Course program, A.Y. 2017-18
| Lesson | Date | Topics | Linked slides and useful links |
| 1 | March 16th, 2018 | introduction to biophysics. Diffusion processes in biology. The diffusion equation and its solutions. The main structural elements in eukaryotic cells. Membranes. | |
| 2 | March 23rd, 2018 |
Dimensional reduction in the diffusion inside cells. Diffusion and potential theory. Absorbing sphere. Receptors on a spherical cell. | |
| 3 | April 6th, 2018 |
Reaction-diffusion and morphogenesis. 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. |
|
| 4 | April 13th, 2018 |
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. Very short refresher of statistical mechanics. The role of the Gibbs free energy in biophysical contexts. |
|
| 5 | April 20th, 2018 (Stella) |
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. |
|
| 6 | April 27th, 2018 | Genetic code. RNA and DNA. Messenger RNA (mRNA) and transfer
RNA (tRNA). RNA Polymerase. Enzymes. Transition state theory. Arrhenius plots. Enzymes and transition state theory. |
|
| 7 |
May 4th, 2018 | Michaelis-Menten kinetics. Transition state stabilization.
Lock-and-key view of enzyme action. 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?". 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. |
|
| 8 |
May 11th, 2018 |
The Laue equations. The data inversion problem. The Patterson
function. The PDB. The contribution of X-ray cristallography to the discovery of the structure of DNA. The diffraction pattern due to a helical structure. Main structural features of DNA from X-ray diffraction. |
|
| 9 | May 18th, 2018 |
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). |
|
| 10 | May 18th, 2018 | Experiment: extraction of DNA from bananas and strawberries. 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). |
|
| 11 | May 25th, 2018 | 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. DNA Repair. Mutations. Mutation rate. DNA damage. DNA repair. Gene modifications linked to cancer; oncogens, tumor-suppressor genes, repair genes. The hallmarks of cancer. |
|
| 12 | June 8th, 2018 (Stella) |
Mathematical models of carcinogenesis. A simple model of
colorectal cancer. Peto's paradox. Basic radiobiology. Cell death and cell survival curves. Biological endpoints. The linear-quadratic (LQ) model. Target theory. Multitarget model. Conditions that influence the shape of the cell survival curve: RBE, OER, etc. Dose-response curves. Use of the LQ model in radiation therapy. The 5 R's of radiobiology. |
|
| 13 | June 12th 2018 (Stella) |
Visit of the beamline dedicated to structural biophysics at ELETTRA | |