Next planned course: Fall 2022
Registration deadline: TBD
Course responsible: Prof. 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 Matlab and Gnuplot installed on your computer prior to the course. Access to Matlab should be available through your University. It is also possible to get access through UiS if need be. Gnuplot is a free download.
Students should register to BioCat through the form at the bottom of this page, as well as:
- UiS students should register as normal through the UiS registration system
- Non-UiS students only need to register to BioCat through the form below.
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 and approved, students work on an essay with a self-chosen (needs to be approved) topic or a given topic related to enzyme kinetics.
Some minor elements of the course may vary from what is detailed below due to the online format.
- Introduction. Students’ backgrounds and Interests.
- Review of basic kinetic principles and terms. Steady states. Catalysis (Ch. 1 and handouts).
- Tools to solve chemical rate equations (handout).
- Historical Perspectives on Enzymes. The Michaelis-Menten Equation and its parameters. Traditional parameter determinations and nonlinear curve fitting methods. (Ch.2 and handouts).
- Computer exercise: Studying rapid equilibrium vs. steady state systems.
- Enzyme assays, cooperativity, choice of pH, temperature (Ch. 4).
- Deriving Steady States (King-Altman method; parts of Ch. 5).
- Hysteretic (non-steady state) enzyme kinetics (handout). Examples.
- Reversible Inhibition and activation (Ch. 6).
- Instrumental methods to study enzyme kinetics
- Lab exercise: Influence of pH on alkaline phosphatase.
- Effect of pH on Enzyme Activity. Diprotic Model. Analyzing the experimental data from the day before.
- Influence of temperature on enzymatic reactions (Ch. 11).
- Regulation of Enzyme Activity (Ch. 12)
- Lab exercise: Using Isothermal Titration Calorimetry in Enzyme Kinetics
- Multi-enzyme systems. Metabolic control analysis and sensitivity analysis.
- Control engineering concepts and robust control. Positive and negative feedback mechanisms (handout). Examples.
- Enzymes and signal transduction: ultra-sensitivity (handout).
- Computer Exercise: Modeling robust homeostasis.
- Multi-substrate systems (Ch. 8)
- Topic(s) of compulsory Essay(s); dependent on students’ interests.
- Course evaluation
Exam and evaluation (including the essay)
After the lectures have been completed and approved, students work on an essay with a self-chosen (needs to be approved) topic or on a given topic related to enzyme kinetics. After the course the student can keep fully working versions of the simulation software they used during the course.
Minimum 80% attendance and approved project work/report.
Lectures are based on: Athel Cornish-Bowden, Fundamentals of Enzyme Kinetics, Fourth Edition, Wiley-Blackwell and handouts/papers. Please install Matlab and Gnuplot on your home computer.
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.