Chemistry Shirts 2009:

1. Chemistry Shirts 2009: Peptide or periodic table designs also available. Order on Fridays pre-seminar in Chem. Library or from Dr. Raymond, CB 243

2. “A role for aneuploidy in genome evolution?”Andreas Madlung, Associate Professor, Biology Dept., University of Puget Sound, Tacoma, WAWednesday, April 8, 2009 at 4 pm in BI 234

3. Chemistry Seminar F 4/10 3:15 pm SL 130 Do try to attend. This guy is good!

4. Office Hours next week: M 12-1 R 2-3

6. Figure 30-28 The replication of E. coli DNA.

7. Figure 30-7 Priming of DNA synthesis by short RNA segments. Page 1139

8. DNA Polymerase I (pol I) from E. coli first DNA polymerase characterized. approximately 400 molecules of the enzyme per cell. large protein with a molecular weight of approximately 103 kDa (103,000 grams per mole). a divalent cation (Mg++) for activity Three enzymatic activities: 1. 5'-to-3' DNA Polymerase activity2. 3'-to-5' exonuclease (Proofreading activity)3. 5'-to-3' exonuclease (Nick translation activity) It is possible to remove the 5'-to-3' exonuclease activity using a protease to cut DNA pol I into two protein fragments Both the polymerization and 3'-to-5' exonuclease activities are on the large Klenow fragment of DNA pol I, and the 5'-to-3' exonuclease activity is on the small fragment.

9. Like all known DNA polymerases, DNA polymerase I requires a primer from which to initiate replication and polymerizes deoxyribonucleotides into DNA in the 5' to 3' direction using the complementary strand as a template. Newly synthesized DNA is covalently attached to the primer, but only hydrogen-bonded to the template. The template provides the specificity according to Watson-Crick base pairing 4. Only the alpha phosphate of the dNTP is incorporated into newly synthesized DNA

10. Figure 30-8b X-Ray structure of E. coli DNA polymerase I Klenow fragment (KF) in complex with a dsDNA (a tube-and-arrow representation of the complex in the same orientation as Part a). Page 1141

12. Figure 30-12 Nick translation as catalyzed by Pol I. Page 1144

13. Figure 30-8a X-Ray structure of E. coli DNA polymerase I Klenow fragment (KF) in complex with a dsDNA. Page 1141

14. Here’s a computer modelhttp://www.youtube.com/watch?v=4jtmOZaIvS0 Overview of DNA and replication http://207.207.4.198/pub/flash/24/menu.swf This is a pretty good outline: http://www.youtube.com/watch?v=teV62zrm2P0&NR=1 Another one with review questions http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html

17. Figure 30-13a X-Ray structure of the  subunit of E. coli Pol III holo-enzyme. Ribbon drawing. Page 1146

18. Figure 30-13b The  subunit of E. coli Pol III holoenzyme. Space-filling model of sliding clamp in hypothetical complex with B-DNA. Page 1146

19. Sliding clamp http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/poliiib_2/poliiib.htm

21. Clamp loading: ·All clamp loaders utilize the energy of ATP to assemble their respective clamps onto replication forks ·Various studies have suggested that the clamp loading complex starts off in a closed form and, upon bind ATP, is drven into an open conformation that binds the clamp ( dimer) One formed, this complex between the clamp loader and the clamp binds to the DNA, inserts the DNA through the open clamp and then hydrolyzes ATP

22. Figure 30-14 Unwinding of DNA by the combined action of DnaB and SSB proteins.

23. Figure 30-15 Electron microscopy–based image reconstruction of T7 gene 4 helicase/primase. Page 1147

24. Figure 30-17 Active, rolling mechanism for DNA unwinding by Rep helicase.

25. Figure 30-19 X-Ray structure of the N-terminal 135 residues of E. coli SSB in complex with dC(pC)34. Page 1149

27. Figure 30-20 The reactions catalyzed by E. coli DNA ligase. Page 1150

28. Figure 30-21 X-Ray structure of DNA ligase from Thermus filiformis. Page 1151

29. Figure 30-22 X-Ray structure of E. coli primase. Page 1151

30. Transcription

31. Figure 31-1 The induction kinetics of b-galactosidase in E. coli. Page 1217

32. Total RNA Pulse-chase MVA Fig. 26.3

33. 3 Major Types of RNA: messenger transfer ribosomal Other small RNAs are involved in splicing.

34. MVA Fig. 4.21

35. (prok) Inh. initiation Euk inhibitor Blocks elongation MVA Fig. 26.4

36. Table 31-1 Components of E. coli RNA Polymerase Holoenzyme. Page 1221

37. RNAP IV!! Table 31-2 RNA Polymerase Subunitsa. Page 1232

38. MVA Fig. 26.8

39. Figure 31-11aX-Ray structure of Taq RNAP core enzyme. a subunits are yellow and green, b subunit is cyan, b¢ subunit is pink, w subunit is gray. What do you notice about this structure? Page 1224

40. Figure 31-13bModel of the open (Rpo) complex of Taq RNAP with promoter-containing DNA showing the transcription bubble and the active site. Page 1225

41. Figure 31-14 The two possible modes of RNA chain growth. Growth may occur (a) by the addition of nucleotides to the 3¢ end and (b) by the addition of nucleotides to the 5¢ end. Page 1226 How could you distinguish between these two possibilities?

42. Cordycepin triphosphate

44. Initiation

45. MVA Fig. 26A. DNA footprinting (Nuclease protection assay)

46. DNA Footprinting http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/F/ Footprinting.html

47. Figure 31-10 The sense (nontemplate) strand sequences of selected E. coli promoters. Page 1223

48. Figure 31-12a The sequence of a fork-junction promoter DNA fragment. Numbers are relative to the transcription start site, +1. Page 1225

49. MVA Fig. 26.6

50. Figure 31-15 RNA chain elongation by RNA polymerase. Page 1227