MOLECULAR BIOPHYSICS
cod. 1006011

Academic year 2021/22
1° year of course - First semester
Professor
ABBRUZZETTI Stefania
Academic discipline
Fisica della materia (FIS/03)
Field
Microfisico e della struttura della materia
Type of training activity
Characterising
52 hours
of face-to-face activities
6 credits
hub: PARMA
course unit
in ITALIAN

Learning objectives

Knowledge and understanding
At the end of the course the student is expected to be able to:
- know and understand the topics of molecular biophysics discussed in the course
- remember and compare the main characteristics of the experimental techniques introduced in class
- to exemplify physical systems and molecular mechanisms to which the methodologies investigated may be applied (experimental and theoretical)
- to understand the context and even advanced concepts of papers of the most recent literature in the field of molecular biophysics
- know and understand issues that extend those addressed in the first level courses and that allow to develop original ideas

Applying knowledge and understanding
At the end of the course the student is expected to be able to:
- apply the acquired knowledge to address the theoretical study of a biophysical topic
- apply the acquired knowledge to identify the experimental methodology suitable for studying a system of biophysical interest, even new and inserted in a wider context
- apply the acquired knowledge to identify the methodology, the model and the approximations to analyze acquired experimental data and apply it with mastery
- apply the acquired knowledge to elaborate the general scheme of a mechanistic model that describes a molecular process
- carry out a steady state absorption and fluorescence experiment
- perform all the calculations required in the data acquisition and analysis with a good degree of autonomy

Making judgements
At the end of the course the student is expected to be able to:
- analyze from a quantitative point of view relevant biophysical processes both at a theoretical and experimental level
- evaluate the elements to develop a mechanistic model that describes a molecular process
- evaluate with a critical sense the limits of validity of the developed models, the advantages / disadvantages of the studied experimental methodologies, the similarities and the differences between the studied physical systems
- critically assess the experimental results obtained

Communication skills
At the end of the course the student is expected to be able to:
- communicate ideas-problems-solutions on biophysical issues in a clear, concise and effective way
- explain the properties that define the structure, dynamics and function of protein systems
- explain the theoretical characteristics of the introduced experimental photo-physical methodologies
- explain the various phases of an absorption and fluorescence measurement and of the relative data analysis
- explain to the group members and the teacher the experimental issues occurred during practical exercises

Learning skills
- connect different issues addressed in the course and in others
- examine in depth biophysical topics discussed in mentioned scientific papers and develop alternative solutions and methodologies
- understand the potentiality of research in Biophysics

Prerequisites

Basics of classical and quantum physics and chemistry.

Course unit content

The course shows how the physical methodologies can provide fundamental tools for understanding biological phenomena and how molecular biophysics is an area of highly interdisciplinary physics but different from biology.
The subject of radiation-matter interaction is dealt with and, therefore, a photo-physical approach to the identification of the molecular mechanisms underlying processes of relevance in the cellular context in evidenced. The course then illustrates what constitutes modern molecular biophysics, in particular bio-photonics, deepening a selection of topics of current interest in Biophysics and some analysis techniques based on spectroscopic methods. The problem of data analysis and the evaluation of mechanistic models for the definition of molecular mechanisms is also explored.

Therefore, it is possible to identify some macro-topics regarding the lectures, completed by a part of the laboratory exercise:
- Chemical-physical properties of protein systems
- Functional properties of proteins
- Radiation-matter interaction: photophysical properties of proteins and nucleic acids
- Modeling of biophysical processes

Practice in lab (students divided into small groups) organized in:
Absorption and fluorescence (steady state)
Data analysis

Full programme

1 The protein system: the relationship between structure, dynamics and function. The function of proteins (binding, enzymatic catalysis, molecular switch, structural). Enzymatic catalysis and binding. The dynamics of proteins.
2 Chemical-physical basics of biophysics. Chemical kinetics: order of a reaction, transition state, rate limiting step. The fundamental interactions in biophysics.
3 Radiation-matter interaction: basic principles of photo-physics.
Absorption
Fermi's golden rule, transition dipole moment, Born-Oppenheimer approximation, selection rules, Franck-Condon principle.
Spectrophotometer. Lambert Beer's Law.
Absorption of proteins and nucleic acids.
Fluorescence
Radiative and non-radiative transitions. Fluorescence. Fluorescence quantum yield. Solvent effect. Kinetics of photophysical processes. Phosphorescence.
Spectrofluorimeter. Emission and excitation spectra.
Fluorescence of chromophores and proteins.
Fluorescence anisotropy.
Fluorescence quenching.
Förster Resonance Energy Transfer.
Circular dichroism of proteins.
Vibrational spectroscopy (only some hints): Vibrational spectra and Raman, Vibrational protein spectroscopy.
4 Modeling biophysical processes: analytical and numerical methods
Mechanistic models to define the relationship between structure-dynamics-function in proteins

Practice in lab (students divided into small groups) organized in:
Absorption and fluorescence at steady state
Data analysis

Bibliography

Papers from recent literature and slides of the lessons (on Elly platform)
"Struttura e funzione delle proteine" G.A. Petsko, D. Ringe, Zanichelli;
"Principles of fluorescence spectroscopy" J. Lakowicz, Kluver Academic/Plenum Publishers
“Proteins” T.E. Creighton, W.H. Freeman and Company

Teaching methods

The lessons will be held in person. The recording of lessons will be available for students attending the course. There will be some laboratory practice where students will have to apply theory to projects proposed and developed according to the methodological criteria outlined in lectures and in bibliographic and didactic material. Some detailed topics will be available on the Elly platform.
The slides used to support lessons and recording will be uploaded at the end of the lesson on the Elly platform. Slides are considered an integral part of teaching material. It reminds non-attending students to check the available teaching material and information provided by the teacher through the Elly platform.

Assessment methods and criteria

There will be a continuous ongoing but informal training evaluation by discussing with the classroom during the Lessons, or at the beginning of the next lesson to see how much the previously explained concepts have been understood. The exam consists in:

1) preparation of laboratory reports for the exercises carried out. Each report will be corrected and discussed with the students, but will be evaluated overall on a scale of 0-30. Honors is given in the case of achieving the highest score on each item and the mastery of the disciplinary glossary.

2) a written exam in which the student will be asked to illustrate three topics discussed during the lessons. The written exam is evaluated with a scale of 0-30, 10 points for each of the three questions. Honors is given in the case of achieving the highest score on each item and the mastery of the disciplinary glossary. The result of the written exam vote is communicated within a week. Please note that the on-line application to the exam is MANDATORY.
The final grade will result considering the marks assigned for the reports, the written exam and the ongoing evaluation. The predominant weight will be assigned to the written exam.

The student will be evaluated based on the achievement of the objectives previously specified in details.
With a view to verifying whether such knowledge and level of competences have been achieved, the aim of the laboratory reports (1) and of the oral exam (2) is to evaluate the ability of the student to re-elaborate, reformulate such knowledge as well as his/her ability to apply the knowledge and skills gained, apply them and examine in depth the problem of the data acquisition and aanlysis (1) and fundamental topics in biophysics using some of the most recent literature papers in biophysics (2).
The evaluation will be considered insufficient if the student is found lacking in any minimum knowledge of topics and specific language; if he/she doesn’t demonstrate skills in analyzing the experimental data (1) and fundamental properties of biophysical systems (2) and formulating independent critical judgements.
A final evaluation of sufficient (18-23/30) is determined if the student is able to show that he/she has mastered the basic notions and contents of the course and is sufficiently able to apply and express them, even simply, to discuss the experiments (1) and the fundamental properties of biophysical systems (2) and formulate independent critical judgements and opinions.
An average mark is awarded to the student who can demonstrate he/she reaches the above learning aims at a more than sufficient (24-25/30) or good (26-27/30) level. The highest marks ( 28-30/30 and merit) are likewise awarded on the basis of a very good to excellent level.

Other information

On Friday, 09:30-11:30 p.m, or in any other day, by appointment (Email).