Learning objectives
At the end of the course, the student should have learnt and understood the main structural features and the functional properties of biological macromolecules, particularly concerning the thermodynamic laws controlling their behavior in the cells. In particular, the student:
• will acquire a solid background concerning the structure of biological macromolecules
• will learn the tight link between structure and function in biopolymers
• will understand the protein folding problem and the thermodynamic laws governing them
• will deepen the key role of water in the macromolecule function
• will acquire the basic principles of the experimental techniques described
Finally, the student should be able to communicate the main concepts studied in complete and incisive manner. Such ability will be exerted during the course, in which the drawing up of a written report of each practice carried out in the laboratory will be required.
Prerequisites
none
Course unit content
Fundamental principles of structural complexity of living organisms. Introduction to the molecular evolution theory. Water: structure, properties and biological role. Structure of the main biological macromolecules. Primary structure of proteins: chemical properties of aminoacids, Newman projections, aminoacid titration. Primary structure of Nucleic Acids and polysaccharides. Secondary structure of proteins: peptide bond, conformational structures, Ramachandran plot, propensity. Secondary structure of Nucleic Acids and polysaccharides. Tertiary structure of proteins: protein folding, chaperones. Tertiary structure of Nucleic Acids. Aqueous solutions. Thermodynamics and biochemistry: reversible and irreversible reactions, free energy. Aqueous solutions of macromolecules: partial molar quantities, chemical potential, Gibbs-Duhem equation, ideality and non-ideality, mixing entropy. Solutions of Macromolecules: folding, stability and hydrophobic effect. Misfolding: amiloid proteins. Hydration water. Lee-Richards model. Water vapor adsorption. Adsorption isotherms. Experimental techniques: Nuclear Magnetic Resonance (NMR), Fourier Transform Infrared Spectroscopy (FTIR), Circular Dichroism (CD).
Full programme
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Bibliography
E. P. Solomon, L. R. Berg, D. W. Martin, Fondamenti di Biologia, 2009, EdiSES
J. M. Berg, J. L. Tymoczko,L. Stryer, Biochimica, 2012, Zanichelli
T. E. Creighton, Proteins. Structure and Molecular Properties, 1993, W. H. Freeman and Co
C. R. Cantor and P. R. Schimmel, Biophysical Chemistry. Part II, 1998, W. H. Freeman and Co
R. B. Gregory, Protein-solvent interactions, 1995, M. Dekker, Inc.
A. Ben-Naim, Molecular theory of water and aqueous solutions, Part I and II, 2010, World Scientific.
Teaching methods
Oral lessons and practices in the laboratory.
For the oral lessons the teacher will use slides that will be part of the educational material. These slides will be uploaded on the "Elly" platform some days before the beginning of each new lesson. In addition, the students will have supplied of literature papers. To download the educational material, the on-line registration to the course is needed.
Experimental laboratory practices are included in the course program
The practical exercises first will be driven by the teacher, then they will be performed personally by the student, to provide them with advanced techniques and methodologies.
A written report of each practice performed in the lab will be required, in which the student will explain the studied system, the methods used, the results obtained, the conclusions and the comments. Such reports could be given during the course or at the end, but, in any case, the reports will be due a couple of days before the exam, and will be corrected and evaluated. Therefore, the delivering of the reports is needed to do the exam.
Assessment methods and criteria
The exam will consist in two parts: a written one and an oral one. The written exam will be a series of 10 open questions on the arguments treated during the lessons. The oral exam will be the analysis of the results obtained during the laboratory practices and the discussion of the reports; some questions on the fundamental concepts of the studied techniques will follow. These two parts have the same weight on the final evaluation.
Other information
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