C7940 Bioanalytics I - Biomacromolecules

Faculty of Science
Autumn 2008
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 11:00–11:50 AK1
Prerequisites
basic knowledge of biochemistry is pre-requisited (C3181 biochemistry I, C4182 biochemistry II). C7895 mass spectrometry of biomolecules 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
there are 16 fields of study the course is directly associated with, display
Course objectives
main objectives of lecture: introduction into bioanalytics; understanding the approaches in analysis of biomacromolecules snd suprabiomolecular structures (nucleic acids, proteins and their complexes, lipidic structures), with special regard to utilisation of mass spectrometry as a versatile analytical tool; managing the important theoretical background for understanding of those approaches
Syllabus
  • 1) analytical approaches in bioanalytics – demands; high throughput, shotgun analysis, standardization
  • affinity methods – principles, carry-out and use (separation, interaction studies), IMAC, APAGE
  • 2) immunoanalytic 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. Edited by John R. Yates. Totowa, NJ: Humana Press, 2002, ix, 198. ISBN 0896039927. info
  • Posttranslational modifications of proteins : tools for functional proteomics. Edited by Christoph Kannicht. Totowa, N.J.: Humana Press, 2002, xi, 322. ISBN 0896036782. info
Assessment methods
the lecture is based on ppt presentation and its explication, presentation its-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 there are no available textbooks covering the subject.
oral examination; students are required to understand and be familiar with the principles and its applications; enumerations, listing of facts and suchs would not be required.
Language of instruction
Czech
Further Comments
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 2007 - for the purpose of the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007.
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