Code Course name CFU Year G6403B Info not available 3 1

Transcription

1 Basic aims The aim of the course is an in-depth discussion of the structureactivity relationships of the main classes of biological molecules. Strategies for synthesis, isolation and structural characterization of biomolecules will be treated. Potential applications in biotechnology will also be discussed, particularly those more closely related to the concept of bioeconomy. Acquired skills The student will be able to critically discuss the structure-activity relationships of the molecular classes presented in the course. He will also acquire knowledge and skills on the most important extraction, preparation/purification and structural characterization methodologies. Finally, the student will be able to use the main experimental and computational methodologies for understanding the mechanisms of macromolecule-ligand interaction. Course contents A general review on structure and chemistry of the main classes of biomolecules: aminoacids and peptides, carbohydrates, nucleic acids and lipids. In particular, the course deals with advanced and up-to-date synthetic methods in solution and in the solid phase. In addition, case studies on specific biomolecules (e.g. insulin) and selected topics will be treated. In addition, the course provides a general introduction to the main spectroscopic techniques for chemical structural analysis of small organic molecules and biomolecules: UV-Vis spectroscopy, chiroptical methods, Nuclear Magnetic Resonance. Particular emphasis is dedicated to practical aspects and applications in structural biology (secondary and tertiary structural analysis, solution structure of small proteins and oligonucleotides, structure-activity relationship studies) and in the food and biotechnology industry (process control).

2 Program Teaching unit 1: Biomolecular Spectroscopy (teacher: Prof. E. M. Ragg) - General introduction. (0.25CFU) Main spectroscopic techniques for chemical structural analysis. The mechanism of interaction between radiation and matter. The electromagnetic spectrum. Fundamental and excited states. Absorption and emission spectroscopies. - Ultraviolet-Visible (UV-VIS) Spectroscopy and Chiroptical methods (0.5 CFU) Electronic transitions and UV-vis absorbance. Electronic, vibrational and rotational energy levels. Molecular orbitals and electronic transitions in isolated and conjugated alkenes, in carbonyl compounds, in benzene and heteroaromatic compounds. Spectral features of purines, pyrimidines, aromatic aminoacids. Chiroptical methods: optical rotation, rotatory optical dispersion, circular dichroism. Applications in biotechnology: determination of melting temperatures of PCR primers. Use of fluorescent probes for DNA staining and binding studies. Secondary structure analysis of proteins and nucleic acids by circular dichroism. - Nuclear Magnetic Resonance (NMR) (1.25CFU). Magnetic properties of the atomic nucleus. Energy and frequency of nuclear spin transitions. Pulsed NMR and Fourier Transform NMR. The chemical shift. Structural factors influencing the chemical shift. Signal multiplicity. Geminal and vicinal couplings. "long range" couplings. Chemical and magnetic equivalence. Examples of analysis of the main spin-systems. The Nuclear Overhauser Effect for the determination of proton-proton distances. - Heteronuclear spectroscopy: 13C-NMR. 31P-NMR, 15N-NMR. Coupled and decoupled spectra. Application examples in the biotechnology and food industry - 2D-NMR spectroscopy. Introduction. The main homo- and hetero-nuclear correlation experiments - Application of NMR spectroscopy for solution structure determination of nucleic acids and proteins and their complexes with small molecules: secondary and tertiary structure analysis

3 of proteins and DNA by NMR; determination of acidity constants by means of chemical shifts ph variations. Thermal stability analysis of biomolecules. Association studies in small moleculebiomolecule interactions Tutorials (1CFU) Class (0.5 CFU): Structure determination of unknown compounds by joint analysis of UV and 1H/13C-NMR spectra Lab.(0.5 CFU): Bioinformatics laboratory on computer analysis of X-Ray and NMR biomolecular structures

4 CFU subdivision Lectures Practise in class Practise in lab. Laboratory Seminar Other 2 0,5 Prerequisites Basic knowledge of the structure and nomenclature of the main functional groups in organic chemistry. Basic knowledge of biochemistry. For any question and further details please contact the teacher at enzio.ragg@unimi.it or andrea.pinto@unimi.it. Preparatory instructions none Learning materials a) E. Rossi, D. Nava, G. Abbiati,G. Celentano,S. Pandini Structure determination of organic compounds, practical exercise Ed. EdiSES; b) Biochemistry- 4th Edition Voet & Voet Wiley; c) Organic Chemistry - 4thEdition - Clayden, Greeves, Warren and Wothers-Oxford University Press, Wiley and Sons; d) Slides of lessons available through the Ariel Web Site Other info MODALITÀ DI ESAME ED ALTRE INFORMAZIONI: The examination is in the written form and will deal with all topics inherent to both course units. Unit 1: a) the student should be able to describe the structure of a simple organic molecule on the basis of the provided spectroscopic data; b) a theoretical question about general aspects of molecular spectroscopy. Unit 2: two questions related to synthetic aspects and the description of structure-activity relationships of specific classes of compounds described in the course. Students should answer to all questions within 2 hours. To each question a formal maximum value of 8 points will be assigned. The exam is considered sufficient when at least 9 points for each unit have been

5 assigned. At least 7 exam sessions per year will be guaranteed. The date of the exam will be published on SIFA platform.