DNA REPLICATION PART 2
PROCESS OF DNA
REPLICATION STEPWISE
The first step is
STEP 1 .ACTIVATION OF NUCLEOTIDES
Here
we are talking of DNA nucleotide now these DNA nucleotides there are of four
types containing four different nitrogen bases and these nucleotides as
they have a pentose sugar, nitrogen base, and one phosphate
group. They are phosphates so we write them as AMP, TMP, CMP, and GMP.MP is
for monophosphates. These are inactive nucleotides that are circulating
all around in the nucleoplasm.
In the case of eukaryotic cells and in the cytoplasm of prokaryotic cells and they are activated by phosphorylates
to the enzyme and all these monophosphates are converted into triphosphates
so it becomes ATP, TTP, CTP, and GTP .so now these are the activated nucleotides
.
STEP NO 2.OPENING
OF THE DNA HELIX
It
doesn't mean that this takes place first and the next step is taking place simultaneously
that means when these are getting activated at the same time that is opening-up
of the DNA helix is also taking place. so for our understanding, we have divided
all the complete process into steps now step number two is opening of the DNA helix.
Now when the DNA helix opens there are multiple steps again involved in the first step
which is involved in the recognition of the site of origin from where it is or no
replicate. So it is RECOGNITION OF THE ORI SITE. Ori (ORIGIN) site is the site where replication starts.
It
is a special nucleotide sequence that needs to be recognized. so first that ORI
site from where the replication is going to start has to be recognized in prokaryotes
Normally, there is one ORI sight, but in the case of eukaryotes, there can be
more than one ORI site. Then HELICASES binds at this ORI SITE and opens up the
helices. It opens up the helix.
Next step the other two enzymes that are
TOPOISOMERASE
and SINGLE STRAND STABILIZING PROTEINS what are they going to do. They will
release the tension from this open up headaches and will hold or stabilize those two separated strands. so by these steps, the headaches open up now here we need to understand that if We are talking
about the linear DNA molecule. it may open from the tip so in that case the
DNA opened up DNA is going to look like an opened helical spring and again we are drawing it for
our convenience this part of the DNA is going to be in the form of zipping and this
opens up part is known as the replication fork.
This is possible in the case of a linear DNA but if the DNA is the
circular DNA then the way we draw the circular DNA is these are the two strands
which are there and the place where these two strands open up .we find that there
is a separation between the two strands. This separated part is known as the replication bubble. So if it is a circular DNA we are going to see something which is called a replication
bubble the place where the two DNA's are
going to get separated and in case of a linear one we are going to draw replication
fork .this is what is opening up of the DNA strands.
Now let us understand a few more things before we take up the
next step. we know that these two strands of DNA are anti-parallel. The third prime
means the third carbon is free here the same strand at the other end will have
the fifth carbon-free and the Strand which is in front of it. The
complementary strand will have the third prime 3 here (opposite) and fifth free here.
OUR NEXT STEP IS GOING TO BE FORMATION OF
THE PRIMER
This take-up we need to know why this
primer is required and where this primer will be for primer or we can even write
that step here. So that by understanding the structure we can also relate those
things .so that become OUR STEP NUMBER 3 THAT IS PRIMER FORMATION and
the enzyme which is required for this is
DNA
DIRECTED RNA POLYMERASE
This
primer is a small segment of RNA nucleotide maybe six, seven, eight, 10 nucleotides
are the nucleotides so if this is, what we are talking of as a primer? The
primer has one end where the third carbon is going to be free and the other end
which is going to be the fifth carbon-free. That means whether we are talking
of DNA or RNA choose that polarity one in has OH free the other end has
phosphoric acid or phosphate group free. Here also this RNA primer which we
have drawn here has a third carbon-free in the fifth end.
The nucleotide
which is coming is getting added at the third end. The reason why it always
gets added at the third end is because at the third end there is a functional
group than this OH. Now let us see the primer formation. if this track that is
parent strand 3 to 5.we are talking of this track if it has to synthesize a new
DNA where should the primer come, the new strand which is going to come here
the RNA primer will have the fifth carbon 3 here .because the new strand which
is going to come here should be anti-parallel .so this end will be 5 and this the end is going to be though, that means here there is going to be OH. This fits
into what we were talking about right now
this is added and if new nucleotide of zero it will come at the third
end then again here then again here.
When
new nucleotides will keep coming let us come to the other strand. The two
strands we are talking about this one which strand we are talking about 5 to 3
prime parents strand. If we make a nuclear this article primer here then what
should come in front of the five prime is three and what would cover the other the end is five .what is at five has phosphate and this has OH and we said the new a nucleotide can come only at the functional group that means here but there is
no DNA to give that complementary nucleotide. Here, so this position of primer
is actually wrong
The primer should fall at the base of the opened-up fragment. in this case, suppose
we take only this opened up part .this end becomes 5 prime and if you are talking
of this end this becomes the third prime, and the RNA primer if is formed here
the in front of three it will have its 5 prime and the other end will have the
third prime and third has the old. So now the DNA nucleotide can come and bind
here as well as here. So one thing which we have to remember is the primer is
formed in front of the third end of the parent strand.
if
we are talking of this cracks the primer is in front of the third carbon of the
parents. if you are talking of this open up strand the primer is again in front
of the third end of the template DNA on which the new DNA is to synthesized. And
one more important thing that we have to remember is that the new DNA or the
strand always grows from five prime towards three prime. this you can say is
the most important thing and we have to strictly follow it because this is how
the new DNA strand is going to get synthesized .this is true even for RNA and
the simple reason for this is that at the third end there is OH or functional
groups if anything new has to come it can come and find only at the third. So
DNA strand is going to grow towards its third prime
We have to remember that primer is
formed in front of the third end of the template strand or the parent strand
and the new DNA or RNA for that grows towards its third prime. That means the
direction is going to be always five-prime towards three prime. so these are the first three steps that is
1. Activation of nucleotides
2. Opening up of the helix
First
the ORI site is recognized that is the place from whether the applications
going to originate then in any case TOPOISOMERASE and SINGLE-STRANDED
SINGLE STRAND STABILIZING in time. They stabilize the helix the two strands
separated this is what we see if it is a linear molecule which is known as
replication fork. Then primer formation primer is a small seven to ten
nucleotide sequence RNA nucleotide sequence.