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DNA Replication
By
Prof. Moushira Abdel-Wahab
Lectures Objectives
 Describe the flow of genetic information
 Define Replication
 List basic rules of replication
 Explain how the problems after denaturation are
overcome
 List steps of DNA replication
List the proteins involved in replications and outline
their functions
Compare leading and lagging strands
Describe Proofreading
List difference of eukaryotic replication vs prokaryote
Central dogma of molecular
biology
DNA Replication = DNA  DNA
Process of duplication of the
entire DNA prior to cell division.
So each daughter cell gets a complete copy
DNA Replication
Basic rules of replication
A. Semi-conservative
B. Starts at the ‘origin’
C. Bidirectional
D. Synthesis always in the 5-3  direction
E. Semi-discontinuous
F. RNA primers required
• DNA Synthesis
 The DNA bases on each
strand act as a template to
synthesize a complementary
strand
• Recall that Adenine (A)
pairs with thymine (T)
and guanine (G) pairs
with cytosine (C)
 The process is
semiconservative because
each new double-stranded
DNA contains one old
strand (template) and one
newly-synthesized
complementary strand
DNA Replication
A
G
C
T
G
T
C
G
A
C
A
G
C
T
G
T
C
G
A
C
A
G
C
T
G
T
C
G
A
C
A
G
C
T
G
T
C
G
A
C
T
C
G
A
C
A
G
C
T
G
Replication is bidirectional:
that is, the replication forks
move in both direction away
from the origin
DNA replication
requirements
DNA
template
Free
nucleotides
Enzymes ATP
The mechanism of DNA replication
Arthur Kornberg, a Nobel prize winner and
other biochemists deduced steps of
replication
The mechanism of DNA replication
– Initiation
• Proteins bind to DNA and open up double
helix
• Prepare DNA for complementary base
pairing
– Elongation
• Proteins connect the correct sequences
of nucleotides into a continuous new
strand of DNA
– Termination
• Proteins release the replication complex
DNA replication steps
Initiation
( Separation of the 2 DNA strands (unwinding)
Replication: 1st step
• Unwind DNA
• Helicase Cleaves the hydrogen bonds between the
two DNA strands and require energy provided by
ATP
• Stabilized by Single stranded binding protein
replication fork
single-stranded binding proteins
helicase
Prepriming complex
Responsible for initiation
and maintaining the
separation of the two DNA
strands
Prepriming complex
Responsible for initiation
and maintaining the
separation of the two DNA
strands
DnaA
Helicase
DNA supercoiling
• As the 2 strands are separated from each
other, this creates coils infront of the
separated part (supercoils) which prevents
further separation of the helix.
• Toposiomerases are enzymes that are
responsible for the elimination of
supercoils.
Toposiomerases
Players of Elongation
DNA Replication
• DNA Polymerase
 Enzyme that catalyzes the covalent bond between the phosphate of one
nucleotide and the deoxyribose (sugar) of the previous nucleotide
DNA Polymerization
3 end has a free deoxyribose
5 end has a free phosphate
DNA polymerase:
 can only build the new strand in
the 5 to 3 direction
 Thus scans the template strand in
3 to 5 direction
DNA Replication
DNA polymerase can not initiate DNA synthesis
DNA Replication
DNA polymerase
DNA polymerase can not initiate DNA synthesis
• Primase (a type of RNA polymerase) builds an RNA primer
(5-10 ribonucleotides long)
• DNA polymerase attaches onto the 3 end of the RNA primer
DNA Replication
DNA polymerase
Primosome complex
Formed prior to RNA
primer synthesis
Elongation
• DNA polymerase uses each strand as a template in the 3 to 5 direction
to build a complementary strand in the 5 to 3 direction
 results in a leading strand and a lagging strand
DNA Replication
Limits of DNA polymerase III
 Unidirectional ,synthesizes DNA
from 5 to 3 direction only
Leading & Lagging strands
5
5
5
5
3
3
3
5
3
5
3 3
Leading strand
Lagging strand
 continuous synthesis
DNA polymerase III


3
5
growing
replication fork
DNA polymerase III
______________________
 built by ________________
 serves as starter sequence for
DNA polymerase III
Limits of DNA polymerase III
 can not initiate DNA synthesis
Starting DNA synthesis: RNA primers
5
5
5
3
3
3
5
3
5
3 5 3
growing
replication fork primase
RNA
Elongation step
RNA primer
synthesis
Chain elongation
Excision of RNA
primers and their
replacement by DNA
5’
5’
3’ 3’
5’
3’
5’ 3’
5’
3’
3’
5’
Excision of RNA primers
and their replacement by DNA
It localizes the 5’end of the
RNA primer and then
cleaves the phosphodiester
bonds of RNA primer one
by one from 5’→3’
RNA primer of each
Okazaki fragment is
removed by DNA
polymerase I enzyme by its
5’→3’ exonuclease activity.
As it removes the RNA, DNA pol I replaces it with
deoxynucleotides, synthesizing DNA in 5’→3’ direction till
the RNA is totally degraded and the gap is filled with DNA
3’
5’
3’
5’ 3’
5’
3’
3’
5’
3’
5’
3’
5’ 3’
5’
3’
3’
5’
DNA Ligase
Then by DNA ligase enzyme, the DNA fragments will be
joined together. The enzyme requires energy, which in
eukaryotes is provided by the cleavage of ATP to (AMP +
PPi). Ligase seals the nick in the sugar-phosphate
backbone
Proof Reading
• Proof Reading of the newly synthesized DNA
(Replication fidelity):
DNA polymerase, is
self-correcting: it has
a proofreading activity
Steps of Proofreading of newly
synthesized DNA
3- A correct base is added by 5’to 3’polymerase activity.A correct
base is then base paired to the template.
2- Incorrect base which had been added by 5’ to 3’ activity is
removed by Pol 3’ to 5’ exonuclease activity
1- Incorrect base had been added by 5’ to 3’ polymerase
(Pol.)activity. Incorrect as it is not complementary to the template,
so not base paired to the template.
Comparison of Prokaryotic DNA
polymerases
Feature Pol I Pol II Pol III
53 exonuclease activity + --- ---
35 exonuclease activity + + +
Synthesis rate (nucleotide/min) 600 30 30000
Replication + --- +
Repair + + +
Eukaryote
Multiple origin of
replication
RNA primers
removed by Rnase H
Different set of DNA
polymerases with
similar functions
Eukaryote DNA replication
Single origin of replication for
prokaryotes
Multiple origin of replication
Prof._Moushira_DNA replication.pdf

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Prof._Moushira_DNA replication.pdf

  • 2. Lectures Objectives  Describe the flow of genetic information  Define Replication  List basic rules of replication  Explain how the problems after denaturation are overcome  List steps of DNA replication List the proteins involved in replications and outline their functions Compare leading and lagging strands Describe Proofreading List difference of eukaryotic replication vs prokaryote
  • 3. Central dogma of molecular biology
  • 4.
  • 5. DNA Replication = DNA  DNA Process of duplication of the entire DNA prior to cell division. So each daughter cell gets a complete copy DNA Replication
  • 6. Basic rules of replication A. Semi-conservative B. Starts at the ‘origin’ C. Bidirectional D. Synthesis always in the 5-3  direction E. Semi-discontinuous F. RNA primers required
  • 7. • DNA Synthesis  The DNA bases on each strand act as a template to synthesize a complementary strand • Recall that Adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C)  The process is semiconservative because each new double-stranded DNA contains one old strand (template) and one newly-synthesized complementary strand DNA Replication A G C T G T C G A C A G C T G T C G A C A G C T G T C G A C A G C T G T C G A C T C G A C A G C T G
  • 8. Replication is bidirectional: that is, the replication forks move in both direction away from the origin
  • 10. The mechanism of DNA replication Arthur Kornberg, a Nobel prize winner and other biochemists deduced steps of replication
  • 11. The mechanism of DNA replication – Initiation • Proteins bind to DNA and open up double helix • Prepare DNA for complementary base pairing – Elongation • Proteins connect the correct sequences of nucleotides into a continuous new strand of DNA – Termination • Proteins release the replication complex
  • 12. DNA replication steps Initiation ( Separation of the 2 DNA strands (unwinding)
  • 13.
  • 14. Replication: 1st step • Unwind DNA • Helicase Cleaves the hydrogen bonds between the two DNA strands and require energy provided by ATP • Stabilized by Single stranded binding protein replication fork single-stranded binding proteins helicase
  • 15. Prepriming complex Responsible for initiation and maintaining the separation of the two DNA strands
  • 16. Prepriming complex Responsible for initiation and maintaining the separation of the two DNA strands DnaA Helicase
  • 17. DNA supercoiling • As the 2 strands are separated from each other, this creates coils infront of the separated part (supercoils) which prevents further separation of the helix.
  • 18. • Toposiomerases are enzymes that are responsible for the elimination of supercoils. Toposiomerases
  • 20. DNA Replication • DNA Polymerase  Enzyme that catalyzes the covalent bond between the phosphate of one nucleotide and the deoxyribose (sugar) of the previous nucleotide DNA Polymerization
  • 21. 3 end has a free deoxyribose 5 end has a free phosphate DNA polymerase:  can only build the new strand in the 5 to 3 direction  Thus scans the template strand in 3 to 5 direction DNA Replication
  • 22. DNA polymerase can not initiate DNA synthesis DNA Replication DNA polymerase
  • 23. DNA polymerase can not initiate DNA synthesis • Primase (a type of RNA polymerase) builds an RNA primer (5-10 ribonucleotides long) • DNA polymerase attaches onto the 3 end of the RNA primer DNA Replication DNA polymerase
  • 24. Primosome complex Formed prior to RNA primer synthesis
  • 25. Elongation • DNA polymerase uses each strand as a template in the 3 to 5 direction to build a complementary strand in the 5 to 3 direction  results in a leading strand and a lagging strand DNA Replication
  • 26. Limits of DNA polymerase III  Unidirectional ,synthesizes DNA from 5 to 3 direction only Leading & Lagging strands 5 5 5 5 3 3 3 5 3 5 3 3 Leading strand Lagging strand  continuous synthesis DNA polymerase III   3 5 growing replication fork
  • 27. DNA polymerase III ______________________  built by ________________  serves as starter sequence for DNA polymerase III Limits of DNA polymerase III  can not initiate DNA synthesis Starting DNA synthesis: RNA primers 5 5 5 3 3 3 5 3 5 3 5 3 growing replication fork primase RNA
  • 28. Elongation step RNA primer synthesis Chain elongation Excision of RNA primers and their replacement by DNA
  • 29. 5’ 5’ 3’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’ Excision of RNA primers and their replacement by DNA It localizes the 5’end of the RNA primer and then cleaves the phosphodiester bonds of RNA primer one by one from 5’→3’ RNA primer of each Okazaki fragment is removed by DNA polymerase I enzyme by its 5’→3’ exonuclease activity.
  • 30. As it removes the RNA, DNA pol I replaces it with deoxynucleotides, synthesizing DNA in 5’→3’ direction till the RNA is totally degraded and the gap is filled with DNA 3’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’
  • 31. 3’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 5’ DNA Ligase Then by DNA ligase enzyme, the DNA fragments will be joined together. The enzyme requires energy, which in eukaryotes is provided by the cleavage of ATP to (AMP + PPi). Ligase seals the nick in the sugar-phosphate backbone
  • 32. Proof Reading • Proof Reading of the newly synthesized DNA (Replication fidelity): DNA polymerase, is self-correcting: it has a proofreading activity
  • 33. Steps of Proofreading of newly synthesized DNA 3- A correct base is added by 5’to 3’polymerase activity.A correct base is then base paired to the template. 2- Incorrect base which had been added by 5’ to 3’ activity is removed by Pol 3’ to 5’ exonuclease activity 1- Incorrect base had been added by 5’ to 3’ polymerase (Pol.)activity. Incorrect as it is not complementary to the template, so not base paired to the template.
  • 34. Comparison of Prokaryotic DNA polymerases Feature Pol I Pol II Pol III 53 exonuclease activity + --- --- 35 exonuclease activity + + + Synthesis rate (nucleotide/min) 600 30 30000 Replication + --- + Repair + + +
  • 35. Eukaryote Multiple origin of replication RNA primers removed by Rnase H Different set of DNA polymerases with similar functions Eukaryote DNA replication
  • 36. Single origin of replication for prokaryotes
  • 37. Multiple origin of replication