F8310 The molecular interactions in biology and chemistry

Faculty of Science
Spring 2021
Extent and Intensity
2/0. 3 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
Teacher(s)
prof. RNDr. Jiří Šponer, DrSc. (lecturer)
Guaranteed by
prof. RNDr. Viktor Brabec, DrSc.
Department of Condensed Matter Physics – Physics Section – Faculty of Science
Contact Person: prof. RNDr. Jiří Šponer, DrSc.
Supplier department: Department of Condensed Matter Physics – Physics Section – Faculty of Science
Prerequisites
There are no specific requirements
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The course explains the modern view on the role of molecular interactions in chemistry and biology. Basic molecular interactions will be described (covalent structure, van der Waals forces, electrostatic interactions, hydrogen bonding) together with some additional types of forces. The role of solvent and entropy will be analyzed. Both the basic classical force field description and full electronic structure (quantum chemical) description will be described. Also, basic experiments to characterise molecular interactions will be explained - physical chemistry experiments and x-ray crystallography. The topics will be illustrated using selected examples, with main emphasize given to the fascinating developments in the field of RNA structure, dynamics and function, with extensive analysis of the function of the ribosome during protein synthesis.
Learning outcomes
The main objective of the course is to provide the students with the ability to
- list and describe the role of molecular interactions in chemistry and biology (both on classical and quantum chemical level)
- list and describe basic experiments to characterise molecular interactions.
Syllabus
  • The role of molecular interaction and why they are so important.
  • Covalent structure
  • Van der Waals forces
  • Electrostatic forces
  • Hydrogen bonding
  • nonadditivity of interactions, induction, charge transfer
  • empirical force fields, molecular mechanics, molecular dynamics
  • quantum chemical description
  • basis sets of atomic orbital
  • Electron correlation
  • Physical chemistry methods
  • X-ray crystallography
  • solvent and entropy
  • Supramolecular assemblies
  • Protein structure
  • DNA structure
  • protein-DNA complexes
  • Structure, dynamics and function of RNA - revolution in biology
  • molecular interactions in RNA
  • Structure and function of large ribosomal subunit
  • Structure and function of small ribosomal subunit
  • elongation cycle on the ribosome
  • Role of molecular interaction in the evolution of ribosomal RNA
  • Biomolecular machines and how they (fundamentally) differ from macroscopic machines.
Literature
  • Computational studies of RNA and DNA. Edited by Jiří Šponer - Filip Lankaš. Dordrecht: Springer, 2006, xi, 636. ISBN 1402047940. info
Teaching methods
Lectures with many case studies, class discussion, practical examples.
Assessment methods
discussions, oral examination - colloquium.
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is taught: every week.
Teacher's information
http://www.ibp.cz/labs/LSDNA/
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019.
  • Enrolment Statistics (recent)
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