Week 1

Assignments for the first week

Feb 09 Aqueous Solutions, Buffers

Reading (to be completed before class!)   

Lehninger
Chp 2: All (required)
 
Example Pre-Assignment      key

In Class Activities

Discussion of Syllabus and Basic Buffer Concepts

Worksheet: Properties of water     key

Class Summary (link)

Problems

Lehninger
Chp 2: 1, 2, 3, 5, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 20, 22, 24, 25, 26, 27, 33

Some Helpful review (solutions)

 


Feb 11 Amino Acids, Primary Structure

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)

Pre-Assignment

  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)

Problems

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


 

Feb 13 Secondary Structure and Modeling

Focus
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.
 

Pre-Assignment

Complete Deepview tutorials (1-8) and bring questions

 

Problems

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

- BRING your LAPTOP to CLASS
- Use Deepview to convert the octapeptide into

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