C7942 Bioanalytics I - Biomacromolecules

Faculty of Science
Autumn 2014
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.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Wed 11:00–12:50 C02/211
Prerequisites
basic knowledge of biochemistry is prerequisited; 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
there are 10 fields of study the course is directly associated with, display
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 utilization 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, 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
Literature
  • 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
Teaching methods
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.
Assessment methods
oral examination; students are required to understand and to 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
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 2012, Autumn 2013, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Autumn 2014, recent)
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