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.
Module 2 (Bigi) - Secondary metabolism. Definition of secondary metabolism. Simplicity and complexity of secondary metabolites: building blocks, enzymes and characteristic reactions. Methods for the isolation and characterization of metabolites. Overview of the biosynthetic pathways and main key intermediates: the acetate pathway (fatty acids and polyketides), shikimate (aromatic compounds), mevalonate (terpenes and steroids). The organic chemistry connected to these biosynthetic pathways will be illustrated following the biosynthesis of some biotechnological substances (at least two for each biosynthetic pathway) in which a working method will be illustrated suitable to connect the transformations that occur to the concepts developed in Organic Chemistry,and identifying the corresponding enzymes. The exercises will focus on making students acquire the working method by autonomous study of cases related to Biotechnologies.
Seminars (Prof. Maggi) on appllications and cases of study. The use of the biotechnologies for the transformation of organic substrates for industrial aims. Biorefineries.
-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
Teachers’ handouts and review articles are available on ELLY platform from the beginning of the course lessons
The teaching activity will be carried out through lectures with the aid of slides. The lessons, possibly carried out in person, will also be usable remotely in the ways that the teacher deems most effective, mainly through the TEAMS platform. The recorded lectures will be available throghout the semester. Classroom teaching involves interactive exercises relative to specific problems, seminars.
At the beginning of each course section, the basic chemical properties of the specific class of compounds are identified with the direct contribution of the students by using their established knowledge in organic chemistry. This approach is useful to verify the starting knowledge of the students in organic chemistry and allow the teacher to fill possible gaps.
Both in the case of frontal and remote lessons there will be spaces for interaction with students
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 with open answer and the time available to complete the test is 3 h. Each question has a value of 3 points contributing to a maximum total score of 30/30 points. The test is considered positively surpassed if a score of at least 18/30 points is reached. For each question the minimal sufficient score (1.8/3) is reached if the basic knowledge on the argument is demonstrated, the maximum score (3/3) is obtained if an in-depth knowledge on the argument also from the structural and molecular reactivity point of view is demonstrated jointly with the ability of correctly representing the molecular structure of the discussed species. The achievement of the maximum score in all questions with definitely both exhaustive answers and appropriate language determines the evaluation "cum laude"
The written test is followed by an oral examination to further evaluate the knowledge emerged from the written test.
It is possible to make separately the written exam relative to module 1 (Sansone) at the end of this part of the course.