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Tuesday, November 01, 2011

Better Biochemistry: The Free Energy of ATP Hydrolysis

This is part of a series on important concepts in biochemistry. I'm concentrating on those concepts that may be widely misunderstood and/or not well described in most textbooks. Naturally, I think we do a pretty good job in our book!

We usually think of ATP as a "high energy" molecule because the hydrolysis of ATP to ADP or AMP releases a lot of energy.1 The standard Gibbs free energy change for the two reactions shown in the large figure aren't terribly relevant because, for simplicity, I've left out a key component of the reaction.

Mg2+ ions are an essential part of the reaction in vivo. They are bound to adjacent phosphate groups as shown below and this ATP:Mg2+ complex has different thermodynamic properties than free ATP.

In addition, the standard Gibbs free energy changes aren't very useful when you're dealing with charged molecules and the ATP hydrolysis reactions have charged molecules—even when some of the negative charges are neutralized by Mg2+ ions. That's why it's better to calculate new values of "standard" Gibbs free energy changes in the presence of Mg2+ ions and an ionic strength that's closer to physiological values.

Recall that the traditional standard Gibbs free energy changes are at 25°C (298 K) and pH 7.0. For reactions like ATP hydrolysis, we want a new "standard" that includes 3mM Mg2+ and ionic strength = 0.25 M.

Robert Alberty and his colleagues have calculated the transformed free energies of hydrolysis for many biochemical compounds (Alberty and Goldberg 1992) and those are the values we should use in biochemistry courses.

The table (below right) shows the standard Gibbs free energy changes for the ATP reactions in the presence of 3 mM2+ and ionic strength = 0.25 M. Note that the values are large and negative. That means a lot of energy is given off. This energy can be captured and used in enzyme catalyzed reactions.

If you've been paying attention to the previous postings in this series—as I'm sure you have—you'll remember that standard Gibbs free energy changes don't mean very much in biochemistry. What really counts is the actual free energy change and that depends on the in vivo concentrations of reactants and products.

You'll also remember that most biochemical reactions reach equilibrium (near-equilibrium reactions). At equilibrium concentrations ....

ΔGreaction = 0 kJ mol-1.

ATP would be completely useless as a "high-energy" compound if the hydrolysis reaction was a near-equilibrium reaction. That's why these reactions can never be allowed to reach equilibrium. Cells would die if this ever happened.

Most of the reactions that use up ATP are regulated. What this means is that the activity of the enzyme is inhibited if the concentration of ATP falls too much, relative to ADP (or AMP). If the concentration of ATP is always high relative to the products then there's still a large negative ΔG for the reaction and this energy can be used to drive other reactions.

So, we know that the actual Gibbs free energy isn't the same as the standard Gibbs free energy but what is it's actual value? The short answer is that in most cases we don't know. It has to be some large negative value but it's very difficult to measure the concentrations of ATP, ADP, AMP, and inorganic phosphate inside cells.

The situation isn't entirely hopeless since there are some good estimates. Unfortunately the best examples come from rat hepatocytes and erythrocytes1. We don't know if this is typical of all cells (bacteria, plants etc.) or whether mammalian cells are special.

We can calculate the actual Gibbs free energy change for ATP hydrolysis (to ADP) given the known concentrations of reactants and products in rat hepatocytes. The answer is ΔG = -48 kJ mol-1. Thus, the actual Gibbs free energy change is 1½ times the standard Gibbs free energy change. This has important consequences when we try to figure out how ATP is synthesized and where that energy comes from.

There's an easy way to tell the difference between a good introductory biochemistry textbook and the other kind. Check out the standard Gibbs free energy change for the ATP → AMP + PPi reaction. If the value is close to -45 kJ mol-1 then it's probably a good textbook. If the book also mentions that the actual Gibbs free energy of the ATP → ADP + Pi reaction is close to -50 kJ mol-1 then it's almost certain to be a good textbook.

1. I put "high energy" in quotation marks because it's really the Gibbs free energy of the reaction (system) that we're referring to and not an individual molecule.

2. Rat liver biochemistry used to be very popular.

Alberty, R.A. and Goldberg, R.N. (1992) Standard thermodynamic formation properties of adenosie 5′-triphosphate series. Biochem. 31:10610-10615.


G Radice said...

Thanks, Larry! I was JUST thinking about this today as I work on my syllabus for next semester's cell biology class.

Anonymous said...

between this, and your post on modified nucleotides, I'm sold. I have to get this textbook...

DK said...

Robert Alberty and his colleagues have calculated the transformed free energies of hydrolysis for many biochemical compounds ... and those are the values we should use in biochemistry courses.

"Should"? Why? Alberty's calculations (I am looking at "Thermodynamics of Biochemical Reactions", 2003) are very much idealized and should be treated as nothing more than back of the envelop estimates. For teaching purposes, it should be perfectly sufficient to say "large negative" with real value in the cell further significantly larger and give some random close enough numbers.

If anything, IMHO, it is essential to emphasize that we don't know what the actual numbers are. And that, in general, there is hardly any single biochemical parameter whose value in the real cell we know with any reasonable degree of precision. This is important because to this day there are many people who believe that a faithful computer model of a whole cell is forthcoming very soon because computers are getting exponentially more powerful.

Allan Miller said...

Rat liver biochemistry used to be very popular.

I remember my visits to the 'rat man'. He would select one of his charges, cradle it and stroke it so as not to stress it, then .... whump! The unfortunate animal would be unceremoniously whacked on the edge of a desk, and its liver neatly snipped out and plopped into our petri dish. I decided to do my PhD on plants.

Allan Miller said...

One thing that has always puzzled me, however (feel free to ignore, or refer me to your book!): what is the role of the nucleoside - the base-ribose group - in energy transfer? The same base-ribose-phospate group appears in FAD and NAD, which would suggest some deep connection with early metabolism. The fact that that same group is also an RNA subunit puts a completely unrelated constraint on it - whatever its role in the energetics of polymerisation, it also needs the stereochemistry to allow it to be stacked in the polymer, and base-paired.

schelle said...

If standard Gibbs free energy change for the ATP → AMP + PPi reaction is close to -45 kJ /mol and the respective value for the PPi hydrolysis is -29 kJ/mol, what is than Gibbs free energy for ADP → AMP + Pi ( -42 kJ/mol? )?

Vladimir Matveev said...

As usual, two important questions were left unanswered.
1. In the decay of a chemical compound, energy is released in the form of heat. How is the heat used to perform the work of the sodium pump and other mechanisms?
2. Why has no one compared the amount of synthesized ATP and the amount of utilized ATP in a cell per unit of time in the last 70 years?

MitoSwitch said...

"The" sodium pump
Can you precisely measure ATP made / ATP used with time resolution?
Where would one get the funding to answer your ill-defined questions?

Vladimir Matveev said...

Thanks for your reply. My questions are simple and understandable. If we can not measure the process X, then we can not say that our interpretation of this process is true (regardless of funding). If you are interested in details, you may run through the article: It seems to me that this article does not solve the problem, but it raises important questions.