Summary
Genome-scale models predict growth and pathway usage under constraints.
In depth
Genome-scale models such as Recon3D link thousands of reactions. Flux balance analysis optimises an objective (e.g. growth). Used for drug target identification and metabolic engineering.
Constraint-based models predict flux with minimal data. Integrating omics improves predictions. Models guide diagnosis and strain design.
Key idea: metabolism is a network, not a set of isolated pathways.
Genome-scale metabolic models (GEMs) reconstruct all known reactions of an organism from its genome annotation into a stoichiometric matrix. The first, for Haemophilus influenzae in 1999, was followed by E. coli, yeast and human (Recon).
Flux balance analysis assumes steady state and optimises an objective such as growth rate, to predict fluxes, gene essentiality and growth on different substrates, without needing kinetic parameters. Models guide strain design and identify drug targets in pathogens and cancer, and integrate omics data. Limits include missing annotations and regulation not captured.
Example: predicting which gene knockouts make E. coli produce more succinate.
Key idea: network-level constraints can explain behaviour that single reactions cannot.
Frequently asked questions
What is Systems Biology of Metabolism?
Genome-scale models predict growth and pathway usage under constraints.
Which area of biology covers Systems Biology of Metabolism, and how advanced is it?
Systems Biology of Metabolism is one of the 53 topics in Metabolism & Bioenergetics. It is rated Advanced, so it suits learners who want specialist depth. Related topics in this area include Metabolic Engineering, Metabolic Flux Analysis, Metabolomics.
Can you give an example of Systems Biology of Metabolism?
Models predict gene essentiality in bacteria.
What should I learn before Systems Biology of Metabolism?
Work through the Beginner topics in Metabolism & Bioenergetics first, such as Metabolism, Anabolism and Catabolism, ATP, then return to Systems Biology of Metabolism. Advanced topics assume the Intermediate vocabulary.
What topics are related to Systems Biology of Metabolism?
The closest topics to Systems Biology of Metabolism are Metabolic Engineering, Metabolic Flux Analysis, Metabolomics, Anabolism and Catabolism. Comparing them side by side is a good way to see how the ideas connect.
How can I check that I understand Systems Biology of Metabolism?
Read the summary and the in-depth section, then use the quick check on the interactive lesson for Systems Biology of Metabolism. To practise the whole of Metabolism & Bioenergetics, use the Metabolism & Bioenergetics quiz.
How is Systems Biology of Metabolism different from Metabolic Engineering?
Systems Biology of Metabolism: Genome-scale models predict growth and pathway usage under constraints. Metabolic Engineering: Rewiring pathways in microbes to produce fuels, drugs and chemicals. Read both side by side and note what each one explains.
How should I study Systems Biology of Metabolism step by step?
First, read the summary and write the definition in your own words. Second, read the in-depth section and note any example. Third, compare it with Metabolic Engineering and explain the difference aloud. Finally, take the Metabolism & Bioenergetics quiz and come back to this page for any question you miss.