C7073 Bioanalytics I - Biomacromolecules

Faculty of Science
Autumn 2022
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 15:00–16:50 C02/211
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
Course objectives
the main objective of the course is to introduce bioanalytics in a form of a group of closely related fields, so-called bio-omics.
Learning outcomes
at the end of the course students should be able:
to manage basic bioanalytical methods - separation of biomacromolecules including use of affinity, mass spectrometry
to understand principles of basic bio-omics fields (genomics, proteomics, glycomics, and lipidomics), including their commonly used bioanalytical approaches and instrumental techniques.
Syllabus
  • analytical approaches in v bioanalytics – demands; high throughput and shotgun analyses, result
  • affinity methods – principles, carry-out, use, affinity electrophoresis, IMAC, MOAC, protein equalisers
  • immunoanalytical methods – principles; immunoanalysis – direct, indirect and immunoassay (FIA, LIA, RIA, EIA, ELISA), IAC, IACE, SELDI…
  • separation of biomacromolecules – gel electrophoresis; principles, carry-out (1D, 2D; polyacrylamide, agarose); blotting; liquid chromatography; principles, carry-out (1D, 2D)
  • basics of mass spectrometry – principles; mass spectrum, basic terminology of MS, ionisation (ESI – spectra deconvolution; MALDI), mass analysis (tandem MS), detection, vacuum technique
  • genomics (analysis of nucleic acids) – fundaments, chemical nature of nucleic acids, functional genomics (analytical approaches: PCR, restriction enzymes); identification of known (hybridisation) and unknown sequence (Sanger sequencing, pyrosequencing, 454, Solid); identification of changes in DNA (RFLP, ASO, DGGE, SSCP, CMC); epigenomics; DNA methylation and its analysis
  • proteomics (analysis of proteins and their complexes) – fundamentals, proteome organisation, chemical nature of proteins, their separation
  • expression proteomics – methodics, protein identification (peptide mapping, MS/MS analysis); quantification (AAA, differential PAGE, MS – direct, indirect, stable isotope labelling); shotgun proteomics
  • functional proteomics – methodics, methods of protein interactions study (qualitative - Y2H; BiFC; mbSUS; SLCA; MeRA; SEAM; ion-mobility strategy; quantitative – MS, QCAT, molar ionisation coefficient; probability approach)
  • structural proteomics – methodics (chemical cross-linking), methods (FTICR MS)
  • post-translational modifications analysis – forms of PTM, MS analysis of PTM – localisation; phosphorylation; PTM extent determination
  • lipidomics (analysis of lipids and cellular membranes) – fundaments; structure and function of cellular membranes, chemical nature of lipids, analytical approaches (extraction, separation, MS analysis), shotgun lipidomics, lipidomic databases
  • glycomics (analysis of glycans) – fundaments; chemical nature of glycans and glycoproteins, structure; analytical approaches (derivatisation, separation, MS), shotgun glycomics, glycomic databases
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
Teaching methods
the lecture is based on ppt presentation and its explication. the presentation itself will be available as 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 in czech language covering certain parts of the subject.
Assessment methods
oral examination: students are required to understand and to be familiar with the principles and their applications. the examination consists of three basic questions, which would be during the examination expanded to let the student demonstrate the extent of topic understanding.
during the course, students will be given ungraded, but mandatory, time-saving tasks to consolidate the acquired knowledge.
Language of instruction
Czech
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 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Autumn 2022, recent)
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