BIOORGANIC CHEMISTRY

The course aims to build upon prior knowledge of Organic Chemistry in order to provide a deeper understanding of the chemistry underlying biological processes. In particular, for students who have already acquired a background in organic chemistry, the course is designed to provide the fundamental tools needed to study, from a chemical perspective, some of the most common reactions occurring in living systems, and to understand the similarities and differences with the same reactions carried out in the laboratory. Indeed, although functional group transformations are formally the same, reaction mechanisms may differ depending on the experimental conditions characteristic of synthetic chemistry or of biological systems. In this context, the main reaction mechanisms occurring in biological environments, such as nucleophilic substitutions, additions, eliminations, redox reactions, and enzyme-catalyzed transformations, will be critically analyzed.

Furthermore, the course aims to provide students, who have already acquired knowledge of chromatography and mass spectrometry, with the fundamentals needed to address the characterization of complex protein mixtures through the combined use of proteomic methods, including electrophoretic and chromatographic separation techniques, in-gel digestion reactions, mass spectrometric analysis, and bioinformatic tools.

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

D1 - Knowledge and understanding: The students are expected to demonstrate a solid knowledge of the most common reactions in organic chemistry and the ability to relate them to the reactions discussed during the course that occur in living systems. The student should also show that they have acquired knowledge of analytical methodologies for the study of complex protein mixtures, as well as their applications in different fields, such as the agri-food sector.

D2 – Applying knowledge and understanding: The students should be able to apply the acquired knowledge appropriately and flexibly, also through the theoretical development of targeted projects for the characterization of complex protein systems. They should also be able to identify the main similarities and differences between common reactions in synthetic organic chemistry and the analogous transformations occurring in biological systems.

D3 - Autonomy of judgment: The students are expected to demonstrate critical thinking skills and, based on the knowledge acquired during the course, to design, for example, an experimental project in the field of characterization of complex protein systems, including the selection of appropriate analytical strategies according to the intended objective.

D4 - Communication skills: The students should be able to communicate clearly, using appropriate and rigorous chemical terminology, the knowledge acquired during the course, and to engage in reasoned discussion based on independently developed judgments on issues related to the topics covered.

D5 - Learning skills: The students are expected to demonstrate, also through the ability to retrieve information from the scientific literature and protein databases, well-developed learning and in-depth study skills regarding the topics covered in the course, in order to effectively address complex and interdisciplinary problems, as well as subsequent study paths.

These skills will be fostered by the teacher through the proposal of in-depth topics, classroom exercises, and laboratory activities.

Information for students with disabilities and/or Specific Learning Disabilities (SLD)

To guarantee equal opportunities and in compliance with the laws in force, interested students can ask for a personal interview in order to plan any compensatory and/or dispensatory measures, based on the didactic objectives and specific needs.

Classroom Lectures: 28 hours in classroom - Direct Instruction (Lectures and instructional activities ). During classroom sessions, the instructor uses PowerPoint presentations to support the clear and effective understanding of the course content.

Classroom Exercises: 15 hours in classroom - Interactive Teaching (Interactive and participatory activities)

Laboratory Training: 15 hours will be focused on the use of the mass spectrometer and bio-informatics softwares for the characterization of protein and peptide mixtures (Interactive Teaching (Interactive and participatory activities). 

If the course is delivered in a blended or fully online format, the necessary adjustments may be made to the arrangements described above in order to ensure that the course syllabus and the planned programme are fully covered.

The students should have basic knowledge of:

- Organic Chemistry

- Chemistry of Biomolecules

- Liquid Chromatography and Electrophoresis

Attendance is mandatory. Students are required to attend at least 70% of the total course hours (see Section 3.4 of the Teaching Regulations).

In accordance with Article 30 of the University Teaching Regulations, partial or full exemptions from attendance requirements may be granted to working students, student-athletes and para-athletes, students experiencing particular difficulties, students with disabilities, and students in detention. Such exemptions are subject to a formal resolution by the relevant Degree Programme Council, following the submission of a duly justified request and its approval by the Council. Where applicable, and in consultation with the instructors responsible for the relevant courses, appropriate additional academic support measures may be arranged to ensure that students can nevertheless achieve the required level of preparation.

Part I: Organic Chemistry Reactions in Biological Systems

Review of the principal functional groups and the most common organic reactions occurring in biological systems. Aliphatic nucleophilic substitution reactions, elimination reactions, nucleophilic addition to carbonyl compounds, and nucleophilic acyl substitution reactions. Formation of glycosidic bonds in carbohydrates. Acetyl coenzyme A. Esterification, thioesterification, and transesterification reactions. Mechanisms of action of penicillin and aspirin. Biosynthesis of glutamine and asparagine from glutamate and aspartate. Carbonyl condensation reactions. Examples and comparison with analogous reactions performed under laboratory conditions. Redox reactions in biological systems: NAD(P)+/NAD(P)H and FAD/FADH2. (6 h)

The phosphate group and phosphate transfer reactions in living organisms. Adenosine triphosphate (ATP) and cellular respiration (glycolysis, the Krebs cycle, and oxidative phosphorylation): esterification (phosphorylation), oxidation, Claisen condensation, aldol condensation, and retro-aldol reactions involved in the stages of cellular respiration. (6 h)

Hydrolysis reactions in biological systems. Hydrolysis of glycosidic bonds in polysaccharides. Ester hydrolysis. The example of acetylcholine and acetylcholinesterase. Hydrolysis of triglycerides. Protein hydrolysis. Proteases and hydrolysis of the peptide bond. Serine proteases: chymotrypsin and trypsin. (2 h)

Part II: Proteomic Approaches

Mass spectrometry applied to the study of peptides and proteins. Tandem mass spectrometry (MS/MS) for peptide sequence characterization. (2 h)

Application of mass spectrometry to protein analysis. Characterization of protein amino acid sequences by mass spectrometry; from single proteins to complex protein systems: the era of proteomics. (4 h)

Characterization of complex protein systems. Protein identification through top-down and bottom-up approaches; gel-based and gel-free methodologies. Interpretation of MS/MS data: de novo sequencing. Biological databases and their structure. Protein database searching using mass spectrometry data: Mascot and PEAKS software. Quantitative proteomics: label-based and label-free approaches. (4 h)

Methods for biological sequence alignment. Sequence alignment, similarity, and homology. Substitution matrices. Similarity searches in biological databases using heuristic algorithms: BLAST. Multiple sequence alignment: the ClustalW software. (4 h)

Classroom exercises and examples of proteomic applications. Exercises on the deconvolution of ESI mass spectra of proteins. Exercises on the interpretation of peptide and protein MS/MS spectra (top-down). Examples and practical applications of proteomic approaches in the study of real-world cases. (15 h)

Laboratory Activities (15 h)

- Preparation of a mixture of two proteins and analysis by direct infusion mass spectrometry. Determination of the experimentally obtained molecular masses.

- Reduction of disulfide bonds and alkylation of thiol groups with iodoacetamide in the previously prepared protein mixture. Determination of molecular masses by direct infusion ESI-MS. Calculation of the number of cysteine residues.

- Analysis of bovine milk whey using a gel-free bottom-up proteomic approach and protein identification through database searching using bioinformatics tools.

Chimica Bio-Organica – J. McMurry, T. Begley - Zanichelli

Proteomica – T. Alberio; M. Fasano; P. Roncada; EDISES

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

Lecture notes, handouts, and lecture slides available through the University of Catania's Moodle / STUDIUM e-learning platform

The exam is an oral test. The exam is aimed at verifying the knowledge and skills acquired by the student, his ability to connect the various topics covered during the lessons, and his ability to use appropriate language.

The final evaluation grade is in the 30/30 range.

Evaluation scale:

Grade 30-30 cum laude: 

Grade 27-29: 

Grade 24-26: 

Grade 21-23: 

Exam failed: 

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

To ensure equal opportunities and in compliance with current laws, students may request a personal interview in order to plan any compensatory and/or dispensatory measures based on educational objectives and specific needs. Students can also contact the CInAP (Centro per l’integrazione Attiva e Partecipata — Servizi per le Disabilità e/o DSA) through the referring professor within the department, (https://www.cinap.unict.it/content/referenti).