93357 - Cellular and Structural Biochemistry

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. The experience with the experimental cellular biochemistry laboratory will allow students to achieve an overall training in the handling of animal cell cultures and basic biochemical methodologies.

Course contents

Part 1: Cellular Biochemistry

Didactic activity planning: introduction to the following aspects of the didactic module: learning outcomes; course contents; readings/bibliography; teaching methods and tools, assessment methods; when and how to meet students (office hours),

During the Cellular Biochemistry module the main biochemical processes responsible for the biosynthesis of molecules with industrial applications in engineered cell models will be analyzed and discussed.

 Part 2: Structural Biochemistry

The first 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:

Necessary educational supports

Students will be provided with further recommended bibliographical references (reviews and original papers). The educational supports will be provided as PDF files and will be available to the students on the Virtual Learning Environment (https://virtuale.unibo.it).

Advised educational supports

The teacher advises students to consult the following textbooks for clarifications on the basic concepts of cellular and structural biochemistry: i) Protein Structure and Function - Petsko and Ringe; ii) Biochemistry - Berg, Tymoczko and  Stryer.

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 or from the teaching site Virtuale.

Teaching methods

Teaching methods

Part 1: The teaching method used is based on lectures during which the contents of the program will be illustrated with 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 will be 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 the teacher to evaluate which teaching support tools are most adequate to make the training course accessible to all students.

Part 2: Lectures and practices in the informatics classroom.

Assessment methods

Part 1: The learning test assessment  will consist of an interview that provides open questions 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 integrate and link the different topics with particular attention to the use of scientific terminology and to the proper 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 2 is verified in the same exam session.

The vote obtained for each teaching Part will contribute to the final mark, determined as the weighted average of the two teaching modules of the Cellular and Structural Biochemistry course. The final vote will be considered valid by the calendar. In order to obtain a final grade of 30/30 with honors, the student must show to know in depth all the topics covered during the lessons. Further, the student must explain and integrate the topics with properties of scientific language. To obtain a final grade of 30/30, the student must explain contents covered during the lessons and show the ability to properly integrate them with properties of scientific language. The final grade will be scaled from 30/30 to 18/30 based on the number of questions to which the student is able to answer and on her/his ability to integrate the topics with properties of scientific language. In particular, to obtain the minimum grade of 18/30 the student must show to have basic knowledge of all the contents discussed during the lessons and not be able to integrate them with properties of scientific language.

Teaching tools

Part 1: 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. The contents of the lectures will be presented using PowerPoint slides and discussed with the whole class through appropriate teaching materials.

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. The exercises will be available through a link to the online teaching site Virtuale.

Office hours

See the website of Anna Maria Porcelli

See the website of Francesco Francia