This is the "green" edition of the textbook.
Here are some handouts from Dr. Deis's Intro Course, in Adobe Acrobat PDF format:
I insist on having all students learn the one-letter abbreviations for the 20 amino acids used in protein synthesis. Once you have learned them, this is a very useful version of the codon chart.
NCBI for sequences, BLASTP, etc.
Please tell me if you find typos in the Companion text, especially if they are not on THE TYPO LIST. Recently added typos (some that were found by students) are listed at the bottom of the page.
I am also interested in any typos you might find in the Berg text. I have told Freeman about many of these. I think there are some wrong homework answers which are not on this list, please let me know if you find any. Berg Typos
The Hemoglobin film I show in class was made using MAGE software. Download a copy for MAC or PC from the FASEB website.
Once you have the software installed, download ProTour8.kin. Save the file to your hard disk as text, and then load it into MAGE.
It should also be very useful for students to visit the Freeman website and try out the conceptual insights etc. If you don't have Netscape, Flash, and Chime installed at home, you can try the "insights" etc. on the computers at LSM, the Library of Science and Medicine. All of their computers should have the correct software for the Freeman website to work perfectly.
Old Freeman Website - sometimes works better!
While it seems odd, you actually do have to use an old version of Netscape Communicator, and an old version of Chime, for all of the parts of the textbook website to work properly -- particularly the Structural Insights and Living Figures. Try clicking the buttons on the Structural Insights page to download. Recently the relevant Netscape files have been harder to get. You might try Sillydog for Netscape -- what you want is Communicator 4.7. Also, don't download the latest version of Chime. You can find the archived versions, and get 2.03 instead of the new 2.6. The newest Chime works elsewhere on the web but not on the Berg/Stryer site. In fact the new Chime even works well with Internet Explorer (try the last link on this page). But neither IE nor the newest Chime 2.6 works with the textbook site. If you have Mac with true OS 9.x or lower, it should work. I obtained Mac Communicator 4.75 from the Rutgers DCS Library server and installed Chime 2.0a, and that works on OS X. I am not sure the installation works in the "Classic" environment though -- I installed it on an OS 9.x machine and then ported it over to the OS X machine. -- The Conceptual Insights seem to work well with any computer that has Macromedia Flash Player installed as a plug-in.
Garrett and Grisham wrote the text used in MBB 407-8. This site has useful exercises, animations, etc.
Wolfgang Junge's page -- he did the wonderful animation of Fo/F1 -- ATP Synthase in the mitochondrion.
Luca Turin, who has the new ideas about Olfaction and quantum tunneling.
The Pima Paradox by Malcolm Gladwell, first appeared in the New Yorker. It is thought provoking and ties in with glycogen, fatty acids, and dieting.
Biochemistry tutoring links from the University of Houston. Excellent!
DNA Learning Center animations. Uses Shockwave, definitely worth the trouble to download.
Protein folding animation -- takes a long time to load. Interesting.
More protein folding -- look at Proteins A, G, and L, down the page.
Prion Helical Wheels including a folding animation. Note the use of Schiffer and Edmundson wheels.
Mol Bio Resources -- long and rich in resources!
Animations by Peter B. Berget note especially the Sliding Clamp animation which shows the formation of the "trombone loop." Chime based files may not work but see below:
The Chime animations in the URL above don't work for me because they are in "gzip" format online. The animations here work better, and some of the same files are presented in the "Hall of DNA Replication."
