Bi7940 Bioanalytics I - Biomacromolecules

Faculty of Science
Autumn 2011
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
doc. Mgr. Jan Havliš, Dr. (lecturer)
Guaranteed by
doc. Mgr. Jan Havliš, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Mon 16:00–17:50 C02/211
Prerequisites
basic knowledge of biochemistry is pre-requisited; mass spectrometry of biomolecules (C7895) is a recommended lecture.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
main objectives of lecture: introduction into bioanalytics; at the end of the course students should be able - to understand approaches in analysis of biomacromolecules and suprabiomolecular structures (nucleic acids, proteins and their complexes, lipidic structures), with special regard to utilisation of mass spectrometry as a versatile analytical tool; - to manage the basic theoretical background for understanding of those approaches
Syllabus
  • 1) analytical approaches in bioanalytics – demands; high throughput, shotgun analysis, standardisation
  • affinity methods – principles, carry-out and use (separation, interaction studies), IMAC, APAGE
  • 2) immunoanalytical methods – principles; immunoanalysis – precipitation, agglutination, immunoassay, methods: FIA, LIA, RIA, EIA, ELISA, IAC, IACE, SELDI…
  • 3) gel electrophoresis – principles, carry-out (1D, 2D); blotting
  • 4) genomics (analysis of DNA) – fundamentals of genetics (structure, function of DNA), analytical approaches: PCR, restriction enzymes; direct and indirect sequencing; DNA methylation and its analysis
  • 5) basics of mass spectrometry – principles; ionisation, mass analysis (tandem MS, vacuum technique), detection; mass spectrum
  • proteomics (analysis of proteins and their complexes) – fundamentals (structure of proteins and protein complexes)
  • expression proteomics – methodology, methods (2D HPLC, 2D PAGE, 2D imaging, MS: bottom-up, top-down)
  • 6) functional proteomics - methodology, methods (TAP-tagging, Two-Hybrid, SEAM strategy, ion-mobility strategy)
  • 7) bioinformatics in MS-assisted proteomics – identification of protein in organisms with and without sequenced genomes (MS BLAST, MultiTag)
  • 8) quantitative analysis of protein complexes – internal standard method; mass tagging (ICAT, ICMT, TMT, MCAT, GIST, SILAC, SIL), absolute quantification of proteins and peptides by MS
  • 9) structural proteomics – methodology (chemical cross-linking), methods (FTICR MS)
  • 10) lipidomics (analysis of lipids and cellular membranes) – fundamentals (structure and function of cellular membranes and their components), analytical approaches: lipid extraction, TLC, GC, LC, SFC, GPC, MS analysis (PIS, HGS, FAS), shot-gun analysis
Literature
  • MUSHEGIAN, Arcady R. Foundations of comparative genomics. 1st ed. Burlington: Elsevier Academic Press, 2007, 265 s. ISBN 9780120887941. info
  • Quantitative proteomics by mass spectrometry. Edited by Salvatore Sechi. Totowa: Humana Press, 2007, x, 218. ISBN 9781588295712. info
  • BENFEY, Philip N. and Alex D. PROTOPAPAS. Essentials of genomics. Upper Saddle River: Prentice-Hall, 2005, xiv, 346. ISBN 013047018X. info
  • MIKKELSEN, Susan R. and Eduardo CORTÓN. Bioanalytical chemistry. Hoboken, N.J.: John Wiley & Sons, 2004, xvii, 361. ISBN 0471544477. info
  • LIEBLER, Daniel C. Introduction to proteomics : tools for the new biology. Totowa, NJ: Humana Press, 2002, ix, 198 s. ISBN 0-89603-991-9. info
  • Posttranslational modifications of proteins : tools for functional proteomics. Edited by Christoph Kannicht. Totowa, N.J.: Humana Press, 2002, xi, 322. ISBN 0896036782. info
Teaching methods
the lecture is based on ppt presentation and its explication. presentation it-self will be available as a study material (black-and-white printable pdf with high resolution and restricted access rights). it is recommended to attend the lecture, because of the explication, which significantly extends the presentation and because of limited availability of textbooks in english covering certain parts of the subject.
Assessment methods
oral examination; students are required to understand and be familiar with the principles and its applications. examination consists of three basic questions, which would be during the examination expanded to let the student demonstrate the extent of topic understanding.
Language of instruction
English
Further comments (probably available only in Czech)
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Autumn 2010 - only for the accreditation, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011 - acreditation.
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