Programme

The course aims to provide the following skills and competencies:
Cultural competences (Knowledge of :) The Course aims to provide students with basic knowledge relating to thermodynamics and the kinetics of biological processes, particularly in relation to experimental activities in the laboratory.
Methodological skills (Know How to:) acquire and use experimental data relating to the study of interactions between proteins and ligands, enzyme kinetics and kinetic of binding
The programs is divided into:
1) Study of the interaction between receptors and ligands: methods at equilibrium and transient kinetics:
a) At equilibrium (thermodynamic parameters: Kd: dissociation constant at equilibrium, cooperativity, number of binding sites)
b) Rapid kinetics (kinetic parameters: k: velocity constants)
2) Study of enzymatic activity: steady state kinetics
a) In Steady State (when [ES] is almost constant during experimental observation)
b) In the presence of inhibitors
3) Time-resolved optical spectroscopy and complex kinetics
4) Absorption spectroscopy, fluorescence and circular dichroism

Core Documentation

Recommended textbooks:
M. C. Bonaccorsi di Patti et al. Metodologie Biochimiche - Casa Editrice Ambrosiana
Ninfa/Ballou Metodologie di base per la Biochimica e la Biotecnologia - ed. Zanichelli
Reed et al. Metodologie di Base per le Scienze Biomolecolari- ed. Zanichelli
P. Silvestroni, Fondamenti di chimica - Casa Editrice Ambrosiana
D.M. Etter Introduction to MATLAB 7– Pearson Education, Inc.

Software to use
EXCEL (Office) or CALC (Open Office) * (for linear methods)
MATLAB (Mathworks) or OCTAVE (GNU Octave) * (for spectral analysis and non-linear methods)
GEPASI (P. Mendes et al.) * Or COPASI (Copasi dev. Group) * (for complex reactions)
(*) indicates free software
Lecture notes and calculation exercises will be provided

The professor receives every day from 8.00 to 9.00 or by appointment via e-mail: giovanni.antonini@uniroma3.it

Type of delivery of the course

The course will take place with lectures and numerical exercises carried out in the classroom by using PCs and specific softwares (Excel / Matlab / Octave) The course could also be followed on-line

Type of evaluation

The practical test will consist of processing the experimental data by using PCs and specific programs. Both the achievement of the correct results and the method of carrying out the exercise will be evaluated. Half of the overall score will be assigned to the practical test. The oral exam will consist in the discussion with the teacher on the theory underlying the binding experiments, the enzymatic kinetics and the binding kinetics and on the modalities of carrying out such experiments. Mid-term tests will be carried out without scoring