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MOLECULAR BIOPHYSICS
FRANCESCO SPINOZZI

Seat Scienze
A.A. 2016/2017
Credits 6
Hours 48
Period 1^ semestre
Language ENG
U-gov code SM04 5S058

Prerequisites

Students are expected to have had basic courses in physics, chemistry, biochemistry and biology.

Development of the course

The course includes theoretical lectures (5 credits, 40 hours) and x-ray laboratory practicals (1 credit, 8 hours). Course attendance, although not mandatory, is strongly recommended. Attendance laboratory practicals is mandatory. 

Learning outcomes

Knowledge:
A better understanding of the physical principles that rule out the molecular processes in living systems, with emphasis on statistical thermodynamics, quantum mechanics, intermolecular forces and structure of water. Knowledge of the main techniques of strucural investigation of biological molecules based on X-ray and neutron scattering..

Ability to apply the knowledge:
Students should be able to identify the main forces that underlie a biomolecular process and that determine structure and stability of protein and lipid aggregates. They will be also able to perform X-ray diffraction experiments on aqueous dispersions of lipids, analyse the results and identify the lipid phase.

Soft skills:
The activity during the x-ray laboratory practicals, carried out in a working group, and the preparation of a laboratory report help to improve student's autonomy and communication skills.

Program

Contents (classroom lectures, 7 CFU, 56 hours):
Concepts of thermodynamics: free energy and chemical potential; Thermodynamic probability and entropy; Concepts of statistical thermodynamics; Concepts of quantum mechanics; Geometry of a polymeric chain; Some fundamentals of electrostatics; Intermolecular forces; The structure of the water, hydration effects; Hydrophobic and hydrophilic molecules; Hydration of proteins; Debye-Hückel theory; Monte Carlo method; Molecular Dynamics method. X rays. The scattering vector. Atomic structure factors. Scattering from a mono-dimensional array of atoms. van Laue's conditions. Scattering from a 3D lattice. Electron density. Multiple isomorph replacement method. Powder diffraction. The Bragg law. Diffraction from lipid / water systems. Lipid phases. Small angle X-ray and neutron scattering. From factor and structure factor of proteins in solution.

Laboratory Practicals (1 CFU, 8 hours):
X-ray diffraction and lipid phases

Development of the examination

Methods for assessing learning outcomes:
The exam consists of an oral test, which also assesses the experimental report on x-ray laboratory practicals. 

Criteria for assessing learning outcomes: 
It will be assessed the student's ability to know the contribution of Molecular Biophysics in the quantitative description of relevant aspects regarding the structure and the transformation of biological molecules.

Criteria for measuring learning outcomes:
The final mark is expressed in a scale from 0 to 30. The exam is passed when the mark is greater than or equal to 18. Students can be awarded with the honour mark (30 cum laude).

Criteria for conferring final mark:
The final mark is attributed evaluating the oral test and taking into account the x-ray laboratory report. The honour mark is given when the student has demonstrated full mastery of the subject.

Recommended reading

Lecture notes.
R. Glaser, Biophysics, Springer
K.E. van Holde, W.C. Johnson, P.S. Ho, Principles of Physical Biochemistry, Prentice Hall.
M. Daune, Molecular Biophysics, Oxford University Press.

Courses

• Biologia molecolare e applicata