BIO-ORGANIC CHEMISTRY

Teachers: 
Credits: 
6
Site: 
PARMA
Year of erogation: 
2021/2022
Unit Coordinator: 
Disciplinary Sector: 
Organic Chemistry
Semester: 
First semester
Year of study: 
1
Language of instruction: 

Italian.
This course offers the “Book exam” option. The lectures are held in Italian, but Erasmus/foreign students can complete the course by choosing the “book exam” option: this means that you read and study the literature specifically agreed on with the lecturer/professor and then take a written examination in English.

Learning outcomes of the course unit

Expected abilities at the end of the course:

- To knowledge and identify the molecular properties of important classes of biomolecules such as lipids, amino acids and peptides, carbohydrates, nucleic acids, their chemical behaviour, the methods for structural determination and purification, the possible, more common synthetic and/or enzymatic modifications to which they can undergo. To knowledge and identify synthetic mimics of these classes of compounds. To knowledge possible applications of these molecules in a biomolecular and cellular context (Knowledge and understanding).

- To apply the knowledge of basic Organic Chemistry and of reactivity of these molecules to identify structure and chemical properties of a molecule, to propose strategies for the preparation of oligomers of these species reported in examples from literature and studies in interdisciplinary contexts related with the molecular biology. To be able of representing from a molecular point of view the chemical species and the transformation they undergo (Applying knowledge and understanding)

- To address critically the study of scientific literature at advanced level and even of interdisciplinary research studies with chemical and biomolecular contents related to the molecular species studied in the course and to elaborate a own autonomous evaluation on the ral value of the reported. To autonomously evaluate a designed proposal of chemical nature for its application in a biomolecular context by combining knowledges and managing complexity for discussion with chemistry researchers (Making judgements).

- To communicate in a clear, efficacious and unambigous way the acquired knowledge with a proper language for specialistic, also chemists, and non specialistic spokespersons and public (Communication skills).

- To autonomously study the molecular context and aspects of Biology, tackling with a rational approach and constructive criticism issues and problems new but relatede to the structural and reactivity aspects of the molecules studied in the course (Learning skills).

Prerequisites

Organic Chemistry

Course contents summary

Chemical, structural and reactivity properties of lipids, amino acids and peptides, carbohydrates, nucleic acids. Main concepts and strategies for their synthesis and for synthesis of mimics. Interaction properties and applications. Introduction to instrumental methods and techniques for their purification and characterization

Course contents

Lipids.
Classification of lipids. Triglycerides, chemical properties and reactivity. Oxidation reactions. Phospho- and glycolipids. Micelles and liposomes. Non hydrolysable lipids.
Peptides.
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.
Carbohydrates.
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 kinetic 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.
Nucleic acids.
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

Recommended readings

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,
Review articles from the literature, examples of exercises discussed in the classroom and object of previouos examination tests.
This material is available on Elly platform from the beginning of the course and constitutes the main support for the preparation of the exam.

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

Teaching methods

Frontal lectures and tutorials with the support of slides. The availability of lessons through online and recorded forms will be soon evaluated. The frontal lectures will be characterized by numerous occasions for discussion and interactions with students.
The principles of chemistry, synthesis methods and techniques of purification and characterization of the main class will biological molecules will be presented.
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.
In the tutorial part, examples of actual cases, also related to researches and studies from the literature, are presented and addressed. The related problems of understanding and the synthetic strategies for the molecule preparations are discussed in an interactive manner with the students.

Assessment methods and criteria

Written Exam followed by possible oral examination.
   
The written test consists of 10 questions with open answer and the time available to complete it 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 evaluation of the written test is transmitted to the student through an e-mail message to the institutiopnal address within the date fixed for the vote registration/possible oral exam.
   
The written test may be integrated by an oral examination upon students' request of trying to improve the evaluation, or when the teacher considers necessary to further evaluate the knowledge emerged from the written exam. In these cases, the mark of the written test is remodulated on the basis of the evaluation of the oral exam to generate the final grade that, then, can remain unvaried, increase or decrease.

The oral examination is based on either the questions of the written test, which had answers with an evaluation of less than 2.4 points, or further issues and cases if all the questions had answer with a score of or higher than 2.4 point.

The participation both to the written exam and to the oral/registration is allowed upon enrolment to one of the exam dates reported on Esse3 system