8.Transcription09

8.Transcription09 - Chapters 9-11 of Genes V VI or VII by...

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Chapters 9 -11 of Genes V, VI, or VII by Lewin may be helpful for understanding transcription. (Copies are on reserve in the Chemistry Resource Center) Some useful websites on replication, repair, and transcription; many with animations and all the animations I showed in class http://www.courses.fas.harvard.edu/~biotext/animations/GeneralRecombination.html http://www.pingrysmartteam.com/RPo/RPo.htm http://www.wiley.com/college/boyer/0470003790/animations/replication/replication.htm http://www.usask.ca/biology/genetics/recombination/recom.htm http://engels.genetics.wisc.edu/Holliday/index.htm http://www.nature.com/nrc/journal/v1/n1/animation/nrc1001-022a_swf_MEDIA1.html http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/F/Footprinting.html (Not an animation) http://bio-alive.com/animations/DNA.htm (links to many animations) http://www.courses.fas.harvard.edu/~biotext/FSVideos/DNA_Glycosylase.mov http://www.lmb.uni-muenchen.de/cramer/pr%2Dmaterials/Videos/RNApol_II_Xray_and_zoom.htm http://www.lmb.uni-muenchen.de/cramer/pr%2Dmaterials/Videos/RNApol_II_NAD.wmv
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Picture 3 From Lehninger Biochemistry, 2000
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Transcription Cycle E. coli   RNA polymerase Core:    5 subunits,  α 2 ββ ' ϖ Sigma:      "initiation" subunit Holoenzyme:  core + sigma Promoter Terminator Coding Sequence Transcription Holoenzyme Core Sigma Regulatory Factor Cycles Termination Elongation Initiation
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DNA Footprinting Lewin Fig. 9.16
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Analysis of a DNA Footprinting Experiment Lewin Fig 9.16
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QuickTime  and a TIFF (LZW) decompressor are needed to see this picture. QuickTime  and a TIFF (LZW) decompressor are needed to see this picture. From: Mechanism of origin unwinding:  sequential binding of DnaA to double- and  single-stranded DNA The EMBO Journal  (2001)  20,  1469 1476,  doi:10.1093/emboj/20.6.1469 Figure 1 DNase I footprint of the AT-rich region.  DNase I footprinting was performed using a  5'-end-labeled 428 bp PCR DNA fragment.  Increasing amounts of ATP- or ADP-DnaA  were added, giving final concentrations of  150, 300, 350, 400, 450, 500, 550 and 600  nM. Incubation was for 10 min at 37 ° C. DnaA  box R1, the AT cluster and the three 13mers  are indicated by bars; the lower strands are  shown.
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Typical E. coli Promoter Lewin Genes VII
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Genes VII, Lewin Sigma is released in transition to elongation
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Genes VII, Lewin Transcript cleavage improves fidelity and prevents and/or rescues dead-end complex formation (GreA and GreB)
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Lewin Genes VII Model of Rho- dependent termination
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Polymerization of RNA chain EC i  + NTP       EC i+1 + PP i Pyrophosphorolysis EC  + PP      EC + NTP Reactions Catalyzed by E. coli RNA polymerase
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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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