What is a coupled reaction and why do cells couple reactions?
I was wondering what exactly a coupled reaction is and why cells couple them. I read the wikipedia article as well as several others, such as life.illinois.edu but I still don't get it. Could someone explain it to me?
It's pretty simple. A reaction occurs that releases energy (like ATP losing a phosphate to become ADP + Pi). If this is uncoupled, the energy will merely turn into heat. If it is coupled, then it can be used to fuel some other process. For instance, if you couple the ATP -> ADP reaction to a certain protein, the energy can be used to modify the shape of that protein.
A reaction where the the free energy of a thermodynamically favorable transformation, such as the hydrolysis of ATP, and a thermodynamically unfavorable one, are mechanistically joined into a new reaction (or may be envisaged to be so joined) is known as a coupled reaction.
To put it another way, two or more reactions may be combined mechanistically such that a spontaneous reaction may be made 'drive' a non-spontaneous one, and we may speak of the combined reaction as being 'coupled' (see, for example, Silby & Alberty (2001), quoted below). The combined reaction may be catalyzed by an enzyme, in which case the 'thermodynamic push' is provided by the coupling agent (such as ATP) and the 'kinetic push' is provided by the enzyme.
We need to take into account a very important point. As pointed out by Atkinson (1977), the coupled reaction is a different reaction to the reaction we are trying to 'drive', with different overall stoichiometry and hence a different overall equilibrium constant (Atkinson, 1977, p52).
A coupled reaction does not "push a reaction past its equilibrium" (see Atkinson, 1977, p52). No enzyme, for example, can push any reaction past its position of equilibrium. This is forbidden by the second law. (If your favourite kinetic mechanism does not obey the second law there is, as Eddington put it, "no hope"). An enzyme (or enzymes) can however, cause a reaction to proceed further than it normally would by catalyzing a different reaction (or series of reactions).
Perhaps (in lysine biosynthesis from aspartate), nature requires the the (NADH-linked) reduction of a carboxylic acid to an aldehyde, a reaction normally considered irreversible. And lets spell this one out: the equilibrium constant for a reaction such as the following:
NADH + carboxylic acid = NAD+ + aldehyde (1)
greatly favors aldehyde dehydrogenation so much so that the left-to-right transformation has never (to the best of my knowledge) been demonstrated (more on this below).
Lets first phosphorylate the carboxylic acid using ATP as coupling agent to give aspartyl-phosphate (aspartate kinase):
aspartate + ATP = aspartate-4-phosphate + ADP (2)
Now let's reduce the 'activated' acid (aspartate-4-phosphate) using NADPH as electron donor, where the equilibrium constant of the following reaction is very much to the right (aspartate semialdehyde dehydrogenase):
aspartate-4-phosphate + NADPH + H+ ⇌ L-aspartate 4-semialdehyde + Pi + NADP+
So we have got our product (the aldehyde) from our 'starting material' (the carboxylic acid), but at the 'expense' (as we would see it) of ATP hydrolysis.
We may think of the above reactions as being 'mechanistially coupled' by the formation of aspartyl-phosphate such that the overall equilibrium constant for the following reaction is much more favourable than that of Eqn (1)
aspartate + ATP + NADPH + H+ ⇌ L-aspartate 4-semialdehyde + Pi + NADP+
Or, perhaps in more abstract terms, the coupled reaction may be represented as folows:
carboxylic acid + ATP + NADPH + H+ ⇌ aldeyde + Pi + NADP+
The reduction of a carboxylic acid to an aldehyde has been given a thermodynamic 'push' by the coupling agent (and a kinetic 'push' by the enzymes).
Before we move on to some specific examples let's consider three further points.
(i) What makes ATP a good coupling agent? To again quote Atkinson (1977, p48), a good coupling agent has two requirements: firstly, it must be thermodynamically unstable. That is, it must be "far from equilibrium in terms of some useful conversion" (Atkinson, 1977, p48). The hydrolysis of ATP nicely fills this criterion. Secondly, a good coupling agent must be kinetically stable. Again ATP 'fits the bill': solutions of ATP in water are stable (Atkinson, 1977, p48).
ATP (-39.7 kJ/mol), of course, is not the only useful coupling agent, or even the 'best' one. phosphoenol-pyruvate (-61.9 kJ/mol) , creatine-phosphate (-43.5 kJ/mol) and acetyl-phosphate (-43.1 kJ/mol) are others. The figures in brackets refer to free energy of hydrolysis and are taken from Silby and Alberty (2001, p 282).
(ii) The coupled reaction need not involve direct hydrolysis of coupling agent. Any reaction in which ATP is converted to ADP has received a 'thermodynamic push equivalent to the free energy of hydrolysis of ATP' (Atkinson, 1977, p49). In essence, the concept of a coupled reaction is an abstraction, created by us for our convenience.
(iii) To state the obvious, a coupled reaction is exactly that: coupled. The coupling may be 'chemical', as in many of the examples below, or may be conformational (as in ATP synthase), but there must be in some sense a mechanistic joining into a new (real) reaction. Two reactions occurring in isolation, even if one is ATP hydrolysis, are not coupled.
An example of a coupled reaction is the glyceraldehyde-3-phosphate dehydrogenase (EC 220.127.116.11; GAPDH) reaction [see here] .
Glyceraldehyde-3-phosphate + NAD+ + Pi → 1,3-diPhosphoGlycerate + NADH + H+
We can think of this reaction in terms of two separate reactions which are coupled mechanistically by the enzyme. (i) The NAD+ linked oxidation of an aldehyde to a carboxylic acid (the aldehyde dehydrogenase reaction) and (ii) the phosphorylation of a carboxylic acid. (Like ATP, a phosphorylated carboxylic acid may be considered a 'high energy' compound, that is one where the equilibrium for hydrolysis lies very much to the left in reaction 2 below).
RCHO + NAD+ + H2O → RCOOH + NADH + H+
Reaction 2 (Pi is inorganic phosphate).
RCOOH + Pi → RC(=O)(O-Pi) + H2O
As stated above, the NAD+-linked oxidation of an aldehyde (reaction 1) is practically irreversible. That is, at equilibrium it has proceeded almost totally to the right. As stated above, the position of equilibrium of reaction 2 lies very much to the left.
How can one 'drive' the formation of a phosphorylated carboxylic acid by coupling it to the (spontaneous) NAD+-linked oxidation of an aldehyde?
A simplified version of the GAPDH reaction is as follows (a more complete mechanism, supported by a lot of experimental evidence, may be found in Fersht (1999), which I quote below).
Step 1. Formation on an enzyme-linked thiohemiacetal.
E-SH + RCHO → E-S-C(R)(H)(OH)
A sulphydryl on the enzyme (part of a Cys residue) reacts with the aldehyde group on the substrate to give a thiohemiacetal. (In the representation above, groups in brackets are all connected to a single (tetrahedral) carbon atom).
Step 2. The thiohemiacetal is oxidized by enzyme-bound NAD+ to a thiol-ester (the key step).
E-S-C(R)(H)(OH) + NAD+ → E-S-C(=O)(R) + NADH + H+
This (enzyme-bound) thiol-ester is a 'high energy' intermediate wherein, it may be envisaged, the free energy of aldehyde oxidation has been 'trapped'.
The final step of the GAPDH reaction is now spontaneous (proceeds to the right).
Step 3. Attack on the thiol-ester by inorganic phosphate
(Pi is inorganic phosphate)
E-S-C(=O)(R) + Pi → E-SH + R-C(=O)(O-Pi)
Thus, the free energy of NAD+-linked aldehyde oxidation has been 'sequestered' and used to 'drive' the thermodynamically unfavourable phosphorylation of a carboxylic acid, by coupling the two reactions via a ('high energy') thiol-ester: the coupled reaction is a different reaction.
The 'thermodynamic price' is that the GAPDH reaction (unlike NAD+-linked aldehyde oxidation) is freely reversible: the coupled reaction has a different overall equilibrium constant.
As stated above, this is a simplified version of the GAPDH reaction. The (tetrameric) enzyme contains a tightly bound NAD+ for a start, and this needs to be taken account of. A fuller account may be found in the following reference:
- Fersht, Alan. (1999) Structure and Mechanism in Protein Science, pp 469 - 471, W.H. Freeman & Co.
For a fuller treatment of coupled biochemical reactions, see
Silbey, R.J. & Alberty, R.A. (2001) Physical Chemistry (3rd Edn) pp 281 - 283.
Atkinson, D. E. (1977) Cellular Energy Metabolism and Its Regulation. Academic Press, New York
Pyruvate kinase (EC 18.104.22.168) [see here] is another great example of a coupled biochemical reaction. In this case the reaction is almost irreversible in the direction of ATP synthesis!
The standard transformed free energy (ΔGo') for the hydrolysis of phosphoenol-pyruvate (PEP) to pyruvate and phosphate is ~ - 62 kJ/mol. This represents an equilibrium constant of about 1010 in favour of hydrolysis! (see Walsh, quoted below, pp 229-230).
For comparison, ΔGo' for ATP + H2O → ADP + Pi is about - 40 kJ/mol.
Thus the pyruvate kinase reaction may be viewed as a coupled biochemical reaction where the free energy of PEP hydrolysis is coupled to (almost irreversible) ATP synthesis.
Why does PEP have such a large negative ΔGo'? The enol form of pyruvate does not exist in appreciable quantites in aqueous solution at pH 7 (Pocker et al., 1969; Damitio et al., 1992). PEP may be considered a 'trapped' form of a thermodynamically unstable enol which is released upon hydrolysis, thus 'pulling' the equilibrium to the right. (see Walsh, quoted below, p 230, for a more thorough explanation).
Personally, I have always considered the reaction catalyzed by PK to be pretty amazing.
In response to this question on the standard free energy of hydrolysis of phosphoenolpyruvate (PEP), I'll add the following.
The thermodynamically stable form of PEP in solution at 'physiological' pH is the enol form. That is, the enol from predominates.
PEP hydrolysis may be formally divided into two parts: (i) the hydrolysis of the phosphate ester to give the enol form of pyruvate, followed by (ii) tautomerization to the (thermodynamically stable) keto form of pyruvate (Chiang et al., 1992). Thus it is the enol form of PEP that predominates in aqueous solution at pH 7, but pyruvate exists predominately in the keto form under similar conditions.
In their in-depth study, Chiang and co-workers attribute 47% of the free energy liberated by the hydrolysis PEP to the ketonization of the enol form of pyruvate, and conclude that "nearly half of the high energy content of this molecule resides in its masked enol function" (And of course, they mean 'high energy' in the Lipmann ('squiggle') sense, that is PEP has a high standard free energy of hydrolysis).
We need to be careful with the following and acknowledge that the language is somewhat loose: we may think of PEP as a molecule where the thermodynamically unstable form of pyruvate (the enol form) is 'trapped' in a (thermodynamically stable) phosphate-ester linkage, which will be 'released' on hydrolysis. And to emphasize, the thermodynamically stable form of PEP is the enol form.
IMO, Chiang et al. (1992) is a very nice paper that rigorously backs up conclusions with strong experimental evidence, but it is surprising that they did not quote Walsh who (again, IMO) is the first to give the correct explanation?
Chiang,Y., Kresge, A. J. & Pruszynski, P. (1992) Keto-Enol Equilibria in the Pyruvic Acid System: Determination of the Keto-Enol Equilibrium Constants of Pyruvic Acid and Pyruvate and the Acidity Constant of Pyruvate Enol in Aqueous Solution J. Am. Chem. Soc. 114, 3103-3107
Damitio, J., Smith , G., Meany , J. E., Pocker, Y. (1992). A comparative study of the enolization of pyruvate and the reversible dehydration of pyruvate hydrate J. Am. Chem. Soc., 114, 3081–3087
Lipmann, F. (1941). Metabolic generation and utilization of phosphate bond energy. Adv. Enzymol. 1, 99 - 162.
Pocker, Y., Meany, J. E., Nist, B. J., & Zadorojny, C. (1969) The Reversible Hydration of Pyruvic Acid. I. Equilibrium Studies. J. Phys. Chem. 76, 2879 – 2882.
Walsh, C. (1979) Enzymatic Reaction Mechanisms. W.H. Freeman & Co.
Perhaps the most important coupled reaction is that which occurs in oxidative phosphorylation where the oxidation of fuels via the respiratory redox chain is coupled to the 'synthesis' of ATP.
I have 'steered clear' up to this point, as it is a very complex area and difficult to do justice to in a few lines.
In the chemiosmotic theory of oxidative phosphorylation (due primarily to Peter Mitchell) electron transport via the respiratory chain to molecular oxygen creates a proton gradient across the inner mitochondrial membrane by pumping protons outwards. This proton gradient, or protonmotive force, is used to 'drive' the following reaction to the right:
ADP + Pi ⇌ ATP + H2O
This is commonly referred to as 'ATP synthesis' but, more correctly perhaps, it maintains our coupling agent "far from equilibrium in terms of some useful conversion" (Atkinson, 1977, p48), that is far from equilibrium in the hydrolysis of ATP.
Although all of oxidative phosphorylation may be considered a coupled reaction, all that will be (very briefly) looked at here is the reaction catalyzed by ATP synthase, which may be considered to catalyze the following coupled reaction.
ADP + Pi + H+(Out) ⇌ ATP + H2O + H+(In)
This is an example of vectorial catalysis, but it is much more. The ATP synthetase has been described as a "splendid molecular machine" (Boyer, 1997b).
- It is an example of sequential, cooperative catalysis between 3 active sites where the the release of products (ATP) at one site is dependent on binding of substrates (ADP and Pi ) at another.
- It is an example of indirect conformational coupling where the proton gradient effects the release of of tightly bound ATP by eliciting sequential conformational changes in all active sites .
- It is an example of a binding-change mechanism, where the proton gradient is responsible release of ATP from the enzyme, but plays no role in its synthesis.
- Perhaps most dramatically, it is an example of rotational catalysis, where the indirect rotation of a protein subunit brings about the sequential conformational changes in the active sites.
Much of the mechanism of ATP synthetase is due to Boyer: this includes the prediction of rotational catalysis and the formulation (and defense) of the binding-change mechanism (see Boyer, 1997a,b). For some nice dynamic diagrams on the mechanism of action, see this SO answer.
Perhaps the most important considerations from the standpoint of the present discussion is the subtlety of the coupling effect or 'mechanistic joining': it is brought about by a conformational change due to rotation of a protein subunit, and it is mediated though the dissociation of ATP from a subunit and not through its 'synthesis' from ADP and Pi at an active site.
[Aside] In a most famous experiment, rotary catalysis was 'physically' demonstrated by Kinoshita and co-workers by attaching an actin filament to the rotating subunit of the enzyme and viewing under a fluorescent microscope (see here), which showed that rotation is anti-clockwise (viewing the enzyme from the 'membrane' side) when the enzyme is hydrolyzing ATP. A nice YouTube video, which seems to be base on the original Noji experiment, may be found here .
Abeles, R.H., Frey, P.A. & Jencks, W.P. (1992) Biochemistry. Jones & Barlett, Publishers.
Boyer, P. D. (1997a) [Nobel Lecture] Energy, Life, and ATP (pdf available here)
Boyer, P. D. (1997b) The ATP Synthase. A splendid molecular machine Annu. Rev. Biochem. 66, 717–749
Mitchell, P. (1978) [Nobel Lecture] David Keilin's Respiratory Chain Concept and Its Chemiosmotic Consequences (pdf available here)
Walker, J. E. (1997) [Nobel Lecture] ATP Synthesis by Rotary Catalysis (pdf available here)
In a coupled reaction energy required by 1 process is supplied by another process. For example: glucose + phosphate becomes glucose.6.phosphate. This is an endergonic reaction and the energy is supplied to this reaction by another reaction which has to be exergonic reaction i.e. ATP which can become ADP+energy.
Coupling process by which two or more chemical reactions depend on each other through energy once one is exothermic another is endothermic, one produce product or intermediate which is used by the another Examples glycolysis and citric acid cycle , phosphorylation and dephosphorylation in steps of glycolysis and many other