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1. DNA REPLICATION
PRESENTED BY :-
LOVYANSH LIFESCIENCE

2. THE CHEMISTRY OF DNA SYNTHESIS
• DNA Synthesis Requires Deoxynucleoside Triphosphates and a
Primer:Template Junction
• For the synthesis of DNA to proceed, two key substrates must be
present
• First, new synthesis requires the four deoxynucleoside
triphosphates—dGTP, dCTP, dATP, and dTTP .
• Nucleoside triphosphates have three phosphoryl groups that are
attached via the 5’ -hydroxyl of the 2’ -deoxyribose. The phosphoryl
group proximal to the deoxyribose is called the a-phosphate,
whereas the middle and distal groups are called the b-phosphate
and the g-phosphate, respectively.
• The second essential substrate for DNA synthesis is a particular
arrangement of single-stranded DNA (ssDNA) and double-stranded
DNA (dsDNA) called a primer:template junction

3. • The template provides the ssDNA that directs
the addition of each complementary
deoxynucleotide. The primer is complementary
to, but shorter than, the template.
• . The primer must have an exposed 3’ -OH
adjacent to the single-strand region of the
template. It is this 3’ -OH that will be extend

5. DNA Is Synthesized by Extending the 3’
End of the Primer
• The chemistry of DNA synthesis requires that the new chain grows
by extending the 3’end of the primer .
• Indeed, this is a feature of the synthesis of both RNA and DNA. The
phosphodiester bond is formed in an SN2 reaction in which the
hydroxyl group at the 3’end of the primer strand attacks the a-
phosphoryl group of the incoming nucleoside triphosphate.
• The leaving group for the reaction is pyrophosphate, which is
composed of the b-phosphate and g-phosphate of the nucleotide
substrate.
• The template strand directs which of the four nucleoside
triphosphates is added. The nucleoside triphosphate that base-pairs
with the template strand is highly favored for addition to the primer
strand.

8. THE MECHANISM OF DNA
POLYMERASE
• The synthesis of DNA is catalyzed by a class of enzymes called DNA polymerases.
Unlike most enzymes, which have one active site that catalyzes one reaction, DNA
polymerase uses a single active site to catalyze the addition of any of the four
deoxynucleoside triphosphates.
• DNA polymerase accomplishes this catalytic flexibility by exploiting the nearly
identical geometry of the A:T and G:C base pairs
• The DNA polymerase monitors the ability of the incoming nucleotide to form an
A:T or G:C base pair, rather than detecting the exact nucleotide that enters the
active site
• when a correct base pair is formed are the 3’-OH of the primer and the a-
phosphate of the incoming nucleoside triphosphate in the optimum position for
catalysis to occur. Incorrect base pairing leads to dramatically lower rates of
nucleotide addition as a result of a catalytically unfavorable alignment of these
substrates .
• This is an example of kinetic proofreading, in which an enzyme favors catalysis
using one of several possible substrates by dramatically increasing the rate of bond
formation only when the correct substrate is present. Indeed, the rate of
incorporation of an incorrect nucleotide is as much as 10,000-fold slower than
when base pairing is correct

9. • DNA polymerases show an impressive ability to distinguish between
ribonucleoside and deoxyribonucleoside triphosphates (rNTPs and
dNTPs). Although rNTPs are present at approximately 10-fold higher
concentration in the cell, they are incorporated at a rate that is
more than 1000-fold lower than dNTPs. This discrimination is
mediated by the steric exclusion Of rNTPs from the DNA
polymerase active site .
• In DNA polymerase, the nucleotide-binding pocket cannot
accommodate a 2’ -OH on the in-coming nucleotide. This space is
occupied by two amino acids that make van der Waals contacts
with the sugar ring.
• Changing these amino acids to other amino acids with smaller side
chains (e.g., by changing a glutamate to an alanine) results in a DNA
polymerase with significantly reduced discrimination between
dNTPs and rNTPs

11. DNA Polymerases Resemble a Hand
That Grips the Primer:Template
Junction
• These structures reveal that the DNA substrate sits in a large cleft that
resembles a partially closed right hand .
• Based on the hand analogy, the three domains of the polymerase are
called the thumb, fingers, and palm.
• The palm domain is composed of a b sheet and contains the primary
elements of the catalytic site.
• In particular, this region of DNA polymerase binds two divalent metal ions
(typicallyMg2þ or Zn2þ) that alter the chemical environment around the
correctly base-paired dNTP and the 3’ -OH of the primer .
• One metal ion reduces the affinity of the 3’ -OH for its hydrogen.
• This generates a 3’OH that is primed for the nucleophilic attack of the a-
phosphate of the incoming dNTP.
• The secondmetal ion coordinates the negative charges of the b-phosphate
andg-phosphate of the dNTP and stabilizes the pyrophosphate produced
by joining the primer and the incoming nucleotide.

13. What are the roles of the fingers and
the thumb?
• The fingers are also important for catalysis. Several residues located
within the fingers bind to the incoming dNTP.
• More importantly, once a correct base pair is formed between the
incoming dNTP and the template, the finger domain moves to
enclose the dNTP .
• This closed form of the polymerase “hand” stimulates catalysis by
moving the incoming nucleotide into close contact with the
catalytic metal ions.
• The finger domain also associates with the template region, leading
to a nearly 90*turn of the phosphodiester backbone between the
first and second bases of the template. This bend serves to expose
only the first template base after the primer at the catalytic site and
avoids any confusion concerning which template base should pair
with the next nucleotide to be added

15. processivity of DNA
Polymerases Enzymes
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16. DNA Polymerases Are Processive
Enzymes
• Catalysis by DNA polymerase is rapid. DNA polymerases are
capable of adding as many as 1000 nucleotides/sec to a
primer strand.
• The speed of DNA synthesis is largely due to the processive
nature of DNA polymerase.
• Processivity is a characteristic of enzymes that operate on
polymeric substrates.
• In the case of DNA polymerases, the degree of processivity
is defined as the average number of nucleotides added
each time the enzyme binds a primer:template junction.
• Each DNA polymerase has a characteristic processivity that
can range from only a few nucleotides to more than 50,000
bases added per binding event

17. DNA polymerase “grips” the template
and the incoming nucleotide when a
correct base pair is made.
• (a) An illustration of the changes in DNA polymerase structure after the
incoming nucleotide base-pairs correctly to the template DNA. The
primary change is a 40* rotation of one of the helices in the finger domain
called the O-helix.
• In the open conformation, this helix is distant from the incoming
nucleotide. When the polymerase is in the closed conformation, this helix
moves and makes several important interactions with the incoming dNTP.
A tyrosine makes stacking interactions with the base of the dNTP, and two
charged residues associate with the triphosphate. The combination of
these interactions positions the dNTP for catalysis mediated by the two
metal ions bound to the DNA polymerase.
• (b) The structure of T7 DNA polymerase bound to its substrates in the
closed conformation. The O-helix; the rest of the protein structure is
shown as transparent for clarity. The critical tyrosine, lysine, and arginine
can be seen behind the O-helix. The base and the deoxyribose of the
incoming dNTP; the primer; template strand; the two catalytic metal ions;
phosphates.

19. llustration of the path of the template
DNA through the DNA polymerase
• The recently replicated DNA is associated with the
palm region of the DNA polymerase.
• At the active site, the first base of the single-stranded
region of the template is in a position expected for
dsDNA.
• As one follows the template strand toward its 5’end,
the phosphodiester backbone abruptly bends 90*.
• This results in the second and all subsequent single-
stranded bases being placed in a position that prevents
any possibility of base pairing with a dNTP bound at
the active site.

21. DNA polymerases synthesize DNA in a
processive manner
• This illustration shows the difference between a
processive and a nonprocessive DNA polymerase.
• Both DNA polymerases bind the primer:template
junction. Upon binding, the nonprocessive
enzyme adds a single dNTP to the 3’ end of the
primer and then is released from the new
primer:template junction.
• In contrast, a processive DNA polymerase adds
many dNTPs each time it binds to the template

23. he tautomeric shift of guanine results
in mispairing with thymidine
• (a) Base pairing between the normal keto
form of guanine with cytosine.
• (b) In the rare instance that guanine assumes
the enol tautomer, it now base-pairs with
thymidine instead of cytosine. Although we
have illustrated the mispairing of the alternate
tautomer of guanine, each of the bases can
form alternate tautomers that change its
base-pairing specificity.

25. • Removal of these incorrectly base-paired
nucleotides is mediated by a type of nuclease
that was originally identified in the same
polypeptide as the DNA polymerase.
• Referred to as proofreading exonuclease, these
enzymes degrade DNA starting from a 3’ DNA end
(i.e., from the growing end of the new DNA
strand).
• Nucleases that can only degrade from a DNA end
are called exonucleases; nucleases that can cut
within a DNA strand are called endonucleases.)

26. Nucleases that can only degrade from
a DNA
• (a) When an incorrect nucleotide is incorporated into
the DNA, the rate of DNA synthesis is reduced because
of the incorrect positioning of the 3’ -OH.
• (b) In the presence of a mismatched 3’ end, the last 3–
4 nucleotides of the primer become single-stranded,
resulting in an increased affinity for the exonuclease
active site. Once bound at this active site, the
mismatched nucleotide (and frequently an additional
nucleotide) is removed from the primer.
• (c) Once the mismatched nucleotide is removed, a
properly base-paired primer:template junction is re-
formed, and polymerization resumes

29. ENZYME USEED IN DNA
REPLICATIONS
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LIFESCIENCE

30. Both Strands of DNA Are Synthesized
Together at the Replication Fork
• The junction between the newly separated template strands and the unreplicated
duplex DNA is known as the replication fork .
• The replication fork moves continuously toward the duplex region of unreplicated
DNA, leaving in its wake two ssDNA templates that each direct the synthesis of a
complementary DNA strand
• The antiparallel nature of DNA creates a complication for the simultaneous
replication of the two exposed templates at the replication fork.
• Because DNA is synthesized only by elongating a 3’end, only one of the two
exposed templates can be replicated continuously as the replication fork moves.
• On this template strand, the polymerase simply “chases” the moving replication
fork.
• The newly synthesized DNA strand directed by this template is known as the
leading strand. Synthesis of the new DNA strand directed by the other ssDNA
template is more complicated. T
• his template directs the DNA polymerase to move in the opposite direction of the
replication fork. The new DNA strand directed by this template is known as the
lagging strand The resulting short fragments of new DNA formed on the lagging
strand are called Okazaki fragments

31. The Initiation of a New Strand of DNA
Requires an RNA Primer
• Primase is a specialized RNA polymerase dedicated to
making short RNA primers (5–10 nucleotides long) on
an ssDNA template.
• Primase activity is dramatically increased when it
associates with another protein that acts at the
replication fork called DNA helicase
• . This protein unwinds the DNA at the replication fork,
creating an ssDNA template that can be acted on by
primase.
• . The requirement for an ssDNA template and DNA
helicase association ensures that primase is only active
at the replication fork.

32. DNA Helicases Unwind the Double
Helix in Advance of the Replication
Fork
• DNA polymerases are generally poor at
separating the two base-paired strands of duplex
DNA.
• Therefore, at the replication fork, a third class of
enzymes, called DNA helicases, catalyze the
separation of the two strands of duplex DNA.
• These enzymes bind to and move directionally
along ssDNA using the energy of nucleoside
triphosphate (usually ATP) binding and hydrolysis
to displace any DNA strand that is annealed to
the bound ssDNA

34. Binding of single-stranded binding
protein (SSB) to DNA.

35. Topoisomerases Remove Supercoils Produced by
DNA Unwinding at the Replication Fork
• The supercoils introduced by the action of the DNA helicase are removed by
topoisomerases that act on the unreplicated dsDNA in front of the replication fork .
• These enzymes do this by breaking either one or both strands of the DNA without
letting go of the DNA and passing the same number of DNA strands through the
break
• . As positive supercoils accumulate in front of the replication fork, topoisomerases
rapidly remove them.
• In this diagram, the action of Topo II removes the positive supercoil induced by a
replication fork.
• By passing one part of the unreplicated dsDNA through a double-stranded break in
a nearby unreplicated region, the positive supercoils can be removed.
• It is worthnoting that this change would reduce the linking number by two and thus
would only have to occur once every 20 bp replicated.
• Although the action of a type II topoisomerase is illustrated here, type I
topoisomerases can also remove the positive supercoils generated by a replication
fork. Note that the positive superhelicity in front of the replication fork is shown as
right-handed toroidal writhe (one complete turn equals a positive writhe of þ1).
Passage of one dsDNA molecule through the other at the site of the writhe changes
this to one complete left-handed toroidal writhe (equal to a writhe of –1).
• This illustrates how the linking number is changed by 2 units by a type II
topoisomerase (for more information regarding DNA topology and writhe, see
Chapter 4, DNA Topology,

37. DNA Polymerases Are Specialized for
Different Roles in the Cell
• . DNA polymerase III (DNA Pol III) is the
primary enzyme involved in the replication of
the chromosome
• , DNA Pol III is generally found to be part of a
larger complex that confers very high
processivity—a complex known as the DNA
Pol III holoenzyme.

39. Sliding Clamps Dramatically Increase
DNA Polymerase Processivity

40. ATP control of sliding DNA clamp
loading.

41. Composition of the DNA Pol III
holoenzyme

43. Prokeriyotic DNA replication
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44. Prokariyotes
• DnaA protein :- replication initiation factor
• pramote unwinding of dna
• Dna B protein :- breaks the H-bonds
• opens up replication fork
• DNA c protein :- loading factor
• loading of Dna A & Dna B
• Dna G protein :- primer formation
• synthesis short strands of RNA
• Dna Gyrase :- cause negative supper coiling of dna
relieves strain while Dna is being unwinding by
helicase
Dna ligase :- join / ligated the strans
forms phosphodiester bond b/w 5’ phosphate & 3’ hydroxil
group

45. • Dna pol : - pol 1 :- gap filling
• pol 2 :- repair
• pol 3 :- Replication 3’ to 5’
• Rnase :- remove ribonucleotides from rna
primer
• Ssb : - single strand DNA binding protein
prevent rejoining
• Tus / Tur protein :- for termination of
replication

47. Model for E. coli initiation of DNA
replication
• The major events in the initiation of E. coli DNA replication are
illustrated.
• (a) Multiple DnaA. ATP proteins bind to the repeated 9-mer
sequences within oriC.
• (b) Binding of DnaA. ATP to these sequences leads to strand
separation within the 13-mer repeats. This is mediated by an
ssDNA-binding domain in DnaA. ATP that elongates and changes the
structure of the associated ssDNA such that it cannot hybridize to
the complementary ssDNA.
• (c) A complex between DNA helicase (DnaB) and the DNA helicase
loader (DnaC) associates with the DnaA-bound origin. An ssDNA-
binding domain in the helicase loader and protein–protein
interactions between DnaA and the helicase/helicase loader
mediate these interactions.
• (d) The DNA helicase loader catalyzes the opening of the DNA
helicase protein ring and placement of the ring around the ssDNA at
the origin.

48. • (e) The DNA helicases each recruit a primase that synthesizes an
RNA primer on each template. The RNA primer causes the helicase
loader to release from the helicase, resulting in the activation of the
DNA helicase. The movement of the DNA helicases also removes
any remaining DnaA bound to the replicator.
• (f ) The newly synthesized primers and the helicases are recognized
by the clamp loader components of DNA Pol III holoenzymes.
Sliding clamps are assembled on each RNA primer, and leading-
strand synthesis is initiated by one of the three core DNA Pol III
enzymes of each holoenzyme.
• (g) After each DNA helicase has moved 1000 bases, a second RNA
primer is synthesized on each lagging-strand template, and a sliding
clamp is loaded. The resulting primer:template junction is
recognized by a second DNA Pol III core enzyme in each
holoenzyme, resulting in the initiation of lagging-strand synthesis.
• (h) Leading-strand synthesis and laggingstrand synthesis are now
initiated at each replication fork. As shown in Figure 9-23, the third
DNA Pol III core enzyme also participates in lagging-strand DNA
synthesis. Each replication fork will continue to the end of the
template or until it meets another replication fork moving in the
opposite direction

52. E. coli DNA Replication Is Regulated by
DnaA.ATP Levels and SeqA
• SeqA bound to hemimethylated DNA inhibits reinitiation from recently
replicated daughter origins.
• (a) Before DNA replication, GATC sequences throughout the E. coli genome
are methylated on both strands (“fully” methylated). Note that
throughout the figure, the methyl groups are represented by red
hexagons.
• (b) DNA replication converts these sites to the hemimethylated state (only
one strand of the DNA is methylated).
• (c) Hemimethylated GATC sequences are rapidly bound by SeqA.
• (d) Bound SeqA protein inhibits the full methylation of these sequences
and the binding of oriC by DnaA protein (for simplicity, only one of the two
daughter molecules is illustrated in parts d –f ).
• (e) When SeqA infrequently disassociates from the GATC sites, the
sequences can become fully methylated by Dam DNA methyltransferase,
preventing rebinding by SeqA.
• (f ) When the GATC sites become fully methylated, DnaA can bind the 9-
mer sequences and direct a new round of replication from the daughter
oriC replicators

55. Chromosome breakage as a result of
incomplete DNA replication.
• This illustration shows the consequences of
incomplete replication followed by chromosome
segregation. The top of each illustration shows
the entire chromosome. The bottom shows the
details of the chromosome breakage at the DNA
level. (For details of chromosome segregation,
• As the chromosomes are pulled apart, stress is
placed on the unreplicated DNA, resulting in the
breakage of the chromosome.

57. Eukaryotic dna replication
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58. Protein of dna replications
• ORC :- origin recognition complex
bind to origin of replication & recruite initiation protein
-CDC6 :- cell division cycle6
- part of pre replicative complex
- loads MCM to ORC
- CDT 1 :- CDS-10 DEPENDENT TRANSCRIPT 1
-chromatin licensing & dna replication
factor-1
- - part of pre-replicative complex
- - bind to orc along with CDC6 & MCM
- -f mit DNA from replication more than ince per
cell cycle

59. - CDK/DDK :- CYCLIN DEPENDENT KINASE / Dbf4 DEPENDENT
KINASE
- CDC-45 :- CELL DIVISION CYCLE 45 (interect with MCM-7 &
POL –ALFA)
- GINS:- co-activator of initiation (from CMG assembaly)
- RFC :- REPLICATION FACTOR C :- DNA CLAMP LOADER
- MCM:- mini chromosome maintanance
- (MCM 2-7) DNA helicase
- RPA :- replication protein A
- - Keep strands from binding to itself (SSBP)
- PCNA :- dna clamp act as processivity factor for dna pol
delta

61. Eukaryotic helicase loading
• Loading of the eukaryotic replicative DNA helicase is an ordered
process that is initiated by the association of the ATP-bound origin
recognition complex (ORC) with the replicator.
• Once bound to the replicator, ORC recruits ATP-bound Cdc6 and
two copies of the Mcm2-7 helicase bound to a second helicase
loading protein, Cdt1.
• This assembly of proteins triggers ATP hydrolysis by Cdc6, resulting
in the loading of a head-to-head dimer of the Mcm2-7 complex
encircling double-stranded origin DNA and the release of Cdc6 and
Cdt1 from the origin.
• Subsequent ATP hydrolysis by ORC is required to reset the process
(illustrated as release from Mcm2-7). Exchange of ATP for ADP
allows a new round of helicase loading.

63. Activation of loaded helicases leads to
the assembly of the eukaryotic
replisome
• As cells enter into the S phase of the cell cycle, two kinases, CDK and DDK,
are activated. DDK phosphorylates loaded Mcm2-7 helicase, and CDK
phosphorylates Sld2 and Sld3.
• Phosphorylated Sld2 and Sld3 bind to Dpb11, and together these proteins
facilitate binding of the helicase-activating proteins, Cdc45 and GINS, to
the helicase.
• Cdc45 and GINS form a stable complex with the Mcm2-7 helicase (called
the Cdc45/ Mcm2-7/GINS, or CMG, complex) and dramatically activate
Mcm2-7 helicase activity.
• The leading-strand DNA polymerase
• (1) is recruited to the helicase at this stage (before DNA unwinding).
• After formation of the CMG complex, Sld2, Sld3, and Dpb11 are released
from the origin. DNA Pol a/ primase and DNA Pol d (which primarily act on
the lagging strand) are only recruited after DNA unwinding.
• The protein–protein interactions that hold the DNA polymerase at the
replication fork remain poorly understood.

65. Helicase activation alters helicase
interactions.
• Before helicase activation, loaded helicases
encircle doublestranded DNA and are in the form
of a head-to-head double hexamer (mediated by
interactions between the Mcm2-7 amino
termini).
• After helicase activation, the Mcm2-7 protein in
the CMG complex is proposed to encircle single-
stranded DNA, and the interaction between the
two Mcm2-7 complexes has been broken.

67. Eukaryotic helicase loading and
activation occur during different cell
cycle stages.
• . During the G1 phase of the cell cycle,
helicase loading is permitted, but helicase
activation is not allowed.
• During the remainder of the cell cycle (S, G2,
and M phases), helicase loading is inhibited,
but loaded helicases can be activated (this will
only occur during S phase because after S
phase all loaded Mcm2-7 complexes will be
removed from the DNA;

72. Cell cycle regulation of CDK activity
controls replication.
• . In S. cerevisiae cells, CDK levels tightly regulate helicase loading
and activation. During G1, CDK levels are low, allowing helicases to
be loaded, but the loaded helicases cannot be activated (because of
the requirement of CDK for this event).
• During S phase, elevated CDK activity inhibits new helicase loading
and activates previously loaded helicases.
• When a loaded helicase is used for the initiation of replication,it is
incorporated into the replication fork and leaves the origin.
• Similarly, passive replication of origin DNA also removes the
helicase from the origin DNA (not shown).
• Because CDK levels remain high until the end of mitosis, no new
helicase loading can occur until chromosome segregation is
complete and the daughter cells have returned to G1.
• Without a new round of helicase loading, reinitiation is impossible