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maybe this is more bioengineering than biology but I didn't find any such group.

So I got the following photo: enter image description here

And I was asked to do the following for the network inside the red area.
1) Write the stoichiometric matrix for the network
2) Draw a pathway map for the network
3) Draw primary metabolite connectivity maps
4) Write the mass balance equations for primary metabolites

I know that for the first one the columns are the reactions taking place and the lines are the "chemicals". Should the markings on the columns be the same as the numbers that are written on each reaction? (like "3.1.1.31") Almost every reaction can go in both direction, is there anything that says which chemical should get minus and which one gets plus? My attempt at the matrix was: enter image description here

As for the pathway map, isn't that basically the photo is given?
And finally what would be a "primary metabolite" in this case?

All help and hints very well appreciated!

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This is not a particularly well written homework question. I'll try to give some hints based on how I interpret it.

1) The stoichiometric matrix. You have exactly the right idea. I would write the reactions as enzyme names or gene names instead of the EC numbers (e.g. G6PD or G6P dehydrogenase instead of 1.1.1.49). For the reversible reactions, there's no a priori reason to write them in one direction or another, but convention would be to make glucose consumption the positive direction. I would not include "glycolysis" as a separate reaction. I would also consider including cofactors and byproducts in the molecules affected by the reaction (e.g. CO2, NADP+, NADPH, (maybe ADP, ATP, NAD+, NADH also if those come up)).

2) Yes, it's basically what you already have. It's not a particularly great diagram, so you could draw it in a clearer way.

3) I have no idea what this means, but perhaps the next point will help.

4) Primary metabolite is not a super well-defined term, but I think in this context, I would say that the way they're intending the question, they're looking for a "total pathway reaction" that describes the net inputs and outputs of the pathway.

Something like this:

$$ X_1 G6P + X_2 NADP+ \implies X_3 GAP + X_4 FBP + X_5 CO_2 + X_6 NADPH $$ (G6P=Glucose-6-phosphate, GAP=Glyceraldehyde-3-phosphate, FBP=Fructose-bis-phosphate)

I'll leave it to you to figure out what the X's are or whether I left anything out (since it's a homework assignment after all.)

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  • $\begingroup$ Thank you so much! But okay since H6PD has the same EC numbers as the two reactions below (1.1.1.49 and 3.1.1.31) should that be considered as a separate reaction or is it enough to only have the other two? Also if glycolysis shouldn't be included as a separate reaction how do I mark down the carbon going in and out of the network? $\endgroup$ – Berghor Feb 4 '17 at 10:20
  • $\begingroup$ Yeah some enzymes will catalyze more than one reaction. You'll have the same problem with transketolase. Nothing wrong with suffixing them _A and _B or whatever. I didn't mean to say that using the EC numbers was wrong either -- I would just say that if you want human-readable names, biologists/biochemists are more likely to recognize gene names. Few people have the entire EC number hierarchy in their head. $\endgroup$ – Victor Chubukov Feb 4 '17 at 16:22
  • $\begingroup$ Sorry, misunderstood your first question. Each reaction should only appear once, however you name it. The EC number (1.1.1.49) refers to the type of biochemical reaction going on. The gene name refers to the enzyme that catalyzes that reaction. They refer to the same reaction, just in different ways. $\endgroup$ – Victor Chubukov Feb 4 '17 at 16:24
  • $\begingroup$ As for carbon going in out, you sort of already have this (e.g. a -1 for G6P in the G6PD (1.1.1.49) reaction. At the end of the day, the point of this matrix is that if you multiply your matrix by a vector of how much flux is going through each reaction, you'll get a vector with an entry for each metabolite that tells you how much is being produced or consumed. For this to be sensible, every reaction should be mass-balanced (so nothing that produces something out of thin air). $\endgroup$ – Victor Chubukov Feb 4 '17 at 16:29

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