Primary Structure with Intro to Molecular Modeling Feb 16

Reading (to be completed before class!)

Lehninger
Chp 3: 3.1, 3.2, 3.4 Amino Acids, Primary Structure
Chp 3: 3,3 (discussed in lab)
Chp 4: Sections 1-2, pages 115-125

Pre-Assignment

  1. PreAssignment Worksheet
  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

Problems

  • If you have one please BRING your LAPTOP to CLASS
  • Molecular Modeling wih Swiss PdbViewer 
    Tutorials 3-6, 8  Please complete by Monday the 19th before class

Deepview Assignment 1 - Views 1-8, DS-1 (view 9 with caption)
Due Friday the 23rd end of day (pleases send all files via email or share with me in a Google folder)


Amino Acids

  • 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

Lehninger
Chapter 3: 5, 10, 11, 13, 15, 21, 22
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)