57339 - Bioorganic chemistry

Course Unit Page

  • Teacher Carla Boga

  • Credits 4

  • SSD CHIM/06

  • Teaching Mode Traditional lectures

  • Language Italian

  • Campus of Bologna

  • Degree Programme First cycle degree programme (L) in Industrial Chemistry (cod. 8513)

SDGs

This teaching activity contributes to the achievement of the Sustainable Development Goals of the UN 2030 Agenda.

Good health and well-being Quality education

Academic Year 2022/2023

Learning outcomes

At the end of the course, the student has knowledge about the chemical basis of the structure and of the properties of biological molecules and is able to understand the logic that regulates the bio-organic chemistry. He has acquired the basic knowledge on the main metabolic pathways (and their regulation) of the most important classes of biomolecules. He may find, on the most known databases, information on the structure of proteins and nucleic acids. He is able to analyze, through the use of three-dimensional visualization programs, the spatial structure and the molecular mechanism of action of these biomolecules. In particular, with the aid of this technique, he is able to explain and to discuss the catalytic mechanism of the main classes of enzymes. He understands the importance, through specific examples, of the knowledge coming from the bioorganic chemistry, in applied fields such as that of the biocatalysis and of the drug-design.

Course contents

Introduction. Organic, bio-organic and industrial chemistry. Organisms and their taxonomy. The cell.

Supramolecular chemistry and importance of the autoassembling in biological systems.

Lipids: classification and structure, biological role.

Membranes and transport mechanisms

Carbohydrates simple and complex: structure, chemical properties, biological role. Metabolism of some carbohydrates.

Peptides: aminoacids and characteristics of the peptide bond.

Classification and biological role of peptides. Non covalent interactions and their energy. Denaturation of proteins. Reactions on protein side chains and their applications. The levels of the proteic structure: primary, secondary, tertiary and quaternary structure.

Nucleosides and nucleotides: structure and chemical and biological properties. Nucleosidic drugs. Nucleic acids. Experimental sessions on the use of data banks of proteins: Protein Data Bank e PDB Sum. The programs to view the 3-dimensional structure of proteins: Chime, RasMol, Swiss PDB Viewer.

The reaction in biological systems. Thermodynamic and kinetic aspects. Catalysts and kinetic of the enzyme-catalyzed reactions. Michaelis-Menten kinetics. The mechanisms of the enzymatic catalysis. Recognition of substrate. Mechanisms of catalysis. Enzyme nomenclature and classification. Examples and experimental sessions. Coenzimes.

Inhibition of enzymes and examples of irreversible inhibitors and their action mechanism.

Biological transformation of biomolecules. Lipids digestion, glicolysis, Krebs cycle. oxidative fosforylation. Fermentations.

Molecular engines.

Experimental sessions: use of ChemBioOffice for the drawing and the stereochemical analysis of organic molecules. Grug data bank. The data banks for proteins: Protein data bank and PDB Sum. Chime, RasMol, Swiss PDB Viewer.

The experimental sessions on PDB will be particular example connected with the theoretical part of the course.

Readings/Bibliography

Material projected during the lectures will be available via web through the dedicated platform .

J. McMurry, T. Begley: 'Chimica Bio-organica'  Ed. Zanichelli 2007.

Teaching methods

The course will beconstituted oflectures and ofexperimental sessionsthat will be held in the Computer Lab. The discussion with the student will be welcome.

Assessment methods

The exam consists of an Assessment of the content and a check on the learning by pursuing the objectives of the course.

The final exam will consist of: an oral discussion on a topic chosen by the student from which the teacher will find inspiration to discuss some topics covered in class, and an analysis by means of three-dimensional visualization programs, such as those used during the exercises, of the spatial structure and mechanism of action of certain proteins or enzymes found in the main protein databases.

Criteria for the assessment of the exam: the final grade will be out of thirty. It will be particularly appreciated the achievement of an organic view of the learned topics, and the student's ability to cope, using the tools acquired during the course, also specific special interest topics.

Teaching tools

Videoprojector and whiteboard for lectures. Computer lab with computers and computer programs useful for exercises on databases (e.g. PDB). Material projected during the lectures is available via web.

Office hours

See the website of Carla Boga