WEBVTT

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- [Voiceover] Let's talk
a little bit in more depth

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about how DNA actually copies itself,

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how it actually replicates,

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and we're gonna talk about

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the actual actors in the process.

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Now, as I talk about
it, I'm gonna talk a lot

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about the 3' and 5' ends
of the DNA molecule,

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and if that is completely
unfamiliar to you,

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I encourage you to watch the video

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on the antiparallel structure of DNA.

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And I'll give a little bit
of a quick review here,

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just in case you saw it but
it was a little while ago.

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This is a zoom-in of DNA,

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it's actually the zoom-in from that video,

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and when we talk about the 5' and 3' ends,

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we're referring to what's
happening on the riboses

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that formed part of this
phosphate sugar backbone.

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So we have ribose right over here,

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five-carbon sugar,

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and we can number the carbons;

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this is the 1' carbon,
that's the 2' carbon,

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that's the 3' carbon,
that's the 4' carbon,

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and that's the 5' carbon.

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So this side of the ladder,

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you could say,

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it is going in the ...

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it is going, let me
draw a little line here,

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this is going in the 3' to 5' direction.

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So this end is 3' and then this end is 5'.

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It's going 3' to 5'.

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Notice three, this phosphate
connects to the 3',

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then we go to the 5'
connects to a phosphate,

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this connects to a 3',

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then it connects--

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then we go to the 5'
connects to a phosphate.

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Now on this end, as we
said it's antiparallel.

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It's parallel, but it's
oriented the other way.

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So this is the 3', this is the 5',

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this is the 3', this is the 5'.

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And so this is just
what we're talking about

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when we talk about the
antiparallel structure.

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These two backbones,

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these two strands are
parallel to each other,

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but they're oriented
in opposite directions.

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So this is the 3' end
and this is the 5' end.

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And this is gonna be really important

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for understanding replication,

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because the DNA polymerase,

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the things that's adding
more and more nucleotides

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to grow a DNA strand;

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it can only add nucleotides on the 3' end.

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So if we were talking
about this right over here,

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we would only be able to add …

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We would only be able
to add going that way.

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We wouldn't be able to add going …

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We wouldn't be able to add going that way.

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So one way to think about it
is you can only add nucleotides

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on the 3' end or you can only extend …

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You can only extend DNA
going from 5' to 3'.

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If you're only adding on the 3' end,

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then you're going from the
5' to the 3' direction.

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You can't go from the
3' to the 5' direction.

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You can't continue to add on
the 5' side using polymerase.

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So what am I talking
about with polymerase.

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Well let's look at this
diagram right over here

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that really gives us an overview

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of all of the different actors.

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So here is just our of our DNA strand,

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and it's, you can imagine
it's somewhat natural,

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in it's natural unreplicated form,

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and you could see we've labeled
here the 3' and the 5' ends,

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and you could follow
one of these backbones.

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This 3', if you follow
it all the way over here,

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it goes, this is the corresponding 5' end.

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So this and this are the same strand,

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and this one, if you follow it along,

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if you go all the way over
here, it's the same strand.

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So this is the 3' end,

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and 3' end of it and then
this is the 5' end of it.

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Now the first thing,

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and we've talked about
this in previous videos

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where we give an overview of replication,

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is the general idea is that
the two sides of our helix,

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the two DNA, the double-helix
needs to get split,

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and then we can build another,

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we can build another side of the ladder

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on each of those two split ends.

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You could really view this
as if this is a zipper,

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you unzip it and then you put
new zippers on either end.

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But there's a lot of--

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in reality, it is far more
complex than just saying

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"Oh, let's open the zipper
and put new zippers on it."

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It involves a whole bunch of
enzymes and all sorts of things

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and even in this diagram,

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we're not showing all
of the different actors,

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but we're showing you the primary actors,

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at least the ones that
you'll hear discussed

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when people talk about DNA replication.

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So the first thing that needs to happen,

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right over here, it's all
tightly, tightly wound.

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So let me write that,

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it is tightly, tightly wound.

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And it actually turns out,

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the more that we unwind it on one side,

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the more tightly wound
it gets on this side.

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So in order for us to unzip the zipper,

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we need to have an enzyme

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that helps us unwind
this tightly wound helix.

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And that enzyme is the topoisomerase.

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And the way that it actually works is

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it breaks up parts of the
back bones temporarily,

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so that it can unwind and
then they get back together,

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but the general high-level
idea is it unwinds it,

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so then the helicase enzyme,

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and the helicase really doesn't look like

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this little triangle
that's cutting things.

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These things are actually
far more fascinating

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if you were to actually see a--

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the molecular structure of helicase.

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But what helicase is doing

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is it's breaking those
hydrogen bonds between our …

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Between our nitrogenous bases,

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in this case it's an adenine
here, this is a thymine

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and it would break that
hydrogen bond between these two.

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So, first you unwind it,

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then the helicase,

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the topoisomerase unwinds it,

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then the helicase breaks them up,

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and then we actually think about

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these two strands differently,

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because as I mentioned,

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you can only add nucleotides

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going from the 5' to 3' direction.

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So this strand on the
bottom right over here

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which we will call our leading strand,

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this one actually has a
pretty straightforward,

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remember this is the
5' end right over here,

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so it can add,

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it can add going in that direction,

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it can add going in that
direction right over here.

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This is the 5' to 3',

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so what needs to happen here
is to start the process,

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you need an RNA primer

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and the character that puts an RNA primer,

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that is DNA primase.

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We'll talk a little bit more about

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these characters up here
in the lagging strand,

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but they'll add an RNA,

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let me do this in a color you can see,

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an RNA primer will be added here,

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and then once there's a primer,

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then DNA polymerase can just
start adding nucleotides,

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it can start adding
nucleotides at the 3' end.

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And the reason why the leading
strand has it pretty easy

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is this DNA polymerase right over here,

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this polymerase, and once again,

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they aren't these perfect
rectangles as on this diagram.

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They're actually much more
fascinating than that.

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You see the polymerase up there,

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you also see you one
over here, polymerase.

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This polymerase can just,

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you can kind of think of it
as following the opened zipper

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and then just keep adding,

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keep adding nucleotides at the 3' end.

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And so this one seems
pretty straightforward.

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Now, you might say wouldn't it be easy

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if we could just add
nucleotides at a 5' end,

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because then we could say

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well this is going from 3' to 5',

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well maybe that polymerase
or different polymerase

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could just keep adding
nucleotides like that,

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and then everything would be easy.

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Well, it turns out that
that is not the case.

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you cannot add nucleotides at the 5' end,

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and let me be clear,
this 3' right over here,

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this, I'm talking about this strand.

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This strand right over here,

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this, let me do this in another color,

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this strand right over here,

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this is the 3' end, this is the 5' end,

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and so you can't,

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you can't just keep adding
nucleotides just like that,

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and so how does biology handle this?

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Well it handles this by adding primers

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right as this opening
happens, it'll add primers,

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and this diagram shows the
primer is just one nucleotide

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but a primer is typically
several nucleotides,

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roughly 10 nucleotides.

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So it'll add roughly 10 RNA
nucleotides right over here,

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and that's done by the DNA primase.

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So the DNA primase is
going along the lagging,

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is going along this side,
I can say the top strand,

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and it's adding,

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it's adding the RNA primer,

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which won't be just one nucleotide,

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it tends to be several of them,

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and then once you have that RNA primer,

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then the polymerase can add
in the 5' to 3' direction,

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it can add on the 3' end.

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So then it can just start adding,

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it can just start adding DNA like that.

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And so you can imagine this process,

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it's kind of, you add the
primase, put some primer here,

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and then you start building
from the 5' to 3' direction.

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You start building just like that,

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and then you skip a little bit
and then that happens again.

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So you end up with all
these fragments of DNA

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and those fragments are
called Okazaki fragments.

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So, it's a Okazaki fragments,

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and so what you have happening
here on the lagging strand,

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you can think of it as,

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why is it called the lagging strand?

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Well you have to do it in this kind of …

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it feels like a sub-optimal way

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where you have to keep creating
these Okazaki fragments

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as you follow this opening,

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and so it lags, it's going
to be a slower process,

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but then all of these
strands can be put together

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using the DNA ligase.

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The DNA ligase; not only will
the strands be put together,

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but then you also have the
RNA being actually replaced

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with DNA and then when all is said done,

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you are going to have a strand
of DNA being replicated,

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or being created right up here.

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So when it's all done, you're
gonna have two double strands,

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one up here for on the lagging strand,

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and one down here on the leading strand.