C7942 Bioanalytics I - Biomacromolecules

Přírodovědecká fakulta
podzim 2013
Rozsah
2/0/0. 2 kr. (plus ukončení). Doporučované ukončení: zk. Jiná možná ukončení: k.
Vyučující
doc. Mgr. Jan Havliš, Dr. (přednášející)
Garance
doc. Mgr. Jan Havliš, Dr.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Předpoklady
basic knowledge of biochemistry is prerequisited; mass spectrometry of biomolecules (C7895) is a recommended lecture.
Omezení zápisu do předmětu
Předmět je nabízen i studentům mimo mateřské obory.
Mateřské obory/plány
Cíle předmětu
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
Osnova
  • 1) analytical approaches in bioanalytics – demands; high throughput, shotgun analysis, standardization
  • 2) affinity methods – principles, carry-out and use (separation, interaction studies), IMAC, APAGE
  • 3) immunoanalytical methods – principles; immunoanalysis – precipitation, agglutination, immunoassay, methods: FIA, LIA, RIA, EIA, ELISA, IAC, IACE, SELDI…
  • 4) separation of biomacromolecules – gel electrophoresis; principles, carry-out and use (1D, 2D; polyacrylamide, agarose); blotting; 2D liquid chromatography
  • 5) genomics (analysis of DNA) – fundamentals of genetics (structure, function of DNA), analytical approaches: PCR, restriction enzymes; identification of known (hybridization) and unknown sequence (Sanger m., pyrosequencing, 454, Solid); identification of changes in DNA; DNA methylation and its analysis
  • 6) basics of mass spectrometry – principles; ionization (ESI –spectra deconvolution; MALDI), mass analysis (tandem MS), detection, vacuum technique mass spectrum, basic terminology of MS
  • 7) proteomics (analysis of proteins and their complexes) – fundamentals (structure of proteins and protein complexes, proteome organization)
  • 8) expression proteomics – methodology (MS: bottom-up, top-down), MS: identification of protein using peptide fingerprints/maps, bioinformatics in MS-assisted proteomics; MS: identification of protein using amino acid sequence; other methods of expression proteomics: 2D HPLC, 2D PAGE, 2D imaging
  • 9) quantitative analysis of protein complexes – quantification using mass spectrometry, input of quantitative information into MS spectrum (internal standard method; mass tagging – ICAT, ICMT, TMT, MCAT, GIST, SILAC, SIL), deciphering the quantitative information in MS spectrum; automation in proteomics (AI problem)
  • 10) functional proteomics – methodology (parallel and sequential analysis), methods of protein-protein interaction study (Y2H; BiFC; mbSUS; MeRA; SEAM –myc, TAP, FLAG, His-tags; ion-mobility strategy); absolute quantification of proteins and peptides by MS (SIL, VICAT, QCAT; molar ionization coefficient; probability approach)
  • 11) structural proteomics – methodology (chemical cross-linking), methods (FTICR MS); shotgun proteomics – hyphenated techniques
  • 12) post-translational modifications analysis – forms of PTM, MS analysis of PTM – localization; glycosylation, phosphorylation; PTM extent determination
  • 13) 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), shotgun analysis
Literatura
  • Quantitative proteomics by mass spectrometry. Edited by Salvatore Sechi. Totowa: Humana Press, 2007, x, 218. ISBN 9781588295712. info
  • BENFEY, Philip N. a Alex D. PROTOPAPAS. Essentials of genomics. Upper Saddle River: Prentice-Hall, 2005, xiv, 346. ISBN 013047018X. info
  • MIKKELSEN, Susan R. a 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
Výukové metody
the lecture is based on ppt presentation and its explication. presentation itself 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.
Metody hodnocení
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.
Vyučovací jazyk
Angličtina
Další komentáře
Studijní materiály
Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován každoročně.
Výuka probíhá každý týden.
Předmět je zařazen také v obdobích podzim 2012, podzim 2014, podzim 2015, podzim 2016, podzim 2017, podzim 2018, podzim 2019, podzim 2020, podzim 2021, podzim 2022, podzim 2023, podzim 2024.