82318 - BIOCHIMICA CELLULARE E STRUTTURALE

Academic Year 2018/2019

  • Moduli: Anna Maria Porcelli (Modulo 1) Francesco Francia (Modulo 2)
  • Teaching Mode: Traditional lectures (Modulo 1) Traditional lectures (Modulo 2)
  • Campus: Bologna
  • Corso: Second cycle degree programme (LM) in Molecular and industrial biotechnology (cod. 9213)

Learning outcomes

At the end of this tutorial, the student will acquire deepened knowledge on: protein structural changes involved in important biochemical functions like catalysis, signal transduction, DNA-protein interactions. The student will be able to advantageously discuss about cellular biochemistry, to understand the methodology utilized in cellular biochemistry, to propose experimental protocols for the study of specific cellular functions.

In the informatics hall, the student will get a basic know how of a molecular graphic program for the analysis of PDB files and for planning mutagenesis experiments based on the detailed study of the proteins structure.

Course contents

Part 1: Cellular Biochemistry

Intracellular signaling: Structural and molecular signatures of the 7TM receptors; structural interactions between 7TM receptors and heterotrimeric G proteins; molecular mechanisms mediated by Gs proteins; structure and function of adenylate cyclase; signaling mediated by cyclic AMP; structure and function of protein kinase A; regulation of protein kinase A by cAMP; the scaffold proteins: AKAPs; in vivo measurements of cyclic AMP levels: use and applications of FRET methodology; structure and function of Grk proteins; molecular interaction between Grk and arrestin; structure and function of arrestin during receptor desensitization, endocytosis and cell signaling pathways.

Mitochondria: Ultrastructural view of mitochondria; mitochondrial cristae as an example of supramolecular organization of biological membranes; morphological and functional heterogeneity of mitochondrial network; methodologies for the analysis of the structure and function (fluorescent probes specific for mitochondria and their use for the analysis of mitochondrial reticulum morphology and mitochondrial membrane potential). Molecular organization of mitochondrial DNA and its role in mitochondrial disorders and cancer; role of oxidative phosphorylation and TCA in metabolic and hypoxic reprogramming in tumor cells; metabolic enzymes and oncometabolites in regulating factor HIF1a and tumorigenesis; dynamics of mitochondrial reticulum: mitofusins, OPA1 and DRP1 in the regulation of fission and fusion processes; quality control of mitochondria: role of PINK1 and Parkin in the regulation of mitophagy.

Calcium as an universal and versatile second messenger: Concept of "calcium-signaling toolkit"; transporters and channels in cell membranes; molecular signature of phospholipases C; structure of IP3 and ryanodine receptors; temporal and spatial aspects of calcium signaling; calcium homeostasis in the mitochondria; calcium microdomains between mitochondria and ER; proteins involved in structural and functional maintenance of MAMs subcompartiment; role of MAMs in Ca2+ homeostasis between mitochondria and endoplasmic reticulum and in the biosynthesis of some lipids.

Part 2: Structural Biochemistry

Part of the tutorial will take place in the informatics hall and dedicated to the following topics:-know how of the main nucleic acid and protein databank and retrieval of the searched information (structure, function, sequence, omology); -learning of the basic functions of a molecular graphics program to visualize and manipulate crystalloghraphic data; -key factors of secondary, tertiary and quaternary protein structure organization, Ramachandran plot; super-secondary structure; ligand induced conformational changes; manipulation of structure to evaluate in silico induced mutations; structural comparison between homologous proteins; -studies on the molecular mechanism utilized by proteins mentioned in the associated lessons of Cellular Biochemistry (Part 1).

Readings/Bibliography

Part 1:

Bibliography

The teacher will provide references (reviews and original papers). Lectures slides will be available to the students, after downloading the PDF files from the IOL platform (https://iol.unibo.it/).

Readings

The teacher prompts the consultation of the following textbooks for clarification /deepening of concepts and basic principles of cellular and structural biochemistry

“Cellule” Lewin et al (Zanichelli, terza edizione)

“Struttura e Funzione delle proteine” Petsko & Ringe (Zanichelli)

“I principi di biochimica di Lehninger” Nelson and Cox (Zanichelli)

Part 2:

students can download on their computer supports all the material used during the exercises (guides, work sheets, scientific articles, introductory lessons) directly from the computers used in the bioinformatics classroom

Teaching methods

Part 1: The teaching method used is based on lectures during which the contents of the program will be illustrated using PowerPoint slides. Attendance to such lessons is not mandatory but it is highly recommended as the contents of the program will be presented and explained by the teacher and discussed with the whole class. This teaching method will facilitate the learning of contents and will allow the achievement of the knowledge and skills by the whole class. Students are encouraged to communicate to the teacher any requirements by e-mail as soon as possible. This will allow teacher to evaluate which teaching support tools are most adequate to make the training course accessible to all students of the course.

Part 2: Lectures and practices in the informatics classroom.

Assessment methods

Part 1: the learning test assessment will consist of an interview that provides at least 3 questions related to the topics covered in the program in order to verify and evaluate the student's knowledge of the contents developed and discussed during the lessons. Moreover, during the interview the student's ability to link and integrate the various topics with particular attention to the scientific terminology used and to correct and accurate exposure will be evaluated.

Part 2: interview aimed at evaluating the comprehension of the topics covered during the exercises in the computer room. The student will begin the exam presenting a report on a crystallized protein structure chosen by him using a power point presentation with images produced using the molecular graphics program learned.

The learning assessment of Part 1 and Part 2must be verified in the same exam session. In order to obtain a final grade of 30/30 with honors, the student must show that he/she knows and has deepened, using the textbooks and bibliography indicated by the teacher, all the topics covered during the lessons. Further, they must explain and integrate the topics with scientific language properties. To obtain a final grade of 30/30, the student must explain contents covered during the lessons and show the ability to correctly integrate them with scientific language properties. The final grade will be scaled from 30/30 to 18/30 based on the number of questions to which the student answers and her/his ability to integrate the topics with scientific properties language. In particular, to obtain a grade of 18/30 the student must show to have superficial knowledge of all the contents discussed during the lessons and not be able to integrate them with scientific language properties. The vote obtained will be considered valid within the calendar year and will contribute to the final mark, determined as the weighted average of the different Parts of the 82318 - BIOCHIMICA CELLULARE E STRUTTURALE teaching.

Teaching tools

Part 1: The contents of the lectures will be presented using PowerPoint slides and discussed with the whole class through appropriate teaching materials. The students are encouraged to communicate to the teacher any requirements by e-mail as soon as possible. This will allow teacher to evaluate which teaching support tools are most adequate to make the training course accessible to all students of the course.

Part 2: Power point lectures, molecular graphic program tutorial, practical exercises in the informatics classroom. Students are asked to inform the teacher of any needs by e-mail as soon as possible. This will allow the teacher to evaluate which teaching support tools are most adequate to make the training course accessible to all students of the course.

Office hours

See the website of Francesco Francia

See the website of Anna Maria Porcelli