CG010 Proteomics

Faculty of Science
Autumn 2022
Extent and Intensity
2/0/0. 2 credit(s) (plus 2 credits for an exam). Type of Completion: zk (examination).
Taught in person.
Teacher(s)
doc. Mgr. Jan Havliš, Dr. (lecturer)
prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
Mgr. David Potěšil, Ph.D. (lecturer)
Mgr. Tomáš Klumpler, Ph.D. (lecturer)
doc. Mgr. Jan Paleček, Dr. rer. nat. (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
Tue 9:00–10:50 C02/211
Prerequisites
basics in biochemistry, analytical and physical chemistry
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
major goal of this subject is to acquaint students overall and generally with proteomics as a field, with its content and main aspects.
Learning outcomes
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.
Syllabus
  • 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 - principles of assembly, modules - molecular machines.
  • 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)
Literature
    recommended literature
  • TWYMAN, R.M. Principles of proteomics. BIOS Scientific Publishers, 2008. ISBN 1 85996 273 4. info
  • Proteomics. Edited by Timothy Palzkill. New York: Kluwer Academic Publishers, 2002. viii, 127. ISBN 0-306-46895-6. info
Teaching methods
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.
Assessment methods
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 an oral examination.
during the course, students will be given ungraded, voluntary, time-saving tasks to consolidate the acquired knowledge.
Language of instruction
Czech
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
Teacher's information
21., 28. 9. a 5. 10. 2020 - jan havliš 12. 10. a 19. 10. 2020 - tomáš klumpler 26. 10. a 2. 11. 2020 - honza paleček 9. 11. a 16. 11. 2020 - david potěšil 23. 11. 2020 - zbyněk dráhal
The course is also listed under the following terms Autumn 2010 - only for the accreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021.
  • Enrolment Statistics (recent)
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