committed step in the TCA

[theonlytycrane]

Kaplan emphases this as isocitrate to alpha-ketoglutarate via isocitrate dehydrogenase. I always learned this as oxaloacetate + acetyl-coa to citrate via citrate synthase. How did you learn it?

This is just me being curious as to what others learned! Knowing the 3 regulated enzymes of the cycle is most important.

---

Members don't see this ad.

 

[Integrated MCAT Course]

Citrate synthase is generally taken to be the committed step. Citrate synthase is extremely exergonic (driven by the thioester substitution) and allosterically regulated, so it has the right properties of the committed step, and there's no major branching pathway between citrate and alpha-ketoglutarate, unlike G6P in glycolysis (which can go towards pentose phosphate or glycogen synthesis) so I'm not sure where Kaplan is coming from with this one.

 

[meg_2020rwj]

Citrate synthase is generally taken to be the committed step. Citrate synthase is extremely exergonic (driven by the thioester substitution) and allosterically regulated, so it has the right properties of the committed step, and there's no major branching pathway between citrate and alpha-ketoglutarate, unlike G6P in glycolysis (which can go towards pentose phosphate or glycogen synthesis) so I'm not sure where Kaplan is coming from with this one.

This is not quite correct, citrate is an intermediate in fatty acid synthesis and can thus shunt into this pathway. The citric acid cycle is not usually considered to have a "committed step" as PFK-1 in glycolysis. As you said, the three enzymes in the citric acid cycle that catalyze reactions with a highly negative free energy are the most highly regulated enzymes: citrate synthase, isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase.
A good resource that explains this is Ferrier's Biochemistry (Lippincott's Illustrated Reviews Series), page 114. As a science writer (for a small startup called Draw it to Know it) and a future medical student (Rutgers RWJMS Class of 2020) I have found Kaplan to be unreliable when it comes to specifics. The start-up I write for has a great MCAT prep course that I genuinely believe is the best resource out there...though I know I am a little biased!

 

[betterfuture]

Kaplan emphases this as isocitrate to alpha-ketoglutarate via isocitrate dehydrogenase. I always learned this as oxaloacetate + acetyl-coa to citrate via citrate synthase. How did you learn it?

This is just me being curious as to what others learned! Knowing the 3 regulated enzymes of the cycle is most important.

Are you talking about the rate determining step?

 

[theonlytycrane]

@betterfuture yep! The 3 highly regulated steps of the TCA are what is most important to know.

@meg_2020rwj Interesting resource for students! I feel like it's a bit pricey though for only videos 😵

 

[betterfuture]

@betterfuture yep! The 3 highly regulated steps of the TCA are what is most important to know.

@meg_2020rwj Interesting resource for students! I feel like it's a bit pricey though for only videos 😵

Wait, so what are the other 2? Are they the 1st, 3rd and 4th step of TCA?

 

[theonlytycrane]

@betterfuture

1. oxaloacetate + acetyl-coa -> citrate via citrate synthase

2. isocitrate -> alpha-ketoglutarate via isocitrate dehydrogenase

3. alpha-ketoglutarate -> succinyl-coa via alpha-ketoglutarate dehydrogenase complex

 

[Lawpy]

Kaplan emphases this as isocitrate to alpha-ketoglutarate via isocitrate dehydrogenase. I always learned this as oxaloacetate + acetyl-coa to citrate via citrate synthase. How did you learn it?

This is just me being curious as to what others learned! Knowing the 3 regulated enzymes of the cycle is most important.

I don't think there are any committed steps in citric acid cycle, because the intermediates play a role in other metabolic pathways. Examples include succinyl-CoA for heme biosynthesis and alpha-ketoglutarate for amino acid metabolism. Even the citric acid cycle enzymes play various metabolic/physiological roles like succinate dehydrogenase for the electron transport chain and aconitase as an iron regulatory protein sensitive to blood iron levels.

If I have to pick a step that's considered committed, it'd probably be citrate synthase, since that's the start of the cycle.

 

[meg_2020rwj]

@betterfuture yep! The 3 highly regulated steps of the TCA are what is most important to know.

@meg_2020rwj Interesting resource for students! I feel like it's a bit pricey though for only videos 😵

The tutorials do come with multiple choice quiz questions...and many medical schools have already bought subscriptions to Draw it to Know it's upper level courses such as Gross Anatomy and Neuroanatomy (like Thomas Jefferson Medical School in Philly, Washington University, etc.) which lends it more credibility than your average test prep company. I didn't think $14.99/month was very pricey compared to the MCAT materials out there, especially considering how scarce existing resources are for the new version. But regardless, you can also find Draw it to Know it on Youtube or follow them on Facebook/twitter for MCAT worthy questions if price is an issue! Hope my earlier citric acid cycle response helped 🙂

 

[aldol16]

I don't think there are any committed steps in citric acid cycle, because the intermediates play a role in other metabolic pathways. Examples include succinyl-CoA for heme biosynthesis and alpha-ketoglutarate for amino acid metabolism. Even the citric acid cycle enzymes play various metabolic/physiological roles like succinate dehydrogenase for the electron transport chain and aconitase as an iron regulatory protein sensitive to blood iron levels.

Well, remember the intermediates have the same number of carbon units as oxaloacetate. In other words, they serve essentially "catalytic" functions. Once acetyl-CoA enters the TCA cycle, the two carbons (not exactly the same two carbons that entered, but two nonetheless) must leave as CO2.

 

[Lawpy]

Well, remember the intermediates have the same number of carbon units as oxaloacetate. In other words, they serve essentially "catalytic" functions. Once acetyl-CoA enters the TCA cycle, the two carbons (not exactly the same two carbons that entered, but two nonetheless) must leave as CO2.

But do they have to? I'm not sure whether the citric acid cycle has to be completed all the way with all the other metabolic pathways going on in the background. So it could be, say, oxaloacetate --> citrate --> isocitrate --> alpha-ketoglutarate, but then shunt away from the cycle and participate in amino acid metabolism or other pathways. So in this case, only one carbon is lost as CO2

That's why i don't think the citric acid cycle itself has a committed step. Rather the pathways shunting citric acid intermediates away from the cycle has the first committed step that is strictly regulated for specific needs.

 

[aldol16]

But do they have to? I'm not sure whether the citric acid cycle has to be completed all the way with all the other metabolic pathways going on in the background. So it could be, say, oxaloacetate --> citrate --> isocitrate --> alpha-ketoglutarate, but then shunt away from the cycle and participate in amino acid metabolism or other pathways. So in this case, only one carbon is lost as CO2

That's why i don't think the citric acid cycle itself has a committed step. Rather the pathways shunting citric acid intermediates away from the cycle has the first committed step that is strictly regulated for specific needs.

Yes, but those intermediates shunted off must eventually be replenished so the TCA cycle can go on - it's a mass balance issue. So once you do the final count, you'll see that two carbons must leave overall as CO2. In other words, it can't ever go back to acetyl-CoA. That's what a committed step is. Once you commit to the pathway, you can't go back. The TCA cycle must complete (eventually at least) and once it completes, two CO2 must have been released.

 

[Lawpy]

Yes, but those intermediates shunted off must eventually be replenished so the TCA cycle can go on - it's a mass balance issue. So once you do the final count, you'll see that two carbons must leave overall as CO2. In other words, it can't ever go back to acetyl-CoA. That's what a committed step is. Once you commit to the pathway, you can't go back. The TCA cycle must complete (eventually at least) and once it completes, two CO2 must have been released.

I agree with that, but then the question lies as to where the committed step is. The best guess I have is citrate synthase, since it uses up the acetyl-CoA synthesized from pyruvate and releases it (eventually/indirectly) in the form of two CO2 molecules.

Coming to think of it more closely, it actually makes sense in most cases for the first regulatory (high negative free energy) step of the metabolic pathway to be a committed step. Of course, this doesn't apply to glycolysis because glucose-6-phosphate is shunted to other pathways, but in most cases it works. Someone mentioned about citrate being used for fatty acid synthesis, but I looked into it and it is essentially just broken down to acetyl-CoA in a reaction that is basically just the opposite to the one catalyzed by citrate synthase. So I guess it'd make sense for citrate synthase to be truly a committed step for citric acid cycle.

 

[Integrated MCAT Course]

I think and aldol16's comments are very useful, that the branches from succinyl-CoA or alpha-ketoglutarate do not invalidate the idea of citrate synthase as the 'committed step' because the oxaloacetate portion is essentially playing a catalytic role. That's just a very good thing to understand. However, I do think Meg2020's point above is very useful too, regarding citrate's role in fatty acid synthesis. In that case, the oxaloacetate portion is acting as a shuttle to transport the acetyl-CoA to the cytosol, with the oxaloacetate returning later (if it isn't used for gluconeogenesis) back to the mitochondrion as malate. However, the second part of the comment which uses this instance to make a general dig at Kaplan might not be so fair, at least in this case, because the branch between oxidative degradation on the one hand or transport to the cytosol for fatty acid synthesis on the other must actually be the rationale for Kaplan's assertion of isocitrate dehydrogenase as the committed step of the TCA. It's not consistent with what I was taught a long time ago but it makes sense.

My own feeling is that the concept of 'committed step' is a little bit loose conceptually. The classic model of a committed step is PFK-1 in glycolysis. It's exergonic, with multiple levels of regulation, and it occurs just after the branch point between glycolysis, the pentose phosphate pathway and glycogen synthesis. You want an idea like 'committed step' to capture what's going on here. However, just because the PFK-1 reaction occurs doesn't mean glycolysis is going to go all the way to the end. 3-phosphoglycerate might become a precursor for serine, cysteine, and glycine, for example, or phosphoenolpyruvvate for phenylalanine, tyrosine, or trypotophan.

 

[aldol16]

I agree with that, but then the question lies as to where the committed step is. The best guess I have is citrate synthase, since it uses up the acetyl-CoA synthesized from pyruvate and releases it (eventually/indirectly) in the form of two CO2 molecules.

Coming to think of it more closely, it actually makes sense in most cases for the first regulatory (high negative free energy) step of the metabolic pathway to be a committed step. Of course, this doesn't apply to glycolysis because glucose-6-phosphate is shunted to other pathways, but in most cases it works. Someone mentioned about citrate being used for fatty acid synthesis, but I looked into it and it is essentially just broken down to acetyl-CoA in a reaction that is basically just the opposite to the one catalyzed by citrate synthase. So I guess it'd make sense for citrate synthase to be truly a committed step for citric acid cycle.

I agree with your first point and it makes sense.

I do not agree with your second point because you're talking about two different processes - Krebs cycle and fatty acid biosynthesis. These are two separate pathways. The citrate is only acting as a "shuttle" in the latter. That means that it must be transported back into the mitochondria to replenish your stores of oxaloacetate - otherwise, fatty acid biosynthesis wouldn't be able to occur at all since oxidative phosphorylation would grind to a halt.

So the only possible objection lies in the fact that oxaloacetate + acetyl-CoA in the mitochondria can be reversed in the cytosol. What people don't remember is that the cleavage of citrate to form OAA and acetyl-CoA in the cytosol requires ATP hydrolysis - in other words, it's highly endergonic. So you can think of that as a "bypass" reaction similar to F1,6BPase in gluconeogenesis, which bypasses a strongly endergonic reaction. That supports the idea of citrate synthase being the committed step in the Krebs cycle. Before somebody objects to this analysis, I'm not saying that a reaction is the committed step of any pathway just by virtue of being strongly exergonic. I'm saying that a reaction being strongly exergonic is highly suggestive of it being a committed step which, when taken with other evidence, becomes convincing.

 

[Integrated MCAT Course]

aldol16 said 'The citrate is only acting as a "shuttle" in the latter. That means that it must be transported back into the mitochondria to replenish your stores of oxaloacetate '

I'm sorry. I'm not really following. By your usage it seems that citrate is a 'shuttle' in either case. Oxaloacetate receives two carbons becoming citrate in the citrate synthase step. Then the path branches towards either TCA or fatty acid synthesis, either of which regenerate oxaloacetate. Citrate synthase does not seal the fate of those two carbons. The up or down regulation of isocitrate dehydrogenase does. Whether those two carbons become CO2 or part of a fatty acid, whichever path is taken, oxaloacetate is going to return.

Am I missing something?

 

[Lawpy]

I agree with your first point and it makes sense.

I do not agree with your second point because you're talking about two different processes - Krebs cycle and fatty acid biosynthesis. These are two separate pathways. The citrate is only acting as a "shuttle" in the latter. That means that it must be transported back into the mitochondria to replenish your stores of oxaloacetate - otherwise, fatty acid biosynthesis wouldn't be able to occur at all since oxidative phosphorylation would grind to a halt.

So the only possible objection lies in the fact that oxaloacetate + acetyl-CoA in the mitochondria can be reversed in the cytosol. What people don't remember is that the cleavage of citrate to form OAA and acetyl-CoA in the cytosol requires ATP hydrolysis - in other words, it's highly endergonic. So you can think of that as a "bypass" reaction similar to F1,6BPase in gluconeogenesis, which bypasses a strongly endergonic reaction. That supports the idea of citrate synthase being the committed step in the Krebs cycle. Before somebody objects to this analysis, I'm not saying that a reaction is the committed step of any pathway just by virtue of being strongly exergonic. I'm saying that a reaction being strongly exergonic is highly suggestive of it being a committed step which, when taken with other evidence, becomes convincing.

aldol16 said 'The citrate is only acting as a "shuttle" in the latter. That means that it must be transported back into the mitochondria to replenish your stores of oxaloacetate '

I'm sorry. I'm not really following. By your usage it seems that citrate is a 'shuttle' in either case. Oxaloacetate receives two carbons becoming citrate in the citrate synthase step. Then the path branches towards either TCA or fatty acid synthesis, either of which regenerate oxaloacetate. Citrate synthase does not seal the fate of those two carbons. The up or down regulation of isocitrate dehydrogenase does. Whether those two carbons become CO2 or part of a fatty acid, whichever path is taken, oxaloacetate is going to return.

Am I missing something?

Sorry i'm a little lost. When i say that a TCA intermediate is being shunted off to another pathway, i mean the intermediate is directly metabolized into another, different product. Like alpha-ketoglutarate being metabolized to glutamate, or succinyl-CoA being metabolized to a precursor molecule for heme synthesis. Since the intermediates are used for very different purposes, the first step in this shunting mechanism is usually strongly exergonic and committed step. Why? Because you want to trap the TCA intermediates for the designated pathway to avoid returning to TCA cycle

Citrate doesn't work in this case. Citrate synthase simply produces citrate from oxaloacetate and acetyl-CoA. The citrate used for fatty acid is basically just producing acetyl-CoA in a reverse reaction catalyzed by an ATP-dependent enzyme. Since citrate itself isn't directly metabolized, it wouldn't be accurate to say citrate is shunted off elsewhere like alpha-ketoglutarate and succinyl-CoA. It's the acetyl-CoA that's being shunted off for fatty acid synthesis.

Of course, this is all semantics, but if citrate isn't metabolized directly, it would make sense for citrate synthase to be a commited step in TCA cycle. However, isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase complex aren't commited steps because the products of these reaction can be directed away to other metabolic pathways. This is analogous to why hexokinase isn't a commited step in glycolysis because glucose-6-phosphate can be used in glycogen synthesis and pentose phosphate pathway.

 

[aldol16]

I'm sorry. I'm not really following. By your usage it seems that citrate is a 'shuttle' in either case. Oxaloacetate receives two carbons becoming citrate in the citrate synthase step. Then the path branches towards either TCA or fatty acid synthesis, either of which regenerate oxaloacetate. Citrate synthase does not seal the fate of those two carbons. The up or down regulation of isocitrate dehydrogenase does. Whether those two carbons become CO2 or part of a fatty acid, whichever path is taken, oxaloacetate is going to return.

For some reason, you're merging two pathways into one extended pathway. If you want to talk about the Krebs cycle, acetyl-CoA going to citrate must be the committed step because once that occurs, those two carbons don't have a choice but to complete the reaction. Why? Because although intermediates can be shunted off into other pathways, you must always replace OAA because it's catalytic. That's the very definition of a catalyst. So if you're talking about the Krebs cycle as a full reaction, the first step is the committed step.

Now, if you're talking about fatty acid biosynthesis, acetyl-CoA + OAA ---> citrate isn't part of reductive biosynthesis. All it does is transport acetyl-CoA to the cytosol for reductive biosynthesis to occur. Once it does that, OAA must be transported back into the mitochondria - otherwise, the Krebs cycle would grind to a halt.

Acetyl-CoA has multiple fates, yes. But once it enters the Krebs cycle, it must produce the two CO2. Because that's the very purpose of the Krebs cycle. Once it enters the fatty acid biosynthesis pathway at the stage of acetyl-CoA carboxylase, it becomes committed to fatty acid biosynthesis. These are distinct pathways.

This is not a clear distinction. That's why people are arguing here. This is also why we usually don't teach a "committed" step in the Krebs cycle. The term itself is loaded and can be interpreted in multiple ways.