Learning outcomes of the course unit
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.
Course contents summary
Chemical, structural and reactivity properties of lipids, amino acids and peptides, carbohydrates, nucleic acids. Main concepts and strategies for theis synthesis and for synthesis of mimics. Interaction properties and applications. Introduction to instrumental methods and techniques for their purification and characterization
Classification of lipids. Triglycerides, chemical properties and reactivity. Oxidation reactions. Phospho- and glycolipids. Micelles and liposomes. Non hydrolysable lipids.
Nomenclature, acidity and basicity, pI, distribution curves of amino acids and peptides.
Hydrolysis of peptide bond. Examples of biologically active peptides.
Principles of the chemical synthesis of peptides; protecting groups and coupling reagents. Solid phase synthesis. Principles of combinatorial chemistry applied to peptide synthesis.
The role in the storage of information for the cell life. Examples of mono-, oligo-, polysaccharides, glycoconjugates and their biological functions. Nomenclature, structural, physico-chemical and reactivity properties. Principles and concepts of the glycoslyation reactions: glycosyl donor and acceptor, protecting and activating groups.
Degradation of polysaccharides by enzymes. Interactions between enzyme and substrate. Use of glycosidases for the synthesis of the glycosidic bond. Thermodynamic and cinetic approach. Glycosynthases and fluorosaccharides. Biosynthesis of the glycosidic bond: the glycosyltransferases. Classification of glycosyltransferases and their use for the synthesis of complex saccharides. Lectins and multivalency.
Structure and chemical properties of nucleosides and nucleotides. Reactivity and stability. Chemical synthesis of oligonucleotides. Examples of significant oligonucleotide mimics.
Examples of common DNA and RNA binders.
Principles of methods for purification and characterization of biomolecules
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, 28.
Lecture notes by the Professor, available at the course web site on Elly platform.
Review articles from the literature.
In depth-study texts:
For the section relative to peptides: Peptidi e Peptidomimetici, V. Santagada, G. Caliendo, Piccin Nuova Libraria, 2003 – S. M: Hecht. Bioorganic Chemistry: Peptides and Proteins. Oxford University Press.
For the section relative to carbohydrates: 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 section 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
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 Test followed by oral examination.
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 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 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.