Experimental and Computational Methods in Biophysics

The updated ‘Guía docente’ can be found in the Faculty web page

Period:  1st (Fall semester)

ECTS:  6

Course contents:

EXPERIMENTAL METHODS IN MOLECULAR AND CELL BIOLOGY

SEMINARS:

Seminar 1.- Basic genetic mechanisms and information flow.
The seminar will deal with one or more of the following topics: DNA replication and reparation, transcription and translation.

Seminar 2.- Internal organization in eukaryotic cells.
The seminar will deal with one or more of the following topics: cellular organelles, synthesis, targeting and secretion of macromolecules, vesicular transport, and mechanisms of energy conversion.

Seminar 3.- Intra- and inter-cellular chemical signals.
The seminar will deal with one or more of the following topics: membrane receptors and intracellular effectors (channels, etc), second messengers (in particular Ca2+ and cAMP), intracellular cascades, regulation of genetic programs, nervous and immune systems and their disturbances.

Seminar 4.- Cell motility and shape, cell división and cell cycle.
The seminar will deal with one or more of the following topics: cytoskeleton, microfilaments, microtubules, muscle contraction, cilia nad flagella, molecular motors, cell division, cell cycle and its disturbances.

Seminar 5.- Cell-cell and cell-matrix adhesion, development and differentiation.
The seminar will deal with one or more of the following topics: cell junctions, types, composition and functions, structure and function of extracelular matrix, basal lamina, mechanisms implicated in development and their regulation, cellular differentiation, cell fate.

PRACTICAL CLASSES:

1. Solutions. Buffers
2. Purification of serum immunoglobulins: fractional precipitation of proteins. Ion exchange chromatography
3. Determination of protein concentration: Lowry
4. SDS-polyacrylamide gel electrophoresis
5. Culture of eukaryotic cells from different tissues. Growth and cell staining.
6. Growth of genetically transformed bacteria
7. Isolation of nucleic acids
8. Plasmid DNA digestion with endonuclease restriction enzymes
9. Separation of DNA molecules by agarose gel electrophoresis
10. Identification of amino acids in casein by thin layer chromatography (TLC).

EXPERIMENTAL AND COMPUTATIONAL METHODS IN PHYSICS

Practical session of MATLAB programming

Introduction to programming in MATLAB: elementary operations with matrices and arrays, representation of functions, scripts.

Function optimization.

Numerical solution of ordinary and partial differential equations.

Statistical analysis.

MonteCarlo Simulations.

Applications to problems of Physics and Biology

Physics labs

Physics experiments designed to study motion, forces and energy, oscillations and waves (sound and light), temperature and heat. Guided by the teacher, the students will plan the goals and experimental design, explore its theoretical foundations and analyze the results.

Bibliography:
Cooper, G.M. and Hausman, R.E. 2009. The cell: a molecular approach. Sinauer. 5th Edition.
URL for info: http://www.sinauer.com/cooper5e/
NCBI online access to 2nd Ed: http://www.ncbi.nlm.nih.gov/books/NBK9839/

. Tymoczko, J., Berg, J., Stryer, L. 2010. Biochemistry: a short course. W. H. Freeman. 1st Edition.URL: http://www.whfreeman.com/catalog/Product/biochemistryashortcourse-firstedition-tymoczko
URL for online access to contents: http://bcs.whfreeman.com/tymoczko1e/default.asp?s=&n=&i=&v=&o=&ns=0&uid=0&rau=0

Brian R. Hunt. A guide to MATLAB for beginners and experienced users. Cambridge University Press, (2006).

Faculty:

Coordinator of Experimental Methods in Molecular and Cell Biology: Catalina Ribas Nuñez

email: cati.ribas@uam.es

Coordinator of Experimental Methods in Physics: David Míguez

email: david.miguez@uam.es

Website: sysbio.openwetware.org

Computational methods lab: Alfredo Levy Yeyati

email: a.l.yeyati@uam.es

 

 

More info on the course official guide (Guía docente)