Re: How do Okazaki fragments work?

How do Okazaki fragments work?
I know they have something to do with how DNA is only transcribed from the 3' end to the 5' end (or visa versa, I can't remember which way) but i don't get how they work when the DNA is unwinding.

A detailed discussion of Okazaki fragments is beyond the scope of our site. However, we do have an answer in our archives that includes a brief discussion of Okazaki fragments (890336238.Mb).

For a more in depth discussion, you should read a college-level Biochemistry textbook, like Biochemistry, by Stryer. This text is available online, and you can search for references to Okazaki fragments within the text.

That search reveals five results:
Okazaki Fragments,
One Strand of DNA Is Made Continuously, Whereas the Other Strand Is Synthesized in Fragments,
DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites,
The Leading and Lagging Strands Are Synthesized in a Coordinated Fashion, and
DNA Ligase Joins Ends of DNA in Duplex Regions

To paraphrase Stryer, the DNA polymerase enzyme operates only in the 5^' to 3^' direction, but the strands of the duplex DNA molecule are anti-parallel, pointing in opposite directions; if the Watson strand points in the 5^' to 3^' direction, then the Crick strand points in the 3^' to 5^' direction. One solution would be to have two DNA polymerase molecules move in opposite directions from the origin of replication, with two replication forks moving at the same time, but that would leave large regions of DNA single stranded (the strand not-being replicated by a given polymerase) and susceptible to damage¹. The cell solves this problem by having one strand (the leading strand) replicated continuously by one polymerase, and the other strand (the lagging strand) replicated discontinuously -- in short fragments discovered by Reiji Okazaki -- by the other polymerase, which loops the lagging strand around itself (as shown in the image to the right). The Okazaki fragments are then ligated together. This allows a single replication fork to move forward in the 5^' to 3^' direction along the leading strand, and minimizes the time that either strand has to spend single stranded.