Course: Experimental Methods in Protein Biochemistry

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Course title Experimental Methods in Protein Biochemistry
Course code UCH/022
Organizational form of instruction Lecture + Lesson
Level of course Master
Year of study 2
Frequency of the course In each academic year, in the summer semester.
Semester Summer
Number of ECTS credits 4
Language of instruction English
Status of course Compulsory
Form of instruction Face-to-face
Work placements This is not an internship
Recommended optional programme components None
Lecturer(s)
  • Štěrba Ján, RNDr. Ph.D.
Course content
Chemistry of peptides and proteins. Physical and Chemical methods applied to the studies of protein structure. Protein Structures in relation to their function. Contents: Chemistry of peptides and proteins: Polymer of amino acid; Threedimensional structure: Secondary structure, Fibrous proteins, Globular proteins, Protein stability, Quaternary structure; Protein folding and dynamics: Protein folding, protein denaturation, folding pathway and prediction of protein structure; Protein dynamics; atomic fluctuations, collective motions and triggered conformational changes; Experimental methods applied to study protein structures: Transport in electric field, interaction of EM radiation with particles (X-rays diffraction by fibrous proteins, NMR, Circular dichroism, Laser raman, Neutron diffraction; Theoretical methods applied to study protein structures: homology modeling, molecular dynamics, ligand/docking; Allosteric regulation;

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Dialogic (discussion, interview, brainstorming)
  • Preparation for classes - 25 hours per semester
  • Class attendance - 39 hours per semester
  • Preparation for exam - 25 hours per semester
  • Preparation for credit - 10 hours per semester
Learning outcomes
Chemistry of peptides and proteins. Physical and Chemical methods applied to the studies of protein structure. Protein Structures in relation to their function. Contents: Chemistry of peptides and proteins: Polymer of amino acid; Threedimensional structure: Secondary structure, Fibrous proteins, Globular proteins, Protein stability, Quaternary structure; Protein folding and dynamics: Protein folding, protein denaturation, folding pathway and prediction of protein structure; Protein dynamics; atomic fluctuations, collective motions and triggered conformational changes; Experimental methods applied to study protein structures: Transport in electric field, interaction of EM radiation with particles (X-rays diffraction by fibrous proteins, NMR, Circular dichroism, Laser raman, Neutron diffraction; Theoretical methods applied to study protein structures: homology modeling, molecular dynamics, ligand/docking; Allosteric regulation;
Final Competences - to have detailed insight in the structure of proteins with respect to protein chemical and biophysical properties - to have insight in the use of prediction methods and molecular modeling techniques - to have knowledge of and to have insight in protein folding in vitro and comparison to in vivo protein folding - to have knowledge of and to have insight in the general principles of protein purification (based on size, charge, hydrophobicity or on biospecific properties) - to have knowledge of possible chemical modification reactions
Prerequisites
knowledge from courses: Biochemistry 1, Biochemistry 2, Biochemistry Laboratory 1, Biochemistry Laboratory 2, Biomolecular NMR Spectroscopy

Assessment methods and criteria
Oral examination, Student performance assessment

The student must pass the practical part, participate on lectures and actively discuss the topics. The students must understand the following topics to successfully pass the exam: protein folding, protein purification techniques, protein structure modelling techniques etc.
Recommended literature
  • Lesk, Arthur M. Introduction to protein science: architecture, function, and genomics / Arthur M. Lesk. 1st ed. Oxford : Oxford University Press, 2004. 310 s..
  • Petsko, G & Ringe, D. Protein Structure and Function, New Science Press in association with Sinauer Associatesand Blackwell Science, London. 2003. 180 pp..


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Secondary Schools Teacher Training in Chemistry (1) Category: Pedagogy, teacher training and social care - Recommended year of study:-, Recommended semester: Summer