So confused with 5' to 3' end of DNA molecule

[scilearner]

Hello everyone,

 

Quick questions. What do they mean by different polarities in anti parallel DNA strands. Are they referring to some chemical polarity or simply the fact they run in opposite directions.

 

I'm confused with DNA replication. DNA polymerase can only synthesize DNA in 5' to 3' direction. I don't understand how this could cause a lagging strand.

 

For example

 

5'------------------------3' (1st strand)

3'------------------------5' (2nd strand)

 

Can't two DNA polymerases work in opposite directions in DNA replication. One from 5' to 3' in the first strand(moving to the left) and the other 5 to 3 in the second strand(moving to the right)

 

They say that RNA polymerase can only synthesize RNA from 5' to 3' direction.

 

5'------------------------3' (1st strand)

3'------------------------5' (2nd strand)

 

So that makes the second strand the template strand. My question is can't RNA polymerase use the first strand as the template strand by synthesizing in the opposite direction (to the left)

 

Thanks a lot

[Mr Skeptic]

Hm, what you are missing is that for the DNA polymerase to work, it needs a "bubble" where the DNA strands are separated. DNA Pol will then proceed in the 5' to 3' direction on each strand. However, the other half of each DNA molecule will be in the wrong direction for DNA pol, leaving a side that is unbound. On this side, primase adds RNA bits that match the DNA molecule. These are needed for DNA polymerase to attach, but on this side the DNA pol is working backwards (still 5' to 3' though), in that it is going towards a part of the DNA that is already paired up with a new strand. However it will hit the RNA primer that is on the end of the strand it is heading towards and replace that with DNA. This takes longer though.

 

We eukaryotes have a system whereby our DNA is replicated from several sites at once. Starting at each end of the DNA strand only would take too long. Also, having unbound DNA of that length would probably be a recipe for disaster.

 

Finally, you might as well learn about telomers. Because DNA Pol works in one direction, and also it needs a certain amount of space before it can start working, a bit of each end of the DNA strand gets lost. We have bits called telomers that are dispensable, attached at each end of the DNA strand. We also have an enzyme called telomerase that can add telomers to the strand for the cells that must not age (stem cells and germ cells).

Edited November 18, 2009 by Mr Skeptic

[scilearner]

Thanks a lot Mr Skeptic. I really appreciate the answer but unfortunately I find DNA replication very difficult. I researched this for the past 2 hours and I still don't get it.

 

<-----------DNA polymerase

5'------------------------3' (1st strand)

3'------------------------5' (2nd strand)

DNA polymerase---->

 

 

If two DNA polymerases work at the same time in opposite direction can't you replicate DNA without lagging strands?

 

Remember DNA polymerase can only synthesize from 5'---->3'

 

I read this sentence a million times but I still don't get why is this relevant when you can have two polymerases. Please excuse my poor understanding!!

 

Is it simply we only have one polymerase?

 

Thanks

[Mr Skeptic]

No there are lots of polymerases. Each replication bubble (several in each DNA being replicated) has two sides though, and I think you don't want to leave an entire length of DNA single-stranded as your suggestion would require

 

 

You correctly surmise that there is a DNA Pol working in each direction. It's just that there's a few working behind it as well.

[CharonY]

The problem is that the DNA helix has to be "unzipped" by a helicase. The enzyme essentially moves along the DNA and separates the two strands. If you follow the point of the unzipping, it is easy to note the difference between the 5-3 and 3-5 strand. More precisely, the lagging strand can be most easily defined at the actual replication fork (the part where the single and double stranded DNA meet). The whole bubble itself is of no consequence for that and maybe even a bit confusing. If you look at the pic above just look closely on either the left or right end, near the fork (and ignore the rest). There you should see why in one direction it is lagging.

Edited November 18, 2009 by CharonY

[Why Not Blue Eyes]

The problem is that the DNA helix has to be "unzipped" by a helicase. The enzyme essentially moves along the DNA and separates the two strands. If you follow the point of the unzipping, it is easy to note the difference between the 5-3 and 3-5 strand. More precisely, the lagging strand can be most easily defined at the actual replication fork (the part where the single and double stranded DNA meet). The whole bubble itself is of no consequence for that and maybe even a bit confusing. If you look at the pic above just look closely on either the left or right end, near the fork (and ignore the rest). There you should see why in one direction it is lagging.

 

So is the real reason why the enzyme does not replicate the bottom strand simultaneously with the leading strand because the lagging strand is litterally lagging behind in the replication fork? It's bubble has not quite been formed like the leading strand, thus it can not replicate as quickly? Doesn't it have segments unlike the leading strand? I do not quite understand why the lagging strand has segments unlike the leading strand?

[Mr Skeptic]

So is the real reason why the enzyme does not replicate the bottom strand simultaneously with the leading strand because the lagging strand is litterally lagging behind in the replication fork? It's bubble has not quite been formed like the leading strand, thus it can not replicate as quickly? Doesn't it have segments unlike the leading strand? I do not quite understand why the lagging strand has segments unlike the leading strand?

 

No. One side of each replication fork is backwards. The one that is backwards is still done 5' to 3', but it has to be done in pieces since the new strand is uncovered in the 3' to 5' direction. Each piece has to be done like starting the replication process, a primase to add a bit of double strand, and then a DNA polymerase needs to get on that and start copying, until it reaches the end of the previous one. But on the other side of the replication fork, the DNA is uncovered 5' to 3', and the DNA polymerase just keeps on going without interruption..