Which end is 5' and 3' ?

[Le Boudin]

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From TBR FL6 #139

DNA polymerase I requires a primer for proper activity. In the repair of pyrimidine dimers, the primer is:

a. provided by the enzyme primase
b. ...
c. the 3' end of the nicked strand
d. ...

C is the best answer. If we look at the diagram, we can see that DNA polymerase I fills in the gap created by the excision. There is no need for a new primer (therefore, primase is not a possible answer), because a primer is already there in the form of a 3'-OH on the nicked strand. Consider the other answers: We already mentioned why primase is incorrect. uvrABC is the enzyme responsible for excising the damaged piece of DNA, making it an unlikely answer. The strand that runs antiparallel to the nicked strand is the template, and not the primer.
OK so first of all it's a trick question? "DNA Pol 1 requires a primer" ... "there is no need for a new primer".

Second of all, the fat grey arrow show extension going from Left to Right, and the 3'-OH of the nicked strand is on the other side of the nick. How could polymerization start there? Unless they mean:

5'-----------3' end of nick ___________ 5' end of nick---------3'

So in a nick, which ends are the 5' of the nicked strand and the 3'?

 

[GeronimoMD]

The grey arrow would be the 3' end of the nicked strand.

http://highered.mcgraw-hill.com/olc/dl/120082/micro18.swf

 

[whiteshadodw]

The grey arrow would be the 3' end of the nicked strand.

http://highered.mcgraw-hill.com/olc/dl/120082/micro18.swf

Geronimo is right. the 3' end of the nick would be the 5' end of the strand. it can't be the other side of the nick because the other side is 5'. DNA is synthesized 5'-->3', but the 3'OH of the nucleotide that's already on the strand makes a phosphodiester bond with the 5' end incoming nucleotide.

 

[GreenRabbit]

OK so first of all it's a trick question? "DNA Pol 1 requires a primer" ... "there is no need for a new primer".

It's not a trick question. Notice the word "new".

 

[Le Boudin]

Thanks for the replies. Thinking about it from the biochemical mechanistic perspective of 3'-OH attacking the new dNTP, etc. makes sense which end is the 3'-OH vs. the 5' end.