DNA Replication ~ 5' to 3' direction?

[Fall 4 U]

Hello All!

I have a Bio Test on DNA Replication tomorrow and I had a quick question. (I'm in 8th grade)

When the textbook states that DNA can only be replicated from the 5' to 3' direction, I don't get it.

If it's like this

PT. B -> 5' ---------- 3'

3' ---------- 5' <- PT. A

Couldn't there be a polymerase working from both point A and B? Since they're both starting at the 5' direction?


(I have read Yggdrasil's response to a similar question, but it was kind of fuzzy to me...)

And if you guys have the time, it would be Awesome if you guys could also add a quick summary of DNA replication too!

Yggdrasil, and all, I would love it if you guys have a quick and easy to understand summary of this topic. Thank you!

 

[Ygggdrasil]

When a textbook states that DNA can only be replicated in the 5' to 3' direction, it is referring to the synthesis of DNA. Each strand of DNA has a 5' end and a 3' end. In order to make that strand longer, you could imagine adding new DNA to the 3' end of the strand or to the 5' end of the strand. As it turns out, DNA polymerases can only add new nucleotides to the 3' end of the strand and not the 5' end of the strand, so DNA gets synthesized in the 5' --> 3' direction.

In your example, you have the right idea. Both strands of DNA can be copied, and when they're being copied the DNA polymerases will be moving in opposite directions. When synthesizing the top strand, DNA polymerase can only synthesize it from left to right (5' to 3'), and when synthesizing the bottom strand, the polymerase will be moving from right to left. You could not have the case where the top strand is synthesized by a polymerase moving from the right to left because DNA polymerase cannot work in the 3' to 5' direction.

Why can't polymerase add nucleotides to the 5' end of the DNA? DNA synthesis is powered by the release of pyrophosphate (the final two phosphates on the nucleotide triphosphates) that occurs during DNA synthesis. These phosphates are attached to the 5' end of the nucleotides. These triphosphate groups are somewhat unstable and can sometimes break off on their own. If nucleotides were added to the 5' end of the DNA, accidental loss of the 5' triphosphate would be a big problem; without the 5' triphosphate, DNA synthesis could not continue. However, if new nucleotides are added to the 3' end of the DNA, it doesn't matter if the 5' triphosphate of the DNA strand gets damaged. For 5' to 3' synthesis, loss of triphosphates from the nucleotides would cause problems, but there are so many nucleotides in the cell that the low rate of tirphosphate loss from the nucleotides does not affect the rate of DNA synthesis.

I hope that clears up your question. Let me know if anything is still unclear.

 

[epenguin]

What you are asking, we are presuming, is why couldn't you have the growing DNA chain with -5'PPP at its end and then a mononucleoside 5'-triphosphate condense its 3'-OH onto that with elimination of pyrophosphate which would give a chain one nucleotide longer with 5'PPP at the end ready to do the same thing again.

Watson in his textbook gives much the same explanation as Ygggdrasil except instead of random loss of the terminal phosphate or pyrophosphate he invokes proofreading, which is the exonuclease eating back the new strand for error correction. This is hydrolysis which is energetically favoured, while if it had to leave PPP at the end of the eaten-back strand, it would have to be an pyrophosphate transfer energetically driven by say ATP at every step. It sounds awkward and hard to imagine it being preferred.

If instead the question is couldn't you have mononucleoside-3'-triphosphates that condense on a 5'OH end of growing DNA and so extend it in the 3'->5' direction I don't know anyone can give a reason. In fact I'd say you could but you don't, in life on earth.

The thing to remember is 5'(mono, di and triphosphates are queens, kings and aces in biochemistry on earth. Think ATP - 5'ATP. This is reflected even in the terminology I think. You could consider a DNA strand to be a polymer either of nucleoside 5' or of 3' phosphates. But considering 5' king, you divide mentally the chain up into 5'-PN-3'OH monomeric units, and so define a 5'->3' direction, the only way I find the terminology not confusing.

The empire of 5'- is not a fact about chemistry. The energetics of phosphate or pyrophosphate transfer from 3'- or 5'- NTP or from dNTP should be about the same. It's a fact of biology. Enzymes recognise and catalyse reactions with the 5'-P- compounds. The reason must go back to the origin and early history of life. I guess a 5' with its extra O-C-O- can explore a much larger volume and variety of interacting complementary structures so a catalyst has a greater chance of evolving.

I have never heard any considerations on this - it's not the sort of thing you are very encouraged to ask in biology. If that reflects on anyone it's not the person asking the question IMHO.

 

[Ygggdrasil]

I suspect the reason why the triphosphate resides on the 5' end comes from the fact that for ribonucleotides, a 5' triphosphate is much more stable than a 3' triphosphate.

In ribonucleotides, the 2' hydroxyl resides right near the 3' hydroxyl and would be capable of nucleophilic attack on a 3' triphosphate group, resulting in the loss of pyrophoshate and formation of a 2',3'-cyclic phosphate intermediate (see for example, http://www.scripps.edu/news/scientificreports/sr2001/images/fedor1.gif). Thus, 3'-rNTPs would over time catalyze their own hydrolysis to 3'-rNMPs, while 5'-rNTPs do not face this problem.

That said, there are exceptions to every rule in biology. As it turns out, there are polymerase enzymes that can add nucleotides to the 5' end of substrates (for example, see http://www.pnas.org/content/early/2013/12/04/1321312111.abstract).

 

[epenguin]

Yes, I'd lost sight of that, makes sense for RNA and it is thought that RNA genes preceded DNA in evolution - plus nucleic acid synthesis is of course very far from the only uses of nucleoside triphosphates.