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Topic: How does ATP release its chemical energy?  (Read 4658 times)

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Offline biomiracle

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How does ATP release its chemical energy?
« on: January 12, 2014, 07:53:53 PM »
Hello!

It is my understanding that the formation of the chemical bond releases the chemical energy and the breaking of the chemical bond requires the energy input.  How can an ATP release its chemical energy during the hydrolysis into the ADP and phosphate group if the breaking of the chemical bond requires the energy input?

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Re: How does ATP release its chemical energy?
« Reply #1 on: January 13, 2014, 03:02:15 AM »
Think about bonds created after phosphate is removed.
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Offline Babcock_Hall

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Re: How does ATP release its chemical energy?
« Reply #2 on: January 17, 2014, 03:34:02 PM »
It is possible that you are confusing thermodynamics and kinetics in your question.  Every chemical reaction has an energy barrier in order to reach the transition state (a kinetic issue).  However, when one tries to understand the role of ATP in a cell, one is usually working in the language of thermodynamics.

Offline Babcock_Hall

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Re: How does ATP release its chemical energy?
« Reply #3 on: January 18, 2014, 01:30:52 PM »
However, when one tries to understand the role of ATP in a cell, one is usually working in the language of thermodynamics.
I need to clarify my previous comment.  One sometimes wishes to explain why ATP is needed in what would be an otherwise unfavorable process.  An example is moving sodium ions against their electrochemical gradient.  This becomes thermodynamically favorable when coupled with the hydrolysis of ATP to ADP and phosphate.  This is a question of thermodynamics, and the OP seems to be primarily concerned with thermodynamics.  However, there are many kinetic issues involving the role of ATP in biochemistry, and my previous comment unintentionally shortchanged this aspect of ATP.  I think it is safe to say that how coupling occurs is the province of kinetics and mechanism.  The question of how enzymes catalyze the reactions of ATP is also in the sphere of kinetics and mechanism.
« Last Edit: January 18, 2014, 04:47:41 PM by Babcock_Hall »

Offline jef6550

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Re: How does ATP release its chemical energy?
« Reply #4 on: February 20, 2014, 07:24:21 AM »
I'll try to give you a simple explanation. It may be long, but I promise the read will be worth it and will answer your question in complete detail from a molecular, physical, and biochemical standpoint.

Contrary the simplicity that we all learned in elementary school and what is commonly found on the web, ATP does not release any energy!

What is actually happening is that a molecule of ATP is manufactured in the cell. By Brownian movement (random, uniform motion) ATP comes into contact with a protein. With this target protein are other proteins called kinases which phosphorylate other molecules, meaning that the kinase can remove a phosphate group from the molecule. In this case, ATP is phosphorylated by an ATP-protein kinase called ATPase which makes ATP into ADP+P. The protein kinase does this by molecular interactions between the specific structure and order of the amino acids in the kinase and the ATP, which results in separation of the phosphate and deposition of the phosphate into the target protein.

Now there is a recycling process for the leftover ADP, but for now we will tag along with the extra phosphate and see what happens next. This is where the physics and biochemistry come in.

Keep in mind that everything in the world has a charge and that proteins are made up of a specific order of different amino acids. Some amino acids may be more positively charged or negatively charged depending upon the type and number of atoms that make up each molecule of amino acid. In fact, proteins get their shape and function from just the natural forces of attraction between the other amino acids in the protein itself.

On the molecular scale, there is no external driving force. Everything just happens automatically based upon the forces of attraction between one another due to the properties of atoms.

Let's get back to that phosphate that was removed from ATP. The phosphate actually binds onto an amino acid in the protein and creates what is called a conformational change in the structure of the protein. A short little flow chart of protein structure goes like this: Proteins are made of multiple subunits, which are made of multiple domains, which are made of multiple arrangements of amino acids that form either helixes or zigzag like sheets, and each helix or sheet is made up of the different amino acids and the forces that are between them such as bonds or natural repulsion and attraction forces.

The shape of the protein changes because phosphate is going to attract or push back surrounding amino acids which causes a chain reaction of movement from amino acid to amino acid throughout the protein.

Here, the shape of the protein is changed, and therefore the function of the protein is changed as well. The newly changed protein can then go off to perform other functions that are perceived as needing "energy", and so hence, we tend to lazily classify ATP as an energy source. Eventually, another protein called a phosphotase will come along and remove the phosphate from the target protein so that the cycle can start all over again!

An example of this taking place is in the brain. In fact, 60% of all the ATP produced in the body is actually used up by your head. This is because ATP in the brain is phosphorylated so that the phosphate can change the structure of proteins called ion pumps which are located the membranes of neurons in order to cause shifts in the domains of the pump which rotates the protein and causes certain ions that are attached to the protein to be expelled outside of the cell which creates a difference in the electrochemical concentration between the intracellular and extracellular fluid which prepares the cell for propagation and depolarization.

I would love to go into more detail about the neurology of this sort of thing, but now we're off topic.

Hope this helped.

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myself; biochemistry, chemistry, physics, and neuroscience major at Virginia Polytechnic and State University

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Re: How does ATP release its chemical energy?
« Reply #5 on: February 20, 2014, 11:24:46 AM »
With respect, I don't agree with your post at all, which is extremely misleading and suggests an incomplete understanding of chemical thermodynamics. Moreover it's filled with a lot of tangential information that doesn't really have much to do with the central question.

I don't feel inclined to pick apart your entire post so I'll stick to just one bit:

On the molecular scale, there is no external driving force. Everything just happens automatically based upon the forces of attraction between one another due to the properties of atoms.

Things don't just happen automatically - this is an absurdly unscientific statement if I've ever heard one. What you perceive as "automatic" is more appropriately referred to as a statistical movement toward lower potential energy: which in chemical systems is free energy, translated into lower enthalpy and higher entropy. "Force of attraction", as you call it, is just a handwaving way of referring to electrostatic potential energy. These forces and energetic interactions determine what is  the statistically favorable endpoint of a system at equilibrium.  All the references you make to proteins changing conformation and so forth may be true, but ultimately these processes are driven by favorable (downhill) changes in free energy. There's no free lunch. On a macroscopic scale, for an energetically unfavorable change to occur in one place, a correspondingly energetically favorable change has to occur somewhere else, and generally these processes have to be in reasonably close proximity to one another in order to be efficient.

ATP is rightly referred to as a universal energy currency because changing ATP to ADP results in a fairly substantial free energy loss, which can be used to drive energetically unfavorable processes elsewhere. This is no different fundamentally from what happens in a test tube on the lab bench in more simple chemical systems. The complication here is that in the cell there are oodles of thermodynamically unfavorable reactions that need to happen and many of these reactions happen far from the region of the cell where energy is directly generated through glucose (or other) metabolism. ATP is a carrier of energy - metabolism and the electron transport chain in the mitochondria drives the endergonic process of ATP production (energy stored), which can then be used elsewhere due to entropic diffusion of ATP throughout the cellular matrix. You are correct that energy is usually not directly released by ATP when it is enzymatically converted to ADP, by which I mean energy is not dumped out into the external medium (in which case it would be dispersed as heat). This is not a useful use of energy, so what good would it do the cell? Rather the stored energy is used to directly form other bonds in other biological molecules, or unfavorable changes in protein conformation, and so forth. In this, the ultimate truth is that biology is simply chemistry and chemistry is simply applied thermodynamics. Heat is the final waste product of everything, and each conversion process does release a little heat. There's always a little waste. Where do you think body temperature comes from?

A simple analogy might be gasoline as an energy carrier for making automobiles move. The chemical energy of gasoline ultimately derives from the sun, but cars can't utilize (directly) solar energy, particularly at night, and so we go to gas stations and put gas in our cars, which allows us to drive (literally) energetically unfavorable processes (going up a hill, say). There is of course always an energetic cost to using an energy carrier because no process is 100% efficient, but ultimately gasoline is a medium of stored solar energy than then is converted to do a thermodynamically unfavorable process elsewhere.

So it is with ATP in the cell. Glucose itself is a chemical energy storage medium of course (produced and utilized by plants as a means of storing solar energy to drive chemistry in plant cells) so one might ask why we didn't evolve to utilize the chemical energy of glucose directly rather than doing a currency exchange, so to speak, from glucose to ATP. I'm not evolutionary biologist but if I were to speculate I'd say it's because animals ingest many different chemical energy sources from their diets (glucose, fructose, fats, proteins, etc.) and it would be extremely ineffecient to have a means for animals cells to utilize each of these types of sources for each cellular process. Much better to have a single cellular energy currency, which is exactly what animals cells have. Metabolism may be appropriately described as the body's means of converting all the various types of energy currency harvested through diet into a single currency which can be used universally by all internal cellular components. The currency analogy is actually rather apt - we don't just throw money out onto the street and expect something good to come of it for us directly. We use it for a directed purpose, we exchange it for something else that would not otherwise just come to us spontaneously. Humans could survive without currency as a placeholder for material property, and in fact did for much of its formative period, when goods were directly exchanged. But could you imagine a complex society surviving without a universal currency to efficiently mediate the exchange of goods between invested parties? I couldn't, and nor would it be feasible for cells to survive without a single currency to efficiently mediate the exchange of energy between invested biomolecules. A single economy is far more efficient, and indeed necessary for a complex organism to exist.
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Offline Yggdrasil

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Re: How does ATP release its chemical energy?
« Reply #6 on: February 21, 2014, 12:20:11 AM »
What is actually happening is that a molecule of ATP is manufactured in the cell. By Brownian movement (random, uniform motion) ATP comes into contact with a protein. With this target protein are other proteins called kinases which phosphorylate other molecules, meaning that the kinase can remove a phosphate group from the molecule. In this case, ATP is phosphorylated by an ATP-protein kinase called ATPase which makes ATP into ADP+P. The protein kinase does this by molecular interactions between the specific structure and order of the amino acids in the kinase and the ATP, which results in separation of the phosphate and deposition of the phosphate into the target protein.

This is not an accurate explanation of how molecular motor proteins convert the chemical energy from ATP into movement, and it confuses two different classes of proteins.

First, protein kinases—enzymes that transfer a phosphate of ATP onto another protein—generally are not involved in generating motion.  Although sometimes phosphorylation of a target will produce a conformational change, these phosphorylation events are not powering energy-dependent motor proteins.  Rather, phosphorylation is acting as a signal to change the protein's interactions with other proteins or to alter the enzymatic activity of the protein.  The prototypical example of a protein regulated by phosphorylation is Src, a proto-oncogene and a protein kinase itself.

Molecular motors—proteins that convert the free energy from ATP hydrolysis into mechanical or chemical energy—however, are different from kinases.  Whereas kinases are classified as transferase enzymes, molecular motors are a class of hydrolases known as ATPases.  The chemical reaction they catalyze is the hydrolysis of ATP: ATP + H2O --> ADP + PO4.  Examples of such molecular motor proteins include, transport motors (such as myosin, kinesis, and dyenin) which use ATP hydrolysis to power directed motion, helicases which use ATP hydrolysis to unwind DNA, and ion pumps (such as the Na/K pump) which use ATP hydrolysis to pump ions across a membrane in order to establish electrochemical gradients.

In all of these cases, the phosphate never gets transferred to the actual motor protein during the hydrolysis reaction.  Rather, the active site of the enzyme adopts different shapes during the various stages of the hydrolysis reaction, from the apo (empty) state, to the ATP-bound state, to the ADP+Pi state, to the ADP-bound state, then back again to the apo state.  These changes to the shape of the active site are coupled to conformational changes elsewhere in the protein such that ATP hydrolysis leads to the desired activity of the motor protein (e.g. moving the leg of kinesin forward on a microtubule).  Probably the motor for which we understand this mechanochemial coupling best is the F1-ATPase (which normally synthesizes ATP in the cell but, when run in reverse, converts ATP hydrolysis into rotary motion).  A good description of how this motor works can be found in the following paper:

Adachi et al. 2007. Coupling of Rotation and Catalysis in F1-ATPase Revealed by Single-Molecule Imaging and Manipulation. Cell 130:309. doi:10.1016/j.cell.2007.05.020.

Of course, there are many other ways the cell can use the chemical energy store in ATP for other useful tasks (for example, many enzymes activate certain bonds by attaching them to an AMP or ADP leaving group in order to allow certain chemical reaction to proceed favorably).

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