SUBJECT

Title

Physical Biochemistry I

Type of instruction

lecture

Level

master

Faculty

Faculty of Science

Part of degree program

Biology MSc

Credits

Recommended in

Semesters 1-4

Typically offered in

Autumn/Spring semester

Course description

1. The basics of reaction kinetics and kinetic theory. Reaction velocity. Reaction mechanisms and rate laws. Models for complex reactions: the rate limiting step, steady-state assumption.

2. Order of the reaction. Determining the order of a reaction. The Michaelis-Menten equation. Integrating rate laws: first and second order reactions. Examples: radioactive decay and DNA renaturation.

3. The reaction rate theory of Arrhenius. Maxwell distribution. Arrhenius equation, activation energy. Arrhenius plot.

4. Reactions in solutions, solvent effects on the reaction rate. Diffusion controlled reactions. Eyring's theory: the concepts of activated complex and activation free energy. Van't Hoff plot.

5. Thermodynamics of solutions, the Gibbs free energy. The fundamental law of solution thermodynamics. Chemical potential. The additivity rule and the Gibbs-Duhem equation. Raoult's law.

6. Real solutions and non-ideality. Activity, activity coefficient and applications.

7. Biological thermodynamics. Hydrolysis: an application of solution thermodynamics. Acid-base reactions. The pH dependence of the reaction free energy. Examples: ATP hydrolysis.

8. Osmotic pressure, colligative properties. The non-ideality term, virial expansion. Macromolecules with bound ions.

9. Thermodynamics of electrolytes. The mean ion standard chemical potential and the mean ion activity coefficient. Fundamentals of electrostatics, electric field strength and potential, Gauss' law. Donnan potential.

10. Debye-Hückel theory. Ionic strength.

11. Multiple equilibria. Law of mass action. Binding site heterogeneity. The equilibrium dialysis experiment, Scatchard plot.

12. Deviations in the Scatchard plot and molecular cooperativity. Donnan and Debye-Hückel effects in electrolytes. Binding site cooperativity, saturation curve. A model for extreme positive cooperativity. Hill plot.

Readings

Kensal Edward Van Holde, W. Curtis Johnson, Pui Shing Ho: Principles of Physical Biochemistry, Pearson/Prentice Hall, 2006