CHIMICA FISICA DEI SISTEMI BIOLOGICI E DELLE BIOINTERFACCEModule Principi di Chimica Fisica Biologica (Modulo 1)
Academic Year 2023/2024 - Teacher: Carmelo LA ROSAExpected Learning Outcomes
The student must learn the quantitative notions and problem-solving of weak forces and interactions, conservation and energy transfers in the form of heat, entropy and thermal machines, chemical equilibrium, phase diagrams, and electrochemistry of reversible processes.
Specifically:
(a) knowledge and understanding skills. The knowledge objective will be achieved by rigorously explaining the basic concepts through the mathematics of differential calculus, integral and differential equations. The goal of understanding the topics covered will be pursued by using examples outside the topics of thermodynamics applied to chemistry, e.g., applications of the laws of thermodynamics to biology and materials in an interactive manner with students.
(b) ability to apply knowledge and understanding. These objectives will be achieved by performing numerical and theoretical classroom exercises of the topics covered.
(c) autonomy of judgment. The autonomy of the judgment test will have been achieved if and only if objectives (a) and (b) are met. If the test is negative, the teacher must take up the unclear topics with new examples and lectures to bridge the remaining lagoons.
(d) ability to communicate. The ability to communicate clearly and rigorously the topics covered will be addressed with lectures at the beginning of the science communication course and a final written test where students expound on a topic covered during the course.
(e) Ability to pursue study independently. This will be achieved and tested at the end of the course using scientific articles related to the program with classroom exposition by students.
Course Structure
Required Prerequisites
Attendance of Lessons
Detailed Course Content
Differential Scanning Calorimetry: Principles, applications to conformational transitions.
Circular Dichroism: Principles, applications to determination of protein secondary structures.
Statistical Thermodynamics: Boltzmann factor, probability of a system, partition function.
Molecular Dynamics: Principles, force field, AA-MD, CG-MD, SMD, REMD, TI-MD, FEP-MD, data analysis.
Solid-state NMR: Principles, Spinning Magic Angle, 31P and 2H.
ESR: Principles, Spin-label.
X-ray diffraction: Principles, determination of the three-dimensional structure of proteins.
Fourier Transform: Properties of TF and anti TF, applications to NMR and IR spectroscopies and X-ray diffraction.
Biological membranes: phospholipids, monolayers and bilayers and self-assembling phenomena, the structure of phospholipid bilayers, gel-liquid crystal phase transitions, structural characterization of bilayers, dynamic characterization of phospholipid bilayers, model membranes, spectroscopic and thermodynamic characterization of phospholipid bilayers.
Proteins: structure and properties of amino acids, peptide binding, protein structure, Ramachandran plot, folding problem, Lumry-Eyring model, three-dimensional determination of protein structures, protein dynamics, membrane-protein interactions, spectroscopic and thermodynamic characterization of protein systems. Amyloidogenic proteins, toxic amyloids and functional amyloids, the structure of amyloids, the interaction of amyloidogenic proteins with phospholipid bilayers.
Nucleic acids: structure and properties of DNA and RNA, interaction with small molecules, liquid crystalline phases, model systems, spectroscopic characterization and thermodynamics.
Textbook Information
| Author | Title | Publisher | Year | ISBN |
|---|---|---|---|---|
| C. La Rosa | Appunti |
Course Planning
| Subjects | Text References | |
|---|---|---|
| 1 | Recalls thermodynamics, kinetics and spectroscopy, structure of liquid water, hydrophobic effect, liquid crystals. | Students will be provided with notes of all lectures at the beginning of the course |
| 2 | Differential Scanning Calorimetry: Principles, applications to conformational transitions. Circular Dichroism: Principles, applications to determination of protein secondary structures. | Students will be provided with notes of all lectures at the beginning of the course |
| 3 | Statistical Thermodynamics: Boltzmann factor, probability of a system, partition function. Molecular Dynamics: Principles, force field, AA-MD, CG-MD, SMD, REMD, TI-MD, FEP-MD, data analysis. | Students will be provided with notes of all lectures at the beginning of the course |
| 4 | Solid-state NMR: Principles, Spinning Magic Angle, 31P and 2H.ESR: Principles, Spin-label. X-ray diffraction: Principles, determination of three-dimensional structure of proteins. Fourier Transform: Properties of TF and anti TF, applications to NMR and IR spectroscopies and X-ray diffraction. | Students will be provided with notes of all lectures at the beginning of the course |
| 5 | Biological membranes: phospholipids, monolayers and bilayers and self-assembling phenomena, structure of phospholipid bilayers, gel-liquid crystal phase transitions, structural characterization of bilayers, dynamic characterization of phospholipid bilayers, model membranes, spectroscopic and thermodynamic characterization of phospholipid bilayers. | Students will be provided with notes of all lectures at the beginning of the course |
| 6 | Proteins: structure and properties of amino acids, peptide binding, protein structure, Ramachandran plot, folding problem, Lumry-Eyring model, three-dimensional determination of protein structures, protein dynamics, membrane-protein interactions, spectroscopic and thermodynamic characterization of protein systems. Amyloidogenic proteins, toxic amyloids and functional amyloids, structure of amyloids, interaction of amyloidogenic proteins with phospholipid bilayers. | Students will be provided with notes of all lectures at the beginning of the course |
| 7 | Nucleic acids: structure and properties of DNA and RNA, interaction with small molecules, liquid crystalline phases, model systems, spectroscopic characterization and thermodynamics. | Students will be provided with notes of all lectures at the beginning of the course |
| 8 | Lab exercises | Students will be provided with notes of all lectures at the beginning of the course |
Learning Assessment
Learning Assessment Procedures
Examples of frequently asked questions and / or exercises
Cellular Membranes, Singer and Nicholson Model.
Order Parameter
Structure of Proteins
Solid State NMR Spectroscopy
Fluorescent probes
amyloids