foreign
polymerization is done Naturally by DNA
and we know that DNA polymerization
process is carried naturally due to the
pyrophosphate that is produced the
hydrolysis of pyrophosphate drives the
reaction forward and we also know that
if there is only one phosphate left any
polymerase cannot seal it
it's called The Nick we need ligase to
add an extra phosphate from ATP and then
cancel the name
now we are going to talk about the
different types of DNA polymerase
different types of DNA polymerase that
are available and in prokaryotic
replication particularly we talk about
different types of polymerases so
here you can see the table in this table
we have DNA polymerase we have three
different types of activities of a DNA
polymerase and ultimately the function
of the DNA polymerase
now a DNA polymerase as I mentioned it
has two kinds of Activity one is the
polymerization
polymerization and the second one is
exonuclease activity or proof reading
right
a proofreading activity
now polymerization direction is
done by all kinds of DNA polymerase
but the exonuclease activity can be of
two different type 5 Prime to three
prime
or
C Prime to five Prime X nucleus activity
but not all the polymer is share same
sort of exonucleus activity different
polymers have different types of
exonuclease activity here we are seeing
five different types of polymerase so
polymer is one
polymerase activity for all the
polymerase are five Prime to three prime
but for polymer is one the exonuclease
activity five to three prime EXO nucleus
activity is present
activity are also present so that means
DNA polymer is one
can go 5 Prime to 3 Prime
polymerization
and it can also
go exonuclease activity
in both Direction
in both the directions
that is a unique feature of DNA
polymerase one unique feature of having
five Prime to three prime exonucleus
activity which is not present in any of
other DNA polymerase
well the rest of the other DNA
polymerase like DNA polymers 2 and 3
they have three prime to five Prime
exonuclease activities
okay
so what are the function of DNA polymer
is one
removes and replaces primers at the end
of DNA replication event due to the
capability of cleaving a DNA strand c25
prime or 5 to 3 Prime they are excellent
choice to utilize them to remove the RNA
or any ribonucleotides from the existing
DNA and fill that Gap
now what is the gap
let's say this is the nearest trend
so these are hydrogen bonds in the
middle
but here are two nucleotides let's say A
and G
no other nucleotide present in the
complementary DNA this region is known
as
a gap
so Gap means
nucleotides are missing Gap means
nucleotida
anything
but a Nick is
when nucleotides are present
only the first four diaster Bond
let me see
this is the difference between a Nick
and a gap
so if there is a gap
what do you need to fill it
nucleotides and polymerase
if there is a Nick then what do we need
to fill it
DNA ligase is needed no nucleotides are
needed and ATP is needed because ligase
requires ATP to function
clear
so the function of polymer is two
polymerase 2 is involved in DNA repair
and
it restarts the replication after damage
DNA Hall synthetic synthesis process
and the polymer is C
is the actual polymerase required for
elongation of the DNA or DNA
replication processing prokaryotes so in
prokaryotic DNA polymerase type DNA
polymerase 3 is the
predominant DNA polymerase for the
process of application
and in prokaryotes polymerase one is
used to fill the gaps
mix never can be sealed by polymerase it
can only be sealed by ligase with ATP
and polymerase 2 is used as a repair
mechanism a polymerase for DNA repair
mechanism
apart from that there are DNA polymers
four and five
four and a four and five both this kind
of DNA polymerase are used very less but
they are mostly used for DNA repair
mechanism
okay and repair mechanism of translation
means if there's a lesion formed in the
DNA lesion means where there is no
proper interaction or pairing of the
nucleotides a soil structure in the DNA
strand those lesions can be removed and
new DNA can be synthesized in that
position by polymerase type 5. but
mainly there are the C Paul 1.2 and Paul
three
the unique feature about DNA polymer is
one is that it carries a 5.3 Prime
exonuclease activity
foreign
foreign
I would like it
so here you'll see the important feature
of DNA polymer is one
you see the DNA polymer is one is a like
it contains two different subunits
so when we treat it with some
proteolytic enzyme
the proteolysis because the protein DNA
polymer is one the proteolysis of
polymerase gives arise to two fragments
one larger fragment and one small
fragment
okay when we do that extracellularly on
the outside of a cell we can do this
outside of the cell
in a environment outside any vitro
process right we add some proteolytic
enzyme it just it degrades of polyvinus
one hollow enzyme Hollow means when the
enzyme is filled with multiple
cellulitis so they separate into two
fragments one large one small the large
fragment is known as cleaner fragment
and the small fragment is basically
having five Prime to three prime
extonuclease activity
now this cleaner fragment contains two
fragments here you can see green and
yellow one with the five Prime to three
prime polymerization activity another
one is another three one into five Prime
exonuclease activity means basically all
the other all two pole three that they
share three to five Prime EXO nucleus
activity which is also being shared by
pole one
so 5 Prime to 3 Prime polymer
polymerization activity C Prime to five
Prime X1 equals activity this is present
in all polymerase one two three
but
the 5 Prime to three prime
exonuclease activity is rare
is found in
only Paul one
and the moment we use the proteolysis we
have these two fragments one large one
small so the large fragment is capable
of carrying out the function of both
five Prime to three prime polymerization
activity 3.5 Prime exonucleus activity
and they rest other the five point three
prime X activity gets separated and this
is not always needed because you know if
you want to delete something or delete
added nucleotide we need to go backward
that is C Prime to five Prime that's why
always the external nucleus activities
are present three to five Prime and not
five to three prime
now we are going to see the examples of
eukaryotic polymerase and look at the
comparison between them
here you can see the eukaryotic
polymerase the polymer is eukaryotes are
named as Alpha Delta Epsilon beta gamma
you can see the Delta and Epsilon are
known as the predominant polymerase is
in eukaryotes they help in elongation of
leading and lagging strength Epsilon
involved with the leading strand Delta
with the lagging strength on the other
hand polymer is Alpha is simply used for
the priming of replication in both the
strands
and polymer is beta involved in DNA
repair polymerase gamma in the
replication of mitochondrial DNA because
Union eukaryotes organelles like
mitochondria have their own DNA and the
mitochondrial DNA
replication is done by polymerase gamma
all right so these are the different
types different DNA polymers is the
classification comparison
now we are going to talk about the DNA
polymerase structure how they look like
this is the DNA polymerase C or policy
structure
basically this is a overall idea of DNA
policy there are different sub uh
assemblies to a ball three structure you
can see it's made with multiple
different subunits
so it looks something like two arms two
hands connected to a body
so consider this as a body known as Tau
unit holding two different mirror
identical sides of the polymerase
together
and the bottom let's say this is the leg
which is built with gamma
Delta Chi
PSI and all these different structures
now these three different portions the
body main bodies the arms made up with
Alpha and this is known as delt Epsilon
Theta and there is beta clamp which will
be loaded here
okay so if you consider this as a
overall structure beta clamp has an
important specific role to play Tau has
a role to hold them together and this
leg which is made with Delta Psi and all
this segment they help to load the beta
note the DNA onto the beta clamp but
beta climb on top of the DNA basically
imagine this is the DNA strand the DNA
strand will be separated
right
once it's separated the polymerase will
load itself
so let's say this is the polymerase
Alpha units Tau connected
okay Alpha m is the body and these are
this is the loader the bitter clamp
will help to load the polymerase
on top of both the template strand
because the DNA replication process that
is going on in the prokaryotes it's
going on in both the strands
both strands simultaneously
both strands simultaneously
so the beta clamp is loaded in both the
strands and the polymerase will move
from five Prime to three prime direction
of newly synthesizing strands Direction
so this was let's say the red one is the
existing parental
C Prime to five Prime
so the New Strand is the blue color 5
Prime to C Prime this is new and
polymerase is movement in this direction
right
so the role of beta clamp is to load the
polymerase
and the alpha units and Tau hold the
structure together
and there is these are known as the
clamp loader and they are also known as
the camp nodal means they load this beta
clamp on top of
the hands you can say the yeah
now Tau the hand means is Epsilon on
this structure so they load it there
this area beta clamp Road so what is the
point of having beta clamp it looks like
a clamp what is the function of a clamp
is to hold something right so there are
two different strands of the DNA here
you can see in this picture and with the
help of the beta clamp
the polymerase is holding
itself on top of the DNA strands so
something like trapezium the trapezoid
that that game you know they have this
uh rulers that hold them into rope for
example two ropes are passing you have
clamp loader with the help of the clamp
loader you're holding in both these
ropes together right
now you'll be moving in the one forward
direction that is 5.3 prime or newly
synthesizing strand without the beta
strand
the polymerase can polymerize but the
rate of polymerization will be very very
low
okay
so what is polymerization rate
number of nucleotides added per minute
or per second that is polymerization
rate
and what is processivity there are two
things one is polymerization
and the second one is
process c v t
what are the difference between the two
polymerization means number of
nucleotides per time per unit time
that is polymerization rate
what is processivity number of
nucleotide added before the fall falls
off
number of nucleotides of polymerase can
attach in one go in one stretch that is
known as the processivity of that DNA
polymerase
the possessivity of DNA polymer 3 is
maximum
that's why DNA polymerase is used as a
primary polymerase for DNA replication
in prokaryotes that is maximum for Delta
in case of okay
so Delta n and the
Epsilon because that's why they are used
for leading and lagging strand
particularly for polymerase it's uh in
broker is Paul three that's working
now without the beta clamp the
processivity drops
polymers can polymerize but let's say 10
off
but with beta clamps loaded with beta
clamps tagged it can polymerize thousand
nucleotides at a time before it falls
off
now the rate of polymerization depends
on the availability of dntps
but processivity is not related to the
availability of dntps
it is also but processivity depends on
both the factors the availability of
dntp as well as the presence of beta
class
okay while polymerization only depends
on
the dntp is the amount of the ntps if
there is no dntp no polymerization in
both the case that's true but in case of
processivity dntp along with dntp beta
clamp
is another important parameter
in this picture you will see a
schematic drawing
of polymerase DNA polymerase 3 a similar
drawing you can see
so you don't need to remember it only
need to know the importance of Tau unit
to hold two identical structures left
and right hand side together as a single
polymerase body
beta clamps are very very important in
order to load the polymerase itself to
the single strands template DN
and what else this gamma and PSI this
structure is a loader of beta clamp the
load beta clamp on top of the strands of
the game
that's all you need to know
okay now one big question comes in
that we know that that this polymerase
you know two different strands are
present in the DNA
this is stand one this is Trend two we
are seeing two different strands and
this strands both are used as a template
strength to synthesize the new Strength
right now let's look at the dilemma here
we have this C Prime to five Prime
existing Strand and we have 5 Prime to
three prime existing strand
so our new Strength synthesis will go
this direction 5 to 3 Prime
and
this is also five to three
this polymerase both are connected
together by Tau
so polymer is at a time can move at Only
One Direction either these or
this
if polymer is moved
right hand side
it's moving five to three prime for this
strand but for this it's opposite
and if polymerase is moving from this 5
Prime to 3 Prime
this is fine but for this trend it's
opposite
if they are not connected by Tau unit
two are separate units they could have
easily polymerized to stand separately
but they are moving in opposite
direction let's assume these are the two
bitter Rings they are moving in opposite
direction but they are connected
together how they move
they should be sharing force and they
should separate
so to prevent that
there is a fold
formation of loop is done
so that concept of DNA looping we'll see
that in a moment so DNA is bent in such
a way that at a time the polymerase will
move only in One Direction of course one
of the Strand will be smoothly
replicated and the Strand with smooth
continuous replication will be known as
leading strand
and the one with breaking small segment
replication at a time will be known as
lagging strand
okay
now this bent is important for the
replication to continue even when the
polymerase are connected the two units
two sides of the polymers are connected
together