HIGHLIGHTS IN BIOPHYSICS
cod. 1006148

Academic year 2016/17
3° year of course - Second semester
Professor
ABBRUZZETTI Stefania
Academic discipline
Fisica applicata (a beni culturali, ambientali, biologia e medicina) (FIS/07)
Field
A scelta dello studente
Type of training activity
Student's choice
52 hours
of face-to-face activities
6 credits
hub: PARMA
course unit
in - - -

Learning objectives

This course is intended to give an overview on the modern molecular biophysics.
The aim of this course is to introduce in a qualitative manner, modern spectroscopic techniques and show selected applications to relevant current topics. It is intended to also show how physical methods can become extremely valuable tools for understanding biological processes.
The selection of topics is intended to guide students to make a more thoughtful choice for their future studies, possibly in Biophysics. It is also intended to give students in Biological Sciences an overview on the modern experimental methods that are available to tackle very complex biological problems.

Knowledge and understanding
The student should prove to know and understand the topics covered by the course, as indicated in the following program.

Applying knowledge and understanding
Students, at the end of the course, will have achieved the ability to apply their knowledge to address the study of a biophysical topic. More specifically: understanding papers of the most recent literature, exploring theoretical and experimental biophysical issues, developing and supporting basic reasoning. The student will have to show to be able to describe the processes of biological systems in a framework of fundamental physics laws, understand the need for a quantitative analysis of the observed processes and possess the ability to develop a mechanistic model to describe a molecular process.

Making judgements
Students, at the end of the course, will have to demonstrate that they have improved their critical thinking skills and judgment capability in particular to collect and interpret data, elaborate on biophysical issues, communicate ideas-problems-solutions in order to develop the learning skills that are necessary to undertake further studies in biophysics or carry out professional activities related to it.

Communication skills
Students, at the end of the course, will have to demonstrate the ability to communicate ideas-problems-solutions about biophysical issues and present them in a clear, concise and effective way. Communication skills will be practiced in class, involving students in the discussion of the covered topics, and during laboratory exercises. Small groups of students will be encouraged to develop their ability to work in groups, discuss possible problems that may arise during measurements, find solutions and alternative methods which the students will have to learn to share with their colleagues and explain to group members and the teacher.

Learning skills
Students, at the end of the course, will have to demonstrate that they have started a path of understanding of the main biophysical issues in any form of expression, comprehension of the most recent research results and translation into professional actions, that should be considered as self-study, research and design of an experiment.

Prerequisites

Basics of calculus, classical physics and chemistry.

Course unit content

1. A modern vision of biophysics: living systems in a framework of physical laws
2. Qualitative description of proteins
Function, structure, and dynamics
3. Spectroscopic methods for the study of macromolecules: theory and practice
4. Qualitative introduction to modern techniques based on radiation-matter interaction, single molecules spectroscopy and super-resolution microscopy.
5. Data analysis: using numerical methods in order to model biophysical processes
6. Elements of photophysics

Practice in lab on steady-state spectroscopic methods (absorption and fluorescence) and data analysis (24 hours)

Full programme

A modern vision of biophysics: living systems in a framework of physical laws
Microscopic and macroscopic world
From Maxwell-Boltzmann to Eyring and Arrhenius equation: the activation energy of a chemical process

Qualitative description of proteins
The structure of proteins
Determination of protein structure
Protein folding: chaperons, Levinthal paradox, free energy landscape, experimental techniques for studying protein folding (absorbance-fluorescence, circular dichroism, stopped flow, laser flash photolysis)
Kinetics of protein folding: time scales, T-jump (technique and examples)
Function of proteins
Relations between function, structure, and dynamics: the globin super-family as an example

Qualitative introduction to modern techniques based on radiation-matter interaction, single molecules spectroscopy and super-resolution microscopy.
Spectroscopic methods for the study of macromolecules: theory and practice
Data analysis: using numerical methods in order to model biophysical processes

A bit of photophysics:
GFP: the revolution of cellular biology
Photoactivable compounds
Photo-chromic and photo-switchable proteins
Photosensitizers and photodynamic therapy

Practice in lab on steady-state spectroscopic methods (absorption and fluorescence) and data analysis (24 hours)

Bibliography

Papers from recent literature and slides of the lessons. "Protein structure and function" G.A. Petsko, D. Ringe, Zanichelli; "Biological Physics. Energy, Information, Life. Updated first edition" Philip Nelson, Palgrave Macmillan and WH Freeman ed.; "Principles of fluorescence spectroscopy" J. Lakowicz, Kluver Academic/Plenum Publishers

Teaching methods

Lessons and practice in the lab.

Assessment methods and criteria

The exam consists in a talk by elaborating on one of the topics covered by the course.
The student will be evaluated based on the achievement of the objectives specified in details, namely the extent to which:
1
the student understands similarities and differences between biophysical systems, can explain experimental data, and methodologies useful to biophysics
2
is able to comprehend the essential aspects of papers in the most recent literature, perform simple experiments, analyze the data and summarize them, use the results to model the biophysical system.

Other information

On Tuesday, 12:30-14:30 p.m, or in any other day, by appointment (Email) at the Department of Physics and Earth Sciences.