1. DNA replication Chapter 16

3. Summary of history Griffith Mice & Strep Transformation External DNA taken in by cell

4. Summary of history Hershey-Chase Bacteriophages Supported heredity information was DNA

5. Bacteriophages

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7. Summary of history Franklin X-ray diffraction Double helix Watson-Crick Double helix model

8. Nucleic acid structure DNA deoxyribonucleic acid RNA ribonucleic acid Nucleotides

9. Nucleotide structure 1. 5 carbon sugar (ribose) 2. Phosphate 3. Nitrogenous base

10. Nucleotide structure

11. Nitrogenous base Purines (2 rings) Adenine(A) & Guanine(G) Pyrimidines (1 ring) Cytosine (C), Thymine (T) DNA only Uracil (U) RNA only

13. Phosphodiester bond Links 2 sugars (nucleotides)

15. Nucleic acids 5 ’ Phosphate group (5 ’ C) at one end 3 ’ Hydroxyl group (3 ’ C) at the other end Sequence of bases is expressed in the 5 ’ to 3 ’ direction GTCCAT 5 ’ pGpTpCpCpApT---OH 3 ’

16. Double helix Complementary Sequence on one chain of DNA Determines sequence of other chain 5 ’ -ATTGCAT-3 ’ 3 ’ -TAACGTA-5 ’

18. Double Helix Complementary Purines pair with pyrimidines Diameter of base pairs are the same Adenine (A) forms 2 hydrogen bonds with Thymine (T) Guanine (G) forms 3 hydrogen bonds with cytosine (C)

19. Double Helix Sugar-phosphates are the backbone Complementary Phosphodiester bonds Strands are antiparrellel Bases extend into interior of helix Base-pairs form to join the two strands

21. Fig. 16-7 Hydrogen bond 3 end 5 end 3.4 nm 0.34 nm 3 end 5 end (b) Partial chemical structure(a) Key features of DNA structure 1 nm

23. Duplication DNA unzips-breaks hydrogen bonds New strand forms based on existing strand Old strand is saved Compliment of new strand New DNA-one old strand & one new strand Semiconservative replication

24. Fig. 16-9-3 A T G C TA TA G C (a) Parent molecule AT GC T A T A GC (c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand (b) Separation of strands A T G C TA TA G C A T G C T A T A G C

27. Duplication study Meselson and Stahl Bacteria 14 N and 15 N Semiconservative method.

28. Fig. 16-10 Parent cell First replication Second replication (a) Conservative model (b) Semiconserva- tive model (c) Dispersive model

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30. Duplication Enzymes DNA helicase: Enzyme opens helix starts duplication Separates parental strands Single-strand binding protein: Binds to unpaired DNA After separation Stabilizes DNA

31. Duplication Enzymes DNA polymerases: Help lengthen new strand of DNA Adds new nucleotides strand Synthesis occurs only one direction 5’ to 3’ Adding new nucleotides to the 3’OH

32. Duplication Enzymes Primer: Section of RNA Complementary to the parental DNA Synthesis occurs only one direction 5’ to 3’ DNA primase: Enzyme creates the primer

33. Duplication Enzymes Topoisomerase: Relieves strain of unwinding DNA DNA pol1: Removes primers Replaces with DNA nucleotides DNA ligase: Creates phosphodiester bonds between Okazaki fragments

35. Duplication OriC Origins of replication Starting point in DNA synthesis Replication is bidirectional Proceeds in both directions from origin 5’to 3’direction

36. Duplication E coli (bacteria) Circular DNA One origin Eurkaryotes Multiple origins

38. Duplication Replication bubble: Separation of strands of DNA Replication of DNA Replication fork: Y-shaped region End of replication bubble Site of active replication

39. Duplication

42. Leading strand: DNA continuous 5’ to 3’ replication (towards fork) Template is 3’ to 5’ Lagging strand: DNA duplicated in short segments (away from fork) Okazaki fragments: Short stretches of new DNA-lagging side

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44. Duplication Unzips (helicase, single-strand binding protein, topoisomerase) Primer DNA polymerase (5’to3’) DNA ligase

46. Duplication

48. Fig. 16-14 A C T G G G GC CC C C A A A T T T New strand 5 end Template strand 3 end 5 end 3 end 5 end 3 end Base Sugar Phosphate Nucleoside triphosphate Pyrophosphate DNA polymerase

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50. Fig. 16-13 Topoisomerase Helicase Primase Single-strand binding proteins RNA primer 5 5 53 3 3

51. Fig. 16-15b Origin of replication RNA primer “Sliding clamp” DNA pol III Parental DNA 3 5 5 5 5 5 5 3 3 3

52. Fig. 16-16a Overview Origin of replication Leading strand Lagging strand Overall directions of replication 1 2

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54. Fig. 16-17 Overview Origin of replication Leading strand Lagging strand Overall directions of replication Leading strand Lagging strand Helicase Parental DNA DNA pol III PrimerPrimase DNA ligase DNA pol III DNA pol I Single-strand binding protein 5 3 5 5 5 5 3 3 3 3 1 3 2 4

55. Fig. 16-16 Overview Origin of replication Leading strand Lagging strand Overall directions of replication Template strand RNA primer Okazaki fragment Overall direction of replication 1 2 3 2 1 1 1 1 2 2 5 1 3 3 3 3 3 3 3 3 3 5 5 5 5 5 5 5 5 5 5 5 3 3

57. Duplication

59. Telomers: Sequences at ends of chromosomes Short nucleotide sequences Repeated 100-1000 times Prevents 5’ end erosion Telomerase: Enzyme that lengthens telomers Usually in germ cells

61. Repairs Mismatched pair: Duplication error Enzymes remove error Nucleotide excision repair: Damaged section removed Nuclease New nucleotides fill gap Complement DNA section not damaged

62. Chromosome packaging Chromatin: Complex composed of DNA and proteins 40% DNA 60% protein Heterochromatin: More compacted chromatin Euchromatin: Loosely packed chromatin

63. Chromosome packaging Double helix Histones: proteins Nucleosome: DNA coiled around 8 histones (10nm) Nucleosomes then coil (30nm) Looped domains attach to chromosome scaffold (300nm) Domains coil form chromosome

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