Learning outcomes of the course unit
The course will give the students a detailed knowledge of the basic aspects and of several advanced aspects of the organic chemistry applied to the most important biological molecules.
Course contents summary
Introduction. Review of the properties of functional groups, in particular aldehydes, chetones, amines, carboxylic acids and their derivatives. Extension of these concepts to biologically relevant molecules.
Lipids. Prrincipal classes of lipids. Triglycerides and their chemical properties. Autooxidation and
Photooxidation of fatty acids. Phospholipids and glycolipids. Micelles and liposomes. Principal classes of non-saponifiable lipids.
Amino acids and peptides: acidity, basicity, isoelectric point, solubility, polarity, spectroscopic properties, chirality, esterification and acylation reactions, synthesis, prebiotic origin. Peptide bond hydrolysis, peptide sequencing, peptide synthesis, peptido-mimetics.
Proteins. Determination of primary sequence, bottom-up approach to the secondary and tertiary structure. Main non covalent interactions, folding. Denaturation and solubility: temperature, pH, ionic strenght, detergents, organic molecules. Native chemical ligation.
Monosaccharides. Stereoisomery, linear and ciclic conformations, alfa and beta configurations, mutarotation. Reduction, oxidation, rearrangements. Tollens and Fehling reactions, reactions with amines, alcohols, glycosides. Hydrolysis of glycosides. Alkylations and acylations.
Oligo- and Polisaccharides. Reactivity. Structure determination. Alginates, agar, carragenans). Peptidoglycan, LPS, lipid A. Synthetic polisaccharides. Cyclodextrin: structure and applications. Chemical synthesis of glycosides and polysaccharides: Koenigs/Knorr reaction, anomeric control.
Nucleosides, Nucleotides. Pyrimidine and purine heterocycles and their properties. Phosphor derivatives and their reactivity. Structure of nucleosides and nucleotides.
Nucleic acids. Polynucleotide structures. Watson-Crick hydrogen bonds, donor and acceptor sites in major and minor groove. Thermal stability: hydrogen bonds, hydrophobic effect, stacking, electrostatic repulsion. DNA chemical synthesis: protecting groups, phosphite triester, phosphoramidite, H-phosphonate methods. Stability of DNA and RNA to hydrolysis. DNA sequencing. DNA reactivity: alkylating agents, interacalating agents, cross-linking, oxidations, photoactivation. Antigene and antisense oligonucleotides, modified oligonucleotides. Nucleic acids as nanotechnology objects. Peptide nucleic acids (PNA): properties and applications.
Origin of life in prebiotic environments. RNA world, prebiotic synthesis of nucleobases and sugars.Pre-RNA world: different sugars, PNA, self-replicating systems. Origin of homochirality: from weak interactions to amplification theories.
Basic textbooks. P.Y. Bruice “Chimica Organica” EdiSES (2005)Brown, Foote, Iveson “Chimica Organica” III Edizione EdiSES (2006)• K. Peter, C. Vollhardt, N.E. Schore “Chimica Organica” 3 Edizione. Zanichelli (2005). J. McMurry “Chimica Organica” 6 Edizione. Piccin (2005).
Course Notes by the Lecturer
Scientific literature found on specialized chemical journals
1) V. Santagada, G. Caliendo. ' Peptidi e Peptidomimetici' PICCIN (2003)
2) S. M: Hecht 'Bioorganic Chemistry: Nucleic Acids' Oxford University Press (1996)
3)S. M: Hecht 'Bioorganic Chemistry: Peptides and Proteins' Oxford University Press (1998).
4)S. M: Hecht 'Bioorganic Chemistry: Carbohydrates' Oxford University Press.(1999)