Thermodynamics question

[Pewl]

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I recall seeing this question somewhere on a qbank or qbook: there's like this reaction going from A--->B--->C--->D--->E---->F and they give you the free energy at each part of this reaction. Then, they ask you at which intermediate will the reaction likely be halted at. I keep forgetting whether it's a negative or positive free energy that causes you to stop where?

anyone know?

 

[Monica Lewinsky]

The negative free energy reactions are the rate-limiting steps.

 

[cyclohexanol]

I recall seeing this question somewhere on a qbank or qbook: there's like this reaction going from A--->B--->C--->D--->E---->F and they give you the free energy at each part of this reaction. Then, they ask you at which intermediate will the reaction likely be halted at. I keep forgetting whether it's a negative or positive free energy that causes you to stop where?

anyone know?

Something like this might show up on the actual exam (hint). I know I started having MCAT flashbacks when I saw it.

 

[penguinophile]

The negative free energy reactions are the rate-limiting steps.

Maybe I am missing something, but I honestly don't see how you are getting that free energy (a thermodynamic principle) dictates the rate limiting step (a kinetic principle).

As far as I know a negative free energy is supposed to mean that the reaction is spontaneous, thus going back to the OPs questions, whenever a Gibbs free energy is positive, that reaction is unfavorable, so unless it is coupled to another reaction or uses a charged reactant (ATP, UDP-glc, Biotin...whatever you need) that reaction shouldn't happen.

 

[R_C_Hutchinson]

Maybe I am missing something, but I honestly don't see how you are getting that free energy (a thermodynamic principle) dictates the rate limiting step (a kinetic principle).

As far as I know a negative free energy is supposed to mean that the reaction is spontaneous, thus going back to the OPs questions, whenever a Gibbs free energy is positive, that reaction is unfavorable, so unless it is coupled to another reaction or uses a charged reactant (ATP, UDP-glc, Biotin...whatever you need) that reaction shouldn't happen.

I think he/she is referring to the notion that generally in a pathway the tightly-regulated, committed (and in-vivo rate limiting) steps are "irreversible," big negative free energy ones. This is the result of evolution and the natural advantage of not building up intermediates when a pathway isn't needed and, less directly, having less propensity for futile cycles and energy waste.

But you're right, if you have an unregulated system of just a bunch of reactions, the slowest, highest delta G would then likely be the part of the reaction that has the biggest influence on where things go. Very low free energies in the reactions "around" such a step can push over an unfavorable reaction via lechatelier's principle.

The question of a rate limiting step in a free, unregulated system of catalyzed or uncatalyzed reactions is dependent on the energy of the transition state, propensity towards proximity of reactants, free thermal energy and how much the catalyst can drop the free energy peak of the transition state. I guess that's just a long-winded way of saying that although a wooden desk and oxygen would be much happier as water and carbon dioxide, the reaction of the desk burning at room temp is extremely slow. Slower still is the fusion of light atomic nuclei, though pound-for-pound it beats anything energywise that can be seen in electron bonds. Other reactions with less negative free energy, like frozen water melting to liquid at room temp go a lot faster not because their free energies are lower but because their peak transitional state energies are so much more easily attained under STP kind of conditions.

 

[Pewl]

Uh.... so given a list of delta G's as answers choices, which would be the correct answer, as far as where the reaction would get stuck at?

 

[Monica Lewinsky]

Maybe I am missing something, but I honestly don't see how you are getting that free energy (a thermodynamic principle) dictates the rate limiting step (a kinetic principle).

As far as I know a negative free energy is supposed to mean that the reaction is spontaneous, thus going back to the OPs questions, whenever a Gibbs free energy is positive, that reaction is unfavorable, so unless it is coupled to another reaction or uses a charged reactant (ATP, UDP-glc, Biotin...whatever you need) that reaction shouldn't happen.

You are right, but usually the large negative free energy steps are the regulated, and thus rate-limiting steps.

In most biochemical pathways, these steps tend to have large negative delta G's whereas the "positive" delta G steps in between tend to have such a small free energy change that the equilibrium gets pushed by forward by the large negative delta G steps ahead (imagine a car going down a somewhat bumpy track, the "positive changes" are well-negated by the overall "negative" energy change).

Pewl, I need more info. about the question. Are they assuming there are biological enzymes there (as opposed to the reactions occuring spontaneously)? Would they actually ask something like this on Step 1?

 

[R_C_Hutchinson]

Would they actually ask something like this on Step 1?

Somewhere on some qbank I remember seeing a question like this:

   1     2     3     4
A --> B --> C --> D --> E
 +.02  -8.6  -3.3  -9.7

The question was something to the effect of "The figure depicts the free energy changes for a pathway involving the metabolism of a compound. Which step is most likely rate limiting?"

Then it had a k-type group of answer choices. As for whether or not it would show up on boards I have no idea. In answer to pewl, I think they'd have to tell you whether you were dealing with a biological pathway or just a set of reaction intermediates. If they gave a graph with reaction as the x axis I'd pick the transition state energy, if they gave a pathway and said it involved enzymes in vivo, I'd pick the first substantial negative energy step.