82311 - Protein Biochemistry

Learning outcomes

MODULE 1: At the end of the course students possess deep knowledge of protein structure, molecular motors in cells, cell cycle regulation and on the main signal transduction mechanisms.

MODULE 2: At the end of the laboratory module, the student knows the RasTop molecular graphic program for visualize the proteins molecular models deposited in the Protein Data Bank as PDB files. Through the knowledge of molecular graphics, the student will be able to inspect the structure of any protein or multi-protein complex deposited in a database, in order to better understand the relationships between structure and function.

Course contents

MODULE 1 (Prof. Giorgio Sartor)

• Aminoacids: structure, chemical properties;
• Peptidic bond: Primary structure and dihedral angles (phi; psi; omega; chi) and their representation (Ramachandran plot).
• Secondary structure of proteins:
  • Helical structures (alpha-helix; pi-helix; 3-10 helix);
  • Beta-sheet; beta-hairpins; turns;
• Tertiary structure of proteins: motifs and doamins
• Quaternary structure of proteins: examples and classification.
• Molecular motor:
  • Generalities: ATP and AAA
  • ATP-Sinthase - Myosin
  • Miosyn - Dynein - Kinesin - Actin
  • Actin and microtubules
  • Miosyn/Actin and muscolar contraction
  • Dynein and microtubules - bacterial flagellum
• Signal trransuction
  • G-Protein Coupled Receptors: Classification and structure of the heterotrimer
  • G-proteins;receptor to ligaind nteraction; GTPase activity: molecular target o f subunits
  • Protein Kinase C; Adenilate cyclase
  • Receptors with intrinsic tyrosin kinase activity: Sos-Ras-Raf
  • Citokins and recpetros
  • Steroid hormones and receptors
• Cell cycle
  • CDK-cyclin (pRb) regulation acnd their interface with signal transduction mechanisms
  • Structure of CDK-cyclin and interaction with E2F
  • INK4 (p16, p15, p18 e p19) and CIP/KIP (p21, p27 e p57) regulation
• Photophysical mechanisms of bioluminescence and GFP
• Protein turn-over
  • Protease mechanisms (serine proteases; aspartate proteases and metal proteases);
  • Ubiquitine-proteosome system; Calpains;

MODULE 2 (Prof. Luisa Iommarini)

The course includes 2 credits for a total of 30 hours of computer lab, and will be divided into the following exercises (4 hours each):

• Learning of the RasTop program
• Exercise on Ciclines and EGFR receptors
• Exercise on the JAK-STAT system
• Exercise on ionic membrane channels
• Exercise on Actin and Myosin
• Exercise on Calcium ATPase
• Exercise on Kinesine

 

Readings/Bibliography

MODULE 1

Biochimica di Jeremy M. Berg, John L. Tymoczko, Lubert Stryer - Zanichelli
Struttura e funzione delle proteine Gregory A Petsko, Dagmar Ringe - Zanichelli
Teaching notes available on-line

MODULE 2

The necessary material (tutorial to the use of the RasTop program, PDB file needed to display the protein models) will be provided in the computer room by the teacher.

Teaching methods

MODULE 1: Frontal lesson with access to literature references to prepare the presentation.

MODULE 2: Introductory lessons in PowerPoint and practical exercises on the computer, following the guide to the tutorial provided by the teacher.

Assessment methods

The principal learning outcomes that will be assessed are:

- deep knowledge of protein structure

- knowledge of the processes:

• of cellular motors
• of cell cycle regulation
• of cellular mechanisms of signal transduction

- ability to communicate preparing a power point presentation (10 slides max) to be followed by a discussion.

Once completed all the exercises, in the first useful window, the learning of the topics covered will be verified by a multiple choice written exam. The assigned score will go from 0 to 5 points and will be added to the score obtained in the Protein Biochemistry module. This score will be considered valid for a calendar year. The student will be able to improve his score with an oral test, to be held on the same dates of appeal of the Protein Biochemistry module. The student may decide not to participate in the written test. In this case the verification will be only by oral examination.

 

Teaching tools

MODULE 1: Teaching material (teacher's slides) and access to scientific references to be used for the presentation.

MODULe 2: Computer lab, tutorial to the use of the RasTop program provided by the teacher, introductory lectures to the exercises in PowerPoint, PDB files. All the material can be downloaded by the students on their IT supports directly in the classroom.

Links to further information

http://www.gsartor.org/pro/didattica/materiale_bt.html

Office hours

See the website of Giorgio Sartor

See the website of Francesco Francia