BIC-30803 Advanced Methods in Biochemical Research

Course

Credits 3.00

Language of instruction:

English

Assumed knowledge on:

BIC-20306 Cell Physiology and Genetics.

Continuation courses:

Thesis Biochemistry

Contents:

Note: This course has a maximum number of participants.
The deadline for registration is one week earlier than usual. See Academic Year:
https://www.wur.nl/en/Education-Programmes/Current-Students/Agenda-Calendar-Academic-Year.htm->Registration for Courses

Advanced Methods in Biochemical Research is a multidisciplinary course in which different spectroscopic methods are used to unravel protein interactions and dynamics. The organization and dynamics of biological systems rely on an intimate interplay of biomacromolecules. Proteins, nucleic acids and other molecular compounds, such as membrane phospholipids, may interact with each other to transduce signals or to build up macromolecular structures that perform catalysis, shape cells or form intracellular organelles. Cell functioning largely depends on protein interaction networks or, as outlined in Alberts (1998), ‘the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines’. Unraveling protein interaction patterns is therefore of key importance to increase our understanding of cellular processes. The scope of the first part of the course is to quantitatively determine several physical properties of fluorescent proteins, e.g. diffusion constants and masses, and to obtain insight in the operation of advanced spectroscopic instruments. We will use steady-state fluorescence spectroscopy, time-resolved fluorescence anisotropy, fluorescence fluctuation spectroscopy and absorption spectroscopy to measure signals from the purified fluorescent proteins. In addition to the fluorescence spectroscopy measurements, mass spectrometry (MS) will be performed on the same protein samples in order to identify and study relative quantitative amounts of proteins present .

Learning outcomes:

After successful completion of this course students are expected to be able to:
- explain which advanced spectroscopic methods can be applied for studying cellular biochemistry in general.
- purify proteins using affinity chromatography handling and characterize of these proteins.
- explain the principles of FRET methodology.
- handle spectroscopic techniques such as steady state spectroscopy, time resolved fluorescence spectroscopy (anisotropy), fluorescence correlation spectroscopy and mass spectrometry.
- use sophisticated data analysis software for quantitative interpretation of protein interactions and dynamics.
- identify and quantify proteins using mass spectrometry analysis.
- write a research paper on the conducted fluorescence- and mass spectroscopy experiments and present the work orally.

Activities:

Lectures. Perform experiments on protein purification and characterization and using advanced (fluorescence) spectroscopy (experiments are compulsory since acquired skills are part of the learning outcome). Use computer programs for data handling and processing. Write a report in the form of a research paper and present the work with an oral presentation.

Examination:

The practical course consists of two separate subjects; mass spectrometry (30%) and fluorescence spectroscopy (70%).
Marks will be given for:
- practical performance (15%);
- written reports (65%);
- oral presentation (20%).

Literature:

A syllabus will be provided at the first day of the course. Blackboard pages contain lecture slides, background literature, links to online material, and student reports on the conducted experiments.