Organic Chemistry for the Biotechnology
Learning outcomes of the course unit
The course aims to provide the basic concepts of Organic Chemistry that can be applied to the molecular description of biological phenomena and the modification of these to obtain biotechnological applications. In particular, the course will provide elements for understanding the chemistry of the main biological macromolecules (peptides, oligonucleotides, oligo- and polysaccharides) and their transformations, and the biological properties and origin of secondary metabolites. Case studies will also be presented where the application of such knowledge has led to important industrial progress, with particular attention to modern life-related nanotechnologies.
The course will provide the acquisition of a formally correct language; the ability to express the content in a clear and immediate way will be stimulated; the links between the different parts of the course and how they contribute to the overall understanding of the biological systems will be emphasized.
Application of knowledge:
The course aims also to provide the tools to interpret rationally and at the molecular level the main properties of biological macromolecule,s and biological pathways leading to the production of secondary metabolites. Such compounds are found only in specific organisms or groups of organisms and are the expression of the individuality of the species. It also stimulates the student's understanding of events that had previously been addressed only in a phenomenological way.
The course also aims to provide students with tools for interdisciplinary and interdisciplinary research on biotechnology and chemistry applied in this field and to discuss / communicate with chemists colleagues.
Organic Chemistry and Biochemistry. Fundamentals of analytic techniques
Course contents summary
Structural and reactivity properties of carbohydrates, peptides, nucleic acids and analogues. Their modifications for biotechnological purposes. Systems for the drug dellivery. Secondary metabolism. Biotechnological strategies for the development of industrial processes based on these classes of molecules
(Sansone) - Chemistry of bio-macromolecules. Carbohydrates: reactivity, biosynthesis and synthesis of the glycosidic bond through chemical and enzymatic methods. Multivalent effect. Glycoconjugates. Complex carbohydrates as pharmaceutical products. Peptides and peptide synthesis. Combinatorial synthesis. Reactivity of nucleic acids. Synthesis of oligonucleotides and analogues commonly used as mimic for biological applications. Non viral transfecting agents. Systems for drug and biomolecule delivery. Principles of methods for characterization and purification of biopolymers from synthesis. Biotechnologies and Nanotechnologies based on peptides, nucleic acids and analogues.
Definition of secondary metabolism. Structural variety of secondary metabolites: building blocks, enzymes and charecteristic reactions. Methods for isolation and characterisation of metabolites. The acetate pathway: fatty acids and polyketides. Saturated, monounsaturated and polyunsaturated fatty acids, prostaglandins, tromboxanes, leukotrienes, lipoxins: physiological role. The shikimate pathway: shikimate biogenesis, aromatic amino acids, tetracyclins. Teprenes: biogenesis, mono-, sesqi- and diterpenes, natural rubber; squalene and fitoene, carotenoids, visual cycle. Steroids: biogenesis from squalene: lanosterol cholesterol, corticosteroids, sex hormones, bile acids: physiological implications. Alkaloids:nomenclature, cassification and bilogical role; biogenesis. Antibiotics: principal classes, biogenesis and mechnisms of action.
Seminars (Prof. Maggi) on appllications and cases of study. The use of the biotechnologies for the transformation of organic substrates for industrial aims. Biorefineries.
Upon request by students and not included in the program for the examination: Prebiotic Chemistry. The mistery of the origin of life (Corradini)
-P.Y. Bruice Chimica Organica 2nd Edition. Edises, 2011. Capitoli 13, 14, 17, 21, 22, 23, 27, 28. - W.H. Brown, C.S.Foote, B.L.Iverson E.V. Anslyn. Chimica Organica. IV Edizione
EdiSES (2009).Capitoli 13,14, 17, 18, 23, 25, 26, 27, 28.
- J. McMurry :Chimica Organica. 7 Edizione. Piccin 2008. Capitoli 12, 13, 20, 21, 24, 25, 26, 27,
P. Mac Dewik Chimica, biosintesi e bioattività delle sostanze naturali Piccin 2012.
- Teachers’ handouts
In depth-study texts:
for the peptide part:- Peptidi e Peptidomimetici, V. Santagada, G. Caliendo, Piccin Nuova Libraria, 2003; - S. M: Hecht. Bioorganic Chemistry: Peptides and Proteins. Oxford University Press
For the carbohydrates part:- The Sugar Code. Fundamentals of Glycosciences, Hans-Joachim Gabius Ed., 2009 Wiley -VCH Verlag, Weinheim- Introduction to Glycobiology, M. E. Taylor, K. Drickamer Eds., 2006 Oxford University Press - Carbohydrate Chemistry: State of the Art and Challenges for Drug Development. An Overview on Structure, Biological Roles, Synthetic Methods and Application as Therapeutics, Ed. Laura Cipolla, Imperial College Press, 2015.
For the part on oligonucleotides:- Bioorganic Chemistry - Nucleic Acids, Sidney M. Hecht, Ed., 1996 Oxford University Press. - Gli Oligonucleotidi Sintetici - Principi e applicazioni, CNR - Progetto Strategico Nucleotidi Antisenso, UTET Periodici
For the part relative to trasfecting agents- DNA Interactions with Polymers and Surfactants, R. S. Dias and B. Lindman Eds, Wiley Interscience, 2008; - DNA and RNA Binders - From small molecules to drugs, M. Demeunynck, C. Bailly and W. D. Wilson Eds., Wiley-VCH, 2003
- Review articles from the literature
Classroom teaching and interactive exercises relative to specific problems, seminars
Assessment methods and criteria
The requested knowledges for a successful examination are: ability in critically facing the study of scientific literature even in a research context; ability in applying the knowledges in basic Organic Chemistry and Instrumental techinques to solve problems of biotechnological interest also in interdisciplinary contexts; ability in communicating with an appropriate and unequivocal language the acquired knowledges. The student must also demonstrate to be able to continue in autonomy the study of the molecular aspects of biotechnologies; to have a proper and detailed knowledge of the properties of principal classes of biomolecules and secondary metabolites, of their chemical behavior, the methods for their characterization and purification.
The written test consists of 10 questions. In order to pass, 6/10 questions have to be correctely answered or, alternatively, if at least 60% of the total content expressed is correct and exhaustive.
The written test is followed by an oral examination to further evaluate the knowledge emerged from the written test.