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During our first lecture of plant physiology, our teacher told us that the separation of biochemical synthesis pathways was advantageous because it was safer and more economical. The problem I got, while studying this back at home, was that he didn't explain why it is so.

I can understand why it is safer (for example, a lysosome could break down a lot of major components of the cell if that lysosome was not restricted to its area), but it's quite difficult for me to understand why it's more economical, in terms of energy. Any clear/simple explanation about this would be greatly appreciated.

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False Economies?

Goodness knows what the poster’s teacher meant by saying that the separation of biochemical pathway is “more economical”! This is not a term usually applied to metabolism and, anyway, in life people who are economical do not always get value for the money they do spend, never mind obtain a better quality of life.

Most treatments of the separation of biochemical pathways justifiably emphasize the advantages of being able to regulate forward and reverse reaction sequences independently. However let us have a look at the separation of pathways in terms of energy, as the poster requested.

Some basic thermodynamics

The poster also requested the explanation be clear and simple. The following is simple, as long as you are familiar with the some basic ideas of chemical thermodynamics. If you are not, I suggest you read the three pages in Section 8.2 of Berg et al. online. (Whether it is clear or not I leave others to judge.)

  • What determines whether a chemical reaction proceeds is the overall (Gibbs) free energy change (ΔG). If it is negative, the reaction is thermodynamically favourable.
  • The actual free energy change depends on ΔG0, the standard free energy change (reflecting the chemistry of the reaction(s)), together with the actual concentrations of reactants and products.
  • Enzymes are necessary to catalyse reactions in living organisms, but do not affect the position of their equilibrium.

Argument

For simplicity, let us consider a series of reactions interconverting compounds M and P:

M ⇄ N ⇄ O ⇄ P

No separation between pathways

Consider a situation in which the forward (M➞P) and reverse biochemical transformations (P➞M) involve the exact same chemical changes catalysed by the exact same enzymes, i.e. no separation between pathways. In order for this to work the overall ΔG0 must be near zero, otherwise reaction in one direction will be very difficult to achieve (require a very high concentration of starting reactant). For a ΔG0 near zero there will be equilibrium (no net reaction) at equal concentrations of M and P. In order to cause a flow of metabolites, say in the forward direction, there must be an increase the concentration of M relative to P.

There are two problems with this.
First, quite a large ratio of M to P, say, would be required to achieve net flow through the pathway, and this would involve having a large pool of unreacted M. (Section 8.2 of Berg et al., cited above, has some calculations that illustrate this.) This may or may be regarded as economical use of thermodynamic energy, but is not particularly economical in the use of resources. However, a ‘pathway’ in which it is employed is glucose transport in the liver (actually a single transport process).
Second, the direction of overall reaction is controlled solely by the ratio of M to P, a situation that lacks flexibility.

Separation between pathways

If separate pathways are involved, the first problem of a single pathway mentioned above is overcome in the following way. Each overall reaction can have a high negative ΔG0, so that it does not require such a large pool of reactant and is essentially unidirectional. One might ask how this can be, as the value of ΔG0 for the chemical reaction, M ⇄ P is fixed. The answer is that separate pathways will involve other reactants, so that the overall forward reaction might be
M + X ➞ P + Y
whereas the reverse reaction might be
P + A ➞ M + B
This is considered for glycolysis and gluconeogenesis in Section 16.3.6 of Berg et al. — with actual equations. The ΔG0, for glycolysis is quoted as – 84 kJ/mol, and that for gluconeogenesis as –38 kJ/mol.

Of course, if both reactions have a thermodynamically favourable values of ΔG0, it is necessary for the cell to prevent the uneconomic cycling of P back to M after it has been formed. However the fact that the pathways are different means that different enzymes will be involved, which are the targets of regulatory molecules that can switch them off and on. These regulatory molecules usual reflect supply and demand, but need not be intermediates in the reaction sequences, and they can act as far more sophisticated ‘switches’ for the enzymes. The particular details of this for glycolysis and gluconeogenesis can be found on the first page of Section 16.4 of Berg et al.

…the price of everything, the value of nothing

So are separated biochemical pathways energetically more economical? The large free energy change that drives these reactions is ‘lost’ as heat, so one could argue that the reverse is actually true. Or, then again, one might say that “you get what you pay for”.

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Imagine the enzyme with four different tasks. Its inhibition disrupts four different pathways. Instead, the separation of pathways into a continuous chain of discrete processes carried out by discrete enzymes prevents "catastrophic disruption," and creates a low-energy landscape for the emergence of new pathways.

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  • $\begingroup$ The concept of modularity in programming (or more specifically in Object Oriented Programming) would be a good analogy. $\endgroup$ – Remi.b Mar 26 '18 at 16:17
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    $\begingroup$ While the claim is intuitive, it would be good to have a reference for this claim. $\endgroup$ – Remi.b Mar 26 '18 at 16:18

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