DNA replication for prokaryote vs. eukaryotes

[joonkimdds]

are they the same or diff?
I only learned one type of replication, but
there are diff types of polymerases for each and I am confused if they r any different.

[doc3232]

Originally Posted by joonkimdds

are they the same or diff?
I only learned one type of replication, but
there are diff types of polymerases for each and I am confused if they r any different.

Prokaryotes dna are circular and have an origin of replication
In general, prokaryotes have much simpler dna replication. Less proteins involved.

Also, prokaryotes have naked DNA, so there is not unwrapping.

[Doa110]

Originally Posted by joonkimdds

are they the same or diff?
I only learned one type of replication, but
there are diff types of polymerases for each and I am confused if they r any different.

Proks. use different systems, for bacteria...>Operon system.
Euks. use the Tarnscription (from nucleous)....>Translation (at the ribosome site in cytoplasm....>Protein synthesis (in cytoplasm).

[joonkimdds]

Originally Posted by Doa110

Proks. use different systems, for bacteria...>Operon system.
Euks. use the Tarnscription (from nucleous)....>Translation (at the ribosome site in cytoplasm....>Protein synthesis (in cytoplasm).

isn't DNA replication different from protein synthesis?

[tranv117]

Originally Posted by joonkimdds

isn't DNA replication different from protein synthesis?

well bacteria are capable of replicating DNA and synthesize proteins all at the the same time. They're capable of this because they do not have a nucleus.

This is a reason why eukaryotes have much more specialized functions. Things are compartmentalized which leads to more and more regulation at each point as opposed to prokaryotes.

[joonkimdds]

hm...I just found out that they have completely different Pre-replication complex.

The Prokaryotic Pre-RC
In prokaryotes, the pre-RC is made up of the following factors :

A helicase such as dnaA, which unwinds the DNA ahead of the replication fork.
A primase such as dnaG, which generates an RNA primer to be used in DNA replication.
A DNA holoenzyme, which is actually a complex of enzymes that performs the actual replication.


The Eukaryotic Pre-RC
In eukaryotes, the pre-RC is made up of the following factors:

A six-subunit complex called Origin Recognition Complex (ORC) which binds to the origin.
Two regulatory proteins called Cdc6 and Cdt1 which are recruited by ORC.
The MCMs (Minichromosome Maintenance proteins), the helicase complex.
These proteins assemble on cellular origins in G1 phase of the cell cycle. Once these proteins are assembled, the MCMs are phosphorylated and DNA replication begins.

[yakuza]

Originally Posted by joonkimdds

hm...I just found out that they have completely different Pre-replication complex.

The Prokaryotic Pre-RC
In prokaryotes, the pre-RC is made up of the following factors :

A helicase such as dnaA, which unwinds the DNA ahead of the replication fork.
A primase such as dnaG, which generates an RNA primer to be used in DNA replication.
A DNA holoenzyme, which is actually a complex of enzymes that performs the actual replication.


The Eukaryotic Pre-RC
In eukaryotes, the pre-RC is made up of the following factors:

A six-subunit complex called Origin Recognition Complex (ORC) which binds to the origin.
Two regulatory proteins called Cdc6 and Cdt1 which are recruited by ORC.
The MCMs (Minichromosome Maintenance proteins), the helicase complex.
These proteins assemble on cellular origins in G1 phase of the cell cycle. Once these proteins are assembled, the MCMs are phosphorylated and DNA replication begins.

I wouldn't even bother with prokaryote vs euk DNA rep.

BUT, I would definitely know their differences in transcription

[yakuza]

Originally Posted by joonkimdds

isn't DNA replication different from protein synthesis?

yes!

[BunsenBurner]

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!

------------------------------------------------------------------------------
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

------------------------------------------------------------------------

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!)

---------------------------------------------------------------------------------

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)

[navneetdh]

Prokaryotes do not have introns therefore faster replication.

[jennyuzzy]

Originally Posted by navneetdh

Prokaryotes do not have introns therefore faster replication.

Well it is true they dont have introns, how ever that is part of the transcription process not replication.

however, Eukaryotes have faster replication because they have many initiation sites and so can start in multiple places making it much faster to get the job done unlike Prokaryotes that have only one initiation site.....i believe