Following are links to class handouts. Dates are approximate.

January 27, 2009: Course syllabus, schedule, why E. coli?, glossary of genetic terms, reactions catalyzed by beta-galactosidase, table of galactosides, cartoons of interrupted mating.

February 3, 2009: Alternative explanations for the effect of removing inducer and for the effect of transferring uninduced cells grown in labeled medium to unlabeled medium containing IPTG.

February 5, 2009: 3-factor cross to determine the order of lacZ and lacI with respect to lacY. The two possible orders are shown and the reciprocal cross is also given.

February 12, 2009: This set of handouts provides supplementary information for the paper by Scaife and Beckwith, including a description of lacOo mutants, properties of nonsense mutations and their suppressors, cartoons of the coupling of transcription and translation, translation on polycistronic mRNAs, the role of rho factor in transcription termination, and the mechanism of polarity; also given are the reasons the lac promoter was thought to lie between lacO and lacZ, and mapping of the lac promoter mutations with respect to lacZ and lacI.

February 19, 2009: This set of handouts provides supplementary information for the paper by Beckwith et al., including the steps in formation of specialized transducing phages by bacteriophage lambda, the steps in formation of strains in which lac has been transposed to a site near the integration site of phage phi 80, and the steps in formation of specialized transducing phages carrying lac in both possible orientations.

February 24, 2009: This handout on deletion mapping will be used in the discussion of the paper by Ippen et al.

March 12, 2009: A set of handouts for the paper by Gilbert and Muller-Hiller. Also, some follow-up handouts on experiments demonstrating that lactose repressor binds the lac operator and the nitrocellulose filter binding assay. Another handout describes how the lac operator was isolated and its sequence determined. And the components of a minimal in vitro transcription system is described and its application to the demonstratration that CAP functions by activating lac transcription. Also shown are data demonstrating that lacO is transcribed.

March 26, 2009:This set of handouts contains data demonstrating how the entire lac regulatory region was initially sequenced and how genetics helped define the boundaries of the various regulatory regions. Also included are handouts describing selected laboratory methods used to study protein-DNA interactions, e.g., methylation protection, ethylation interference, DNase I footprinting, and gel mobility shift assays.

April 2, 2009: Handouts supplementing the paper by Ogata and Gilbert. One handout shows how UV-irradiation of BU-dR substituted DNA leads to strand-breakage of cross-linking to the side group of a closely bound protein, e.g., lactose repressor. The other describes the steps to prepare a DNA fragment labeled on one end of one strand.

April 2, 2009: Handouts describing the mechanism of repression by lactose repressor. Included are DNaseI footprinting data from a paper by Galas and Schmidtz.

April 7, 2009: Handouts supplementing the 1984 paper by Ebright et al. by providing a cartoon depicting the DNA-binding, helix-turn-helix motif of lambda repressor. Images of the three-diminensional structures of lambda cro protein and CAP are given as is the consensus sequence of the DNA bound by CAP, which shows its dyad symmetry.

April 7, 2009: A second set of handouts providing descriptions of molecular biology methods. Included are handouts of the chain-termination (Sanger) method of DNA sequencing, PCR, "soeing", which is a PCR method that enables two DNA fragments to be "spliced" together, the fluorescence, PCR-based method for DNA sequencing and the Quik-Change method of mutagenesis.

April 16, 2009: Handout providing a supplement to the second paper by Ebright et al.

April 21, 2009: Handouts for the first paper by Zhou et al. One describes the abortive initiation assay and the other provides better copies of the last two figures.

May 7, 2009: Handout summarizing information from the Busby and Ebright papers of 1994 and 1999 on the UP element as a third promoter recognition element and the protein-protein interactions that mediate CAP-dependent activation at class I and class II promoters.

May 7, 2009: Handout summarizing the paper by Niu et al. in which mutants specifically defective in activation of class II CAP-dependent promoters are isolated and characterized.

May 7, 2009: Handout showing the ternary complex of DNA-bound CAP and the alphaCTD, as published by Benoff et al.

Not Used, 2009: A figure depicting schematically the ChIP and ChIP-chip approaches used by Grainger et al.

Not Used, 2009: A figure comparing the recruitment and pre-recruitment mechanisms of transcription activation and a figure providing genetic evidence for pre-recruitment. For use with the paper by Grainger et al.

Not Used , 2008: Action of chemical mutagens, e.g., hydroxlylamine.

Not Used , 2009: Summary of the data describing the binding of AraC protein to araI as obtained by Schleif and by Lee et al.

Not Used , 2009: Handout illustrating supercoiled DNA

Not Used , 2000: Handout summarizing the forms of AraC during repression and induction with respect to the light switch mechanism.

Not Used , 2009: Handout describing some remaining unanswered questions about the ara system and also some suggestions for new mutants to isolate.

Not Used , 2009: Handout describing the action of CAP at Class II CAP-dependent promoters.

Not used in 2009: Handouts introducing gene regulation in phage lambda including its genetic map, a table summarizing the stages of transcription, a description of the assembly and action of the N protein anti-termination complex, a "scorecard" of the genes involved in lambda development, a figure describing the regulatory circuits involved in lambda development, and a figure showing the action of repressor and Cro at the rightward lambda operator/promoter region.

Not used in 2000: Handout of electron microscopy experiments demonstrating DNA looping by lambda repressor.

Not used in 2009: Handout illustrating the effect of DNA looping by lambda repressor on expression from the Prm promoter and use of this system to isolate mutants defective in the protein-protein interactions underlying repressor-mediated cooperativity.

Not used in 2009: Handout describing the isolation of new specificity mutants of lambda 434 repressor.

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