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Advanced biochemistry course taught at University of Oregon, Winter 2018
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CH662: Advanced Biochemistry

Lecture material for CH662 Advanced Biochemistry taught at the University of Oregon in Winter 2018.

Course objectives

  • Prepare students to do research in molecular biology by helping them think molecularly and by introducing tools to study binding interactions.
  • This will be achieved by:
    • Introducing students to controlling conceptual frameworks in biochemistry, with an emphasis on quantitative reasoning.
    • Introducing methods used to study biomolecular properties and function, with an emphasis on binding interactions.
  • By the end of this course:
    • Understand the difference between microscopic and macroscopic phenomena and know the conceptual tools used by biochemists to link the two scales.
    • Be able to employ simple mathematical models to describe both the thermodynamics and kinetics of biomolecluar interactions.
    • Reason about the effects of mutations on molecular structure.
    • Have a working understanding of a collection of methods used to probe molecular mechanisms, with an emphasis on those used for binding interactions.

How to use this repo:

View currently hosted material:

View visuals

Download and host locally:

  • Fork the project on github and then clone it locally.
  • Run in the man directory. Hit Enter at all prompts. This will install grunt dependencies in the directory. I have tested this on an Ubuntu machine. You might have to tweak npm install for your environment.
  • In the cloned directory, type grunt serve. This should load index.html in your default browser.

Download and host on github:

If you have a gh-pages branch, github will host this material directory.

  • Fork the project on github and then clone it locally.
  • Push changes to the gh-pages branch: git push origin gh-pages
  • Access via, replacing harmsm with your own user name.


Types of content:

  • Visuals (material I showed as slides). The base directory has lecture_xx.html that hold this material. The material for each lecture -- images, videos, etc. -- are all in the presentation-data/xx/ directory for that discussion.
  • pre-class: materials that students should have looked at before class. In the pre-class/xx directory.
  • in-class: material I scribbled on the board or handed out in class. These live in the in-class/xx directory for each lecture.


Course material is made available under the unlicense. I have attempted to credit all source material I used to construct the visuals where appropriate. Reveal.js presentation technology is released under their own license (see LICENSE_reveal.js).


This is built on the reveal.js platform (check it out!):

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