CHIMICA BIOORGANICA CON ELEMENTI DI PROTEOMICA

Aim of the course is to improve the knowledge of the key concepts of the Organic Chemistry for a better knowledge of the Chemistry of biological processes.

In particular, the course is aimed to provide the fundamental tools to study, through a chemical approach, some of the reactions occurring in living systems, and to understand that they follow the same rules of reactivity and the same mechanisms of the reactions that take place in the laboratory.

The course also intends to provide students, who have already acquired the knowledge of chromatography and mass spectrometry, the knowledge of the key concepts for the characterization of complex protein mixtures by proteomic approaches.

Furthermore, in reference to the so-called Dublin Descriptors, this course helps to acquire the following skills:

D1 - Knowledge and understanding: The students will have to demonstrate their mastery of basic knowledge about the organic chemistry. Students will have to correlate the basic knowledge about the organic chemistry with the main reactions treated during the course occuring in living systems.

D2 - Ability to apply knowledge: The students will have to show knowledge and understanding of organic reactions treated during the course of organic molecules involved in living systems.

D3 - Autonomy of judgment: The students will have to apply their knowledge, understanding and skills. Particularly, the students must show his ability to critical reasoning and their ability to identify the most appropriate proteomic approaches for the characterization of complex protein systems.

D4 - Communication skills: The students must be able to communicate clearly with a correct property of language and terminological rigor their conclusions.

D5- Learning skills: The students will have to develop learning skills that will enable them to continue studying in a self-directed or autonomous way.

Classroom Lectures: 38 hours in classroom

Laboratory Training: 4 hours will be focused on the use of the mass spectrometer and bio-informatics softwares for the characterization of protein and peptide mixtures.

Should teaching be carried out in mixed mode or remotely, it may be necessary to introduce changes with respect to previous statements, in line with the programme planned and outlined in the syllabus.

Learning assessment may also be carried out on line, should the conditions require it.

PART I

Review of the main functional groups and the most common organic reactions in living systems.

The phosphate group and the transfer reactions of phosphate groups in living systems. Adenosine triphosphate (ATP). Phosphorylation of alcohol groups. Kinase enzymes. Enzymatic reactions of phosphorylation and dephosphorylation.

Carbonyl addition reaction in living systems. Semiacetals and acetals. Formation of glycosidic bonds in carbohydrates. N-glycosidic bonds. The glycosyltransferases. Hydrolysis of glycosidic bonds.

Nucleophilic acyl substitution reaction in living systems. Esters and thioesters. Acetyl-coenzyme A. Esterification, thioesterification and transesterification. Formation of amides and biosynthesis of glutamine and asparagine.

The hydrolysis reactions of esters, thioesters and amides in living systems. Proteases and hydrolysis of the peptide bond. Serine proteases: chymotrypsin and trypsin.

Redox reactions in living systems: NAD(P) ⁺ and NADH(P); FAD and FADH₂

PART II

Mass Spectrometry in the characterization of peptides and proteins: Tandem mass spectrometry (MS/MS) for the characterization of a peptide sequence.

How to study proteins by mass spectrometry: Characterization of the amino acid sequence of a protein by mass spectrometry; from a single protein to complex protein systems: the proteomics “era”.

Characterization of complex protein systems: Protein identification by top-down and bottom-up approaches; gel-based and gel-free approaches. Interpretation of MS/MS data: de novo Sequencing; protein identification by homology by BLAST (Basic Local Aligment Software Tool). Protein database search by mass spectrometry data: Mascot and PEAKS software. Quantitative Proteomics: SILAC, ICAT and iTRAQ approaches and label-free approaches. Examples and practical applications.

About Bioinformatics: Biological databases; database structure; methods for aligning biological sequences; Dot Matrix and Replacement Matrices; search for similarities in databases using heuristic algorithms: FASTA and BLAST; Multiple Sequence Alignment: The ClustalW software.

Chimica e Propedeutica Biochimica – Bettelheim; Brown etc. – EDISES

Chimica Organica – W.H. Brown; C.S. Foote; EDISES

Computational Methods for Mass Spectrometry Proteomics – I. Eidhammer; K. Flikka; L. Martens; S.O. Mikalsen; WILEY

Proteomics in Practice: A Laboratory Manual of Proteome Analysis – R. Westermeier; T. Naven; WILEY

Appunti, dispense e slides di lezione reperibili tramite il portale STUDIUM di UNICT.