Learning objectives
To acquire knowledge on the molecular details and properties of some important biological compounds:lipids, amino acids, peptides and proteins, carbohydrates, and nucleic acids.
To learn the synthesis of artificial molecules mimicking the behaviour of biological compounds: amino acids, peptides, carbohydrates and oligonucleotides. Principa concept in prebiotic chemistry. Principles of instrumental methods for the characterization and study of the structural properties of the biological components. To understand the role of Bioorganic Chemistry for the acquisition of new knowledge and for the development of new applications in Biology.
Results expected:
detailed knowledge of the principal classes of biomolecules, in particular biopolymers, and of their chemical properties, of the methods used to determine their structure, of purification methods and of the methodology to mimick or to modifiy them. Ability to undersand and critically evaluate the theoretical basis and experimental details of studies concerning lipids, carbohydrates, oligo- and polypeptides, nucleic acids and their analogs.
Prerequisites
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Course unit content
Part I Organic Chemistry of Biomolecules
Lipids. Principal 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.
Peptides. Nomenclature. Cis-trans isomers of the peptide bond bond. Acid-base properties of peptides, isoelectrivc point. Acidic and basic hydrolysis. Examples of peptides with biological activity. Peptide synthesis: protecting groups, activation, methods in solution and on solid phase; Boc and Fmoc strategies. Conjugated peptides, cyclic peptides, peptido-mimetics. Combinatorial chemistry applied to peptide libraries.
Carbohydrates. Monosaccharides. Stereoisomery, linear and ciclic conformations, alfa and beta configurations, mutarotation. Reduction, oxidation, rearrangements. Tollens and Fehling reactions, reactions with amines, alcohols; glycoside formation. Hydrolysis of glycosides. Reaction of the monosaccharides. Examples of biologically relevant glycosides and glycoproteins. Oligo- and Polisaccharides. Reactivity. Structure determination. Examples of biologically relevant disaccharides and oligosaccharides Cyclodextrin: structure and applications. Synthetic oligosaccharides. Polysaccharides: classification and structure of biologically relevant structures.
Nucleosides and Nucleotides. Pyrimidine and purine heterocycles, nucleobases and their properties. Acid base properties, tautomerism, reactivity. Nucleosides: structure and biological properties. Phosphor derivatives and their reactivity. Nucleotides. Nucleic acids. Polynucleotide structures. Double helices and factors affecting their stability: hydrogen bonds, hydrophobic effect, stacking, electrostatic repulsion. DNA chemical synthesis: protecting groups, phosphoramidite, H-phosphonate methods. Chemical synthesis of RNA. Stability of DNA and RNA to hydrolysis. DNA reactivity: alkylating agents, interacalating agents, minor groove binders, cross-linking, oxidations, photoactivation. Chemical DNA sequencing and comparison with present sequencing technologies.
Simple models of prebiotic systems. Origins of homochirality.
Part II Methods in Bioorganic Chemistry
Introduction to experimental methods for the study of biomolecules. Spectroscopy, chromatography, mass spectrometry, diffractometry and nuclear magnetic resonance (NMR). Examples of experimental protocols for the purification and characterization of lipids, peptides, carbohydrates and nucleic acids in complex mixtures and in biological samples
Part (III) Applications
Principal applications of the methodologies above described for the development of new applications and for the acquisition of new knowledge. The molecules described in part I and the methods described in part II in “omic” studies.
Interactive analysis of literature studies in this field on several examples and discussion of the methods described.
Full programme
http://scienzebiologiche.unipr.it/cgi-bin/campusnet/corsi.pl/Show?_id=01c1;sort=DEFAULT;search=%7bdocente%7d%20%3d%7e%20%2f%5cbrcorradini%5cb%2f;hits=1
Bibliography
W.H. Brown, C.S.Foote, B.L.Iverson E.V. Anslyn. Chimica Organica. IV Edition
EdiSES (2009).Chapters 13,14, 17, 18, 23, 25, 26, 27, 28.
K. P. Vollhardt, N.E. Schore :Chimica Organica. third Edition, Zanichelli Editore,
2005. Chapters 19,20,21,24,25,26
P.Y. Bruice Chimica Organica. Edises, 2005. Chapters 13, 14, 17, 21, 22, 23, 26, 27.
J. McMurry :Chimica Organica. 7 Edition. Piccin 2008. Chapters 12, 13, 20, 21, 24, 25, 26, 27,
28.
Copies of lectures available at the course web site.
Text for Further reading:
V. Santagada, G. Caliendo :Peptidi e Peptidomimetici. PICCIN Editore, 2003.
S. M: Hecht. Bioorganic Chemistry: Nucleic Acids. Oxford University Press
S. M: Hecht. Bioorganic Chemistry: Peptides and Proteins. Oxford University Press
S. M: Hecht. Bioorganic Chemistry: Carboydrates. Oxford University Press
Teaching methods
Frontal lectures.
Assessment methods and criteria
Written examination
Other information
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