BIOORGANIC CHEMISTRY - MOD. 2

This course is part of the core education activities of the Biomolecular Chemistry curriculum of the Master’s Degree Programme in Sustainable Chemistry and Technologies. Both Mod. 1 and Mod. 2 of the course deliver key theoretical notions and practical lab experiences aiming at integrating the main Organic Chemistry concepts with the organic reactivity observed in biological systems. Through the course lectures students will develop the theoretical and critical evaluation tools necessary to identify the main mechanistic and reactivity analogies and differences occurring between synthetic organic chemistry and biological processes. The laboratory sessions are designed to provide the key practical competences necessary to develop simple experiments employing biologically relevant organic compounds and/or biocatalysts, as well performing an adequate structural characterization, evaluation of the stereochemical and/or biological properties, and formulation of reaction mechanism hypothesis.

Knowledge and understanding
Upon completing the course students will acquire:
a) a comprehensive knowledge of the key structure and reactivity concepts of organic chemistry, which will be integrated to the main reactivity patterns and supramolecular interactions regulating the reactions occurring in living systems;
b) ability to identify the main classes of biological and biomimetic reactions as well as the main bonding and weak-bonding interactions involved;
c) a complete understanding of the principles of organic reactivity applied to reactivity of biological systems and to the development of biomimetic systems.

Ability to apply knowledge and understanding
Students will apply the theorical notions of the course to the critical discussion of relevant biosynthetic and biomimetic processes using the appropriate technical terminology and symbolism. The theoretical notions will be further integrated in the foreseen lab experiences, focusing on reactions of biological interest and actively applied to experimental data processing. Moreover, students will identify and understand the main practical challenges associated to reaction monitoring, quantitative determinations, bio-based compounds purification as well as regio- and stereochemical control in enzymatic reactions on biochemically relevant substrates and/or with biomimetic catalyst.

Judgement skills
a) Ability to critically determine, in a simple and appropriate manner, the main correlations between reactivity of organic compounds and biological systems;
b) Critical analysis of the experimental data acquired during the lab experiences;
c) Ability of proposing suitable experiments for the development of biomimetic systems.

Communication skills
a)Appropriate and pertinent use of the terminology and symbolism learnt during the theoretical course;
b) Dynamic, effective and proper interaction with both lecturers and course mates;
c) Constructive communication with both the instructor(s) and lab mates during the laboratory sessions, aiming at maintaining a high level of attention and full understanding of the experimental work that should be performed;
d) Choosing and applying the correct technical terminology and nomenclature in a laboratory context as well as in concise written reports.

Learning ability
a) Taking lecture notes effectively, highlighting the topics according to their importance;
b) Integrate autonomously the course material provided by the instructors and lecture notes;
c) Record the observed experimental results, such as macroscopic and chromatic variations observed in the course of the experiments, and relate them to the information acquired during the theoretical part of the course and the introductory laboratory lessons;
d) Drafting clear, succinct and exhaustive lab reports of a few pages which include the objective of the experience, the experimental data and the related discussion of the results.

In order to ensure complete understanding of the laboratory experiences, students should have already acquired the basic Organic Chemistry learning objectives regarding, in particular, functional groups reactivity. Students should be familiar with the main physico-chemical properties of organic compounds as well as the reactivity patterns of mono and polyfunctional organic molecules which are the main learning objectives of Organic Chemistry 1 and Organic Chemistry 2. Moreover, students should know the main classes of biologically relevant organic molecules and their role in primary metabolism, which are the main learning objectives of Biochemistry.

- Functional groups in biological chemistry.
- Specific and general acid-base catalysis. Brønsted equation. Nucleophilic and electrophilic catalysis. Acidity and basicity in bioorganic chemistry and enzymes.
- Origin of chirality in living systems. Chirality in biological systems, general concepts, effect in drugs. Chirality of biomolecules, proteins, saccharides, nucleic acids.
- Weak supramolecular interactions: H bond, halogen bond, electrostatic interaction, ion-dipole interaction, ion-π, dipole-dipole, van der Waals interaction, classical and non-classical hydrophobic effect.
- Examples of supramolecular interactions in biological systems, DNA double helix, protein secondary structure, cell membrane, examples of recognition of biological molecular messengers and drugs. Non-covalent interactions in molecular recognition.
- general structural features of enzymes, active site, allosteric regulation, competitive and non-competitive inhibition, kinetic effects.

Lab Experiences
- Glucose mutarotation;
- Supramolecular chemistry: cyclodextrins as complexing agents;
- NMR techniques to determine the structure of a dipeptide.
Please note that laboratory attendance is mandatory.

Richard B. Smith “Biochemistry. An Organic Chemistry Approach” CRC Press, 2020, ISBN: 978-0-8153-6713-0.
David Van Vranken, Gregory A. Weiss "Introduction to Bioorganic Chemistry and Chemical Biology" Garland Science 2012, ISBN: 978-0-8153-4214-4.

Learning outcome assessment is common for both Module 1 and Module 2. It is mandatory to hand in lab reports prior to the final examination. Learning assessment will be performed in two steps consisting of a preparatory written test composed of both multiple choice and open answer quizzes of approximately 2 h to assess the comprehension of the theoretical notions of the course, followed by a viva voce oral examination to further verify the acquired knowledge of the main theoretical outcomes of the course as well as understanding of the lab experiences and critical discussion of the lab reports. A minimum grade of 18/30 for the written test is required for admission to the oral examination. Grading will be provided in a scale of 30, ranging from 18 (sufficient) to 30 (excellent).
Exam evaluation consists of the weight average grade between the written and oral examination (70 % of the final grade) and lab reports (30 % of the final grade).

Theoretical course: theoretical lessons will be provided as 1.5 hours lectures.
Laboratory experiences: the course includes a series of 3 practical laboratory activities, each lasting 5 h, that will be held at the Teaching Laboratory of Organic Chemistry, Beta Building, 1st floor. These lab activities will be preceded by a series of introductory lessons providing a description of the experiments and concise insights on the main analytical tools employed in the laboratory experiences.
At the beginning of the first day of laboratory students will be reminded of: i) the main rules regulating the behavior to be kept during the lab sessions and ii) the importance of the use of personal protective equipment and the proper handling of chemicals.
Copies of the lectures slides, experimental procedures and experimental data will be available through the course Moodle space.

English

Accessibility, Disability and Inclusion

Accommodation and support services for students with disabilities and students with specific learning impairments:
Ca’ Foscari abides by Italian Law (Law 17/1999; Law 170/2010) regarding supportservices and accommodation available to students with disabilities. This includes students with mobility, visual, hearing and other disabilities (Law 17/1999), and specific learning impairments (Law 170/2010). In the case of disability or impairment that requires accommodations (i.e., alternate testing, readers, note takers or interpreters) please contact the Disability and Accessibility Offices in Student Services: disabilita@unive.it.

written and oral