CG910 Proteomics

Přírodovědecká fakulta
podzim 2023
Rozsah
2/0/0. 2 kr. (plus 2 za zk). Ukončení: zk.
Vyučující
doc. Mgr. Jan Havliš, Dr. (přednášející)
prof. RNDr. Zbyněk Zdráhal, Dr. (přednášející)
Mgr. David Potěšil, Ph.D. (přednášející)
Mgr. Tomáš Klumpler, Ph.D. (přednášející)
doc. Mgr. Jan Paleček, Dr. rer. nat. (přednášející)
Garance
doc. Mgr. Jan Havliš, Dr.
Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Dodavatelské pracoviště: Národní centrum pro výzkum biomolekul – Přírodovědecká fakulta
Předpoklady
basics in biochemistry, analytical and physical chemistry
Omezení zápisu do předmětu
Předmět je nabízen i studentům mimo mateřské obory.
Mateřské obory/plány
Cíle předmětu
At the end of the course students should be able: to understand and to explain terms related to proteomics (protein biosynthesis, sequence, structure, and interactions); to know relations between protein properties and methods of their study, to be able to use this knowledge on proteins and their complexes to follow their role in organisms.
Výstupy z učení
at the end of the course students should be able:
to understand and to explain terms related to proteomics (protein biosynthesis, sequence, structure, and interactions);
to know relations between protein properties and methods of their study
to use this knowledge on proteins and their complexes to follow their role in organisms.
Osnova
  • Jan Havliš
  • Introduction into proteomics – definition of proteome and proteomics. Why it is so important to study proteome and its changes: postgenomic era and what to do with information, which we cannot read, genotype vs. phenotype, what does happen during expression, from gene to protein and back. Approaches of contemporary proteomics: Expression, purification and analysis of recombinant proteins, analysis of relations between structure and function, differential proteomics, analysis of post-translational modifications
  • Proteins - biosynthesis of proteins, basic structure hierarchy, basic protein properties (size and shape, polarity, charge, reactivity). Expression proteomics - the conditions and regulation of gene products expression (under different conditions, also ontogenically), protein identity: protoprotein, protein splicing (intein, extein), post-translational modifications, transport, localisation of proteins (eg. cell membrane proteins, secretome), degradation, relations between genotype and phenotype.
  • Tomáš Klumpler
  • structural proteomics - domains, tertiary structure, protein folding, structure and environment relations, allostery, structure modelling
  • Jan Paleček
  • Protein interactions - domains, surface - bond types - interactome (maps, evolution) - protein complexes - simple (dimers), multicomponential (SMC...), molecular machinery.
  • David Potěšil
  • Bioinformatics and proteins - Mw, pI, primary structure, PTMs, domains, tertiary structure, gene ontology (GO), phylogenetic similarity (mutations, proteins from organisms with unsequenced genomes), protein complexes.
  • Zbyněk Zdráhal
  • Importance and utilisation of proteomics - role of proteomics in basic research, application of proteomics (disease diagnostics, pathogene identification)
Literatura
    doporučená literatura
  • TWYMAN, R.M. Principles of proteomics. BIOS Scientific Publishers, 2008. ISBN 1 85996 273 4. info
  • Proteomics. Edited by Timothy Palzkill. Boston: Kluwer Academic Publishers, 2002, viii, 136. ISBN 0792375653. info
Výukové metody
the lecture is based on ppt presentations and their explication. presentations themselves will be available as study material. it is recommended to attend the lecture because of the explication, which significantly extends the presentations, and because of the limited availability of textbooks in english covering certain parts of the subject.
the subject will be eventually lectured if the number of enrolled students exceeds number 5; otherwise, students will be given a chance to pass the subject without lecturing, combining study materials and on-demand tutorials at max 2x2h per semester; contact the lecturer to set up the schedule.
Metody hodnocení
the basic written examination takes 90 minutes and consists of a single-choice test with sixty questions, five choices per question. to pass the test, it is necessary to answer correctly at least 60 % of the questions; the test covers the complete content of the course. the examination will conclude with a brief oral examination.
at the beginning of the course, the document containing voluntary running tasks to consolidate the acquired knowledge will be uploaded to the study materials section.
Vyučovací jazyk
Angličtina
Informace učitele
the number of enrolled students did not reach the critical mass for this subject given by the study regulations; the course remains open, but will not be lectured, see above in the section "teaching methods/výukové metody".
Další komentáře
Studijní materiály
Předmět je vyučován každoročně.
Výuka probíhá každý týden.
Předmět je zařazen také v obdobích podzim 2016, podzim 2017, podzim 2018, podzim 2019, podzim 2020, podzim 2021, podzim 2022, podzim 2024.