C8490 - Metabolic and Structural Biochemistry

Learning outcomes

"The course aims to provide students with a thorough understanding of metabolic biochemistry, with particular emphasis on the main biosynthetic pathways, the structure of key enzymes involved, and their regulatory mechanisms. These topics will also be addressed from an applied perspective, with reference to the use of engineered cell models for the production of compounds of industrial or therapeutic interest. Upon completion of the course, students will be able to: - Analyze and discuss with advanced competence topics related to metabolic biochemistry, both theoretical and applied; - Critically understand the structure-function relationship of enzymes; - Use advanced molecular graphics programs to analyze protein structure, conformational changes induced by mutations or interactions with regulatory elements, and to get acquainted with the role of cofactors in enzymatic catalysis. "

Course contents

The course consists of two modules: Metabolic Biochemistry (Module 1) and Structural Biochemistry (Module 2).

During the Module 1, students will examine the major biochemical processes regulating cellular metabolism and the biosynthesis of molecules of industrial and therapeutic interest, using Saccharomyces cerevisiae as both a model organism and a production platform.

Module 1 consists of lectures and seminar activities.

The lecture component (2 CFU, 14 hours) covers the following topics:

• organization of central carbon metabolism and the regulatory mechanisms governing glycolysis, alcoholic fermentation, and respiratory metabolism;
• principles of metabolomics and their application to the study of cellular metabolism and metabolic flux analysis;
• principles and strategies of metabolic engineering applied to S. cerevisiae, with particular emphasis on the design of high-productivity strains through the modification of key enzymes and optimization of metabolic pathways;
• pyruvate, acetyl-CoA, and ethanol metabolism, together with the major biosynthetic pathways involved in the production of high-value metabolites, including 2,3-butanediol, fatty acids, oleochemicals, and other biotechnologically relevant compounds.

The seminar component (1 CFU, 12 hours) involves the individual study of a topic related to the module through reading, critical analysis, and discussion of the relevant scientific literature. Each student will prepare a PowerPoint presentation illustrating the biochemical basis of the metabolic processes under investigation, the metabolic engineering strategies employed, and the main experimental findings reported in the literature. The presentation will be followed by a discussion with the instructor and the rest of the class, aimed at both deepening subject-specific knowledge and developing transferable skills. This activity is designed to enhance students' ability to retrieve and critically evaluate scientific literature, interpret experimental data, formulate evidence-based conclusions, communicate scientific information clearly and effectively, and engage in rigorous scientific discussion with both the instructor and their peers. The presentation will be assessed by the instructor, and the mark obtained will contribute to the final grade for the module, according to the assessment criteria described in the relevant section. Although attendance at the seminar/tutorial activities is not compulsory, participation in all 12 hours is strongly recommended, as these activities form an integral part of the learning pathway and are intended to support the acquisition of both subject-specific and transferable skills.

Module 2 consists of lectures (1 CFU, 7 hours) and computer laboratory sessions (2 CFU, 26 hours), both delivered in a computer laboratory. The lecture component provides the theoretical background required for practical computer-based activities.

The first part of the module introduces the major online databases for nucleic acids and proteins, together with molecular graphics software for the visualization and manipulation of crystallographic structures. The following topics will be covered:

• key features of protein secondary structure and the Ramachandran plot;
• supersecondary, tertiary, and quaternary protein structures;
• substrate- and ligand-induced conformational changes (induced fit);
• manipulation and analysis of crystallographic structures;
• oligomeric proteins;
• structural comparison of homologous proteins.

Part of the computer laboratory sessions will be devoted to the study of the molecular mechanisms of proteins discussed during the lectures of the Metabolic Biochemistry module.

Readings/Bibliography

Module 1

Required and supplementary reading: The instructor will provide the relevant bibliographic references (review articles and original research papers) covering the topics included in the module. Teaching materials presented during the lectures will be made available to students as PDF files through the University Virtual Learning Environment (https://virtuale.unibo.it [https://virtuale.unibo.it/] ).

Recommended textbooks: Students are encouraged to consult the following textbooks for clarification and further study of the fundamental concepts and principles of cellular and structural biochemistry:

i) Protein Structure and Function – Petsko & Ringe

ii) Biochemistry – Berg, Tymoczko & Stryer

Module 2

The instructor will provide the bibliographic references (review articles and original research papers) related to the laboratory activities. All teaching materials used during the practical sessions will be made available to students as PDF or Word files through the University Virtual Learning Environment (https://virtuale.unibo.it [https://virtuale.unibo.it/].

Recommended textbooks: See the recommended references for Module 1.

Teaching methods

Module 1: The teaching approach is based on classroom lectures, during which the course topics are presented using PowerPoint slides. Although attendance is not compulsory, students are strongly encouraged to attend, as the course content is presented and explained by the instructor and discussed with the class. This teaching approach is designed to facilitate learning and enable students to achieve the intended learning outcomes and acquire the knowledge and skills covered by the module.

The tutorial sessions are held in the classroom and form an integral part of the module. Although attendance is not compulsory, participation in all 12 hours is strongly recommended to fully develop the subject-specific knowledge and transferable skills addressed by the course.

Module 2: The module consists of introductory lectures followed by practical computer-based sessions. The practical sessions are held in a computer laboratory, where students’ complete exercises assigned by the instructor to reinforce and assess their understanding of the topics covered during the lectures.

As concerns the teaching methods of this course unit, all students (including all the international incoming exchange students, i.e. ERASMUS) must attend Module 1, 2 online [https://www.unibo.it/it/servizi-e-opportunita/salute-e-assistenza/salute-e-sicurezza/sicurezza-e-salute-nei-luoghi-di-studio-e-tirocinio].

Students with learning disorders and\or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en ) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, considering the teaching objectives.

Assessment methods

Assessment for the course, which is divided into Modules 1 and 2, is carried out jointly. The assessments for both modules must be taken during the same examination session and within the same exam call. The final grade is calculated as the weighted average of the marks obtained in the two modules. This grade is then combined, as a weighted average, with the grade obtained in the Applied and Functional Genomics to determine the final grade for the Advanced Biochemistry and Genomics integrated course.

In accordance with Article 16, paragraph 5, of the University Teaching Regulations, students may decline the registration of a passing final grade only once.

Module 1 and Module 2

Students may use Artificial Intelligence (AI) tools to support their independent study, for example to deepen their understanding of course topics, clarify concepts, and summarize the scientific literature. However, students remain fully responsible for critically evaluating the accuracy, reliability, and correct interpretation of any information obtained through AI tools. The use of AI tools is not permitted in the preparation or development of the PowerPoint presentation required for the tutorial activitieFurthermore, the use of AI during the in-person examination is strictly prohibited. Any unauthorized use of AI constitutes a violation of academic integrity.

Module 1

Assessment consists of an oral examination including questions covering the topics addressed during the course. The examination is designed to evaluate students' knowledge and understanding of the course content. Students will also be assessed on their ability to relate and integrate different topics, using appropriate scientific terminology and communicating concepts accurately and effectively. The mark obtained in the oral examination will be averaged with the mark awarded for the tutorial presentation. This average will contribute to the final grade for the Metabolic and Structural Biochemistry course (6 CFU).

Module 2

Assessment consists of an oral examination combined with a practical computer-based test. At the beginning of the examination, students are required to give a presentation on a structural biochemistry topic of their choice, demonstrating their ability to use molecular graphics software to analyse crystallographic structures. Students may also be asked questions on the topics covered during both the lectures and the practical sessions to assess their knowledge and understanding.

Students with learning disorders and\or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en ) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, considering the teaching objectives.

Students who have been officially granted working student status should refer to the dedicated University webpage (https://www.unibo.it/it/studiare/guida-alla-scelta-del-corso/conciliare-studio-e-lavoro ) for information on the application procedure and the support measures available.

To obtain the highest grade (30/30), students must demonstrate a comprehensive knowledge of all course topics and present them accurately, in an integrated manner, and using appropriate scientific terminology. Final grades range from 18/30 to 30/30 and are awarded according to the number of questions answered correctly, the student's ability to integrate the different topics covered during the course, and the appropriate use of scientific language. A grade of 18/30 is awarded to students who demonstrate only a basic and superficial knowledge of all course topics, with limited integration of concepts and insufficient command of scientific terminology.

Teaching tools

Module 1

The module content will be delivered through PowerPoint presentations supplemented by diagrams, figures, graphs, scientific articles, and other teaching materials made available to students in digital format via the University Virtual Learning Environment. Whiteboards and other multimedia resources may also be used during lectures to facilitate the understanding of the topics covered.

Module 2

Teaching resources include PowerPoint presentations, instructional materials for learning the molecular graphics software and completing the practical exercises, all provided by the instructor, together with the use of the computer laboratory facilities.

Module 1 and 2:

Students with learning disorders and\or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en ) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, considering the teaching objectives.

Office hours

See the website of Anna Maria Porcelli

See the website of Francesco Francia