Structure and functions of biomolecules

Module A - 'Structure and function of biomolecules'.
Amino acids and peptides. Structure and properties of amino acids and peptides. Nitrogen protecting groups: insertion and removal. Possible secondary reactions. Protecting groups of carboxylic and hydroxyl groups. Methods for activation and coupling. Possible racemization phenomena and mechanisms. Methods of solid phase synthesis. Resins and cleavage conditions. Fundamentals of Amino acid biosynthesis and metabolism. Amino acids as biosynthetic precursors. Primary structure determination of proteins.- Carbohydrates. Structure, properties, nomenclature. Anomeric effect. Oxidation and reduction reactions. Glycosylation reactions: concept of glycosyl donor and glycosyl acceptor, promoters, protecting groups. Chemo-enzymatic synthesis of glycosidic bond. Oligosaccharide and glycoconjugates synthesis on solid phase. Structural polysaccharides: cellulose and chitin. Storage polysaccharides: starch and glycogen. Carbohydrates as renewable raw material for fine chemicals. - Nucleic acids. Structure, properties and nomenclature. Nucleosides and nucleotides. Purine and pyrimidine heterocycles. DNA bases. Acid-base characteristics, tautomeric forms, and reactivity. Nucleosides: structure and biological properties. Phosphate, pyrophosphate and triphosphate esters. Nucleotides. Nucleic acids. Polynucleotide structure. Chemical stability and main reactions of DNA and RNA: hydrolysis, oxidation and alkylation. Chemical sequencing of DNA and its scope of use. Chemical synthesis of DNA, protector groups, phosphoramidite, H-phosphonate method. RNA chemical synthesis. Modified nucleic acids and mimics. - Lipids. Structure and properties. Lipid classification. Auto-oxidation and photo-oxidation reactions. Synthesis of complex lipids: some examples. Phospholipids and glycolipids. Micelles and liposomes. Main classes of non-saponifiable lipids

Module B - 'Biomolecular spettroscopy'.
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) (1.25 CFU). 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 (1 CFU) 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