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ATP Hydrolysis

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shefv

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Can someone explain this questions? I am confused between A and D.
Here is how I approached this questions:

Its asking for spontaneity so I thought of G = H - TS equation.
I thought that ATP hydrolysis increases S and H so it can only be spontaneous under high temperatures. If the temperature is lowered, it may become non spontaneous.

I ruled out D because for a reaction to be non spontaneous, Keq should be small so less products made and more reactants left, meaning that ADP:ATP ratio should be small. But answer choice D is saying the opposite of that.

What am I doing wrong here?

Thanks!
 

texasdevil

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It is important to recognize that Keq is constant at a constant temperature. Therefore, the amount of reactants / products will never change Keq. However, these amounts do change Q, which is defined the same way as Keq, but with reactant and product concentrations that are NOT in equilibrium.

Lets move through these by crossing out the incorrect answers.

A is incorrect because of the wording. It can be safely assumed that a temperature *slightly* below 37C can still be body temperature (as 37C is the typical value for body temperature). It does not make any sense that ATP hydrolysis would be non-spontaneous in this scenario, as therefore all humans would die due to lack of ATP to drive bodily functions.

B is incorrect because ATP hydrolysis produces an H+ ion through its hydrolysis. Therefore, we could infer that ATP hydrolysis would be spontaneous in more basic solutions because -OH is consumed in the reaction (and therefore spontaneity through Le Chatelier's principal)

C is incorrect because enzymes never alter the equilibrium and therefore spontaneity of a reaction, they only alter the rate at which it occurs

D is correct because we would expect ADP and ATP to reach equilibrium conditions.

To help rationalize it, it is important to recognize that ATP hydrolysis is spontaneous at 37C, and a slight change in temperature will rarely if ever alter the spontaneity of the reaction in a biological setting, just because of the variability of bodily systems. In general, systems will always equilibrate if a mechanism exists for the reaction (and ATP hydrolysis definitely has a mechanism :p).
 

shefv

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Thanks!

I have a few other questions on the topic of ATP hydrolysis:

1. Can ATP hydrolysis happen on its own or does the process always require ATPase?
2. Where exactly inside the cell does ATP hydrolysis takes place? It seems that since ATP hydrolysis drives many different processes forward, it would take place almost everywhere in the cell - plasma membrane (for active transport), ribosomes (for protein synthesis), nucleus (for RNA synthesis and DNA replication) etc.
3. If ATP hydrolysis takes place in all the organelles in the cell, would ATPase enzyme also be found everywhere in the cell? I know that there are different names for ATPase based on the type of reaction the ATP hydrolysis is driving forward.
4. Under what conditions does the ATP completely hydrolyze to AMP? Why does the process stop at ADP - why not go all the way to AMP and use up the one ATP molecule to the most of its potential before hydrolyzing another ATP molecule?
 

MrRed

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1. ATP hydrolysis can happen on its own. Every chemical reaction can happen on its own without a catalyst. Even endothermic reactions (reactions that are "non-spontaneous") can happen on their own if the particular conditions the reaction will take place in are favorable.

However, for a reaction to happen several things must occur:
1. the energy of the reactants must be of sufficient magnitude such that a collision between the reactants has enough energy to generate the unstable, high energy transition-state. The transition state is a fleeting entity, a combination of the reactants (in this case ATP + H2O) as they undergo some reaction. This is where enzymes come into play -- by lowering the activation energy; or the energy necessary to generate the transition state from the reactants. They do this by stabilizing the transition state, thus lowering its inherent energy, and making it easier to compose.

2. the reactants must be oriented in such a way that the necessary components of each reactant molecule to participate in the reaction can physically interact with one another. Enzymes can orient the molecules in such a way that the correct parts of each reactant can interact with one another. In the case of ATP hydrolysis, the Oxygen atom of water must be able to directly interact with a phosphorus atom in ATP. The respective enzyme will orient this interaction in the most efficient way possible.

As a quick aside the factors that contribute to the relatively large, negative change in free energy of ATP hydrolysis are:
1. the negative charge repulsion of the phosphate groups bound to each other
2. the greater resonance stabilization capabilities of Pi and ADP on their own as compared to ATP
3. stabilization due to hydration: more H2O molecules can interact with Pi and ADP on their own to stabilize them as opposed to the phosphoanhydride linkage of ATP.

So, we can see that ATP hydrolysis can happen on its own if a water molecule and ATP molecule with sufficient energy collide with one another in just the right way in that the oxygen is oriented in a precise manner which allows it to exchange electronic-density with the phosphorus (this is simplified, you can look up the mechanism of ATP hydrolysis). It comes down to statistics, how many of the H2O and ATP molecules in our body will collide in this precise manner without enzyme catalysis to initiate the reaction? Surely, some will due to the sheer number of molecules of each present in the body, but the proportion is rather low.


2. ATP hydrolysis (more specifically ATP decomposition, not necessarily always required a water molecule itself as the molecule used to break ATP into ADP + Pi) can take place anywhere inside the cell. As just discussed ATP hydrolysis "can" happen on its own. Aside from that, all that is necessary for ATP decomposition to occur very readily is an enzyme that can utilize ATP hydrolysis/decomposition to power some other cellular process, and the right cellular conditions that activate that enzyme. Consider enzymes such as hexokinase, citrate lyase, pyruvate carboxylase, and DNA polymerase.

Hexokinase is a key enzyme in gycolysis, utilizing ATP to phosphorylate glucose into glucose-6-phosphate, a key intermediate in glycolysis and the pentose phosphate pathway. Where does this happen? In the cytoplasm.

Citrate lyase, the enzyme that catalyzes the cleavage of citrate (used as a transport form to get OAA and acetyl CoA from the mitochondria into the cytoplasm) into acetyl-CoA and oxaloacetate utilizing ATP. This again, happens in the cytoplasm.

Pyruvate carboxylase, the enzyme which can generate oxaloacetate from pyruvate using ATP, is found in the mitochondria.

Lastly, DNA polymerases -- the wonderful enzyme family that allow for the replication of DNA -- must utilize the cleavage of a pyrophosphate from deoxynucleotides (either dATP, dCTP, dTTP, or dGTP) to add the respective base (either A, C, T, or G) to the growing DNA strand. Of course, this takes place in the nucleus.


3. As just discussed, ATPases, or enzymes that somehow utilize the cleavage of ATP (or some molecule bearing similar properties; thus it is better to think of all XTPases where X = G, C, A, or T; or even U; as having the potential to power cellular reaction). Yes, we typically think of the Na+/K+-ATPase (and other transmembrane ATPases) which utilizes the hydrolysis of ATP to pump 3Na+ out of and 2K+ into the cell, but in reality all of the enzymes just discussed above (and many, many more!) are ATPases in the sense that they break down ATP into ADP + Pi and use this energy to power another reaction.

4. ATP (adenosine TRIphosphate) can be completely hydrolyzed to AMP under a number of circumstances. However, when ATP is being used rapidly an enzyme called adenylate kinase can actually form more ATP from 2ADP in the reaction: ADP + ADP <--> ATP + AMP. The reaction of DNA polymerase, as an example, cleaves dATP directly to PPi + AMP (which is attached to the DNA strand).
Although I'm not complete sure why the cell does not use ADP as readily as an energy source, I would have to imagine the cleavage of an inorganic phosphate from ADP is simply less energetically favorable than is the cleavage of a phosphate off of ATP. You can look further into this by considering the factors that would come into play (charge distribution on ATP vs ADP, size, enzyme specificity, solvation factors, relative energy of the terminal phosphoanhydride linkages of ATP vs ADP, steric factors, etc.).
 
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MrRed

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Also as an aside your first question can be answered simply and quickly by considering the equation G = Go + RT ln(Q).
G = actual change in free energy
Go = standard change in Gibbs free energy (in the body measured at a pH of 7 and temperate of 25C).
T = temperature in kelvin
R = gas constant; 8.314J/K
Q = reaction quotient. For ATP hydrolysis Q would be [ADP][Pi]/[ATP]
Q is always products over reactants (solids and liquids dont appear), the same as any equilibrium constant K. The difference is that Q is the relative values of the products/reactants NOT at equilibrium.
Since the standard change in free energy per mol of ATP hydrolysis is generally accepted to be -31 to -32kJ/mol, this is Go.

By instantly considering this equation (what you should do on the MCAT when you see spontaneous vs nonspontaneous, aside from the other equation G = H - TS) you can see that if we make [ATP] very low and [ADP} very high then the term RTlnQ becomes very large and positive, thus likely canceling the -32kJ that we set as Go; and thus the reaction will be non-spontaneous.
 
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shefv

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Thank you so much for taking the time to thoroughly explain the topic. It has been a great help :)

Just to clarify, are you saying that ATPases not only dephosphorylates ATP (i.e. are a type of phosphotases) but actually phosphorylates other molecules?

Also, I know the mechanism by why ATP exits the mitochondria but can ATP leave one cell where it is made and enter another cell that might need it?
 

MrRed

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ATPases, by definition, are simply enzymes that catalyze the decomposition of ATP into ADP + Pi and generally use the free energy released in this reaction to power other processes in the cell. So, an ATPase does not necessarily have to phosphorylate another molecule (think about the Na+/K+-ATPase).
However, enzymes that phosphorylate other molecules are called kinases or phosphorylases. Phosphorylases add a phosphate group by using orthophosphate (inorganic phosphate) directly added to its substrate.

Kinases (aka phosphotransferases) always need a nucleophilic -OH present in their target molecule (substrate). The oxygen atom of this -OH group serves the exact same role as does the oxygen atom of water during the hydrolysis of ATP. Thus, kinases are a type of ATPase if they use ATP, in the sense that they are catalyzing the decomposition of ATP into ADP + Pi, however they are more adequately defined by their primary purpose - to add phosphate groups to target molecules. However kinases do not have to use ATP to add a phosphate to another molecule, they can actually add phosphate back on to ADP. Review glycolysis to see examples of this (pyruvate kinase, phosphoglycerate kinase).

ATPase's are generally thought of only as a specific class of enzyme, which is why you usually only think about pumps and some transporters (Na+/K+-ATPase, H+-ATPase, etc) as true classified ATPases. My purpose for using the term ATPase so broadly was to illustrate the fact that in fact the decomposition of ATP to ADP + Pi occurs everywhere in the cell and is used to power a majority of cellular processes. However, it is more correct - in terms of convention - to refer to enzymes by their most specific function. Thus -- you wouldn't refer to protein kinase A (a cAMP dependent kinase activated in the glucagon signaling pathway) as a true ATPase, even though it has an inherent ATPase activity in that it must breakdown ATP to ADP + Pi in order for the phosphorylation reaction to proceed.

In general this is how you classify enzymes by standard nomenclature:

Kinase = adds phosphate group to target molecule using a high phosphoryl transfer potential molecule (Ex. Protein Kinase A). Kinases are actually a subclass of transferases.
Phosphatase = removes phosphate group from target molecule (Ex. Protein Phophatase A)
Oxidoreductases = catalyze oxidation reduction reactions (Ex. lactate dehydrogenase)
Ligases = join two molecules at the expense of ATP hydrolysis (Ex. DNA ligase)
Lyases = adds groups to double bond or removes groups to form double bond (Ex. fumarase)
Hydrolases = cleaves molecules by the addition of water (Ex. trypsin)
Isomerases = move functional groups within the same molecule (Ex. triose phosphate isomerase)
Transferases = transfer functional groups between two different molecules
 
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MrRed

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If I may -- I would recommend reading the section on Enzymes in the book Lehninger Principles of Biochemistry. This book will literally have everything you need to know about enzymes, and can likely describe it much better than I can myself.

Alternatively, you can do what I do most of the time and wikipedia the terms. Then hop around, click all the links on that wikipedia page and read them, by the end you will probably have a good idea of whatever it is you were searching for.

To the question about if ATP can exit the cell and go to another cell that needs it. I would say in general, from what I understand, ATP is both produced and used within the cell that needs it; the majority of the time. This is why blood glucose levels are so important -- glucose needs to be in the blood (simplified, as cells can and do use other molecules as substrates for ATP production pathways) so that cells can take it up and make ATP with it.

So, in general, I would assume that again: the majority of ATP is both produced and used within the same cell. However, like anything in biology -- this is most likely not an absolute. You'll have to do more research on the topic.
 
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