cod. 1004199

Academic year 2014/15
1° year of course - First semester
Academic discipline
Chimica organica (CHIM/06)
Attività formative affini o integrative
Type of training activity
47 hours
of face-to-face activities
6 credits
hub: PARMA
course unit
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Learning objectives

to acquire the ability to address critically the study of scientific literature at advanced level and even of research studies. Ability to apply the knowledge of Organic Chemistry and of instrumental techniques to solve problems of biological interest in interdisciplinary fields related to Molecular Biology.
Ability to combine knowledge of different fields and to manage complexity, and to express opinions on issues of the chemical aspects of Molecular Biology.
Ability to communicate clearly and unambiguously the acquired knowledge to specialists and non-specialists; development of the ability to learn which enable to continue the studies in molecular context and in the molecular aspects of Biology also autonomously.
to acquire knowledge on the molecular details and properties of some important biological compounds, of the methods for structural determination, of purification techniques and of synthetic modifications. To stimulate the ability to understand and critically evaluate the theoretical basis and experimental details of studies concerning lipids, carbohydrates, oligo- and polypeptides, nucleic acids and their analogs.


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Course unit content

Methods in Bioorganic Chemistry
Introduction to experimental methods for the study of biomolecules. Spectroscopy, chromatography, mass spectrometry; brief introduction to diffractometry and nuclear magnetic resonance (NMR)methods.

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. Carbohydrates as source of information in intercellular and intermolecular interactions. Examples of oligo-polysaccharides, glycoconjugates and their biological functions. Structure, nomenclature, chemico-physical properties and reactivity. Glycosidic bond formation. Concept of glycosyl donor and acceptor, protecting groups. Activation of the anomeric position. Chemical modification of monosaccharides and chemical synthesis of oligosaccharides. Interconversion and biosynthesis of monosaccharides. Polysaccharides degradation. Glycosidases, transglycosidases, phosphorylases, lyasis. Depolymerization mechanisms. Interactions between enzyme site and saccharide substrate. Use of glycosidases for the synthesis of the glycosidic bond. Thermodynamic and cinetic approaches. Regio- and stereoselectivity. Use of engineered glycosidases (glycosynthases). Biosynthesis and interconvertion of glycosylnucleotides. Biosynthesis of glycosidic bond. Glycosyltransferases. Chemoenzymatic synthesis of oligosaccharides, glycoconjugates and polysaccharides. From in vitro to in vivo synthesis. Post-synthetic modifications of oligo- and polysaccharides. Saccharide receptors lacking enzymatic activity: lectins. Concept of multivalency and glycoside cluster effect. Multivalent ligands for lectin inhibition.
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. Chemical stability and principal reactions of DNA and RNA; hydrolysis, oxidation, alkylation. Chemical DNA sequencing and comparison with present sequencing technologies. DNA chemical synthesis: protecting groups, phosphoramidite, H-phosphonate methods. Chemical synthesis of RNA. Oligonucleotide anologs.
Examples and discussion of applications.

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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, 2011. Chapters 13, 14, 17, 21, 22, 23, 27, 28.
J. McMurry :Chimica Organica. 7 Edition. Piccin 2008. Chapters 12, 13, 20, 21, 24, 25, 26, 27,

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 and tutorials.
During the lectures the principles of chemistry, synthesis methods and techniques of purification and characterization of the main class will biological molecules will be presented. In the tutorial part examples of actual cases, also related to literature data, the related problems of understanding the descripton therein, will be discussed in an interactive manner with the students.

Assessment methods and criteria

Written Exam.
The knowledges required to pass the exam are:
Ability to discuss critically the study of the scientific literature also at the research level. Ability to apply knowledge of basic organic chemistry and instrumental techniques to solve problems in subjects of biological interest, and in interdisciplinary contexts related to Molecular Biology.
Ability to integrate knowledge and handle complexity, and formulate judgments about problems in the complex filed of molecular biology.
Ability to communicate clearly and unambiguously the acquired knowledge; evidence of skills enabling to continue to study the molecular aspects of biology also autonomously.
Detailed knowledge of the properties of the main classes of biomolecules, their chemical behavior, methods of determination of the structure, purification and synthetic methods applied to these. Ability to understand the theoretical principles and experimental details of scientific studies of lipids, carbohydrates, oligo-and polypeptides, nucleic acids and their analogues.
The written exam consists of 10 questions. In order to pass, 6/10 questions are correctely answered or, alternatively, if at least 60% of the total content expressed is correct and exhaustive.
The written examination may be integrated by an oral examination upon students' request, or in cases when the teacher consider necessary to furhter evaluate the knowledge emerged from the written exam.

Other information

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