Bioorganic Chemistry
A.Y. 2024/2025
Learning objectives
Aim of the course Is to illustrate how the principles of mechanistic organic chemistry can be applied to the study of the reactions involved in metabolic processes. It provides knowledges about the fundamentals of enzymatic catalysis by illustrating the application of conceptual tools, experimental techniques and informatics tools to the study of enzyme-catalyzed reactions. Part of the course will be devoted to the use of enzymes for preparative purposes in organic synthesis.
Expected learning outcomes
Students will acquire knowledges about the most common enzymatic mechanisms used by Nature. Students will also be able to apply the already acquired knowledges in Organic Chemistry and the interdisciplinary tools from Bioorganic Chemistry in order to formulate hypothesis about an enzyme-catalyzed reaction and to propose experiments aimed at verifying the postulated hypotheses. Finally, students will acquire a general knowledge about the possible use of enzymes as catalysts in organic synthesis.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
Second semester
Course syllabus
Introduction: aims and instruments of Bioorganic Chemistry.
Structures and functions of enzymes: recap on protein structure; the enzyme active site.
Mechanisms of enzymatic catalysis.
Cofactors and coenzymes.
The IUBMB classification of enzymes.
IT tools and internet resources for the study of bioorganic chemistry.
Application of the above-described tools through case studies of:
- Enzymatic reactions with group transfer: hydrolysis, phosphorylation, transamination.
- Biocatalyzed carbon-carbon bond-forming and bond-breaking reactions: aldol condensation, Claisen condensation; reactions catalyzed by thiamin-dihosphate- and pyridoxal phosphate-dependent enzymes; decarboxylation and carboxylation reactions.
- Redox reactions: formal transfer of hydride ions; Reactions catalyzed by Flavin-dependent enzymes; oxidases, monooxygenases, dioxygenases. Reactions catalyzed by heme-containing enzymes.
- Enzymatic radical reactions.
Where appropriate, the use of some classes of enzymes as biocatalysts for preparative purposes in organic synthesis will be illustrated.
Structures and functions of enzymes: recap on protein structure; the enzyme active site.
Mechanisms of enzymatic catalysis.
Cofactors and coenzymes.
The IUBMB classification of enzymes.
IT tools and internet resources for the study of bioorganic chemistry.
Application of the above-described tools through case studies of:
- Enzymatic reactions with group transfer: hydrolysis, phosphorylation, transamination.
- Biocatalyzed carbon-carbon bond-forming and bond-breaking reactions: aldol condensation, Claisen condensation; reactions catalyzed by thiamin-dihosphate- and pyridoxal phosphate-dependent enzymes; decarboxylation and carboxylation reactions.
- Redox reactions: formal transfer of hydride ions; Reactions catalyzed by Flavin-dependent enzymes; oxidases, monooxygenases, dioxygenases. Reactions catalyzed by heme-containing enzymes.
- Enzymatic radical reactions.
Where appropriate, the use of some classes of enzymes as biocatalysts for preparative purposes in organic synthesis will be illustrated.
Prerequisites for admission
Some basic knowledge deriving from the completion of the bachelor degree is considered necessary for successful attendance at lectures. In particular, knowledge of acid-base theories, the principles of chemical kinetics and the fundamentals of stereochemistry are required. A fundamental prerequisite is the knowledge of the structure, properties and reactivity of the functional groups of organic chemistry (Chimica Organica 1 and 2 of the Bachelor degree). Knowledges of the main metabolic pathways (Biological Chemistry) and of the most common spectroscopic techniques (UV-vis; IR; NMR; mass spectrometry, deriving from Analytical Chemistry and Applicazioni di Chimica Analitica Strumentale)) are desirable, although not essential.
Teaching methods
In-class lessons. Attendance policy: strongly recommended.
Teaching Resources
T. D. H. Bugg. Introduction to enzyme and coenzyme chemistry, Third Edition. Wiley, 2012.
For the use of enzymes as biocatalysts in preparative organic synthesis:
References to reviews and original papers can be found within the slides of the lectures available at the Ariel web site.
For consultation:
R. B. Silvermann. The organic chemistry of enzyme-catalyzed reactions. Academic Press, 2000.
J. McMurry, T. Begley. Chimica bio-organica. Zanichelli, 2007
For the use of enzymes as biocatalysts in preparative organic synthesis:
References to reviews and original papers can be found within the slides of the lectures available at the Ariel web site.
For consultation:
R. B. Silvermann. The organic chemistry of enzyme-catalyzed reactions. Academic Press, 2000.
J. McMurry, T. Begley. Chimica bio-organica. Zanichelli, 2007
Assessment methods and Criteria
Oral exam: the exam consists of an interview that, starting from a topic covered in class, will develop so as to allow the assessment of:
Degree of understanding and knowledge of the topics;
Proper language and clarity of explanation;
Ability to link between different topics;
Mastery of conceptual and experimental tools used in bioorganic chemistry;
Ability to deal with different problems on the basis of the acquired skills.
Degree of understanding and knowledge of the topics;
Proper language and clarity of explanation;
Ability to link between different topics;
Mastery of conceptual and experimental tools used in bioorganic chemistry;
Ability to deal with different problems on the basis of the acquired skills.
CHIM/06 - ORGANIC CHEMISTRY - University credits: 6
Lessons: 48 hours
Professors:
Bassanini Ivan, Morelli Carlo
Educational website(s)
Professor(s)
Reception:
from Monday to Friday by appointment
Professor's office, Department of Chemistry.