As far as POLYMERASES go, don't get DNA Pols mixed up with RNA Pols
(I did this a long time ago)
DNA POLYMERASES (replication)
Prokaryotes - 3 types of DNA Pols
* DNA Pol III
o 5' --> 3' DNA synthesis
o 3' --> 5' exonuclease
* DNA Pol II
o Unknown (for the purposes of the MCAT) - but don't take my word for it!
* DNA Pol I
o 5' --> 3' DNA synthesis
o 3' --> 5' exonuclease
o 5' --> 3' exonuclease
+ Allows for removal of RNA primer (while simultaneously putting down DNA in its place w/ the 5' --> 3' DNA synthesis)
Eukaryotes - DNA Pols
* As far as DNA polymerases go...???? I think I slept through that lecture or didn't attend. Either that OR the scientific community needs to shift some of its focus from E.coli and Drosophila melanogaster to Homo sapiens!
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RNA POLYMERASES (transcription)
Prokaryotes - only one type of RNA Pol
* 5' --> 3' synthesis
* No exonuclease activity (Why? - proofreading at mRNA level is not NEARLY as important in comparison to DNA level---but that's another topic).
Eukaryotes - 3 types of RNA Pols
* All have 5' --> 3' synthesis )and no exonuclease activity as far as I understand).
o RNA Pol I --> rRNA
o RNA Pol II --> mRNA (functions most similarly to the core RNA pol in prokaryotes)
o RNA Pol III -->tRNA
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OTHER STUF CONCERNING DNA/CHROMOSOMES/REPLICATION
Prokaryotes vs. Eukaryotes
Shape
* Eukaryotes - linear
* Prokaryotes - circular
Number of chromosomes
* Eukaryotes - Humans have 23 pairs of chromosomes, but this number varies depending on species.
* Prokaryotes - Just one chromo!
o Don't worry abou pairs thing because prokaryotes are haploid!
o May have plasmid (also circular) - This is just extra-chromosomal material
Packaging DNA:
* Eukaroytes- Nucleosomes (DNA wrapped around histones) and then formation of more and more compact structure
* Prokaryotes - DNA gyrase (introduces positive supercoils)
Origin of Replication (ORC)
* Eukaryotes - Several ORCs--> therefore several replication bubbles
* Prokaryotes - One ORC, and since they have a single circular chromosome, the replication bubble formed is going to make the entire thing look like the Greek letter Theta (why it is called Theta Replication).
Doubling time (mass) - Multiple replication forks?
* Eukaryotes- NO!
* Prokaryotes - YES...especially during exponential growth!
o E.coli has a 20 minute doubling time. How is this possible if DNA Pol is a one speed machine - AKA 40 minutes is the quickest one complete copy of the genome can be made?
+ This is only possible if the newly replicated DNA starts dividing before the original circular chromosome is even finished replicating its genome!!!
+ DO NOT GET THIS CONFUSED WITH MULTIPLE ORCs (only eukaryotes) because that refers to a single generation gap.
o This multiple replication fork thing is hard to describe without a picture, so I'll use an analogy. It is kind of like you're pregnant, but your unborn child is also pregnant...and quite possibly the unborn child of your unborn child is pregnant! In other words --> There is 1 pregnant lady, however a total of 4 generations!!!
o Now, let's say human replication = 40 min and if the unborn child of your unborn child's child was conceived at t = 0 min...., then at t = 40 min, you would have 4 completely separated people (and they would already have new generations brewing).
o Basically, in a matter of 40 minutes, you went from 1 --> 4.
+ That is a total of 2 doublings (2^2 = 4) in 40 minutes!
+ Therefore, 1 doubling / 20 minutes.
o LUCKILY, this phenomena is only reserved for bacteria...phew...AND...also be thankful that the Earth is a planet of limited resources (otherwise the net weight of E. coli on the planet....um...would weigh more than the planet....in less than a month's time!)
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OTHER STUFF CONCERNING TRANSCRIPTION
EUKARYOTES
* Post transcriptional modification
o splicing (get rid of introns)
o 5' methyl / guanine cap
o Poly(A) tail
* Location - nucleus
* Monocistronic - one transcript, one polypeptide
* Transcription initiation - memorization nightmare, so I don't remember details..BUT I think I remember the following -->
o Pre-initiation complex required
o Bringing the RNA-pol to the promoter requires A LOT of sequence specific binding factors.
* Transcription termination - Something to do with the poly(A) tail.
PROKARYOTES
* No post transcriptional modification
o Soon as the RNA pol leaves behind the transcript, that transcript starts getting translated! (simultaneous transcription and translation) -> therefore, no need to protect end of mRNA with 5' cap!
o No introns - No splicing
* Location - cytoplasm
* Polycistronic - There can be more than one polypeptide produced from a single transcript. Think of the lac operon. I believe there were 3 different genes that the RNA pol could cruise over. Pretty much, one mRNA can produce more than one polypeptide (however usually they are related in function). I would think the gene products from the lac operon all have to do with processing lactose (wild guess).
* Transcription initiation
o No Pre-Initiation complex needed
o Promoter -->
+ -10, -35, upstream sequences
+ sigma factor, as part of the core RNA pol aids in finding this promoter (I think).
* Termination - Rho dependent (protein that helps pol fall off DNA) or rho independent (like forming a hairpin loop)
