Chapter 3: read pp. 41-56 skim the rest Problems:1, 2

1. Chapter 3: read pp. 41-56 skim the rest Problems:1, 2 Chapter 23: read pp. 725-732, 737-751, 761-770 skim the rest Problems: 2, 6 Chapter 24: read pp. 773-789, 797-799 skim the rest Problems: 2, 8

2. VVP Fig. 23-41 T4

3. VVP Fig. 23-2

4. VVP Fig. 23-15

5. VVP Fig. 23-16

6. VVP FIG. 23-17

7. VVP p. 749

8. VVP Fig. 23-29

9. VVP Fig. 23-29

11. *Each human cell has 2 meters of DNA. (E. coli has 1.4 mm.) *The total length of DNA in an average person is 2 x 1010 km-- compare that to the earth's diameter of 4 x 104 km!! *A human liver cell nucleus has a diameter of µm and must contain 46 chromosomes each ca. 4.3 cm long. Since the largest human chromosome contains 2.4 x 108 bp it would have a length of 8.2 cm if the DNA were stretched out in the B conformation. *In fact, the length of this chromosome during metaphase (when it is most condensed) is about 10 µm or about 1/8000 the length it could have as B DNA!!!

12. MVA Fig. 28.7 A mitotic chromosome

13. VVP Fig. 23-43

14. VVP Fig. 23-47

15. prolate ellipsoid 100 x 70 Angstroms.

16. Properties of histones residues MW %arg %lys H1 215 23.0 1 29 H2a 129 14 9 11 H2b 125 13.8 6 16 H3 135 15.3 13 10 H4 102 11.3 14 11

17. VVP Fig. 23-45

18. VVP Fig. 23-44b

19. MVA Fig. 28.12

20. VVP Fig. 27-31 Chromosome Puffs where transcription is occurring.

22. VVP Fig. 24-25 Chemical mutagenesis

23. VVP Fig. 24-23

24. VVP Fig. 24-28

25. VVP Fig. 24-29

26. VVP Fig. 24-30

27. VVP Fig. 24-25 Chemical mutagenesis

28. VVP Fig. 24-28

29. VVP Fig. 24-29

30. VVP Fig. 24-30

31. VVP Fig. 23-32b

32. VVP Fig. 23-32c

33. VVP Fig. 23-32a

34. VVP p. 790

36. VVP Fig. 24-1 Meselson and Stahl Experiment

39. VVP Fig. 24-2

40. DNA replication requires: 1.A DNA template to be replicated. 2.DNA helicase - this enzyme unwinds the helical DNA at replication forks. 3.Primase - this enzyme lays down the primers that are necessary for DNA polymerase activity. The primers are composed of RNA. 4.DNA polymerase III - this is the polymerase that does the bulk of the DNA replication using its 5'(3' polymerase activity. 5.DNA polymerase I - the function of this polymerase during replication is to remove the RNA primers (after they have done their job of initiating DNA replication) using a 5'--->3' exonuclease activity. It then uses its 5'--->3' polymerase activity to fill in the resulting gaps (Figure 5.23). 6.DNA ligase - this enzyme seals nicks in DNA by linking up 3' hydroxyl groups with adjacent 5' phosphate groups (Figure 5.23). DNA Ligase will connect DNA to DNA but not DNA to RNA - so there is never a danger of RNA primers being stitched into the nascent DNA. 7.SSB = single-strand DNA binding protein - this protein binds single-stranded DNA at the replication fork and physically blocks potential hybridization - i.e. it makes sure that the DNA is single-stranded when the polymerization machinery is ready to replicate it.

41. DNA polymerases are unable to melt duplex DNA (i.e., break the interchain hydrogen bonds) in order to separate the two strands that are to be copied. All DNA polymerases so far discovered can only elongate a preexisting DNA or RNA strand, the primer; they cannot initiate chains. The two strands in the DNA duplex are opposite (5’-3’ and 3’-5’) in chemical polarity, but all DNA polymerases catalyze nucleotide addition at the 3’-hydroxyl end of a growing chain, so strands can grow only in the 5’-3’ direction.

42. VVP Fig. 24-3 Replication Eye

43. VVP Fig. 24-4

44. Consensus sequence of the minimal bacterial replication origin based on analyses of genomes from six bacterial species. Similar sequences constitute each origin; the 13-bp repetitive sequences (orange) are rich in adenine and thymine residues. The 9-bp repetitive sequences (brown) exist in both orientations; that is, the lower-right sequence, read right to left, is the same as that of the upper-left sequence, read left to right. These sequences are referred to as 13-mers and 9-mers, respectively. Indicated nucleotide position numbers are arbitrary. [See J. Zyskind et al., 1983, Proc. Nat'l. Acad. Sci. USA 80:1164.]

45. Model of initiation of replication at E. coli oriC. The 9-mers and 13-mers are the repetitive sequences. Multiple copies of DnaA protein bind to the 9-mers at the origin and then “melt” (separate the strands of) the 13-mer segments. The sole function of DnaC is to deliver DnaB, which is composed of six identical subunits, to the template. One DnaB hexamer clamps around each single strand of DNA at oriC, forming the prepriming complex. DnaB is a helicase, and the two molecules then proceed to unwind the DNA in opposite directions away from the origin. [Adapted from C. Bramhill and A. Kornberg, 1988, Cell 52:743, and S. West, 1996, Cell 86:177.]

46. VVP Fig. 24-11 SSB

47. Staged assembly of the replisome occurs at the DnaA-oriC complex. IHS - Integration host factor FIS - Factor for inversion stimulation DnaB - helicase DnaC - helicase associated factor SSB - single stranded binding protein

49. VVP p. 787 Replication of X174. Big bubbles are the primase!