08970 - Biological Physical Chemistry

Learning outcomes

The students will be provided with the main subjects of physical biochemistry in order to learn how to use the physical chemistry to understand and measure the properties of large molecules of biological interest. At first they will be introduced to the levels of structure in biopolymers, using the quantitative approach to characterizing structures, and discussing in details the symmetry found at nearly all levels of macromolecular structures. The forces and interactions responsible for creating the characteristics of organized biological structures will be illustrated. The ideas of thermodynamics that are valuable in biochemistry and molecular biology will be reviewed and applied to measurements of properties and functionality of biopolymer. The physiological function of proteins and nucleic acids that is manifested through interactions with ligands will be considered. Students will be accounted for the conformational changes in proteins and nucleic acids according to a statistical thermodynamics approach. They will understand how to use many experimental techniques, as sedimentation, electrophoresis and isoelectric focusing to analyze and separate biopolymers. Finally they will learn how to use the UV-VIS spectroscopy to characterize the biopolymer structure.

Course contents

1. Biological macromolecules: macromolecules, configuration and conformation; molecular interactions in macromolecular structures; symmetry; a quantitative view of structures of proteins, nucleic acids and polysaccharides. Stabilizing interactions in macromolecules.
2. Biochemical applications of Thermodynamics. Electron transfer and biological red-ox reactions.
3. Macromolecules in solution, thermodynamics and equilibria: the chemical potential of ideal and nonideal solutions; applications of chemical potential to physical equilibria; membrane equilibria; sedimentation equilibrium; sedimentation equilibrium in a density gradient; steady-state electrophoresis.
4. Thermodynamics of transport processes: diffusion; transport across membranes, passive, facilitated, active transport; selective ion transport and membrane potential, Goldman equation; sedimentation.
5. Chemical Equilibria involving macromolecules : specific and nonspecific binding of small ligands to proteins and nucleic acids; cooperative and non-cooperative binding; multiple equilibria.
6. Methods for the separation and characterization of macromolecules: moving boundary sedimentation and zonal sedimentation; electrophoresis and isoelectric focusing; gel electrophoresis of nucleic acids, SDS-GE of proteins, capillary electrophoresis, other two-dimensional techniques.
7. Statistical Thermodynamics: models for structural transitions in biopolymers; coil-helix transition in polypeptides; structural transitions in polynucleotides and DNA.
8. UV-VIS absorption spectroscopy applied to the structural analysis of proteins and nucleic acids; Franck- Condon principle; polarization of electronic transitions; exciton theory; solvent effect.

Readings/Bibliography

1.  K. E. van Holde, W. C. Johnson, P. S. Ho, Principles of Physical Biochemistry , Prentice-Hall, 1998.
2. C. Cantor and P. Schimmel Biophysical Chemistry , Freeman and Company, 1980. 

 

Teaching methods

The course contents will be explained in a series of lectures. Both a qualitative and quantitative description of biopolymer properties and structures will be pointed out. The equations  to calculate some of physical properties of biopolymers will be derived and their application field will be specified. These equations will be used to solve numerical exercises. The exposition of course contents will be accompanied with the related scientific experimental results.

Assessment methods

In the final oral examination the student will explain and discuss some of the subjects of course The student could be asked to solve exercises related to physical biochemistry. The examination is passed if the student gets 18/30 marks, being 30/30 the full marks.

Links to further information

http://www2.fci.unibo.it/~etabeta/

Office hours

See the website of Elisabetta Canè