Biochem 650

Basic principles of Statistical Thermodynamics (From basic quantum mechanical models to collections of macromolecules); Binding and Linkage

Lentz; 966-5384, uncbrl@med.unc.edu; 9/25/13-10/28/13; MWF 11:00 AM; 3007 GM.  Registration limited to 12 except with permission Course Director.  (Recitation will meet on Tuesdays and Thursdays, Time and location will be determined)

Atoms & Molecules

9-25-13            W Lec 1 (Models of Molecular Motions: Rigid Body View of a Protein:); H&L Chapt 2.

9-26-13            Th Rec 1 Discuss Transition Problems 1 & 2.  Q1.

From Molecules to Experiments: Statistics

9-27-13            Fri Lec 2 (Ensembles; Boltzmann); Prob. 1 (particle in box) due. H&L Chapt 5

9-30-13            M Lec 3  (Molecular PF: A “Rigid Body Protein”); Prob. 2 (particle in box 2) due

10-1-13            T Rec 3:Q2; discuss Problems 1 & 2

10-2-13            W Lec 4 (Canonical PF); H&L Chapt 6 Prob. 3 (microcanonical & canonical) due

10-3-13            Th Rec 4 Q3;

10-4-13            F Lec 5 (Use of Q: 1] Mixtures & Solutions, QM picture) Prob 4 due EXAM 1 handout (partition function)

10-7-13            M Lec 6 (Use of Q: 2] Solutions & Liquids, Classical picture; 3] A View of Binding: Enthalpy versus Entropy) Prob. 5 (entropy of binding) due;

10-8-13            T Rec 4: Q4  questions about Exam 1

10-9-13            W F Lec 7 (Basic Stoichiometric Binding Theory; Molecular versus Stoichiometric Species); H&L Chapt 8 Prob 6 (entropy of binding expanded) due

10-10-13          Th Rec 5: Q5

10-11-13          Lec 8 (Grand Canonical PF); H&L Chapt 6

Binding and Biology

10-14-13          M Lec 9; (Semi-Grand Canonical PF and Molecular Grand PF: Read Derivation of MGPF H&L Chapter 11 (due

10-15-13          T Rec 6; Q6 EXAM 1 due; EXAM 2 handout

10-16-13          W Lec 10 (Molecular Grand PF: statistical weights, site binding theory versus stoichiometric binding theory); Discuss Prob 7; Prob 7 due. questions about Exam 2

10-17-13          Th Rec 7:Q7 questions about Exam 2.

10-18-13          F Lec 10: Statistical Weights, Binding, and “What Is a Macromolecule?”

10-21-13          M Lec 11: Site Binding Analyses

10-22-13          T Rec 8:Q8

10-23-13          W Lec 12; (Linkage between Protein Binding Sites: Cooperativity, Allostery; MGPF); H&L Chapt 13, Prob 8 due

10-24-13          Th Rec 9:Q9

Binding is Biology

10-25-13          F Lec 13: (Mechanisms of Linkage) H&L Chapt 12;

10-26-13          M Lec 14: (Hemoglobin: MGPF; Sequential vs. Concerted Models) Prob. 10 due. EXAM 2 due. EXAM 3 handout

10-27-13          T Rec 11:Q10: Discuss Prob 9 due & discuss Exam 3

11-8-12            W Lec 4 (DLVO theory).  Hermans

11-9-12            Th Rec

11-10-12          F Lec 5. (Protein titration and pI). Hermans

Simulations of Macromolecules

11-12-12          M Lec 6 (Computer simulations of biosystems.)  MC and MD techniques.  Hermans

11-13-12          Tu

11-14-12          Lec 7.  (Calculation of the free energy change.) Hermans.

11-15-12          Th Rec

11-16-12          F Lec 7 (Potential of mean force (PMF).   Radial distribution function (RDF)

11- 19-12         M Lec 8 (Connection between PMF and RDF).

11-20-12          Tu Rec

11-21-12          W Lec 9 (Elements of theory of simple liquids). Hermans.

11-22-12          Th Thanksgiving

Water & the Hydrophobic Effect

11-27-121        M Lec 10. Water, special properties: Lentz

11-28-12          Tu Rec

11-29-12          Lec 11 Water: structural nature: MD result:, Lentz

11-30-12          Th Rec

12-1-12            F Lec 12. Hydrophobic Effect: Lentz

12-3-12            M Lec 13. Conformational Dynamics of RNA structure: Zhang