Leading and lagging strands in DNA replication | MCAT | Khan Academy

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. If that is completely unfamiliar to you, I encourage you to watch the video on the anti-parallel structure of DNA. 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. When we talk about the five prime and three prime ends, we're referring to what's happening on the riboses that form part of 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 side of the ladder, you could say, is going in the—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, and then we go to the five 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 three prime, this is the five prime, this is the three prime, this is the five prime. 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 three prime end, and this is the five prime end.

This is going to be really important for understanding replication because the DNA polymerase, the thing that's adding more and more nucleotides to grow a DNA strand, it can only add nucleotides on the three 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 five 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. Here is just our DNA strand, and you could imagine it's just somewhat natural in its natural unreplicated form. You could see we've labeled here the three prime and the five prime ends, and you could follow one of these backbones. This three prime, if you follow it all the way over here, goes—this is the corresponding five prime end. So this and this are the same strand.

If you follow it along, if you go all the way over here, it’s the same strand. So this is the three prime end and three prime end of it, and then this is the five prime end of it. Now the first thing we—and we've talked about this in previous videos where we gave an overview of replication—is the general idea that the two sides of our helix, the two DNA double helices, need to get split. Then we can build another side of the ladder on each of those two 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 in reality, it is far more complex than just saying, "Oh, let's open a zipper and put new zippers on it." It involves a whole bunch of enzymes and all sorts of things, and even in this diagram, we're not showing all of the different actors, but we're showing you the primary actors, at least the ones that you will hear discussed when people talk about DNA replication.

The first thing that needs to happen right over here—it’s all tightly, tightly wound. Let me write that—it is tightly, tightly wound. 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 an enzyme that helps us unwind this tightly-wound helix, and that enzyme is the topoisomerase.

The way that it actually works is 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—the helicase really doesn't look like this little triangle that's cutting things. These things are actually far more fascinating if you were actually to see the molecular structure of helicase. But what helicase is doing is breaking those hydrogen bonds between our nitrogenous bases. In this case, this is an adenine here; this is a thymine. It would break that hydrogen bond between these two.

So first, you unwind it; then the topoisomerase unwinds it, then the helicase breaks them up. Then we actually think about these two strands differently because, as I mentioned, you can only add nucleotides going from the five 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 five prime end right over here, so it can add going in that direction. It can add going in that direction.

Right over here, this is the five prime to three prime, so what needs to happen here is to start the process, you need an RNA primer. The character that puts an RNA primer—that is DNA primase. 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 added 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. The reason why the leading strand has it pretty easy is this DNA polymerase right over here. This primase—and once again they aren't these perfect rectangles as on this diagram. They're actually much more fascinating than that. You see DNA polymerase up there; you also see one over here, polymerase. This primase can just, you can kind of think of 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, 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 five prime end, and let me be clear: this three prime right over here— 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 just keep adding nucleotides just like that. 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 a primer as just one nucleotide, but a primer is typically several nucleotides, roughly 10 nucleotides.

So it'll add roughly 10 RNA nucleotides right over here, and that's done by the DNA primase. So the DNA primase is going along the lagging; it's going along this side, you could say, the top strand, and it's adding—it's adding the RNA primer, which won't be just one nucleotide; it tends to be several of them. Once you have that RNA primer, then the polymerase can add in the five prime to three prime direction. It can add on the three 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, the primase puts some primer here, and then you start building from the five prime to the three 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 the Okazaki fragments—and so what you have happening here on the lagging strand—you could 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 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 created right up here. When it's all done, you're going to have two double strands—one up here for the lagging strand and one down here on the leading strand.