Primary Structure with Intro to Molecular Modeling Sept 11th

Reading (to be completed before class!)

  • Chp 3: 3.1, 3.2, 3.4 Amino Acids, Primary Structure
  • Chp 3: 3.3 (discussed in lab)

Terms and Figures to know and understand:

  • Section 3.1: Bold terms (except uncommon amino acids), Fig 3-2 and 3-5, Assign stereoisomersim (Fig 3-3), Box 3-1 and Fig 3-6 (know amino acids that absorb light and Beer's Law), pI,
  • Section 3.2: Know terms in bold, Fig 3-13, Fig 3-14, be able to draw the formation of a peptide bond. You do not have to memorize specific phi and psi angles, Fig 3-7 (formation of disulfide bonds)


  1. PreAssignment Worksheet: Amino acids and the primary and secondary structure of proteins
  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

Upcoming Assignments

  • Molecular Modeling wih Swiss PdbViewer 
    Tutorials 3-8  Please complete by Mon the 18th before class
  • Deepview Assignment 1 - Views 1-8, DS-1 (view 9 with caption)
    Due Fri the 20th end of day (pleases send all files via email or share with me in a Google folder)


Amino Acids (see table 3-1 and Fig 3-5)

  • Memorize Names and 3 and 1 Letter Abbreviations
  • Know 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

Problems: Lehninger
Chapter 3: 1, 2, 3a, 4b,c, 6, 7, 11
Chapter 4: 1
Chp 3 (Methods Problems): 5, 10, 15*, 17
(Methods problems are assigned to support lab. These are review problems and not covered in class. Please see me ASAP if you need assistance)