BCH 341 – ASU ONLINE – iCourse – Spring 2018

J.P. Allen, BioPhysical Chemistry, Wiley-Blackwell, 2008. (free PDF version for ASU students)

Chapter 8: problems 2, 4, 5, 7 and 15.

Additional Problems

6-1A: Ideal gases are often used to introduce statistical thermodynamics.  Try calculating Enthalpy, Entropy and Gibbs Free Energy of  standard pressure and temperature ideal gases using partitional functions formalism for the thermodynamic energies.  This is a great way to start getting sense for the vibrational, rotational and translational contributions to energies, heat capacities and other common thermodynamic quantities. You will need to expand from monatomic gases to at least diatomic gases to start working with vibrational and rotational degrees of freedom.  Also, ‘thermochemistry’ electronic structure ab-initio computational methods are a great way to expand your statistical thermodynamic understanding beyond the pencil/paper problems found in textbooks.

6-2A: A good starting statistical thermodynamic model for biochemical systems is the ‘Helix-Coil’ Transition model.  This is often used in both polypeptides (proteins) and nucleic acids (DNA).  The transition temperature for the helix-coil transitions of DNAs correlate well with the base composition of the DNA.  While becoming generally familiar with this transition model is the goal, it often helps to have a defined problem.  So, how about this:

Sequence dependence of the ‘melting’ curves for short double-stranded DNA helices is commonly used in experimental biochemistry.  Replacing an A and a T in the middle of the sequence with a C and a G cause a change in the ‘melting’ temperature (helix-coil transition).  This would typically be done at mM concentration DNA and 100+ mM salt (NaCl) concentration.  Using a helix-coil transition model, plot the predicted ‘melting curve’ (% single stranded DNA versus Temperature) for A3TAT3, A3ATT3, A3GCT3 and A3CGT3  (and/or A4T4, A5T5, A6T6 and A7T7, to show the length dependence of the ‘melting curve’).