ORGANIC CHEMISTRY OF BIOMOLECULES
Learning outcomes of the course unit
At the end of the course, the student is expected
- Knowledge and understanding:
to know and understand properties and reactivity-properties correlation of biologically relevant organic molecules such as carbohydrates, amino acids and peptides, nucleic acids, lipids, their mimics; to know and understand methods for their chemical modification; to know the correct representation of the molecules object of the course and the reaction mechanisms of their transformations.
- Applying knowledge and understanding:
To be able to exploit the acquired theoretical knowledge to propose proper synthetic strategies for the achievement of complex molecules, foreseeing properties and also suggesting their possible application in different fields of science and technology; to be able to plan and design the synthetic strategies critically considering potentiality, limits and difficulties correlated with these classes of compounds; to be able to find and exploit bibliographic sources useful to reach these aims; to be able of correctly representing molecula structures and reaction mechanisms.
- Making judgements:
To be able to evaluate problems of design related with synthesis procedures and applications of these classes of molecules; to understand and critically evaluate the literature data relative to these classes of compounds; to express personal and autonomous evaluation and consideration on the application and use of these compounds in technological, medical and biological contexts.
- Communication skills:
To be able to correctly use the structural representation of the used chemical compounds; to be able to describe with correct scientific language his/her own knowledge and the proposed strategies; to be able to discuss with researchers having a scientific background in different areas such as biology, biochemistry, biotechnology having well clear the role of these classes of compounds in those scientific contexts.
- Learning skills:
To have the knowledge to autonomously continue the study on the classes of compounds object of the course, being able to tackle new interdisciplinary issues related with the classes of compounds studied in the course, also with the support of information present in the literature, databases, web.
Organic Chemistry 1 and 2
Course contents summary
Chemico-physical properties and reactivity of carbohydrates, amino acid and peptides, lipids and nucleic acids.
Modification of their structure and synthesis of corresponding oligomers.
Artificial mimics, properties and synthesis.
Use as raw material for the production of chemicals.
Noncovalent interaction with molecular and macromolecular species.
Amino acids and peptides
Why to synthesize a peptide. Structure and properties of amino acids and peptides. Nitrogen protecting groups: insertion and removal. Possible secondary reactions. Protecting groups of carboxylic and hydroxyl groups. Methods for activation and coupling. Possible racemisation phenomena and mechanisms. Methods of solid phase synthesis. Resins and cleavage conditions.
Role of carbohydrates in non metabolic biological processes. Structure, properties, nomenclature. Anomeric effect. Oxidation and reduction reactions. Glycosylation reactions: concept of glycosyl donor and glycosyl acceptor, promoters, protecting groups. Enzymatic synthesis of glycosidic bond. Oligosaccharide and glycoconjugates synthesis on solid phase. Synthesis of glycosidic clusters and concept of multivalency and glycoside cluster effect. Carbohydrates as renewable raw material for fine chemicals.
Structure and properties. Synthesis. Modified nucleic acids and mimics. Antigene and antisense strategies. DNA and RNA binders. Nucleic acids as smart material for nanotechnology
Structure and properties. Autooxidation reactions. Synthesis of complex lipids: some examples. Self-assembly of lipids: double layers, lamellar phases, vesicles, liposomes. Delivery applications. Determination of size and zeta potential by DLS. Investigation through AFM and TEM
Lecture notes by the Professor, Review articles from the literature, examples of exercises and cases of study proposed during the examination. All this material is available at the website on Elly platform from teh beginning of the course. It constitutes the main support for the preparation of the exam
In dept-study texts:
for the part relative to amino acids and peptides:
- Peptidi e Peptidomimetici, V. Santagada, G. Caliendo, Piccin Nuova Libraria, 2003
for the part relative to carbohydrates:
- The Sugar Code. Fundamentals of Glycosciences, Hans-Joachim Gabius Ed., 2009 Wiley -VCH Verlag, Weinheim
- Carbohydrates in Chemistry and Biology, B. Ernst, G. W. Hart, P. Sinay Eds., Vol. 1-4, 2000 Wiley -VCH Verlag, Weinheim
- Carbohydrates as Organic Raw Materials, Frieder W. Lichtenthaler Ed., VCH Weinheim, 1991
- 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.
- The Molecular and Supramolecular Chemistry of Carbohydrates, S. David Ed., 1997 Oxford University Press
for the part relative to nucleic acids:
- 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
- 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
Classroom teaching and solution of problems relative to identification and synthesis of derivatives belonging to the illustrated classes of compounds. The resolution of exercizes and problems is done with the direct participation and contribution of the students.
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 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.
Assessment methods and criteria
Oral examination based on the resolution and discussion of exercises on the reactivity and synthesis of lipids, saccharides, amino acids and peptides, nucleic acids, theri mimics.
It is verified the acquired knowledge relative to strategy of modification of amino acids, carbohydrates and nucleotides; synthetic strategy of peptides, oligosaccharides, oligonucleotides; possible application in scientific fields of these classes of molecules thanks to their ability in giving interactions with biologically and medically relevant substrates and species and thanks to their self-assembly properties.
During the examination, questions relative to each of the four course sections (lipids, saccharides, amino acids and peptides, nucleic acids) are posed to the student. It is given to the student the possibility of starting the exame with a topic of own choice.
Specifically, some relatively complex molecules, generally taken from study and research cases present in literature, are proposed to the student for the presentation of their properties and as synthetic targets. In this way the acquired ability is evaluated of planning a correct strategy of synthesis based on the methodologies shown in the course, by using protecting and activating groups, by estimating advantages and drawbacks of the various possibilities and experimental conditions, analysing problems occuring and possible solutions. During the exame, the student has to show to be able to use a correct and appropriate scientific language and the correct representation of reaction mechanisms, molecular structures and functions.
The demonstration of a basic knowledge of tghe course contents, including the main properties of the studied compounds and their reactivity, determines an evaluation of 18-21/30 points; if some of the answers are characterized by a punctual description of reactions and molecules the score reaches 21-24/30; exhaustive answers like these for all the issues discussed during the exam determine a score of 24-27/30; a deep discussion of the topics, even evidencing the ability of the student in tackling new problems and targets, together with the ability of pointing out problems and applications of the compounds under investigation, determines a score of 27-30/30. Definitely exhaustive answers and discussion, with the use of a proper language together with a rigorous representation of molecules and reaction mechanims bring to “laude”.