Kinetics of Cellular Reactions

Fundamentals of Steady State (Michaelis-Menten, Briggs-Haldane,...); Detection of Reaction Intermediates; Mathematical Descriptions of Kinetic Models; Allosteric Models; Single-molecule Kinetics; Examples: Kinesin, Processivity and Randomness; Proofreading Mechanisms

After successful completion of the module the students are able to:

• understand and apply all fundamental kinetic models.
• transfer kinetic schemes to quantitative models (using Mathematica or other computer languages).
• discern global kinetic models and kinetic steps.
• understand the differences between ensemble measurements and single-molecule assays.

Basic understanding of physical chemistry (e.g. CH1104: Chemistry for Physicists)

This module consists of a lecture and an excercise class.

The lecture develops how to set up reaction schemes for (bio-)chemical reactions, and how to describe them by systems of ordinary differential equations. Further, solutions based on 'classical', approximation procedures, computer-based numerical calculations, and stochastic simulations are presented and discussed.

The exercises apply this theoretical background to important cellular and biochemical reactions. Finally, primary literature is studied to show the relevance of the topic for current research.

Lecture with script, example Mathematica programs, exercises, seminar talks

The literature on which the module is based on, will be available via Moodle.

The achievement of the competencies given in section learning outcome is tested exemplarily at least to the given cognition level using final projects independently prepared by the students. The exam of 25 minutes consists of the presentation of the project’s results and a subsequent discussion.

For example an assignment in the exam might be:

• Set up the reaction scheme of enzyme XY, and deduce the kinetic model!
• In which cases does it make sense to use Monte Carlo simulations to solve a kinetic system?
• Which physical limitations restrict the maximal velocity of biochemical reactions?

Participation in the tutorials is strongly recommended since the exercises prepare for the problems of the exam and rehearse the specific competencies.