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Posts Tagged ‘Okazaki

a DNA dialogue 6: Okazaki fragments, as promised

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Canto: Okay, so first off, why are Okazaki fragments so called?

Jacinta: Well as anyone would guess, they’re named after someone Japanese, in this case two, the husband and wife team Reiji and Tsuneko Okazaki, who discovered these short, discontinuously synthesised stretches of DNA nucleotides in the 1960s.

Canto: Yes their story is intriguing – tragic but also inspiring. Reiji, the husband, was born in Hiroshima and died in 1975 from leukaemia, related to the 1945 A-bomb. He was only 44. Tsuneko Okazaki continued their research and went on to make many other contributions to genetics and molecular biology, as a professor, teacher, mentor and director of scientific institutes. Her achievements would surely make her a Nobel candidate, and she’s still alive, so maybe…

Jacinta: Now the key to Okazaki fragments is this lagging strand. Its directionality means that the DNA primase, followed by the DNA polymerase, must work ‘backwards’, away from the replication fork, to add nucleotides. This means that that they have to have periodic breaks – but I’m not sure exactly why – in creating this lagging strand. So the entire replication process is described as semi-discontinuous because of this fundamental difference between the continuously created leading strand and the stop-start ‘fragmentary’ (at least briefly) lagging strand.

Canto: But we need to know why this ‘backward’ movement has to be stop-start, and I’d also like to know more about this primase and polymerase, thank you.  

Jacinta: Well the Okazakis and their team discovered this semi-discontinuous replication process in studying the replication of good old Escherichia coli, the go-to research bacterium, and it was a surprise at the time. Now, I’m looking at the explanation for this necessarily discontinuous process in Wikipedia, and I confess I don’t really understand it, but I’ll give it a go. Apparently the Okazakis ‘suggested that there is no found mechanism that showed continuous replication in the 3′ to 5′ direction, only 5′ to 3′ using DNA polymerase, a replication enzyme’, to quote from Wikipedia. So they were rather cleverly hypothesising that there must be another mechanism for the 3′ to 5′ lagging strand, which must be discontinuous. 

Canto: And another way of saying that, is that the process must be fragmentary. And they used experiments to test this hypothesis? 

Jacinta: Correct, and I won’t go into the process of testing, as if I could. It involved pulse-labelling. Don’t ask, but it has something to do with radioactivity. Anyway, the test was successful, and was supported by the discovery shortly afterwards of polynucleotide ligase, the enzyme that stitches these fragments together. Now, you want to know more about primase, polymerase, and now ligase no doubt. So here’s a bit of the low-down. DNA primase is, to confuse you, an RNA polymerase, which synthesises RNA from a DNA template. It’s a catalyst in the synthesis of a short RNA segment, known as a primer. It’s extremely important in DNA replication, because no polymerase (and you know how polymerase keeps getting associated with primase) can make anything happen without an RNA (or DNA) primer.

Canto: But why? This is getting so complicated.

Jacinta: I assure you, we’ve barely scratched the surface….

Canto: Well, Socrates was right – there’s an essential wisdom in being aware of how ignorant you are. We’ll battle on in our small way.    

 

 

 

 

Written by stewart henderson

February 27, 2020 at 5:48 pm