C4 – Enzyme kinetics
Key information
Next planned course: December 2-6, 2024
Registration deadline: Nov 18, 2024
Format: Digital/Remote (hosted by UiS)
Course responsible: Peter Ruoff
Grading: Minimum 80% attendance and evaluation of project work/report (pass/fail)
Credits: 5 ECTS
UiS course code: BIO910
Software requirement: Please note that you need to have access to Matlab and Gnuplot during the course. Matlab should be available through your University. It is also possible to get access through UiS if need be. Gnuplot is a free download. See further details at the UiS Canvas site.
Registration
All students much register in two ways:
- Directly to BioCat through the form at the bottom of this page.
- Registration to UiS will be done through this link, whether you are a UiS student or an external student.
Content
The course is aimed at PhD students with interests in enzyme kinetics and mathematical modelling of enzymatic/metabolic reactions. The course covers traditional enzyme kinetics topics, but also newer concepts from signal transduction kinetics and robust control (integral feedback) are included. Dependent on the students’ backgrounds and their thesis-work some of the topics may be given in more depth.
After the lectures have been completed, students work on a compulsory delivery.
Teaching
The course (Mon-Fri 9h-15/16h with breaks) will be completely digital and recorded (using Canvas Conferences). Some minor aspects of the course may vary from what is detailed below. Travel for this course will not be required.
Monday
Presentation of participants, their interests, with a brief overview of the course. Practical aspects: Use of Canvas Conferences and orientation about the compulsory delivery. Overview of gnuplot/Matlab and alternative computational methods, such as python. Basic kinetic concepts. Historical aspects about catalysis, enzymes, and the Michaelis-Menten mechanism. Enzyme classes. Introduction into experimental set-ups to record reaction velocities. Spectroscopy primer.
Tuesday
Steady state versus rapid equilibrium solutions (Matlab). Determination of Vmax and Km values by graphical methods as well as using gnuplot and Matlab. Recording of reaction rates by UV-VIS spectroscopy with and without inhibitors (video). Recording of calibration curves.
Wednesday
Inhibition & activation mechanisms. Influence of environmental variables on enzymatic systems: salinity, pH, temperature. The two-protic model. Analysis of experimental alkaline phosphatase data with respect to pH by gnuplot.
Thursday
Reversible MM-mechanism. King-Altman method. Multisubstrate mechanisms. Hysteretic enzymes, Allosteric/cooperativity and ultrasensitivity. Sensitivity analysis (Metabolic Control Analysis).
Friday
Feedback and robust (integral) control in reaction kinetic systems. Homeostasis. Formulation and deadline for the compulsory delivery. Course evaluation.
Exam and evaluation (including the essay)
- Pass/fail
Work requirement
After the lectures have been completed, students work on a compulsory delivery.
Minimum 80% attendance and approved compulsory delivery.
Syllabus
Lectures are based on: Athel Cornish-Bowden, Fundamentals of Enzyme Kinetics, Fourth Edition, Wiley-Blackwell and handouts/papers. Prior to the lecture, please get a Matlab licence from your university (or UiS) and install gnuplot on your computer. For details about installing Matlab and gnuplot see the Welcome page in the ‘Announcements’ tab on Canvas.
Learning outcome
The candidate will be able to design and conduct enzyme kinetic experiments, has knowledge and general competence about the different classes of enzyme mechanisms, including inhibition, activation, and allosteric mechanisms. The candidate learns experimental and computational skills, methods how to extract rate parameters from experiments, estimate their significance and sensitivities, how to set up reaction kinetic models and how to perform simulation calculations.
