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Bioinformatics thus makes it possible to better describe and understand metabolism,

to predict essential genes and resulting antibiotics as well as metabolic responses, for

example in tumour growth or for bacterial cell wall synthesis. ◄

4.3

Exercises for Chap. 4

As an introduction, it is advisable to work through the exercises in Chap. 11 (Sect. 11.1,

11.2, 11.3, 11.4, 11.5, and 11.6).

Modelling metabolic networks:

Task 4.1

Describe how metabolic pathways can be calculated bioinformatically. Also state possible

problems with metabolic modelling.

Task 4.2

Name a computational program for metabolic pathways.

Task 4.3

Explain how to compile all the enzymes of glycolysis for a metabolic pathway. What

advantages do you have in each case when you compare several databases?

Task 4.4

Explain what is meant by elemental mode analysis.

Task 4.5

You want to develop a new antibiotic. Which enzymes in your metabolic pathway could be

interesting antibiotic targets?

Task 4.6

Perform elementary mode analysis on the citrate cycle/citric acid cycle in E. coli. First

download Metatool (https://www.bioinfo.biozentrum.uni-­wuerzburg.de/computing/meta­

tool_4_5/). Then create the Metatool file for the citrate cycle/citric acid cycle in E. coli

yourself and carry out an analysis.

Look at the metabolic network in Metatool and answer the following questions:

1. How many modes do I get?

2. How do I interpret my found modes in terms of finding drugs/targets against

bacteria?

To better understand an elemental mode analysis, you should also answer the following

questions:

4.3  Exercises for Chap. 4