Reading (to be completed before class!)

Lehninger 6th ed (required review)
Chp 3: 3.1, 3.4
Chp 3: 3.2, 3,3 (these methods will be discussed in lab - you are responsible for them on the exam)


  1. PreAssignment Worksheet    Key
  2. Download Deepview (SwissPDB viewer) to your computer.
    Read The Intro to the Deepview turorial and do parts 1 (Getting Started) and 2 (Windows)

In Class Activities

  1. Short lecture/discussion
  2. Activity
    • If you have one please BRING your LAPTOP to CLASS
    • Molecular Modeling wih Swiss PdbViewer 
      Tutorials 3-6, 8
Summary of the Discussion (link)


Deepview Assignment 1 - Views 1-8, DS-1 (view 9 with caption)
Due Tuesday the 17th at noon
Amino Acids
Memorize Names and 3 and 1 Letter AbbreviationsKnow Categories to which each AA belongs (nonpolar, neutral polar charged, etc)
Be able to match structure of the AA to its name
Know approximate pKas for backbone amines and carboxylic acids, charged side chains

Lehninger 6th ed
Chp 3: 1, 2, 4, 11, 12, 13, 21, 22
Chp 3 (Methods Problems): 5, 10, 15*, 17
(These are review problems and not covered in class. Please see me ASAP if you need assistance)

Rework PreAssignment and InClass Worksheet  


Online Resource Amino Acids