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Lecturer(s)
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Berka Karel, prof. RNDr. Ph.D.
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Šponer Jiří, prof. RNDr. DrSc.
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Course content
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Key biomolecules such as DNA, RNA and proteins realise even those tiniest biological functions based mainly on their unique three dimensional (3D) structures. Throughout the evolution nature developed a huge number of variety in 3D structures of biomolecules. Finding the relationship between the primary genetic information and 3D structure of encoded biomolecules is vital for understanding all biochemical processes. Basic types of molecular interactions and forces that create 3D structure of nucleic acids. The mutual effect of these contributions is analysed as well as identified their roles in particular classes of nucleic acids. In direct follow up to other lectures also basic levels also basic levels of description of these interactions from quantum chemistry to empirical potentials with a focus on specific problems associated with studying the fundamental aspects of nucleic acids. The main types of RNA and DNA are discussed with a focus on the principles and their shaping, relation between primary sequence, 3D structure and function, and local or global confirmation variability. The issues are demonstrated on the analysis of the structure and function of ribosomes or other non-cataytic RNA molecules and extraordinary DNA structures such as guanine quadruplexes.
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Learning activities and teaching methods
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Dialogic Lecture (Discussion, Dialog, Brainstorming)
- Preparation for the Exam
- 0 hours per semester
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Learning outcomes
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The lecturese are focused on advanced study of a variety of aspects connected with nucleic acids.
ability to gather information, recognize the structure relations of nucleic acids
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Prerequisites
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unspecified
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Assessment methods and criteria
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Oral exam
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Recommended literature
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Bevilacqua P.C., Brown T.S., Nakano S., Yajima R. (2004). Catalytic roles for proton transfer and protonation in ribozymes. Biopolymers 73, 90-109.
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Moore P.B., Steitz T.A. (2003). The structural basis of large ribosomal subunit function. Rev. Biochem., 72, 813-850.
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Ogle J.M., Carter A.P., Ramakrishnan V. (2003). Insights into the decoding mechanism from recent ribosome structures. Trends Biochem. Sci. 28, 259-266.
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Réblová K., Špačková N., Šponer J.E., Koča J., Šponer J. (2003). Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucl. Acids. Res. 31, 6942-6952, 1.
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Voet D. a kol. (2006). Fundamentals of Biochemistry. New York.
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