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Current time:0:00Total duration:10:19

AP.BIO:

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let's talk a little bit in more depth about how DNA actually copies itself how it actually replicates and we're going to talk about the actual actors in the process now as I talk about it I'm going to talk a lot about the three prime and the five prime ends of a DNA molecule and if that is completely unfamiliar to you I encourage you to watch the video on the anti parallel structure of DNA and I'll give a little bit of a quick review here just in case you saw it but it was a little while ago this is a zoom in of DNA it's actually the zoom in from that video and when we talk about the five Prime and three prime ends we're referring to what's happening on the the ribose is that form part of this this phosphate sugar backbone so we have ribose right over here five carbon sugar and we can number the carbons this is the one prime carbon that's the two prime carbon that's the three prime carbon that's the four prime carbon and that's the five prime carbon so this this side of the the ladder you could say it is going in the it is going let me draw a little line here this is going in the three prime to five prime direction so this end is three prime and then this end is five prime it's going three prime to five prime notice three this phosphate connects to the three prime then we go to the five prime connects to a phosphate this connects to a three prime then it connects then you go to the 5 prime connects to a phosphate now on this end as we said it's anti parallel it's parallel but it's oriented the other way so this is the 3 prime this is the 5 prime this is the 3 prime this is the 5 prime and so this is just what we're talking about when we talk about the anti parallel structure these two backbones these two strands are parallel to each other but they're oriented in opposite directions so this is the 3 prime end and this is the 5 prime end and this is going to be really important for understanding replication because the DNA polymerase the things that's adding more and more nucleotides to grow a DNA strand it can only add new Clio tides on the 3-prime end so if we were talking about this right over here we would only be able to add we would only be able to add going that way we wouldn't be able to add going we wouldn't be able to add going that way so one way to think about it is you can only add nucleotides on the three prime end or you can only extend you can only extend DNA going from five prime to three prime if you're only adding on the three prime end then you're going from the five prime to the three prime direction you can't go from the three prime to the five prime direction you can't continue to add on the 5 prime side using polymerase so what am I talking about with polymerase well let's look at this diagram right over here that really gives us an overview of all of the different actors so here is just our DNA strand and it's and you could imagine it's just somewhat natural in its natural unreplicated form and you can see we've labeled here the 3 prime and the 5 prime ends and you could follow one of these backbones this 3 prime if you follow it all the way over here it goes this is the corresponding 5 prime end so this and this are the same strand and this one if you follow it along if you go all the way over here is the same strand so this is a 3 prime end and 3 prime end of it and then this is the 5 prime end of it now the first thing we and we've talked about this in previous videos where we give an overview of replication is the general idea is that the the to the the 2 sides of our of our helix the two DNA the the the double helix needs to get split and then we can build another we can build another side of the ladder on each of those 2 split ends you could really view this as if this is a zipper you unzip it and then you put new zippers on either end but there's a lot of it's an in reality it is far more complex than just saying always open a zipper and put new zippers on it it involves a whole bunch of enzymes and all sorts of things and and even in this diagram we're not showing all of the different actors but we're showing you the prime marry actors at least the ones that you will hear discussed when people talk about DNA replication so the first thing that needs to happen right over here it's all tightly tightly wound so let me write that it is tightly tightly wound and it actually turns out the more that we unwind it on one side the more tightly wound it gets on this side so in order for us to unzip the zipper we need to have a nun enzyme that helps us unwind this tightly wound helix and that enzyme is the topoisomerase and the way that it actually works is it it breaks up parts of the backbones temporarily so that it can unwind and then they get back together but the general high-level idea is it unwinds it so then the helicase enzyme and the helicase really doesn't look like this little triangle that's cutting things these things are actually far more fascinating if you were XGC a aim of the molecular structure of helicase but what helicase is doing is it's breaking those hydrogen bonds between our between our nitrogenous bases in this case this is an adenine here this is the thymine it would break that hydrogen bond between these two so first you you unwind it then the gila kate the topoisomerase unwinds it then the helicase breaks them up and then we actually think about these two strands differently because as I mentioned you can only add nucleotides going from the 5 prime to the three prime direction so this strand on the bottom right over here which we will call our leading strand this one actually has it pretty straightforward remember this is the 5 prime end right over here so it can add it can add going in that direction it can add going in that direction right over here this is the 5 prime to 3 prime so what needs to happen here is to start the process you need an RNA primer and the character that puts an RNA primer that is DNA primates we'll talk a little bit more about these characters up here on the lagging strand but they'll add an RNA let me do this in a color you can see an RNA primer will be it here and then once there's a primer then DNA polymerase can just start adding nucleotides it can start adding nucleotides at the three prime end and the reason why the leading strand it has pretty easy is it this this DNA polymerase right over here this preliminaries and once again they aren't these perfect rectangles is on this diagram they're actually much more fascinating than that you see DNA eliminators up there you also see one over here pull limb erase this preliminary scan just you can kind of think of it as following the open zipper and then just keep adding keep adding nucleotides at the three prime end and so this one seems pretty straightforward now and you might say well wouldn't it be easy if we could just add nucleotides at a five-prime end because then we could say look this is going from three prime to five prime well maybe that polymerase or different polymerase could just keep adding nucleotides like that and then everything would be easy well it turns out that that is not the case you cannot add nucleotides at the at the five prime end and let me let me be clear this three prime right over here this I'm talking about this strand this strand over here this let me do this in another color this strand right over here this is the three prime end this is the five prime end and so you can't you can't just keep adding nucleotides just like that and so how does biology handle this well it handles this by adding primers right as this opening happens it'll add primers and this diagram shows the primer is just one nucleotide but a primer is typically several nucleotides roughly ten nucleotides so it'll add roughly ten RNA nucleotides right over here and that's done by the DNA primase so the DNA primase is going along the lagging is going along this this side this I could say the top strand and it's adding it's adding the RNA primer which won't be just one nucleotides it tends to be several of them and then once you have that RNA primer then the polymerase can add in the 5 prime to 3 prime direction it can it can add on the 3 prime end so then it can just start adding it can just start adding DNA like that and so you can imagine this process it kind of you add a the the prime ace put some primer here and then you start building from the 5 prime to the 3 prime direction you start building just like that and then you skip a little bit and then that happens again so you end up with all these fragments of DNA and those fragments are called Okazaki fragments so ouka Okazaki fragments and so what you have happening here on the lagging strand you can think of it as why is it called the lagging strand well you have to do it in this kind of it feels like a suboptimal way where you have to keep creating these Okazaki fragments as you follow this opening and so it lags it's going to be a slower process but then all of these these strands can be put together using the DNA ligase the DNA ligase not only will the strands be put together but then you also have the RNA being actually replaced with DNA and then when all is said and done you are going to have a strand of DNA being replicated or being being created right up here and so it's all done you're going to have two double strands one up here for on the lagging strand and one down here on the leading strand

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