Then we need to understand how replication happens.
What is the general pattern and then we will
step into the details. First we are going to
begin by looking at
prokaryotic replication. In prokaryotic replication,
you recall the bacteria have a single circular
chromosome. It may not look like a circle,
it could be all crumbled up in the nucleus,
but it is single and it is circular and so
each of them will have a specific origin of
replication and a specific sequence that says
termination of replication.
In this bacterial chromosome, we will see
a replicon opened up or a space opened up
in which we can have our enzymes or enzymes
machinery. We call that machinery a replisome
and those replisomes will proceed bidirectionally
around the circular chromosomes until they
both run into the terminus at which case the
two new chromosomes will separate from each
other and go into their respective cells.
Pretty simple process right? Well not quite.
It is the machinery that is in the two replicons
in the replisome that is involved in the whole
replication process that we have to get to
know in this lecture. Key again here I might
have repeat it because it comes up over and
over is that DNA polymerase are primary enzyme
that is laying down at nucleotides can only
read in the three prime to five prime directions.
The other key piece of information is that
DNA polymerase also needs that three prime
OH group. Those three prime OH group that
I keep emphasizing is really important to
know. It needs a three prime OH group to grab
on to the previous nucleotide and lay down
the next nucleotide. Let us say we are looking
at a template strand and we are looking at
the newly synthesized strand. We will say
that the three prime is on this template strand
and we are proceeding in this direction. DNA
polymerase has to read the template strand
in this direction, but it is laying down a
complimentary strand in this direction.
So we have one nucleotide with the three prime OH
hanging out on that end, and another nucleotide
with three prime OH hanging out on that end.
The newly synthesized strand is now going
to be oriented in the five prime to three
prime directions. Three prime OH is critical
reading, always three prime to five prime, laying
down new nucleotides five prime to three
prime. Critical to understand in order
to see why DNA replication can get quite confusing.
Let us look at more details.
Here is our nucleotide. We will emphasize
the piece with the sugar. We have our three
prime OH and our five prime phosphates. Super
important parts of a molecule to understand
how they are all put together on the newly
synthesized DNA strand. These parent strands
are going to be antiparallel. We have a replication
fork. When that replication fork opens up,
we can see that the template strands are sort
of in opposite orientation. We have a leading
strand that is oriented from three prime,
the green piece, three prime to five prime
no problem whatsoever. DNA polymerase can run
along that strand and lay down nucleotides
continuously. However, the other strand, the
old complimentary strand has a little bit
of an issue because now we can only read at
that replication fork, there is a five prime
end sticking out on top and the green strand
goes to a three prime end in which case DNA
polymerase has an issue because he cannot
read five to three. It has to read the green
strand from three prime to five prime and
lay down nucleotides in an antiparallel fashion.
So that requires a little bit of jumping back.
We will look at the details of how that works
shortly, but as we jump back, we need to create
different fragments. We call these fragments
Okazaki fragments. I will show you how we
will deal with them shortly. But Okazaki fragment
is a word that you need to know. Keep in mind
that replication is bidirectional. There is
a replication fork on both ends. One side
we have talked about. Here we have a lagging
strand up on top, a leading strand down below.
On the other end, the lagging strand is going
to be on the bottom and the leading strand
is going to be on the top, but it is on this
bottom strand now that we are reading the
template from five to three that doesn't work
out for DNA polymerase. So we are going to
have Okazaki fragments on this lower strands
also, bi-directional replication.