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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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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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Monologic Lecture(Interpretation, Training)
- Preparation for the Exam
- 60 hours per semester
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Learning outcomes
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The subject is aimed on finding the relationship between the primary genetic information and 3D structure of encoded biomolecules is vital for understanding all biochemical processes.
ability to associate information, recognize the structure relations in 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.
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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.
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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., Voeth J.G., Pratt C.V. (2002). Fundamentals of Biochemistry, Upgrade Edition.. John Wiley and Sons.
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