Most of this material is review. In this class we will focus on
  • understanding phi and psi
  • relationship between phi and psi and structure
  • using the Ramachandran plot
  • working with the molecular modeling program to visualize structure

Reading (to be completed before class!)

Required Review Reading
Lehninger 6th ed (required review)
Chp 3: 4.1, 4.2
Supplemental Reading
Berg Biochemistry
Chp 3: 3.2
Mostly repeat of above, however, it may help with understanding torsion angles,
cis and trans peptide bonds, and the Ramachandran plot.


Complete Deepview tutorials (1-8) and bring questions



Lehninger 6th ed
Chp 4: 1, 4, 5, 6, 10

Berg Biochemistry
Chp 3: problem 15

Voet 4th ed
Chp 8: 2, 4

Begin to Browse the resources available a ExPASy
  • Expert Protein Analysis System
  • Molecular Biology computing tools
  • available on Server in Geneva, Switzerland

In Class Activities

  1. Activity

- Use Deepview to convert the octapeptide into

1) a 3-10 helix            > doc octapeptide
2) a α-helix
3) a β-strand              >  brief instructions