Enzymes contribute energy to a reaction?

[araganzar]

Everything I read says enzymes are organic catalysts and do not supply energy for chemical reactions. My understanding is they speed up reactions by providing alternate pathways that have a lower activation energy.

A quiz I took asked "What type of energy do enzymes contribute to chemical reactions?" I answered that enzymes do not contribute energy. The answer I was given was "kinetic energy." In class, the professor said kinetic energy does not affect the thermodynamics or the free energy change in a reaction. He said it was obvious enzymes were contributing kinetic energy because they were bouncing into the substrate.

My question is, how is that a contribution? If you contribute energy, you are giving it up, and you are supplying it to the reaction.

Yes, the enzymes are of course moving around, and yes, they depend on kinetic stability to hold substrates in place. But are they giving kinetic energy to the reaction, or is there just some interchange going on? I know some enzymes actually operate by placing the substrate under physical stress, but not all enzymes. Otherwise, for every instance where some part of an enzyme imparts momentum to some part of a substrate, there are collisions where the opposite is occurring.

I mean, if I gave you 20 bucks and took it back an hour later, you wouldn't say I "contributed" it to you. And if they are giving kinetic energy, how does that not change the energy of the participants in the reaction? If an enzyme imparts kinetic energy to a substrate, I feel like that is definitely if not useful work at least something that changes the free energy in the system.

This seems to kind of violate the central dogma I keep hearing about catalysts. What am I getting wrong?

 

[madcat8000]

Question number one is what class is this?

As far as my education takes me its been properly drilled into me that there is NO energy exchange what so ever...enzymes and catalysts merely lower (or increase) the activation energy at which an reaction can take place. This has the effect of allowing the present energy to be used to do more work because each individual reaction consumes less energy.

 

[madcat8000]

https://www.physicsforums.com/showthread.php?t=41653

this other thread explains it perfectly.

 

[Ygggdrasil]

If all an enzyme does to speed up a chemical reaction is contribute kinetic energy by bumping into the substrate, then why can't any arbitrary large molecule catalyze the reaction?

Clearly this explanation is wrong because it cannot explain the specificity of enzyme catalysis.

Furthermore, for a system at thermal equilibrium, all molecules have the same average kinetic energy. Therefore, when an enzyme and substrate collide, it is equally probable that the substrate will be transferring kinetic energy to the enzyme.

 

[araganzar]

It's a molecular biology class. My problem is, I can't find a reference that explicitly says enzymes *don't* contribute kinetic energy, or don't contribute any kind of energy that doesn't affect the thermodynamics of the reaction (which is another issue with me, how can you contribute energy and not impact thermodynamics? But I'm willing to accept I don't understand that well enough.) In fact I can find very little about the cost of an enyzme's participation in catalysis.

I agree with everything said here, in fact the thread referenced is what brought me here. Like you guys I kind of thought that was the whole deal with catalysts, so this is a major conceptual stumbling block for me. But I feel like if I am going to bring this up with my professor again I really need to have my ducks in a row.

I come from the understanding that there is not an energy exchange in catalysis, too. I think the issue is with the word "contribution." Clearly there is a cost involved with enzymes. They have to be built in the first place, and there is going to be loss due to the binding and unbinding at the active site. But the fact that it costs energy to construct a protein, and that that protein is built with a certain conformation and different polarities in different places, doesn't mean it makes a contribution to the reactions it is catalyzing. *Something* has to be happening to lower that activation barrier, but even though I find different theories on how that transition state is achieved, none of them assert there is any kind of addition of kinetic energy by the enzyme.

I also agree the kinetic effects involved with collision are random and should sum up to no contribution. But the prof is saying the fit involves the enzyme both making a conformational change in the substrate (stressing certain bonds, etc.) and the substrate taking advantage of the kinetic stability of the enzyme. To me this is like saying a coke bottle is making a contribution of kinetic energy to the liquid it is funneling.

Anyway, I feel like if I can't come back to him with an authoritative source he's going to think I'm blowing smoke. But I don't know what to do when the people I am reading and citing think it's so obvious there is not a contribution they don't mention it, and he thinks it's so obvious there *is* one he doesn't see the need to defend it. And I also don't want to be a jerk about it when there might be a very simple semantic or logical difference that we're not seeing eye to eye on.

 

[Kglocc]

Man I just flipped through my copy of "Principles of Biochemistry" by Lehninger et. al. and it appears very vague concerning the actual contribution of energy from enzymes to catalysis.
What it does say (and what you probably already know) is that enzymes bond to the substrate to from an enzyme/substrate (ES) complex. The ES complex induces the substrate into the transition state by means of transitory covalent and non-covalent bonds, which lower activation energy. The example they give is a metal "stick" (substrate) bound to a row of magnets (enzyme). The product is obtained by breaking the stick into two sticks. So the magnets would bind the substrate into a bent stick. That lowers the activation energy needed to completely break the stick in two.
Maybe kinetic energy your professor talks about is the conformational change induced by binding to the active site on the enzyme? The change in activation NRG equals the kinetic NRG? I don't know, I wouldn't necessarily consider that kinetic, wouldn't it be chemical? bond making/breaking and all... I guess I'd like to see a source clarifying this... sorry for the vague rant. Bump.

 

[araganzar]

As far as it being vague, yes. I've read the comments here. I talked to another professor, as well as read the articles on Tom Bruice's site extensively. What both seem to indicate is there is no clear picture of energy exchange in enzymatic catalysis. In fact even the induced fit model, which every class I have taken uses, is thought by much of what I read to be flawed to the point many think it is in need of revision.

I think the main problem in finding citations supporting the statement that enzymes do NOT contribute kinetic energy (or any other kind of energy) to the chemical processes they are catalyzing is that it is a negative assertion. It is difficult for me to find peer-reviewed articles discussing this even in passing because it's considered to be a pretty basic assumption when dealing with catalysts. The best I can find is a discussion of the mass defect involved in the inevitable energy loss from forming and dissolution of the binding interactions between enzyme and substrate.

So how do I come back to my professor on this? I feel it's not something I can just let go, because it's really thrown a spanner in my conceptual wheels. But I do not wish to be confrontational, and I certainly do not want to have a discussion with him about this when I have nothing to back it up. Is it fair of me to say "I don't want to waste more of your time on this, but I cannot find this in our textbook. Can you give me any references so I can look into it further?"

Here is how I would present my objection to my professor's assertion:

- there is no such thing as contributing "bad" or "non-useful" energy to a reaction. If the energy exchange involved in an interaction is not used to perform some kind of work, then you cannot say the enzyme "contributed" energy. And if it IS used to do work, you cannot say this did not impact the free energy / thermodynamics of the reaction.

- the movement of enzymes in solution with substrate (among other molecules and structures) is stochastic (brownian, random). Even though an enzyme might bounce off a substrate, or "stick" and impart momentum (or more accurately each molecule moves based on their summed momentum), overall within the system the net effect of this kinetic energy exchange with regards to the enzyme is zero. This is a pretty basic principle and doesn't need defending.

- the correlative motion of enzymes in orientation with a substrate is electrostatic in nature and does not involve the transfer of any kind of kinetic energy. The enzyme might donate or receive charge, protons, etc. and it might undergo conformational change, as well as the substrate. But the big rule of enzymes, and all catalysts, is that at the end of the day they are unchanged by the reaction they participated in. Again, change may occur but the net sum for enzymes is zero. And if a molecule is unchanged, it cannot have more or less energy than it started with any more than it can have more neutrons or more carbon atoms. Therefore, if a molecule "contributed" any kind of energy (whether or not you qualify it as "useful" energy) it has undergone a permanent change and therefore cannot be said to be a true catalyst.

- This is not to say that enzymes cannot contribute energy to a reaction. What it says is if this DOES occur on a consistent basis, the enzyme is not functioning purely as a catalyst and is in fact an active participant in the reaction. And if this is supported, then many of the other statements made about enzymes in our courses need to be corrected.

Is this sufficient? What stupid mistakes have I made that a sharp teacher can use to deflate my argument?

 

[gerben]

I would assume you can just ask your teacher nice and friendly about this, no need to make it such a big confrontation. Just tell him that you do not understand how an enzyme contributes any energy. Where are the enzyme's losses?

I'd be really interested in what he has to say, it just seems silly to say it contributes kinetic energy.

 

[madcat8000]

Yeah don't be a know it all, try to get his perspective by asking for more information on it, he might realize his error or leave you perfect oppertunity to interject a counter point while in the middle of a friendly exchange. He doesn't have to be right, just make sure you get an A in the class and walk it off. I've done that manytimes myself.

 

[araganzar]

Yeah don't be a know it all, try to get his perspective by asking for more information on it, he might realize his error or leave you perfect oppertunity to interject a counter point while in the middle of a friendly exchange. He doesn't have to be right, just make sure you get an A in the class and walk it off. I've done that manytimes myself.

This is very good advice. I tried this. I sent him an email where I repeated the statement from the quiz. I said our textbook says enzymes do not supply energy to chemical reactions and allowing it seems to conflict with what I've been taught about catalysts. I said I did not want to argue the point on the quiz, but that I was having a really hard time seeing how if the enzyme was contributing any kind of useful energy it wouldn't affect the free energy change.

His response:

We can talk about this, but your book does mention...as I did in class...that enzymes contribute kinetic energy. Kinetic energy is about speed and thus does not effect thermodynamics.

Well, it's not in our book. And I made a serious effort to find that statement, or a similar one, anywhere. So I responded:

Yeah, I wanted to ask about this in class but it seemed like nit-picking or splitting hairs. I generally get in trouble with teachers when I start doing that during class time, and with arguably good reason. I hate to waste your time when I could research this on my own. I'm just having a really hard time finding where our book, or any source I can find, states this. I'm happy to go figure it out on my own if you can point me in the right direction.

He started the next class by having me ask the question out loud to the class, against my objections that I didn't want to do it that way. Then he gave the responses I have mentioned above - enyzmes are moving, they have to create transition states, they are moving themselves AND moving the substrate around so obviously they are contributing energy. And he said he told us the answer in class already so I should have known it.

What could I do at that point, in front of a hundred students? I shut up and took it.

He is a very reasonable guy and I know he would be open to discussing it. But he clearly is pretty invested in this idea.

I think you guys have given me some very reasonable responses with very good points. But this is a guy who is pretty sharp and everything else he has said is spot-on. He will say the same thing any of you would to me if I here and made an assertion you didn't think was correct. He will ask me if I have any evidence from peer-reviewed material that supports my assertion. And he's right to do so. And I got nothing.

I would love to sit down in his office hours and have a friendly discussion about it. I wouldn't present what I did here, I would just listen to what he has to say. But I have already asked three times, and been told three times I am wrong. I can't ask him about this again without a single reference to back me up when I'm pressed.

 

[alxm]

Okay, well I know this; (being a chemical physicist who studies enzyme mechanisms) I knew mol-bio folks are bad at phys chem, but your professor is simply wrong and making an *** of himself if he said that enzymes contribute kinetic energy which is somehow not energy. I may not be a full professor, but I'm quite confident I have a greater level of expertise on this particular subject.

First the basics: A catalyst lowers the energy of the transition-state of the reaction (or cause it to take a different route entirely, with a lower barrier). This increases the reaction rate, i.e. the number of molecules reacting per second, because you have a statistically greater number of molecules with sufficient energy to overcome the barrier. Sloppily, people may say that this increases the 'speed' of the reaction (in the sense that the amount of time it takes to form a given amount of product is shorter). This is a bad term, since what's happening is that the reaction is occurring more often. It's not necessarily faster in-itself.

I can only assume this "increased speed" is what made your professor assume that kinetic energy is being transferred. This isn't the case. For the record, kinetic energy is exactly what chemical energy is. The rotational, translational and vibrational motions of atoms and molecules. More kinetic energy means a higher temperature (and vice-versa). This is basic chemical/statistical thermodynamics. The substrate in the enzyme has the same thermal energy, and the same random fluctuations in energy, that everything around it has. It's the same temperature.

The catalyst, and this includes enzymes, does not contribute any (net) energy to the reaction, and that's the end of that. Otherwise they'd somehow 'run out' - it has to come from somewhere or you would be violating the first law of thermodynamics.

Now, unlike most catalysts (e.g. metal surfaces), enzymes aren't always passive; they don't necessarily just sit there. Due to conformational changes in the enzyme, they can temporarily transfer energy to the reacting molecule by changing their conformation (i.e. some other part of the enzyme moves about, lowering its energy, but stressing the reactant molecule), and the energy released in the reaction may be then used to restore the enzyme to its original conformation. They may also transfer energy from one reaction (e.g. ATP hydrolysis) to perform another. But none of these things lead to any net transfer of energy from the enzyme.

The detailed thermodynamics of enzyme reactions is actually very tricky, even for physical chemists. And I wouldn't be terribly surprised if your textbook was wrong as well; Molbio/biochem textbooks often get this stuff wrong*. I don't know anyone who hasn't been confused by some enzyme at one time or another. But the overall thermodynamics is obvious: After a reaction cycle, the enzyme is in the same state it was before the reaction cycle. It must have the same energy. Nor can it spontaneously channel kinetic (i.e. thermal) energy to any point. That would mean making one spot hotter and one spot colder without expending any energy, also in violation of basic thermodynamics.

Anyway, no need to take my word for it. Forward your discussion to someone at your physical chemistry department, and they'll set him straight.

*If I may disgress: I know more than a few misstatements of how entatic states work. And some stuff which is really widespread is just crazy IMO, such as "Anfinsen's dogma" which holds (or is usually stated as) that the conformation of an enzyme is a global minimum (and thus determined only by the AA sequence). Which I've always held to be blatant wishful-thinking without much supporting rationale. So, why do up to 30% of proteins misfold? And how could "silent" mutations, which don't change the AA sequence, cause conformational changes - which we know they can? Ah well, that's a topic for a different thread.

 

[araganzar]

I don't think he's being a jerk. I think it's an undergraduate class and it is unusual for students to think this critically about statements the professor makes. The whole class murmured and agreed when he said he had told us the answer in class, as though that should be proof enough.

I think we just have a disconnect here, and it's one I was hard-pressed to address because as a relative newbie I don't have a lot of credibility with a tenured professor who has a strong opinion. I am a big believer in the free market of ideas, but this is not a free market. :) But anyway, I think it would be counter-productive to sic a physical chemist on him. While it might address this disconnect, it would not stand me in good stead with the biology faculty and it also seems like the same kind of ambush I complained about getting in class.

The catalyst, and this includes enzymes, does not contribute any (net) energy to the reaction, and that's the end of that. Otherwise they'd somehow 'run out' - it has to come from somewhere or you would be violating the first law of thermodynamics.

This is the basic premise I was proceeding from as well. It's why this was so confusing to me.

The points about reaction rate and net transfer/change are extremely good. I feel like I have enough of a handle on this to discuss this with him in a friendly fashion without either being confrontational or getting my butt handed to me again. If anyone can find a reference or go on record, that would certainly be cool, but you guys have given me PLENTY go on and been extremely helpful. And just as importantly, you've pointed out corrections I needed to make while being kind about it. Thanks!

 

[araganzar]

*If I may disgress: I know more than a few misstatements of how entatic states work. And some stuff which is really widespread is just crazy IMO, such as "Anfinsen's dogma" which holds (or is usually stated as) that the conformation of an enzyme is a global minimum (and thus determined only by the AA sequence). Which I've always held to be blatant wishful-thinking without much supporting rationale. So, why do up to 30% of proteins misfold? And how could "silent" mutations, which don't change the AA sequence, cause conformational changes - which we know they can? Ah well, that's a topic for a different thread.

Also, let me know if you start that thread, because I am extremely interested in mutations and genetic expression. I've read some stuff on biased gene conversion and its contribution to non-adaptive mutation until I got to the point I realized I needed to know a hell of a lot more than I did to digest it.

 

[alxm]

Also, let me know if you start that thread, because I am extremely interested in mutations and genetic expression. I've read some stuff on biased gene conversion and its contribution to non-adaptive mutation until I got to the point I realized I needed to know a hell of a lot more than I did to digest it.

Aha, well that's really one area (gene expression in general) which I'll happily concede that the molecular biologists know a lot more than I do. I'm not even sure I remember which ones are introns and which ones are exons. :uhh:

Reactions, thermodynamics and such I know, what their significance is in the biological context is of less concern to me. (In fact, I can't always remember offhand what organism the enzyme I might be studying comes from) :)

 

[araganzar]

Reactions, thermodynamics and such I know, what their significance is in the biological context is of less concern to me. (In fact, I can't always remember offhand what organism the enzyme I might be studying comes from) :)

I feel the same way in reverse. I find physical chemistry and entropy to be almost inexhaustibly interesting, but they are a distraction the same way genetics or epigenetics would be a distraction to you. We all have a limited amount of time to learn and get stuff done, and unfortunately that sometimes means turning away from something compelling because it's taking one down a side road.

I might just let this go with this professor for that reason. I think I understand it and unless I think the class would benefit there's no reason to push it.

 

[madcat8000]

Actualy you should push this. Privately this time. If alxm would be pleasnt enough to provide some authoratative refrences on how this has been derived you can simply email them to him privately. Respect has to be taken by force if nessicary. It might do well for your future to see it out.

 

[gerben]

His response:
" We can talk about this, but your book does mention...as I did in class...that enzymes contribute kinetic energy. kinetic energy is about speed and thus does not effect thermodynamics."

Well, it's not in our book. And I made a serious effort to find that statement, or a similar one, anywhere. So I responded:

"Yeah, I wanted to ask about this in class but it seemed like nit-picking or splitting hairs. I generally get in trouble with teachers when I start doing that during class time, and with arguably good reason. I hate to waste your time when I could research this on my own. I'm just having a really hard time finding where our book, or any source I can find, states this. I'm happy to go figure it out on my own if you can point me in the right direction."

He started the next class by having me ask the question out loud to the class, against my objections that I didn't want to do it that way. Then he gave the responses I have mentioned above - enyzmes are moving, they have to create transition states, they are moving themselves AND moving the substrate around so obviously they are contributing energy. And he said he told us the answer in class already so I should have known it.

What could I do at that point, in front of a hundred students? I shut up and took it.

I can understand if you just want to drop this here. This teacher seems to have some peculiar conceptions of energy and entropy, and if you were to win the argument you probably would have taught him a few things...

However just as some general advice, just ask your teachers questions and do not excuse yourself for taking their time. Do not say things such as "if I can find it out myself I will". While it is good to find things out yourself there is no need to tell your prof you are willing to do so in order to save them from spending time on you. It is part of their job to answer students' questions, and the good ones are always pleased to discuss any conceptual problems you may have. Nobody is going to blame you for asking questions.

When you get a response, as say "enzymes contribute kinetic energy. kinetic energy is about speed and thus does not effect thermodynamics", then reply to just that and only focus on the things that were said. For example you might reply with "Then does the enzyme lose kinetic energy in every reaction in which it participates? And will it lose all its motion after a certain amount of reactions?", or with any other question relating to whatever you have a problem with in the response. This way your prof will have to respond to your question and you may get a useful exchange of ideas.

Just be respectful and friendly, phrase your questions so that it is clear that you just want to learn. Your profs should be clever enough to recognize that you are not nit-picking but just genuinely trying to learn.

 

[epenguin]

Maybe you shouldn't push because it sounds like you are not going to get anything profitable from him! It's just called diplomacy. Your first reaction was right, I haven't read the site but it doesn't come much better than Bruice, alxm is right too.

What enzymes do which isn't magic but is marvellous is direct chemical reactions, i.e. get them to go from A to B which B is lower free energy but fast and without going to the alternatives C, D, and E which they might in messy nonenzymatic catalysis. Particularly go to products with necessarily less total free energy but not so much less as the nonenzymatic reaction, e.g. transfer a phosphate group to an organic molecule rather than to water as you will come presently up against many examples of. Maybe your teacher has something like that, or the transition state stabilisation (ground state destabilisation) that was mentioned above.