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Lecturer(s)
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Kutá Smatanová Ivana, prof. Mgr. Ph.D.
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Schneider Bohdan, prof. Ing. CSc.
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Course content
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One week course at the Institute of Biotechnology of the Czech Academy of Sciences, usually in the first or second week of January. Introduction to crystallography as the most important method of determination of molecular structures. Why study molecular structures, structure-function relationships in chemistry and biology? Experimental setup, crystal growth, sources of radiation (x-ray lamps, synchrotron etc.) Data collection and reduction. Crystallographic symmetry Structure determination. Solution of the phase problem? Reflections, electron densities and Fourier transforms Structure refinement. Improvement of the molecular model Validation and analysis of structures Comparison of crystallography to other experimental methods as electron microscopy, NMR, and other spectral methods, and to methods of computer simulations by quantum mechanics and methods of empirical potential (molecular dynamics). Finding structures: Structural databases. Practical introduction to the most important databases CSD (for organic molecules) and PDB (the primary repository for 3-D macromolecular structures). Other internet databases important for structural biology. mmCIF and other formats used for archiving structures Comparing structures by tools of structural bioinformatics. Stereochemistry of the building blocks of biomolecules, amino acids and nucleotides. Sequence alignments, relationship between amino acid sequence and protein structure and fold. Methods of structure comparisons. Structural motives of the protein secondary structure, tertiary structure motives, classifications of protein folds. Structures of nucleic acids. I. Helical conformations. II. 3D folding of RNA and DNA.
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Learning activities and teaching methods
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Monologic (reading, lecture, briefing), Dialogic (discussion, interview, brainstorming), Excursion
- Class attendance
- 39 hours per semester
- Field trip
- 6 hours per semester
- Preparation for exam
- 25 hours per semester
- Preparation for classes
- 30 hours per semester
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Learning outcomes
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Introduction to crystallography as the most important method of determination of molecular structures. Why study molecular structures, structure ? function relationships in chemistry and biology Experimental setup, crystal growth, sources of radiation (x-ray lamps, synchrotron etc.) Data collection and reduction. Crystallographic symmetry Structure determination. Solution of the ?phase problem? Reflections, electron densities and Fourier transforms Structure refinement. Improvement of the molecular model Validation and analysis of structures Comparison of crystallography to other experimental methods as electron microscopy, NMR, and other spectral methods, and to methods of computer simulations by quantum mechanics and methods of empirical potential (molecular dynamics). Finding structures: Structural databases. Practical introduction to the most important databases CSD (for organic molecules) and PDB (the primary repository for 3-D macromolecular structures). Other internet databases important for structural biology. mmCIF and other formats used for archiving structures Comparing structures by tools of structural bioinformatics. Stereochemistry of the building blocks of biomolecules, amino acids and nucleotides. Sequence alignments, relationship between amino acid sequence and protein structure and fold. Methods of structure comparisons. Structural motives of the protein secondary structure, tertiary structure motives, classifications of protein folds. Structures of nucleic acids. I. Helical conformations. II. 3D folding of RNA and DNA.
Students gain a basic knowledge of structural biochemistry and X-ray crystallography. Practical part takes places at the Institute of Biotechnology of the Czech Academy of Sciences.
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Prerequisites
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Knowledge of biochemistry, organic chemistry, molecular biology is expected.
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Assessment methods and criteria
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Combined exam
For the exam, students need to understand the principles of theoretical as well as practical aspects covered in lectures and actively participare at the excercises. To pass the course, a student must obtain at least 50% of points in the final exam.
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Recommended literature
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A.M. Lesk: Introduction to Bioinformatics. Oxford University, Oxford (2002).
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B. Alberts; A. Johnson; J. Lewis; M. Raff; K. Roberts; P. Walter: Molecular Biology of the Cell, Garland, New York.
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C. Brandén & J. Tooze: Introduction to Protein Structure. Second Edition, Garland, New York (1998).
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G. Rhodes: Crystallography made crystal clear. Elsevier, Amsterdam (2006).
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J. Drenth: Principles of protein x-ray crystallography. Springer, New York (1994).
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J. Gu & P.E. Bourne: Structural Bioinformatics. Second Edition, Wiley-Blackwell, Hoboken (2009).
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J.P. Glusker; M. Lewis; M. Rossi: Crystal Structure Analysis for Chemists and Biologists. VCH, New York (1994).
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S. Neidle: Nucleic acid structure and recognition, Oxford University, Oxford (2002).
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