Course Materials

Biochemistry/Microbiology 917: Regulation of Gene Expression Seminar

Per current UW guidelines for classes through the end of the spring semester, we are moving journal club to an online platform. We will use Webex for the journal club each week at the following link. The link is the same for each week. As a reminder, the Webex app is more user-friendly than the web browser version.


We recognize there has been a lot of anxiety about use of Zoom of late and, while we’re confident that Zoom can be used safely, we don’t want people to worry about it when there is so much else to worry about these days. If you have the Zoom app installed on your computer, update the software and use it wisely to communicate with colleagues and friends. We may return to it in the future as it has some advantages over other platforms. As always, don’t share confidential information on social media (ie, meeting links and passwords) and don’t click on links in chats or emails unless you are 100% confident that they are safe. If you have concerns about the journal club operations, please communicate them to Bob Landick,


Microbiology 612: Prokaryotic Molecular Biology


  • Geszvain K, Landick R. The Structure of Bacterial RNA Polymerase. [PDF]
  • Zhang J, Landick R. Substrate Loading, Nucleotide Addition, and Translocation by RNA Polymerase. [PDF]


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RNA polymerase II in motion

Example of a true molecular dynamics movie. Physically realistic if you note the time scale. The entire movie shows 6 microseconds of RNAPII motions, meaning that it could be repeated over 150 times in the time it takes for you to blink your eye. An eye blink takes about 1 millisecond (1/1000th of a second or 1000 microseconds). Movie provided by Xuhui Huang and Daniel-Adriano Silva, Dept. of Chemistry, Hong Kong University of Science and Technology.

RNA polymerase II nucleotide addition cycle, transcript cleavage, and backtracking

Example of a morph movie. Not physically realistic, but illustrative of the nucleotide addition cycle. Adapted from Cheung and Cramer, 2012 Cell 149:1431.

Nucleotide addition cycle, elemental pausing, and hairpin-stabilized pausing and swiveling

Schematic movie illustrating nucleotide addition cycle, elemental pausing, and hairpin-stabilized pausing and swiveling. Credit: Seth Darst.


Model of expressome (ribosome-RNAP complex) based on cryoEM structure from Kohler et al., 2017 Science 356:194 with added elements from other ribosome and RNAP structures.

Swivel domain

Molecular model of E. coli RNAP illustrating the swivel domain and its movements upon pause hairpin formation. From Kang et al., 2018 Mol Cell 69:802. Credit: Jin Young Kang.

Conserved core

Conserved core double-psi beta-barrel domains in the beta and beta-prime subunits of bacterial RNAP (illustrated with Thermus thermophilus RNAP, pdb 205i).