Week 2

Feb 16 - Thermodynamics

Reading (to be completed before class!)

Whitford - Proteins: Structurer and Function: pages 53-58
This is the best prepartion for the worksheet

Voet 4th ed
Chp 3: all
Chp 8, Sect 4
We will pay careful attention to the role of thermodynamic principles in governing protein stability.
Weak Forces, Hydrophobic effect, clathrates, free energy changes. This is one of the most important sections since the principles govern protein-substrate and drug interactions, stability of DNA, RNA, and Lipid structures, etc.


Voet Chp 3: 3, 9, 13
Voet Chp 8: 13, 14

Define the hydrophobic effect and explain how it can
influences protein folding?

Additional Review Questions

Explain the following statement

"The folding process can occur when the combination of the entropy associated with the hydrophobic effect and the enthalpy change associated with hydrogen bonds and van der Waals interactions makes the overall free energy negative."

In Class Activities

- BRING YOUR BOOK or have online reference available in CLASS

- Group Problem on Intermolecular forces, thermodynamics, and protein stability - Key


Your general chemistry chapter on thermodynamics


Class Summary (please contribute)


Feb 18 - 3D Structure of Proteins

Reading (to be completed before class!)

Required Review Reading

Lehninger 6th ed (required review)
Chp 4: 4.3
Supplemental Reading
Berg Biochemistry
Chp3: 3.3, 3.4, 3.5 Protein 3D Structure

- Jmol Animation on Protein Structure

Deepview Assignment 1 - reminder due feb 17th noon


Berg Chp 3 (5th ed): 2, 6, 7, 9

Voet: Chp8: 4 (also using Swiss PDBviewer), 18 (also support your answer using SwissPDBviewer), 22  Solutions

In Class Activities

- Molecular Modeling wih Swiss PdbViewer
Tutorials 7, 10 , 11 (Try tutorial 10 with 1 HHO.pdb , READ Note!)


The majority of this material should be review.
Thus, the focus for this class is to gain further expertise with an essential biochemistry tool, the molecular modeling program, and using it to help us understand the following concepts:

  • tertiary packing and the hydrophobic effect
  • stabilizing factors in 3o and 4o structure
  • working with oligomeric proteins
    • comparing hemoglobin and myoglobin


Feb 20 - Loops, Turns, Motifs

Reading (to be completed before class!)

Reading on Loops and Turns

  1. Whitford
    • This first reading is very short but provides a nice introduction to the topic.
  2. Chou Analytical Biochemistry 2000
    • Read just through beta-turns
      • Note there is a mistake in the phi and psi angles for residue i+1 in the type II' turn in table I. They should be phi = 60o psi = -120o
      • You do not have to focus on history of development of b-turns
  3. Voet
    • B. Tertiary Structure, a through i, p245-p256
    • Focus of this reading is on Motifs (supersecondary structure)


Topology and Turns

You can practice looking at turns and loops using the identified structures from this paper
Protein Structure 1973 Lewis
Go to table II. Find some of the identified β-turns and then confirm in DeepView using the PDB structures of those enzymes

In Class Activities

  • In Class QUIZ (on material from week 1 and last Mon)
  • Discussion of Chou and Voet readings
  • Turns and loops as secondary structure analyzed - using molecular modeling software
    • Inspect the structures of the following protein.
      • 1TNF (Note: we actually did 1HEW in class)

Identify two β-turns (according to the nomenclature of Chou), identify the residues in the turn, and discuss an stabilizing interactions in the turn.

This material will be addressed later ...