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Facoltà di Scienze Agrarie e Alimentari Università degli Studi di Milano
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Structure and functions of biomolecules: biomolecular spettroscopy
Codice: G6403B
Docente:  Enzio Maria Ragg
Anno di corso: 
Quadrimestre/semestre: 
CFU: 
Articolazione dei CFU: Lezioni frontali: 2
Esercitazioni in aula: 0,5
Esercitazioni in laboratorio: 0,5
Obiettivi formativi:  The aim of the course is an in-depth discussion of the structure-activity 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.
Competenze acquisite:  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.
Sintesi del programma:  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).
Programma:  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 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 molecule-biomolecule 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
Prerequisiti:  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.
Propedeuticità:  none
Materiale didattico:  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
Modalità d'esame e altre 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
assigned. At least 7 exam sessions per year will be guaranteed.
The date of the exam will be published on SIFA platform.
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