First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
Faculty of Medicine and Surgery
MEDICINE AND SURGERY
Course unit
PROTEIN STRUCTURE AND FUNCTION
MEN1038624, A.A. 2013/14

Information concerning the students who enrolled in A.Y. 2012/13

Information on the course unit
Degree course 6 years single cycle degree in
MEDICINE AND SURGERY
ME1727, Degree course structure A.Y. 2009/10, A.Y. 2013/14
N0
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Degree course track Common track
Number of ECTS credits allocated 4.0
Type of assessment Mark
Course unit English denomination PROTEIN STRUCTURE AND FUNCTION
Department of reference Department of Medicine
Mandatory attendance
Language of instruction Italian
Branch PADOVA
Single Course unit The Course unit CANNOT be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge FULVIO URSINI BIO/10
Other lecturers STEFANO TOPPO BIO/10

Mutuating
Course unit code Course unit name Teacher in charge Degree course code
MEN1038624 PROTEIN STRUCTURE AND FUNCTION FULVIO URSINI ME1726

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines BIO/10 Biochemistry 4.0

Course unit organization
Period First semester
Year 2nd Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Lecture 4.0 40 60.0 No turn

Calendar
Start of activities 01/10/2013
End of activities 25/01/2014
Show course schedule 2019/20 Reg.2015 course timetable

Examination board
Board From To Members of the board
1 STRUTTURA E FUNZIONE DELLE PROTEINE - COMMISSIONE D'ESAME A.A. 2013/2014 01/10/2013 30/09/2017 URSINI FULVIO (Presidente)
TOPPO STEFANO (Membro Effettivo)

Syllabus
Prerequisites: Good knowledge of spoken and written English is required
Target skills and knowledge: The course aims to provide students with basic concepts of structure and function of proteins. Students will acquire the knowledge of the most advanced technologies of Mass Spectrometry in proteomics.
Examination methods: The examination is typically 1 hour and a half in length and closed book in format. The test is with open-ended questions on the entire contents of the course. Also planned seminar activity and evaluation
Assessment criteria: The objective is to assess students’ ability to engage critically with the material covered on the course and provide personal interpretation
Course unit contents: BIOCHEMICAL CONCEPTS
1) Basic concepts on general properties of amino acids, secondary structures, protein domains, and common folds
2) Interactions forces in proteins from quantum chemistry to molecular mechanics and dynamics
3) Introduction to force fields in molecular mechanics and the different interaction forces bonded and non-bonded.
4) Protein folding from Anfisen to modern theories: hydrophobic collapse, diffusion and collision, funnel theories and the Levinthal’s paradox. Lattice simulations in a Hydrophobic Polar model
5) Protein folding in the cell: Folding Accessory proteins and mechanism in Eukaryotes and Prokaryotes: PDI, GroEL/GroES, Heat Shock Proteins. Brief introduction to ER stress and protein misfolding, amyloid formation
MASS SPECTROMETRY IN PROTEOMICS
1) Mass spectrometry MS: the basic principles of proteomics techniques up to mass spectrometry present era
2) Description of MS instrumentations
a. ESI and MALDI sources
b. Mass Analyzers: Quadrupole, stability diagram, Mathieu equations
c. 3D and linear Ion Trap: stability diagram and working process as ion ejections and fragmentation
d. Time Of Flight and equations of ion trajectories
e. Orbitrap basic principles
3) Mass Spectrum interpretation: m/z ion detection, isotope distribution, mass accuracy, resolution, Deconvolution and charge state determination
4) Fragmentation rules and ion series
5) MS fingerprinting and MS/MS data identification analysis
6) Interpreting a MS/MS spectrum: algorithms techniques implemented in Mascot and Sequest, PeptideProphet
7) Parametric and non-parametric methods, FDR, decoy sets, spectral clustering
8) Mass spectrometry quantification techniques: label free, tag-based techniques
9) Signal processing, statistical analysis, normalization, Clustering and classification, Gene Set Enrichment Analysis (GSEA), Hypergeometric testing, Statistical experiment design
Planned learning activities and teaching methods: lectures and learning through the preparation of journal clubs
Additional notes about suggested reading: material provided in class. Slides of the lectures
Textbooks (and optional supplementary readings)