1. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Macromolecular assemblies in DNA- associated functions DNA structures: Chromatin (nucleosome) Replication complexes: Initiation, progression Transcription complexes: Initiation, splicing, progression Other complexes: Repair, recombination December 23, 2004 TIGP-CBMB Molecular biophysics I

2. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 29-1aStructure of B-DNA. (a) Ball and stick drawing and corresponding space-filling model viewed perpendicular to the helix axis. Page 1108

3. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 29-21Toroidal and interwound supercoils. Page 1124

4. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 29-22Sedimentation rate of underwound closed circular duplex DNA as a function of ethidium bromide concentration. Page 1125

5. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 29-23X-Ray structure of a complex of ethidium with 5- iodo-UpA. Page 1125 Figure 31-17X-Ray structure of actinomycin D in complex with a duplex DNA of self- complementary sequence d(GAAGCTTC).

6. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 29-26X-Ray structure of the Y328F mutant of E. coli topoisomerase III, a type IA topoisomerase, in complex with the single-stranded octanucleotide d(CGCAACTT). Page 1127

7. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 29-27Proposed mechanism for the strand passage reaction catalyzed by type IA topoisomerases. Page 1128

8. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 29-28X-Ray structure of the N-terminally truncated, Y723F mutant of human topoisomerase I in complex with a 22-bp duplex DNA. Page 1129

9. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 29-31a Structures of topoisomerase II. (a) X-Ray structure of the 92-kD segment of the yeast topoisomerase II (residues 410–1202) dimer. Page 1131

10. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 29-32Model for the enzymatic mechanism of type II topoisomerases. Page 1131

11. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-1 Electron micrograph of a human metaphase chromosome and of D. melanogaster chromatin showing that its 10-nm fibers are strings of closely spaced nucleosomes. Page 1423

12. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-7aX-Ray structure of the nucleosome core particle. (a) The entire core particle as viewed (left) along its superhelical axis and (right) rotated 90° about the vertical axis. Page 1426

13. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-8X-Ray structure of a histone octamer within the nucleosome core particle. Page 1427 Figure 34-3 The amino acid sequence of calf thymus histone H4. This 102-residue protein’s 25 Arg and Lys residues are indicated in red.

14. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-9Model of the interaction of histone H1 with the DNA of the 166-bp chromatosome. Page 1427

15. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-10 Electron micrographs of chromatin. (a) H1-containing chromatin and (b) H1-depleted chromatin, both in 5 to 15 mM salt. Page 1428 Figure 34-13 Model of the 30-nm chromatin filament. The filament is represented (bottom to top) as it might form with increasing salt concentration.

16. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Macromolecular assemblies in DNA- associated functions DNA structures: Chromatin (nucleosome) Replication complexes: Initiation, progression Transcription complexes: Initiation, splicing, progression Other complexes: Repair, recombination December 23, 2004 TIGP-CBMB Molecular biophysics I

17. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-1 Action of DNA polymerase. DNA polymerases assemble incoming deoxynucleoside triphosphates on single-stranded DNA templates such that the growing strand is elongated in its 5  3 direction. Page 1137 Figure 30-2Autoradiogram and its interpretive drawing of a replicating E. coli chromosome.

18. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-28The replication of E. coli DNA. Page 1155

19. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-5Semidiscontinuous DNA replication. In DNA replication, both daughter strands (leading strand red, lagging strand blue) are synthesized in their 5  3 directions. Page 1138

20. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Table 30-1Properties of E. coli DNA Polymerases. Page 1145

21. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-8aX-Ray structure of E. coli DNA polymerase I Klenow fragment (KF) in complex with a dsDNA. Page 1141

22. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-9bX-Ray structure of Klentaq1 in complex with DNA and ddCTP. (a) The closed conformation. (b) The open conformation. Page 1142

23. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-13aX-Ray structure of the  subunit of E. coli Pol III holoenzyme. Ribbon drawing. Page 1146

24. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Table 30-3Unwinding and Binding Proteins of E. coli DNA Replication. Page 1146

25. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-14Unwinding of DNA by the combined action of DnaB and SSB proteins. Page 1147

26. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Table 30-4Proteins of the Primosome a. Page 1152

27. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-15Electron microscopy–based image reconstruction of T7 gene 4 helicase/primase. Page 1147 X-Ray structure of the helicase domain of T7 gene 4 helicase/primase.

28. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-19X-Ray structure of the N-terminal 135 residues of E. coli SSB in complex with dC(pC) 34. Page 1149

29. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-22X-Ray structure of E. coli primase. Page 1151 Figure 30-25 Electron micrograph of a primosome bound to a fX174 RF I DNA. Such complexes always contain a single primosome with one or two associated small DNA loops.

30. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-23 The synthesis of the M13 (–) strand DNA on a (+) strand template to form M13 RF I DNA. Page 1152 Figure 30-27 The synthesis of the fX174 (+) strand by the looped rolling circle mode.

31. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-29A model for DNA replication initiation at oriC. Page 1156

32. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Table 30-2Components of E. coli DNA Polymerase III Holoenzyme. Page 1145

33. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-32X-Ray structure of the  –  complex. Page 1158

34. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-33X-Ray structure of the  3  clamp loading complex. Page 1159

35. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-34Schematic diagram of the clamp loading cycle. This speculative model is based on a combination of structural and biochemical information. Page 1159

36. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-39X-Ray structure of RB69 DNA polymerase (RB69 pol) in complex with primer–template DNA and dTTP. Page 1164

37. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Macromolecular assemblies in DNA- associated functions DNA structures: Chromatin (nucleosome) Replication complexes: Initiation, progression Transcription complexes: Initiation, splicing, progression Other complexes: Repair, recombination December 23, 2004 TIGP-CBMB Molecular biophysics I

38. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-42Immunofluorescence micrograph of a lampbrush chromosome from an oocyte nucleus of the newt Notophthalmus viridescens. Page 1449

39. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-47Assembly of the preinitiation complex (PIC) on a TATA box–containing promoter. Page 1452

40. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-48aX-Ray structure of Arabidopsis thaliana TATA box– binding protein (TBP). (a) A ribbon diagram of the protein in the absence of DNA. (b) TBP with a 14-bp TATA box–containing segment DNA. Page 1453

41. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-49Model of the TFIIA–TFIIB–TBP–TATA box– containing DNA quaternary complex. Page 1454

42. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-50EM-based image of the human TFIID– TFIIA–TFIIB complex at 35-Å resolution. Page 1454

43. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-9An electron micrograph of E. coli RNA polymerase (RNAP) holoenzyme attached to various promoter sites on bacteriophage T7 DNA. Page 1222

44. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-10The sense (nontemplate) strand sequences of selected E. coli promoters. Page 1223

45. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-11aX-Ray structure of Taq RNAP core enzyme.  subunits are yellow and green,  subunit is cyan,  subunit is pink,  subunit is gray. (b) The holoenzyme viewed as in Part a. Page 1224

46. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-21bX-Ray structure of an RNAP II elongation complex. Page 1234

47. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-47The sequence of steps in the production of mature eukaryotic mRNA as shown for the chicken ovalbumin gene. The consensus sequence at the exon–intron junctions of vertebrate pre- mRNAs. Page 1258

48. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-49The sequence of transesterification reactions that splice together the exons of eukaryotic pre-mRNAs. Page 1259

49. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-51aThe self-splicing group I intron from Tetrahymena thermophila. (a) The secondary structure of the entire 413-nt intron. (b) The X-ray structure of P4-P6 viewed as in Part a. Page 1261

50. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-56An electron micrograph of spliceosomes in action. Page 1265

51. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-57A schematic diagram of six rearrangements that the spliceosome undergoes in mediating the first transesterification reaction in pre-mRNA splicing. Page 1265

52. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-60A model of the snRNP core protein. Page 1267

53. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 31-61aThe electron microscopy-based structure of U1-snRNP at 10 Å resolution. (a) The predicted secondary structure of U1-snRNA. (b) The molecular outline of U1-snRNP. (c) The U1-snRNA colored as in Part a. Page 1268

54. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Macromolecular assemblies in DNA- associated functions DNA structures: Chromatin (nucleosome) Replication complexes: Initiation, progression Transcription complexes: Initiation, splicing, progression Other complexes: Repair, recombination December 23, 2004 TIGP-CBMB Molecular biophysics I

55. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-54b The structure of E. coli Ada protein. (a) The X-ray structure of Ada’s 178-residue C-terminal segment, which contains its O 6 - alkylguanine–DNA alkyltransferase function.(b) The NMR structure of Ada’s 92-residue, N-terminal segment, which mediates its methyl phosphotriester repair function. Page 1175

56. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-55The mechanism of nucleotide excision repair (NER) of pyrimidine photodimers. Page 1176

57. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-57 X-Ray structure of human uracil–DNA glycosylase (UDG) in complex with a 10-bp DNA containing a U·G base pair. Page 1178 Figure 30-55 The mechanism of nucleotide excision repair (NER) of pyrimidine photodimers.

58. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-64The Holliday model of homologous recombination between homologous DNA duplexes. Page 1184

59. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-67a Electron micrographs of intermediates in the homologous recombination of two plasmids. (a) A figure-8 structure. This corresponds to Fig. 30-66d. (b) A chi structure that results from the treatment of a figure-8 structure with a restriction endonuclease. Page 1186 Figure 30-66 Homologous recombination between two circular DNA duplexes. This process can result either in two circles of the original sizes or in a single composite circle.

60. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-68An electron microscopy–based image (transparent surface) of an E. coli RecA–dsDNA–ATP filament. Page 1187

61. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-71The RecA-catalyzed assimilation of a single- stranded circle by a dsDNA can occur only if the dsDNA has a 3 end that can base pair with the circle (red strand). Page 1188

62. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-72A hypothetical model for the RecA-mediated strand exchange reaction. Page 1189

63. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-75aProposed structure of the T. thermophilus RuvB hexamer. (a) EM image reconstruction of RuvB complexed with DNA (not visible). Page 1191

64. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 30-76Model of the RuvAB–Holliday junction complex. The model is based on electron micrographs such as that in the inset. Page 1191

65. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 34-117aCryoelectron microscopy–based images of the apoptosome at 27-Å resolution. (a) The free apoptosome. (b) The apoptosome in complex with a noncleavable mutant of procaspase-9 in oblique top view. Page 1513