KKR063 Metabolic Engineering: design of microbial metabolism

Course objectives
The objective of the course is to provide the students with an overview of the different tools available to analyze metabolism and enable them to propose strategies to meet a metabolic design objective. In this course, the students will be presented with several models of microbial metabolism and the advantages and disadvantages of each kind of model will be discussed extensively. Broadly, two kinds of metabolic models will be addressed in this course – steady-state models (stoichiometric models, elementary flux modes, etc) and dynamic models (kinetic models). The students will also get a hands-on experience working with each of the models as part of their assignments, which will be used to design metabolism for selected applications. The assignments are geared to help the student understand metabolism, rather than on model development. Consequently, there will be a strong emphasis on interpreting the results obtained from the models. The overall aim of the course is to train the students such that they will be capable of working independently in the area of metabolic engineering.

Learning objectives
At the end of the course, the students should be able to:

  • Understand the principles of enzyme function and kinetics
  • Describe physiology in a quantitative manner
  • Learn stoichiometry and energetics of metabolism
  • Extend stoichiometric analysis of metabolism to mass balancing
  • Learn to apply concepts of linear programming to metabolic models
  • Implement these concepts to genome-scale metabolic models
  • Understand the use of radiolabeled tracers in metabolic studies
  • Analyze metabolic pathway utilization in product formation
  • Appreciate the contribution of technology to understanding metabolismImprove oral and written presentation skills

Course prerequisites
Students interested in taking this course are expected to have basic knowledge of biology and algebra. Programming skills in any language are not required, but will be useful.

The medium of instruction, assignments and examination will be in English. The course will be held on Tuesday and Thursday afternoons. This time will be dedicated to lecture and providing directions to complete the assignments. The class will meet in Rooms KS91 or KS11.
Detailed information on the course, hand-outs for the lectures, assignments, etc will be available from the website ( The username and password will be given to course participants on the first meeting time.

The final grade will depend on a group project that is worth 40%, assignments 30% and an examination, the remaining 30%. For the project, the students will form groups of 2-3 and select a metabolic objective in consultation with the instructor. They will work towards designing metabolism to meet the objective. The results will be presented in the form of a report as well as an oral presentation.

Teaching material
The relevant reading material will be posted as lecture notes on the course website. Frequently, references will be made to the textbook Metabolic Engineering that is available in electronic form from the Chalmers library. The slides used during the lecture will also be made available on the website. Additional literature pertaining to the specific lecture will also be mentioned.


Jens Nielsen:

Sergio Bordel:

Chalmers University of Technology,
Department of Chemical and Biological Engineering, Systems Biology,
Kemivägen 10,
SE-412 96 Göteborg, Sweden