- [Voiceover] So let's say we have a piece of
double stranded DNA, and DNA is really a
very, very long molecule so we're gonna
put in arrows at the ends of all
of our DNA strands to remember that.
And when DNA's ready to get replicated
it's going to start bubbling out in many different spots.
And each one of these places is called
an origin of replication and the origin
of replication is simply a sequence of nucleotides
that tells all of the enzymes involved
in replication that oh, this
is where you should start working.
Let's take a closer look at one of these
origins of replication, and sometimes it's
called a bubble of replication or a replication bubble
and let's label our replication bubble.
So, this is the five prime end.
This is going to be the three prime end
and DNA strands are anti parallel to each other.
They run in opposite directions,
so it means that the bottom is going to be
five prime there, and three prime over here.
And an enzyme's going to come along.
This enzyme is DNA polymerase.
And let's see what DNA polymerase is going to do.
So, we'll start with the bottom strand.
DNA polymerase is going to lay down an RNA primer
and the purpose of this RNA primer is
it acts as a piece of nucleic acid onto
which DNA polymerase can then hook the nucleotide.
So, the DNA polymerase will then
add nucleotides in this direction.
Let's look at our top strand.
DNA polymerase lays down an RNA primer
and then proceeds to add nucleotides in this direction.
Let's look at the strands that are being synthesized,
so DNA synthesized always in the
five prime to three prime direction.
So label our top strand, we always go from
five prime to three prime.
So, synthesis is happening in the five prime
to three prime direction, but if you look
at the parental strands, the original strands of DNA,
they're actually being read in the opposite direction.
They're being read from three prime to five prime.
So, let's make this very clear.
DNA is synthesized in the five
prime to three prime direction.
And, again, that's referring to the strand
that's being put together, but DNA is read,
and when I say that I'm referring
to the parental or template strands.
DNA is read in the three prime to five prime direction.
And now let's take our origin of replication,
or replication bubble, and let's cut it in half so that
we can take a closer look at what's really happening.
And I drew it here, except that instead of
a curve, I drew it as a straight line,
but it's really the same thing.
And let's label our replication fork.
This is a replication fork because
as you can see it just looks like a fork.
Let's label the strands.
So, let's say that this is five prime.
That means this is going to be three prime.
And of course the other strand
goes in the opposite direction.
And let's pretend like we are a DNA polymerase.
What are we going to do?
Let's start with the bottom strand.
We're gonna lay down a primer.
Remember, it's made up of RNA.
And we're going to proceed to
add nucleotides in this direction.
And even though I'm drawing the nucleotides
as separate units, remember they're really
being connected to each other, but I just
want to, you know, emphasize the fact that
synthesis is happening so I'm drawing them
as separate units, but you know, try to remember
they're really connected to each other.
And, just to remember, again, synthesis
goes from five prime to three prime.
Let's look at our top strand.
We put an RNA primer over here,
at the five prime end.
Then we proceed to add nucleotides in this direction
and I'm going to label that strand as well.
It goes from five prime to three prime.
Let's analyze what's happening here.
In the bottom strand, we added an RNA primer
and then we proceeded to add nucleotides
in this direction and when this part of the fork
opens up, this part right here,
we can just add more and more nucleotides.
But look at the top strand.
When you add an RNA primer and then add a nucleotide
in this direction, and then when we wanna
kind of continue to replicate
this part of the DNA, well, we can't.
We kind of have to wait 'til the fork
opens up with enough room for us to, you know,
put down a primer and then add nucleotides.
So, let's see what this replication
fork looks like a few seconds later.
So in our bottom strand, we had an RNA primer,
and we kind of just added nucleotides in this direction
and as the fork opened we just kept adding primers.
I'm sorry, nucleotides.
And in this strand, here is the first primer
that we added and then when the fork opened up
with enough room, we lay down another primer,
and then proceed to add nucleotides in this direction.
Let's see what this looks like a few seconds later.
So, again, in our bottom strand we had
only one RNA primer and then
we added a bunch of nucleotides.
And in our top strand, that's our first primer,
and then we added some nucleotides and then we put
in another primer, and then added nucleotides.
Then we put in another primer and we added nucleotides
and I think you get the point.
And so in the bottom strand, synthesis was continuous
and we call that strand the leading strand.
But in the top strand, synthesis was not continuous
and we call that strand the lagging strand
because it's always kind of lagging behind
and it's always waiting for the fork
to open up with enough room so it can put down
another primer and then add all the nucleotides.
And these fragments have a name.
They're actually named after the person who discovered them.
They're called Okazaki fragments.
And just to give you an idea of what's
really going on over here, I'm drawing
maybe five or six nucleotides per second,
but in real life, this happens at a staggering pace.
In fact, the bacteria e. coli, the DNA
polymerase in e. coli will string
together 1,000 nucleotides in one second.
So that's a really large amount
and we humans are a bit slower.
We put together about 50 nucleotides per second.
But still, these are really impressive numbers.
You know, you could just imagine DNA polymerase
zipping down a piece of DNA and stringing
together 1,000 nucleotides in one second.
That's a very, very impressive thing.
Let's go to our next step.
So, we've finished synthesizing our strands of DNA.
But we have all these RNA primers here
and we don't want RNA primer
stuck in the middle of our DNA.
So an enzyme, RNase is going to come along
and remove all these primers and then
a different enzyme will kind of fill
in the gaps of DNA.
And I just want to point out to you,
if you remember before I told you
that really all these nucleotides are bonded together
and just, you know, lifted out,
because I was trying to show you
how it was just being synthesized.
But remember, these are all connected to each other.
But not only that, these nucleotides,
and again, I didn't draw this in the previous diagrams,
as they're being synthesized, they're also
being connected to the corresponding nucleotides
on the parental strand.
So just bear in mind that these are all bonds
and just remember that this is how it really is.
And I'm not gonna fill in the rest,
but I think you get the point.
And our last step is, an enzyme, DNA ligase,
will come and string together all of the disparate
or separate fragments of DNA so that we have
one continuous piece of DNA.
Here's our newly synthesized pairs of DNA.
So, we have two pairs of DNA and each
pair is going to have one parental strand,
that's the original strand that we were
using as a template and one daughter strand.