In class we will have several demos of macromolecular structure and function.  If you would like to explore these demos in more detail I would encourage you to download an educational version of PyMOL from www.pymol.org.  Here is a PyMOL wiki to get you started.  There are also many tutorials to get you started, such as this one on youtube.

Alcohol Dehydrogenase (ADH) as an example of how enzymes work – lecture 7
Click here to download PyMOL session file (4.3 MB) with introduction to the ADH structure.
Click here to download PyMOL session file (1.8 MB) with comparison of free enzyme and ADH binding NAD+.
Click here to download PyMOL session file (1.4 MB) with a focus on active site, Zn coordination and proton relay used to get proton off alcohol and to the solvent.
Click here to download the powerpoint file on ADH shown in class.  Due to the 3 embedded videos it is rather large (177 MB).

Chymotrypsin – mechanism of a serine protease – lecture 9
Click here to download a PyMOL session file (1.5 MB) which shows the active site Ser, His, Asp active site residues, the hydrophobic pocket, and the oxyanion hole.
Click here to download the .mov file of this demo (201 MB).

Enoyl-CoA Hydratase – from fatty acid catabolism – lecture 16
Click here to download a PyMOL session file (6 MB) which introduces the ES crystal structure (pdb code 1EY3).

Double Helix B-form DNA – intro to DNA/RNA – lecture 19
Click here to download a PyMOL session file (1.5 MB) which introduces DNA Watson-Crick base pair, B-form DNA and major groove binding by a transcription factor (pdb code 1b01).

DNA Replication – lecture 20
Click here to download a PyMOL session file (1.8 MB) which shows DNA pol-beta structure with mismatched dNTP bound (pdb code 4LVS).
Click here to download a PyMOL session file (6.1 MB) which shows DNA pol-III, alpha subunit with a ddNTP at end of primed strand and the proper dNTP in the ES complex (pdb code 3E0D).

RNA Transcription – lecture 21
Click here to download a PyMOL session file (12.1 MB) which shows the yeast RNA polymerase bound to DNA-RNA hybrid from “bubble” of mechanism (pdb code 1i6h).