ORGANIC CHEMISTRY OF BIOMOLECULES
Learning outcomes of the course unit
The aim of the course is to give an adequate knowledge of
- properties and reactivity of biologically relevant organic molecules: carbohydrates, amino acids and peptides, lipids, nucleic acids;
- modification of their structure, synthesis of derivatives and mimics;
- their application in different fields of science
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.
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 available at the website on Elly platform
Review articles from the literature
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 e solution of problems relative to identification and synthesis of derivatives belonging to the illustrated classes of compounds
Assessment methods and criteria
Oral examination with exercises on the reactivity and synthesis of saccharides, peptides and nucleic acids.
It is verified the acquired knowledge relative to
- strategy of modification of amino acids, carbohydrates and nucleotides;
- synthetic strategy of peptides, oligosaccharides, oligonucleotides;
- application in scientific fields of peptides, oligosaccharides, oligonucleotides and lipids thanks to their ability in giving interactions with biologically and medically relevant substrates and species and thanks to their self-assembly properties;
It is verified the ability to critically analize the literature data relative to these topics.
During the examination, some relatively complex molecules are proposed to the students as synthetic targets in order to evaluate their acquired ability in 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 illustration of the synthetic strategies, the students have to show to be able to use a correct and appropriate scientifi language and the correct use and presentation of the molecular structures and functions.