82311 - Protein Biochemistry

Learning outcomes

MODULE 1: By the end of the course students possess deep knowledge of protein structure, assembly and turnover. Moreover, students will understand the structural bases of energy production, cell cycle regulation, and key 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. Luisa Iommarini)

The 6 CFU module of frontal teaching includes the following topics:

BASICS OF PROTEIN STRUCTURE:

- Amino acids: their structure, chemical properties, acid-base properties.

- Formation of the peptide bond: primary structure of proteins.

- Secondary structure of proteins: dihedral angles and their representation, helical structures and their geometric and structural classifications, sheet structures.

- Tertiary structure of proteins and classification into motifs and domains.

- Quaternary structure of proteins with some structural examples.

- Online resources for studying proteins, their structure, and interactions.

THE LIFE CYCLE OF PROTEINS:

- Protein synthesis and folding.

- Post-translational modifications and protein sorting.

- Proteolysis and turnover.

- Protein engineering.

FROM STRUCTURE TO FUNCTION:

1. Signal Transduction Pathways:

- General concepts of cellular signaling.

- G protein-coupled receptors: classification and general structure of receptors, types and structure of G proteins, ligand-receptor interaction, G protein activation mechanism and their GTPase activity; molecular targets of the subunits and activation of downstream pathways.

- Receptors with intrinsic tyrosine kinase activity: structural diversity, activation mechanisms, and molecular targets.

- Cytokines and their receptors: structural characteristics, activation mechanisms, and molecular targets.

- Nuclear receptors for steroid hormones: structural characteristics, activation mechanisms, and molecular targets.

- Ion receptors: structural characteristics, activation mechanisms, and molecular targets.

2. Structural Bases of Cell Cycle Regulation:

- CDK-cyclin regulation and their interface with signal transduction mechanisms, structure of CDK-cyclin complexes, and interaction with E2F.

- Regulation through INK4 (p16, p15, p18, and p19) and CIP/KIP (p21, p27, and p57).

3. Structural and Functional Organization of Oxidative Phosphorylation Complexes:

- Structure and function of isolated OXPHOS complexes.

- Supramolecular organization of respiratory complexes and ATP synthase dimers and their functions.

MODULE 2 (Prof. Francesco Francia)

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 G protein

Readings/Bibliography

MODULE 1

- Biochimica by Jeremy M. Berg, John L. Tymoczko, Lubert Stryer – Zanichelli

- Struttura e funzione delle proteine by Gregory A Petsko, Dagmar Ringe – Zanichelli

- Introduzione allo studio delle proteine by Marcello Duranti - Zanichelli

- Material provided by the lecturer available online on Virtuale.

MODULE 2

The necessary material (guide to using the RasTop program, PDB files needed to visualize protein models) will be provided by the lecturer.

Teaching methods

MODULE 1: Lectures using PowerPoint.

MODULE 2: Introductory lessons in PowerPoint and practical computer exercises, following exercise guide sheets provided by the lecturer.

Assessment methods

MODULE 1

The final evaluation aims to define the achievement of the teaching objectives and consists of a written test with open and multiple-choice questions. The score will be in thirtieths and will be averaged with the other modules of the course. The student can improve their score with an oral exam. The optional oral exam (at the student's request) will consist of a discussion of the written test and an in-depth examination of the topics.

MODULE 2

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 score assigned will be out of thirty and will be a weighted average with the other modules of the course. In order to take advantage of the only written test scheduled for each academic year, attendance at at least 4 exercises is required. The student will be able to improve his score with an oral test. The student may also decide not to participate in the written test. In this case the verification will only be through an oral exam, which must also be taken by students who have attended fewer than 4 exercises.

Teaching tools

MODULE 1: The presentations used during the lessons and the scientific publications used for their preparation will be available on Virtuale.

MODULE 2: Computer lab, guide to using the RasTop program provided by the lecturer, introductory lessons to the exercises in PowerPoint, PDB files. All material can be downloaded by students onto their devices directly in the exercise room or on Virtuale.

Office hours

See the website of Luisa Iommarini

See the website of Francesco Francia