SubjectsSubjects(version: 855)
Course, academic year 2019/2020
  
Experimental techniques of structural biology - P320011
Title: Experimentální techniky strukturní biologie
Guaranteed by: Department of Biochemistry and Microbiology (320)
Actual: from 2019
Semester: both
Points: 0
E-Credits: 0
Examination process:
Hours per week, examination: 3/0 other [hours/week]
Capacity: winter:unknown / unknown (unknown)
summer:unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type: doctoral
Note: you can enroll for the course in winter and in summer semester
Guarantor: Ulbrich Pavel doc. Ing. Ph.D.
Spiwok Vojtěch doc. Ing. Ph.D.
Hrabal Richard prof. Ing. CSc.
Is interchangeable with: AP320011
Annotation -
Last update: Hrabal Richard prof. Ing. CSc. (08.11.2018)
The course is aimed at post-gradual students which should learn practical aspects of modern instrumental techniques like mass spectrometry, nuclear magnetic resonance spectroscopy, X-ray crystallography, optical and electron microscopy, and surface plasmon resonance. The fundaments of each method together with various applications in biochemistry, microbiology and other biological sciences will be covered in the course. The introductory lectures will also cover the methods of visualisation of biomolecules, computational methods and work with databases.
Aim of the course -
Last update: Hrabal Richard prof. Ing. CSc. (12.07.2018)

The students will get overview of modern analytical techniques common nowadays in life sciences. They will learn the fundaments of each method and their practical applications.

Computational methods: visualization and manipulation with biomolecules, fundaments of computational methods, database handling... Within the framework of this block the students will work on their own project, which will be evaluated.

NMR: physical fundaments of NMR spectroscopy, utilization of this method for determination of three-dimensional structure of biomolecules, study of their interactions and other physico-chemical properties

Electrom microscopy: basic characteristics and principals of electron microscopy and scanning microscopy including sample preparation and analysis of experimental data

X-ray diffraction: crystal preparation, physical fundaments of the method, technology for determination of the structure of biomolecules

Mass spectrometry: bases of the method, overview of experimental techniques and their practical applications

Physical fundaments of Surface plasmon resonance and it's utilization for study of biomolecular complexes

Optical microscopy: bases of confocal microscopy, high-resolution microscopy, practical applications

Literature -
Last update: Hrabal Richard prof. Ing. CSc. (02.11.2018)

R: http://www.vscht.cz/nmr/mol_model_bioinfo/

A:Egerton R. F.: Physical principles of electron microscopy, 2nd edition, Springer 2006.

R:https://www.amazon.com/Physical-Principles-Electron-Microscopy-Introduction/dp/3319398768

A: H. Günther: NMR Spectrosocopy John Wileay and Sons, 2.vydání, 2001

A: Orsburn B.C., Handbook of basic mass spectrometry for biologists and medical technologists: What you really need to know to get started, Bench to Bedside Press, New York, 2010, 0615434983.

A: de Hoffmann E., Stroobant V., Mass spectrometry: Principles and Applications, Chichester, 2007, 978-0-470-03310-4.

A: A. Fiser, A. Sali. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374, 461-491, 2003.

Learning resources - Czech
Last update: Hrabal Richard prof. Ing. CSc. (12.07.2018)

Výpočetní metody: http://web.vscht.cz/spiwokv/modelovani/

EM: http://www.paru.cas.cz/lem/book/index.html

NMR: http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance

Requirements to the exam - Czech
Last update: Hrabal Richard prof. Ing. CSc. (12.07.2018)

Nejsou.

Syllabus -
Last update: Hrabal Richard prof. Ing. CSc. (12.07.2018)

Structural databases and their utilization, mutual comparing of biomolecular structures, molecular electrostatics, structure prediction, docking, virtual screening, molecular mechanics. QM/MM, molecular dynamics and protein folding

Fundaments of NMR spectroscopy, chemical shift, interaction constant, basic parts of modern spectrometer, technology of determination of three-dimensional structure of biomolecules, study of biomolecular complexes, practical examples

Introduction to X-ray crystalography, preparation of crystals, diffraction theory, acquiring of diffractional data, solution of biomolecular structures, phase problem, model building, their validation and visualization

Principals and techniques of transmission electron microscopy (TEM) and scanning electron microscopy (SEM), practical applications of both techniques, atomic force microscopy (AFM) and scanning tunneling microscopy (STM)

Introduction to mass spectrometry of peptides and proteins, ionization techniques and analyzers, fragmentation techniques, practical application of MS in life sciences (determination of molecular mass, protein identification, sequential analysis, conformational analysis, study of interactions.

Fundaments of optical microscopy, basic techniques a applications, high-resolution microscopy

Surface plasmon resonance and it's role in the study of interactions of biomolecules

Entry requirements - Czech
Last update: Hrabal Richard prof. Ing. CSc. (12.07.2018)

Základní znalosti z předmětů biochemie, fyzikální, anorganická a organická chemie, fyzika.

Registration requirements - Czech
Last update: Hrabal Richard prof. Ing. CSc. (12.07.2018)

Nejsou.

Course completion requirements -
Last update: Hrabal Richard prof. Ing. CSc. (12.07.2018)

Working out a project

Written test and optional oral exam

 
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