Course program, A.Y. 2016-17
| Lesson | Date | Topics | Linked slides and useful links |
| 1 | March 3rd, 2017 | introduction to biophysics. Diffusion processes in biology. The diffusion equation and its solutions. The main structural elements in eukaryotic cells. Membranes. | |
| 2 | March 10th, 2017 |
Dimensional reduction in the diffusion inside cells. Diffusion and potential theory. Absorbing sphere. Receptors on a spherical cell. Reaction-diffusion and morphogenesis. | |
| 3 | March 17th, 2017 |
The (bio)physics of water. The properties of water. Water in the environment. Energy and length scales in the cellular environment. Colloids. The Debye-Hückel theory. The hydrogen bond. Configurational entropy of ice. Dynamics of the hydrogen bond in water: water ions and the Grotthuss mechanism. Ice as a protonic semiconductor. | |
| 4 | March 24th, 2017 |
Very short refresher of statistical mechanics. The role of the Gibbs free energy in biophysical contexts. Chemical kinetics. Equilibrium constants. Dissociation reactions, the pK. Redox reactions and the Nernst equation. Proton pumps in membranes, molecular machines and proton pumps. Biomimetic photosynthesis. CGI of the molecular machines in a cell. | |
| 5 | March 31st, 2017 | X-ray crystallography and its applications to the structural
problems of biology. The basic ideas of crystallography. The
discoveries of von Laue and of the Bragg's. The Laue equations.
The data inversion problem. The Patterson function. The PDB. |
|
| 6 | April 7th, 2017 | The structure of DNA. Griffith's experiment. The experiment of
Avery, MacLeod and McCarty. The paper by Timofeev-Ressovsky,
Zimmer and Delbrück and its relationship with Schrödinger's
"What is life?". The race to uncover the structure of DNA. The
contribution of X-ray cristallography. The diffraction pattern
due to a helical structure. |
|
| 7 |
April 21st, 2017 | Experiment: diffraction from helical structure. From the DNA shape to the DNA structure. The structural elements of DNA: bases, sugars, phosphates. The elements that make up a nucleotide. The hierarchical packaging of DNA in the cell (nucleosomes, chromatin, chromosomes). A glimpse of DNA in present day biophysical research. Experiment: extraction of DNA from bananas and strawberries. |
|
| 8 |
April 28th, 2017 |
A description of the mechanism of DNA replication and the
replisome. The statistical mechanics of DNA. Molecular zipper
model of DNA. Helix to coil transition in DNA (thermal DNA denaturation). DNA unzipping and helicase dynamics. Polymerase chain reaction (PCR). |
|
| 9 | May 5th, 2017 |
Proteins. Lysozyme as an example of
a small protein. Aminoacids. Peptide bonds. Disulfide bonds.
Proteins as polypeptide chains. Geometry of peptide bonds. The
Ramachandran plot.The secondary structure of proteins, alpha
helices and beta sheets. The shape of proteins: the case of
hemoglobin and sickle cell anemia. Other generalities on
proteins. Ribosomes and proteasomes. |
|
| 10 | May 12th, 2017 | Genetic code. RNA and DNA. Messenger
RNA (mRNA) and transfer RNA (tRNA). RNA Polymerase. DNA Repair. Mutations. Enzymes. Transition state theory. Arrhenius plots. |
|
| 11 | May 19th, 2017 | Enzymes and transition state theory.
Michaelis-Menten kinetics. Transition state stabilization.
Lock-and-key view of enzyme action. Viruses. The shape of viruses. The Tobacco Mosaic Virus (TMV). Bacteriophage phi X 174. Thermodynamics of viral self-assembly. |
|
| 12 | May 26th, 2017 | Viral nanotechnology. Mutations. Mutation rate. DNA damage. DNA repair. The Delbrück-Luria experiment. Gene modifications linked to cancer; oncogens, tumor-suppressor genes, repair genes. The hallmarks of cancer. Mathematical models of carcinogenesis. A simple model of colorectal cancer. Peto's paradox. |
|
| 13 | May 29th, 2017 | Visit of the beamline dedicated to structural biophysics at ELETTRA | |
| 14 |
May 31st, 2017 |
Seminar on computational topics in cellular biophysics by Dr. S. Stella |