CG910 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).
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
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
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.
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 - 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)
Literature
    recommended literature
  • 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
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.
the subject will be eventually lectured if the number of enrolled students exceeds number 5, otherwise, students will be given the chance to pass the subject without lecturing combining study materials and on-demand tutorial at max 2x2h per semester; contact the lecturer to set up the schedule.
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 a brief oral examination.
during the course, students will be given ungraded, voluntary, time-saving tasks to consolidate the acquired knowledge.
Language of instruction
English
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
The course is taught: every week.
Teacher's information
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. to ensure, that also foreign students have a chance to pass the course in english even it is not lectured, we offer you to pass the subject by substituting the lecturing by the combination of study materials and tutorial (max 2x2 h per semester).
The course is also listed under the following terms Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Autumn 2022, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2022/CG910