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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, 2004TIGP-CBMB Molecular biophysics I

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Figure 29-1a Structure of B-DNA. (a) Ball and stick drawing and corresponding space-filling model viewed perpendicular to the helix axis.

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Figure 29-21 Toroidal and interwound supercoils.

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Figure 29-22 Sedimentation rate of underwound closed circular duplex DNA as a function of ethidium bromide concentration.

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Figure 29-23 X-Ray structure of a complex of ethidium with 5-iodo-UpA.

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Figure 31-17 X-Ray structure of actinomycin D in complex with a duplex DNA of self-complementary sequence d(GAAGCTTC).

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Figure 29-26 X-Ray structure of the Y328F mutant of E. coli topoisomerase III, a type IA topoisomerase, in complex with the single-stranded octanucleotide d(CGCAACTT).

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Figure 29-27 Proposed mechanism for the strand passage reaction catalyzed by type IA topoisomerases.

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Figure 29-28 X-Ray structure of the N-terminally truncated, Y723F mutant of human topoisomerase I in complex with a 22-bp duplex DNA.

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Figure 29-31aStructures of topoisomerase II. (a) X-Ray structure of the 92-kD segment of the yeast topoisomerase II (residues 410–1202) dimer.

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Figure 29-32 Model for the enzymatic mechanism of type II topoisomerases.

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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.

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Figure 34-7a X-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.

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Figure 34-8 X-Ray structure of a histone octamer within the nucleosome core particle.

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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.

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Figure 34-9 Model of the interaction of histone H1 with the DNA of the 166-bp chromatosome.

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Figure 34-10 Electron micrographs of chromatin. (a) H1-containing chromatin and (b) H1-depleted chromatin, both in 5 to 15 mM salt.

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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.

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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, 2004TIGP-CBMB Molecular biophysics I

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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.

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Figure 30-2 Autoradiogram and its interpretive drawing of a replicating E. coli chromosome.

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

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Figure 30-5 Semidiscontinuous DNA replication. In DNA replication, both daughter strands (leading strand red, lagging strand blue) are synthesized in their 5 3 directions.

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Table 30-1 Properties of E. coli DNA Polymerases.

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

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Figure 30-9b X-Ray structure of Klentaq1 in complex with DNA and ddCTP. (a) The closed conformation. (b) The open conformation.

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Figure 30-13a X-Ray structure of the subunit of E. coli Pol III holoenzyme. Ribbon drawing.

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Table 30-3 Unwinding and Binding Proteins of E. coli DNA Replication.

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

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Table 30-4 Proteins of the Primosomea.

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

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

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

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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.

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Figure 30-23 The synthesis of the M13 (–) strand DNA on a (+) strand template to form M13 RF I DNA.

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Figure 30-27 The synthesis of the fX174 (+) strand by the looped rolling circle mode.

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Figure 30-29 A model for DNA replication initiation at oriC.

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Table 30-2 Components of E. coli DNA Polymerase III Holoenzyme.

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Figure 30-32 X-Ray structure of the – complex.

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Figure 30-33 X-Ray structure of the 3 clamp loading complex.

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Figure 30-34 Schematic diagram of the clamp loading cycle. This speculative model is based on a combination of structural and biochemical information.

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Figure 30-39 X-Ray structure of RB69 DNA polymerase (RB69 pol) in complex with primer–template DNA and dTTP.

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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, 2004TIGP-CBMB Molecular biophysics I

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Figure 34-42 Immunofluorescence micrograph of a lampbrush chromosome from an oocyte nucleus of the newt Notophthalmus viridescens.

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Figure 34-47 Assembly of the preinitiation complex (PIC) on a TATA box–containing promoter.

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Figure 34-48a X-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.

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Figure 34-49 Model of the TFIIA–TFIIB–TBP–TATA box–containing DNA quaternary complex.

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Figure 34-50 EM-based image of the human TFIID– TFIIA–TFIIB complex at 35-Å resolution.

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Figure 31-9 An electron micrograph of E. coli RNA polymerase (RNAP) holoenzyme attached to various promoter sites on bacteriophage T7 DNA.

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

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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.

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Figure 31-21bX-Ray structure of an RNAP II elongation complex.

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Figure 31-47 The 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.

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Figure 31-49 The sequence of transesterification reactions that splice together the exons of eukaryotic pre-mRNAs.

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Figure 31-51a The 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.

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Figure 31-56 An electron micrograph of spliceosomes in action.

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Figure 31-57 A schematic diagram of six rearrangements that the spliceosome undergoes in mediating the first transesterification reaction in pre-mRNA splicing.

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Figure 31-60 A model of the snRNP core protein.

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Figure 31-61a The 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.

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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, 2004TIGP-CBMB Molecular biophysics I

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Figure 30-54bThe structure of E. coli Ada protein. (a) The X-ray structure of Ada’s 178-residue C-terminal segment, which contains its O6-alkylguanine–DNA alkyltransferase function.(b) The NMR structure of Ada’s 92-residue, N-terminal segment, which mediates its methyl phosphotriester repair function.

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Figure 30-55 The mechanism of nucleotide excision repair (NER) of pyrimidine photodimers.

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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.

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Figure 30-55 The mechanism of nucleotide excision repair (NER) of pyrimidine photodimers.

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Figure 30-64 The Holliday model of homologous recombination between homologous DNA duplexes.

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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.

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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.

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Figure 30-68 An electron microscopy–based image (transparent surface) of an E. coli RecA–dsDNA–ATP filament.

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Figure 30-71 The 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).

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Figure 30-72 A hypothetical model for the RecA-mediated strand exchange reaction.

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Figure 30-75aProposed structure of the T. thermophilus RuvB hexamer. (a) EM image reconstruction of RuvB complexed with DNA (not visible).

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Figure 30-76 Model of the RuvAB–Holliday junction complex. The model is based on electron micrographs such as that in the inset.

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Figure 34-117a Cryoelectron 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.

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