Unit PHYSICS OF DNA AND OTHER BIOMOLECULES
- Course
- Physics
- Study-unit Code
- 55A00008
- Curriculum
- Fisica medica
- Teacher
- Alessandro Paciaroni
- Teachers
-
- Alessandro Paciaroni
- Hours
- 42 ore - Alessandro Paciaroni
- CFU
- 6
- Course Regulation
- Coorte 2017
- Offered
- 2017/18
- Learning activities
- Affine/integrativa
- Area
- Attività formative affini o integrative
- Academic discipline
- FIS/03
- Type of study-unit
- Opzionale (Optional)
- Type of learning activities
- Attività formativa monodisciplinare
- Language of instruction
- Italiano
- Contents
- 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. - Prerequisites
- 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
- Chemical composition and primary structure of DNA. Geometry and spatial secondary structure of DNA. Forces stabilizing of the secondary structure. DNA polymorphism. Tertiary structure of DNA. Approximate models of the structure of DNA. Introduction to X-ray diffraction Diffraction from single and double helix. DNA structure by X-ray diffraction pattern of Watson and Crick. Introduction to X-ray and neutron scattering Small angle Scattering. Scattering length. Fermi's pseudopotential. Coherent and incoherent scattering. Isotopic contrast. Low angle scattering of neutrons. Small angle scattering technique applied to G-quadruplex.
Amminacids. Primary, secondary and tertiary structure of proteins. Dynamics of proteins and relationship with biological fucntionality. Theory of the conformational substates.
Cooperative transitions in biomolecules. Elastic models of biopolymers. Entropic forces. Stretching experiments on single molecule DNA and interpretation. Two-states model: freely jointed chain 1D model. Cooperativeness. Cooperative model of 1D chain. Transfer matrix. Helix-coil transition in proteins.