Università degli Studi di Perugia

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Study-unit Code
Fisica della materia
Alessandro Paciaroni
  • Alessandro Paciaroni - Didattica Ufficiale
  • 42 ore - Didattica Ufficiale - Alessandro Paciaroni
Course Regulation
Coorte 2018
Learning activities
Attività formative affini o integrative
Type of study-unit
Opzionale (Optional)
Type of learning activities
Attività formativa monodisciplinare
Language of instruction
Structural properties of DNA and proteins. X-rays and neutron diffraction to study the structure do DNA and proteins. Dynamical properties of biomolecules.
Non-cooperative and cooperative transitions in biomolecules
Reference texts
-Philip Nelson-Biological Physics_ Energy, Information, Life-W. H. Freeman (2003)
-Ken A. Dill, Sarina Bromberg-Molecular Driving Forces_ Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience-Garland Science (2010)
-Amit Kessel_ Nir Ben-Tal-Introduction to proteins _ structure, function, and motion-CRC Press (2011)(Chapman & Hall_CRC mathematical and computational biology series (Unnumbered))
Educational objectives
This course is the first detailed presentation of experimental and theoretical physical methods applied on molecular biological systems (DNA and proteins), with particular attention to their structural and dynamic properties.
The course's main objective is to provide students with the basis for: 1) understanding the basic mechanisms underlying the functional processes related to the biological activity of DNA and proteins 2) dealing with the experimental and theoretical study of the structure and dynamics of biomolecular systems.
The main acquired knowledge will concern:
- Basic elements of intra- and inter-molecular interactions in DNA and proteins
- Basic elements of diffraction and scattering at small angle from biomolecules
- Modeling of tertiary structures of biomolecules
- Modeling linear and non-linear dynamics of biomolecules
- Modeling of elastic properties of biomolecules
- Basic elements on phase transitions in biomolecules
The main skills (ie the ability to apply their knowledge) will be:
- Analyze the response of biomolecules due to external mechanical, thermal or chemical perturbation
- Interpret the results of experiments on biomolecules in terms of their microscopic properties
- Design experiments to probe, and if necessary, optimize properties of structural flexibility and mechanical and thermal stability of biomolecules.
Necessary prerequisites in order to understand and be able to apply many of the topics covered in this Course is to have taken the course of Physics of Condensed Matter and the course of Laboratory for Physics. The student must have solid knowledge on quantum mechanics and on condensed matter subjects.
Teaching methods
The course consists of classroom lectures on all the topics of the program.
Other information
Lectures will be given at the Physics Department.
Learning verification modality
The exam includes an oral test. This test consists of an interview with the objective to ascertain the level of knowledge and the understanding reached by the student on the theoretical and methodological implications listed in the program (bases of the experimental techniques of neutron scattering, basics of experimental techniques of synchrotron radiation, introduction to experimental techniques with free electron laser). In the oral examination it is assessed the student's ability to communicate clearly and independently about the theoretical contents of the course and to design in detail an experiment in order to investigate a scientific problem. The oral exam takes about 50 minutes, depending also on the ease of exposure of the student.
Extended program
DNA structure. Nitrogenous bases. DNA polymorphism. Primary structure and secondary structure and intramolecular bonds. Hydrogen bonds and stacking bonds.

X-ray diffraction. The Watson-Crick-Wilkins experiment for the determination of the double-stranded DNA structure. Atomic form factor. Structure factor. Structure factor of the propeller pitch. Characteristic diffraction pattern of DNA.

Classification of biomolecules and their role in cell metabolism. Proteins and their biological role. Enzyme activity. Structural complexity of proteins. Primary, secondary and tertiary structure. Amino acids and their properties. Peptide bond. Non-covalent interactions in proteins. Electrostatic interactions. Van der Waals interactions. Non-polar interactions: hydrophobic effect. An important biological molecule: water.

Configuration of amino acids. Chirality. Secondary structure of proteins. Still on the peptide bond. Ramachandran Plot. Alpha propellers and beta sheets. Tertiary structure of proteins.

Dynamics in cell metabolism. Brownian Motorcycle.
Self-aggregation of lipids: micelles. Phase transitions and biomolecules. Stability curves and phase coexistence. Miscibility and immiscibility of liquids. Landau model for phase transitions. Helix-coil transitions in proteins. Non-cooperative model. Two-state model. Cooperative model. Stability of biomolecules. DNA stretching. Melting of proteins. Experience in the laboratory of circular dichroism for myoglobin melting.

Dynamics of biomolecules. Relationship between dynamics and biological activity of proteins. Relationship between fast dynamics (picoseconds) and biological activity of proteins. Theory of conformational substates. Example of myoglobin. Experimental evidence of the existence of conformational substates. Lock and key models, induced fit and conformational selection for the action of enzymes.
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