1. Chapter 9 Replication of DNA
Chapter 9 Opener

2. DNA synthesis requires
Figure 9-1
DNA synthesis requires
Figure 9-1
DNA synthesis requires 2

3. Figure 9-1a
Figure 9-1a 3

4. Figure 9-1b
DNA is synthesized by extending the 3’ end of the primer (made of RNA by primase)
Figure 9-1b
DNA is synthesized by extending the 3’ end of the primer 4

5. Figure 9-2
Figure 9-2 5

6. DNA polymerases use a single active site toatalyze
Figure 9-3
DNA polymerases use a single active site toatalyze
Figure 9-3
DNA polymerases use a single active site to catalyze 6

7. Steric constraints (입체적 장해) prevent DNA Pol from using rNTP
Figure 9-4
Steric constraints (입체적 장해) prevent DNA Pol from using rNTP
Figure 9-4
Steric constraints prevent DNA Pol from using rNTP 7

8. Figure 9-5
Figure 9-5 8

9. Two metal ions bind to DNA Polymerase catalyze nucleotide addition
Figure 9-6
Two metal ions bind to DNA Polymerase catalyze nucleotide addition
Figure 9-6
Two metal ions bind to DNA Polymerase catalyze nucleotide addition 9

10. Figure 9-6a
Figure 9-6a 10

11. Figure 9-6b
Figure 9-6b 11

12. Figure 9-7
DNA polymerase grips template and incoming nucleotide when a correct base pair is made.
Figure 9-7
DNA polymerase grips template and incoming nucleotide when a correct base pair is made. 12

13. Figure 9-7a
Figure 9-7a 13

14. Figure 9-7b
Figure 9-7b 14

15. O-helix Base and dNTP Primer Figure 9-7c Figure 9-7c O-helix Primer15

16. Figure 9-8
Figure 9-8 16

17. Figure 9-9
Figure 9-9 17

18. Incorrect base is removed by proofreading exonuclease.
Figure 9-10
Incorrect base is removed by proofreading exonuclease.
(c.f. endonuclease)
Figure 9-10
Incorrect base is removed by proofreading exonulcease. 18

19. Figure 9-11a
Figure 9-11a 19

20. Mismatched 3-4 nucleotide exposed to exonuclease
Figure 9-11b
Mismatched 3-4 nucleotide exposed to exonuclease
(DNA Pol itself)
Figure 9-11b
Mismatched 3-4 nucleotide exposed to exonuclease (DNA Pol itself) 20

21. Figure 9-11c
Figure 9-11c 21

22. Figure 9-12
Replication fork
Figure 9-12
Replication fork 22

23. Primase is a specialized RNA polymerase dedicated to make short RNA primers(5-10 nuleotides long)
Primase initiate RNA synthesis using an ssDNA template of trimer (GTA in case of E. coli) when helicase unwinds dsDNA at the replication fork.
Primase is a specialized RNA polymerase dedicated to make short RNA primers(5-10 nuleotides long)

24. Figure 9-13
Removal of RNA primer
Figure 9-13 24

25. Figure 9-14
DNA helicase separate two strands of double helix before replication fork
has 5’-3’ polarity
Figure 9-14
DNA helicase (have 5’-3’ polarity)
separate two strands of double helix before replication fork 25

26. Central channel Hexameric helicase Phosphate of ss DNA
Figure 9-15
Central channel
Hexameric helicase
Phosphate of ss DNA
Figure 9-15
Hexameric helicase
Central channel
Two hairpin structure
Phosphate
Two hairpin structure 26

27. Figure 9-15a
Figure 9-15a 27

28. Figure 9-15b
Figure 9-15b 28

29. Figure 9-16
Binding of SSB to DNA
Figure 9-16
Binding of SSB to DNA.
Only after SSWbs bind to completely coated initially bound ssDNA does bind occur on other molecules.
Only after SSBs bind to completely coated initially bound ssDNA, does binding occur on other molecules. 29

30. Action of topoisomerase at the replication fork
Figure 9-17
Action of topoisomerase at the replication fork
Figure 9-17
Action of topoisomerase at the replication fork 30

31. Table 9-1
Table 9-1 31

32. (Specialization of DNA polymerases)
Table 9-2
(Specialization of DNA polymerases)
Table 9-2
Specialization of DNA polymerases 32

33. DNA polymerase switching during eukaryotic DNA synthesis
Figure 9-18
DNA polymerase switching during eukaryotic DNA synthesis
DNA Pol α has low processivity and switched with DNA Pol delta.
Figure 9-18
DNA polymerase switching during eukaryotic DNA synthesis 33

34. Figure 9-19
With assistance of sliding clamp, DNA polymerase delta increases processivity(fast replication).
Figure 9-19
With assistance of sliding clamp, DNA polymerase delta increases processivity. 34

35. Slow replication Normal replication Figure 9-20 Figure 9-2035

36. Eukaryotic sliding camp(PCNA) T4 phage Sliding camp
Figure 9-21
E. coli sliding camp
Figure 9-21
E. coli sliding camp
T4 phage
Eukaryotic (PCNA)
Eukaryotic sliding camp(PCNA)
T4 phage
Sliding camp 36

37. ATP control protein function: Loading a sliding camp
Box 9-3-1
DNA pol
ATP control protein function: Loading a sliding camp
Box 9-3-1
ATP control protein function: Loading a sliding camp
DNA pol 37

38. Composition of DNA Pol III holoenzyme
Figure 9-22
Composition of DNA Pol III holoenzyme
Figure 9-22
Composition of DNA Pol III holoenzyme 38

39. Figure 9-23
“Trombone” model for coordinating replication by two DNA polymerase s at E. coli replication fork.
Figure 9-23
“Trombone” model for coordinating replication by two DNA polymerase s at E. coli replication fork. 39

40. Figure 9-23a
Figure 9-23a 40

41. Figure 9-23b
Figure 9-23b 41

42. Figure 9-23c
Figure 9-23c 42

43. Figure 9-23d
Figure 9-23d 43

44. Figure 9-23e
Figure 9-23e 44

45. Figure 9-24a
Binding of DNA helicase to DNA pol III holoenzyme stimulate the rate of DNA strand separation
Figure 9-24a
Combination of all of the proteins than function at the replication fork referred to as REPLISOME(DNA pol, Helicase, Primase)
Combination of all of the proteins than function at the replication fork referred to as REPLISOME(DNA pol, Helicase, Primase) 45

46. Figure 9-24b
Figure 9-24b 46

47. (particular origin of replication) model
Figure 9-25
Initiation of DNA replication: specific genomic DNA sequence direct the initiation
Replicon
(particular origin of replication) model
Figure 9-25
Initiation of DNA replication: specific genomic DNA sequence direct the initiation
Replicom model 47

48. Structure of replicator
Figure 9-26
Structure of replicator
DNA element that facilitate DNA unwinding (blue)
Initiator binding site (green)
Figure 9-26
Structure of replicator
DNA element that facilitate DNA unwinding (green)
Site of initial DNA synthesis
Site of initial DNA synthesis (red) 48

49. Figure 9-27
Figure 9-27 49

50. Figure 9-27a
Figure 9-27a 50

51. Figure 9-27b
Figure 9-27b 51

52. Figure 9-27c
Figure 9-27c 52

53. Figure 9-27d
Figure 9-27d 53

54. Figure 9-27e
Figure 9-27e 54

55. Figure 9-27f
Figure 9-27f 55

56. Figure 9-27g
Figure 9-27g 56

57. Figure 9-27h
Figure 9-27h 57

58. Eukaryotic chromosomes are replicated exactly once per cell cycle.
Figure 9-28
Eukaryotic chromosomes are replicated exactly once per cell cycle.
Figure 9-28
Eukaryotic chromosomes are replicated exactly once per cell cycle.
Chromosome breakage as a results of incomplete DNA replication
Chromosome breakage as a results of incomplete DNA replication 58

59. Replicators (of daughter DNA) are inactivated by DNA replication
Figure 9-29
Replicators (of daughter DNA) are inactivated by DNA replication
Replicator 1 is not reached by adjacent fork before initiation and normally initiated.
Figure 9-29
Replicator 1 is not reached by adjacent fork before initiation and normally initiated.
No replication in daughter 59

60. Eukaryotic helicase loading
Figure 9-30
ORC: origin recognition complex
Eukaryotic helicase loading
Figure 9-30
ORC: origin recognition complex 60

61. Figure 9-31
Binding of Sld2, Sld3, Dpb11 facilitate binding of Cdc45 and Gins
Kinase
Helicase activating protein
Activation of loaded helicases leads to assembly of eukaryotic replisome
Figure 9-31
Activation of loaded helicases leads to assembly of eukaryotic replisome
Kinase
Binding of Sld2, Sld3, Dpb11 facilitate binding of Cdc45 and Gins
Helicase activating protein (Cdc45 and Gins) 61

62. Helicase activation alters helicase interaction
Figure 9-32
Helicase activation alters helicase interaction
Figure 9-32
Cdc45-Mcm2-7-Gins (CMG)
Helicase activation alters helicase interaction
Cdc45-Mcm2-7-Gins (CMG) 62

63. Figure 9-33
In each cell cycle, only one opportunity for helicase to load on origins.
Figure 9-33
In each cell cycle, only one opportunity for helicase to load on roigins. 63

64. ORC: origin recognition complex
Figure 9-34
ORC: origin recognition complex
Figure 9-34 64

65. Topoisomerase II catalyzes decatenation of replication products
Figure 9-35
Topoisomerase II catalyzes decatenation of replication products
Figure 9-35
Topoisomerase II catalyzes decatenation of replication products 65

66. Topoisomerase II catalyzes decatenation of replication products
Figure 9-36
Topoisomerase II catalyzes decatenation of replication products
Figure 9-36
Topoisomerase II catalyzes decatenation of replication products 66

67. Figure 9-37
Protein priming as a solution to end replication problem (in linear chromosome of certain bacterial species and viruses)
Figure 9-37
Protein priming as a solution to end replication problem (in linear chromosome of certain bacterial species and viruses) 67

68. Replication of telomeres by telomerase in eukaryotes
Figure 9-38
Replication of telomeres by telomerase in eukaryotes
Head to tail of TG rich DNA sequences
Figure 9-38
Replication of telomeres by telomerase
Head to tail of TG rich DNA sequences 68

69. Figure 9-39
Figure 9-39 69

70. Telomere binding proteins
Figure 9-40
Telomere binding proteins
Yeast
Human
Figure 9-40
Telomere binding proteins
Yeast
Human 70

71. Telomere length regulation by telomere binding proteins
Figure 9-41
Telomere length regulation by telomere binding proteins
Figure 9-41
Telomere length regulation by telomere binding proteins 71

72. Telomere binding proteins protect chromosome ends
Figure 9-42
Telomere binding proteins protect chromosome ends
Figure 9-42
Telomere binding proteins protect chromosome ends 72

73. Figure 9-42b
Figure 9-42b 73