repair, a base-specific glycosylase recognizes the damaged base. AP-endonuclease creates a nick and exposes a free 3-OH.

Is anyone aware of additional info regarding any of the biochemical enzymes that might be important (whether encountered in QBanks or wherever)??

 

[MrBeauregard]

Absolutely know which enzymes have 3' --> 5' exonuclease and/or 5' --> 3' exonuclease activity; that's one of the most important aspects of those enzymes that I picked up from my qbanking. And make sure to include virion-associated enzymes in this list.

 

[Phloston]

Absolutely know which enzymes have 3' --> 5' exonuclease and/or 5' --> 3' exonuclease activity; that's one of the most important aspects of those enzymes that I picked up from my qbanking. And make sure to include virion-associated enzymes in this list.

As far as I understand, DNA polymerase III and I have 3-5 and 5-3 exonuclease activity, respectively.

Could you be more specific about your last sentence?

 

[Convalaria]

Just finished review of these enzymes:

DNA pol I:
- proofreading: 3'-5' exonuclease activity
- DNA repair: 5'-3' polymerase activity
- RNA primase removal: 5'-3' exonuclease activity

DNA pol II:
- DNA repair: 5'-3' polymerase activity

DNA pol III:
- DNA synthesis: 5'-3' polymerase activity
- proofreading: 3'-5' exonuclease activity

all exonuclease activity is performed in 3'-5' direction, except RNA primase removal by DNA pol I.

 

[Phloston]

Just finished review of these enzymes:

DNA pol I:
- proofreading: 3'-5' exonuclease activity
- DNA repair: 5'-3' polymerase activity
- RNA primase removal: 5'-3' exonuclease activity

DNA pol II:
- DNA repair: 5'-3' polymerase activity

DNA pol III:
- DNA synthesis: 5'-3' polymerase activity
- proofreading: 3'-5' exonuclease activity

all exonuclease activity is performed in 3'-5' direction, except RNA primase removal by DNA pol I.

Cheers for posting that, although I'm a bit confused as to how DNA pol I and II differ here.

Also, are you familiar with the eukaryotic polymerases at all?

 

[Convalaria]

Eukaryotic polymerases:

DNA pol a (alpha):
- synthesis of primer

DNA pol b (beta):
- DNA repair
- base excision repair
- gap filling synthesis

DNA pol g (gamma):
- mt DNA

DNA pol d (delta), e (epsilon):
- proofreading - 3'-5' exonuclease activity

Actually I don't know what is the difference btw DNA pol I and II.
If I remember right I found this info on wiki, maybe you can find more details there

 

[Phloston]

Eukaryotic polymerases:

DNA pol a (alpha):
- synthesis of primer

DNA pol b (beta):
- DNA repair
- base excision repair
- gap filling synthesis

DNA pol g (gamma):
- mt DNA

DNA pol d (delta), e (epsilon):
- proofreading - 3'-5' exonuclease activity

Actually I don't know what is the difference btw DNA pol I and II.
If I remember right I found this info on wiki, maybe you can find more details there

Thanks again. I wasn't aware that gamma does mitochondrial DNA, so I'm glad you mentioned that.

I had picked up somewhere that although alpha does the "primer" activity by polymerizing the first ~20 bases, delta takes over after that, which is why I was equating DNA polymerase III to delta in the first post, and wanted someone's opinion on that.

 

[Convalaria]

Thanks again. I wasn't aware that gamma does mitochondrial DNA, so I'm glad you mentioned that.

I had picked up somewhere that although alpha does the "primer" activity by polymerizing the first ~20 bases, delta takes over after that, which is why I was equating DNA polymerase III to delta in the first post, and wanted someone's opinion on that.

You're welcome 🙂

Also, just found in Kaplan Biochemistry and Med.Genetics:
Leading strand synthesis - DNA pol d
Lagging strand synthesis - DNA pol a
About DNA pol gamma Kaplan also says that it replicates mt DNA

 

[Phloston]

You're welcome 🙂

Also, just found in Kaplan Biochemistry and Med.Genetics:
Leading strand synthesis - DNA pol d
Lagging strand synthesis - DNA pol a
About DNA pol gamma Kaplan also says that it replicates mt DNA

If DNA polymerase alpha does the lagging strand in eukaryotes, then its function is the lagging strand + primers, whereas on the leading strand, delta picks up where alpha left off (i.e. after ~20 bases).

The confusion here is that prokaryotes don't use DNA primase for the lagging strand, which doesn't match up with the fact that eukaryotes use alpha for it. Prokaryotes just use DNA polymerase III for the lagging, which would be the equivalent of eukaryotes using delta for it.

Yet again, pros and eus are different.

Thanks again,

 

[ijn]

They don't ask about specific eurkaryotic DNA polymerases on the exam. The research is still too unsettled. Prokaryotic polymerases are high yield.

 

[Phloston]

They don't ask about specific eurkaryotic DNA polymerases on the exam. The research is still too unsettled. Prokaryotic polymerases are high yield.

I don't think you can say that. You're not a USMLE test-writer.

There's enough research to ask simple questions or analogy-based ones on eukaryotic polymerases. I've also encountered quite a few questions on eukaryotic information so far.

 

[ijn]

Find me a single question that asks anything about specific eurkaryotic DNA polymerases on a CBSE, CBSSA, UWorld, Kaplan, or USMLERx and I'll say you're not completely wasting your time. I predict allocating brain cells on alpha/beta/delta polymerases lowers your STEP 1 score by at least one point three points (on average.)

FWIW, that comment came from the guy who does Kaplan's genetics videos. He probably sees feedback from hundreds of students every year. Look at the wikipedia article on eurkayotic polymerases. It's full of comments along the lines of "this is still a matter of debate." You are not taking a graduate genetics examination. You're taking an exam meant for second year US medical school graduates.

 

[Phloston]

Find me a single question that asks anything about specific eurkaryotic DNA polymerases on a CBSE, CBSSA, UWorld, Kaplan, or USMLERx and I'll say you're not completely wasting your time. I predict allocating brain cells on alpha/beta/delta polymerases lowers your STEP 1 score by at least one point three points (on average.)

FWIW, that comment came from the guy who does Kaplan's genetics videos. He probably sees feedback from hundreds of students every year. Look at the wikipedia article on eurkayotic polymerases. It's full of comments along the lines of "this is still a matter of debate." You are not taking a graduate genetics examination. You're taking an exam meant for second year US medical school graduates.

Lol. It's in Gunner Training. Considering its co-founder, Frank Lau, is a resident at Harvard Plastics, and he's reviewed the QBank questions, I'd believe the GT material, in full, is legitimate for testing purposes. I also think it's interesting that you threw USMLE Rx in the mix per your list above. The fact that you'd consider that QBank an indicator of potential USMLE material indicates that GT is comparable.

 

[ijn]

Unfortunately a plastic surgery residency doesn't confer infallibility. It'd be sweet if it did, though.

If those kinds of zero yield topics are at all common in GT, then I would really start to question its utility in terms of STEP 1 preparation.

 

[Phloston]

Unfortunately a plastic surgery residency doesn't confer infallibility. It'd be sweet if it did, though.

If those kinds of zero yield topics are at all common in GT, then I would really start to question its utility in terms of STEP 1 preparation.

I would say that you generally shouldn't worry about what other people want to learn for the boards.

 

[wisdom is key]

For anyone who is still looking at this thread- eukaryotic DNA polymerases can definitely be tested (I had a UWorld question on this, and saw it in DIT).

A good way to remember it:
Alpha = Lagging strand, primer synthesis
Beta = Base excision repair
Delta = Leading strand
Gamma = Mitochondrial DNA

 

[Transposony]

@Phloston
So in hindsight do you still recommend to know eukaryotic DNA polymerases for Step 1 ?

 

[Phloston]

@Phloston
So in hindsight do you still recommend to know eukaryotic DNA polymerases for Step 1 ?

Qbanks tend to discuss some of this stuff in detail just for the sake of completeness and understanding if you ask me. The specifics are horribly low-yield. Know RNA pol I, II and III, and merely know what it means to be a reverse transcriptase or telomerase or whatever they're describing. USMLE is more concerned about mechanistic understanding, not whether you know it's gamma or delta.