Cellular and Molecular Biology

BIOPHYSICS

BIOPHYSICS

Academic year 2021/2022

Sommario del corso

• Course objectives
• Results of learning outcomes
• Course delivery
• Learning assessment methods
• Support activities
• Program
• Suggested textbooks and readings
• Teaching tools

Course objectives

This teaching contributes to the learning objectives included into the Biomedical and Biomolecular area of the Master in Cellular and Molecular Biology, providing knowledge and applicative abilities to critically investigate biophysical functions of the cells. In particular, detailed biophysical features of ion channels will be discussed from the quantitative and experimental points of view. The course aims to foster the training of students in the application of the physical sciences and engineering to fundamental biological questions at the molecular, cellular, and systems levels. Additional objective points to a quantitative analysis of some conceptual and technical approaches to signal transduction mechanisms from a molecular and postgenomic point of view, with particular emphasis on selected themes.

Results of learning outcomes

• Using multiple experimental and computational tools to solve a biological problem in cell physiology
• Extending and applying knowledge of Biophysics to new contexts
• Re-analyzing information
• Selecting robust information from a variety of sources
• Making reasoned predictions and generalizations from experimental evidence and theoretical information
• Drawing valid conclusions and giving explanations supported by evidence/justification
• Drawing on knowledge and understanding of Biophysics to make accurate statements, describe complex information, provide detailed explanations and integrate knowledge
• Critically evaluating scientific publications and media reports
• Discuss the strength and limitations of the results published on research papers, eventually identifying sources of errors and biases
• Communicating biophysical findings and concepts fully, appropriately, and using a variety of different modalities
• Understanding the mathematical formalism used in Biophysics to model specific cellular dynamics

Course delivery

Teaching includes 6 CFUs (48 hours of face-to-face lectures).

The lessons will be held in presence and in streaming, recorded and published on the Moodle platform.

In particular, the teaching will be delivered in the form of: 

1. Lectures, interactive simulations, and discussion in presence on the topics of the program with critical approach and in relation to the most recent literature;
2. Recordings of the streaming of lectures uploaded on the Moodle platform;
3. Integrative activities:
   • specific readings available on Moodle platform;
   • exercises and self-assessment questions provided on Moodle platform;
   • in-depth videos on specific topics uploaded on the Moodle platform.

Learning assessment methods

The final learning assessment will be held in presence, in written form (Moodle platform) with optional oral integration (relative weight written/oral 3/1).

Students belonging to specific categories will be allowed to participate in online written exams (webex platform), followed by a mandatory oral exam.

Support activities

Supplementary activities

1. selected readings provided on the Moodle platform;

2. online exercises for self-evaluation provided on the Moodle platform;

3. in-depth videos on specific topics uploaded to the Moodle platform.

Program

The main objective of the course is to convey to the students the ability to

1. critically analyze scientific papers on biophysical topics;
2. design integrative experimental protocols to address functional questions, taking into account the strengths and limitations of the different approaches;
3. use mathematical and computational tools to model basic biophysical systems.

Topics:

• Ion Fluxes: from Fick to Nernst-Planck. Nernst Law: Equilibrium and Reversal Potential. GHK Law: Membrane Potential. Equivalent circuits: resistance, capacitance, conductance. Electrical signals: amplitude and frequency coding. Spatial propagation. Receptor potentials. Postsynaptic potentials. Integration. Ionic basis of Action Potential and excitability in neurons and muscles.
• Interactive simulation for the equilibrium potential of multiple ion species and membrane resting potential using Nernst and GHK equations.
• From macro to micro bio-electrical events. Electrophysiology: experimental measurement of ion fluxes through biological membranes. History and techniques. Voltage clamp and the Hodgkin-Huxley model for the ionic basis of action potential. Patch Clamp. Single channel kinetics. Gating, conductance, permeability, selectivity.
• Interactive simulation of the action potential according to the HH-model, under both voltage- and current-clamp configurations.
• Structure and function of ion channels. Ion channels classification: leak channels, gated channels. Common properties of ion channels: gating and selectivity. Molecular basis of voltage sensor. Molecular basis of voltage-gated channels inactivation. Molecular basis of ligand-gated mechanism. Molecular basis of ion selectivity.
• Markov Chains as a useful mathematical tool to model state transitions in ion channels and ionotropic receptors.
• Intracellular messengers. Interplay between cAMP and Ca²⁺ signals in live cells.
• Mathematical modeling of the cellular calcium toolkit and calcium dynamics.
• Cell volume regulation. Water fluxes and aquaporins.
• Genetic approach to control living cells. Optogenetics, chemogenetics and magnetogenetics. Mechanosensitive channels: Piezo and TRP channels.

All the video-lectures, recorded webex streming lessons and discussions, slides, selected papers, e-books and websites are fully available on Moodle.

• Teaching materials
• Exams and finals
• Go to Moodle
• Visit the forums