3. ATP Synthesis

ATP Synthesis

Energy + ADP + Pi —> ATP

ATP Synthesis is energetically unfavorable. The Free Energy of the product is higher than that of the substrate. So, where does the necessary energy come from? Two sources:

  • There’s a source of energy in the proton motive force (PMF)
  • Based on the structure of ATP Synthase, that this energy drives conformations changes, which drive ATP binding

So how to get from ATP binding to energy input and catalysis?

Binding is closely linked to energy. A traditional enzyme binds to transition state of substrate. The resulting binding energy released lowers the activation energy and accelerates reaction. But it’s not necessarily the case that an enzyme bind to the transition state.

Experiments on purified F1 subunits show ADP/ATP exist at equilibrium in the active site of the subunit. The ATP Synthase/ADP Complex (ES: the enzyme substrate complex) has roughly the same free energy as the ATP Synthase ATP complex (EP: the enzyme product complex).

F1 binds ATP so well that it reduces the energy input for ADP->ATP conversion to ~0. But it comes with a high energy barrier to overcome for the release of ATP from ATP Synthase. That’s where the conformation changes of the beta chain fit in.

Lecture slide from HarvardX. All rights are theirs.
Lecture slide from HarvardX. All rights are theirs.


Paul Boyer developed a model on PMF drive called the Binding Change Model (Nobel Prize, 1997):

ATP Synthesis through conformation changes of beta chain. Rotation of asymmetric stalk cycles beta through three conformations with different ATP binding proteins. The protons flowing back to F0 induce oration of the c-ring, which drives the oration of the stalk. Thus, the beta changes.

For each T-state, the beta chain has different binding properties.

Lecture slide from HarvardX. All rights are theirs.
Lecture slide from HarvardX. All rights are theirs.

L-state: traps bound-ADP and Pi

O-state: open, low affinity for ATP and ADP

T-state: tight t-conformation.

States alternate!

Once O-state accepts ADP/PI, the chain (stalk) rotates 120 degrees. O->L, trapping ADP/PI, then L->T. Here ATP will be produced but not released. Then finally, T->) and ATP is released, ready for new substrate.

After each rotation, each beta releases 1 ATP, thus three ATP released per turn.

How many protons needed to make one molecule of ATP?

In the F0 subunit, the c-ring contains between 10-15 chains. Assume 10, for example. A full turn of a 10-chain c-ring needed for 10 protons to flow through F0. Thus, each ATP needs 10/3, or 3.333…. protons. If the c-ring contains 10 c-chains, 3 protons must flow back for the production of 1 ATP.

Only a portion of the PMF is used for ATP Synthesis: most ATP is used outside the mitochondria. Two processes reduce the PMF.


Adenine Nucleotide Translocase coordinates the ATP/ADP exchange across membranes.

ATP has four negative charges to ADP’s three. So, a net transfer of one negative charge into the IM => transfer is favored by the positive membrane potential of the IM.

PMF drives this exchange, but it also neutralized part of its energy potential. It reduces the PMF.

The inorganic phosphate Pi also needs to be transported to the matrix. Phosphate Translocase moves Pi and a proton into the matrix. Net transport = 0 (since the Pi has a charge of -1: see below). This is favored by the transmembrane proton gradient and the import of Pi is also driven by PMF, but Pi reduces PMF (chemical potential) since protons are entering the matrix outside of ATP Synthase.

So the transport of ATP out of the mitochondria is not handled by the PMF, nor is the transfer of protons into the IMS by the ETC.

Note: at physiologic pH, the inorganic phosphate, Pi, is actually the ion H2PO4 ion. Net charge -1.

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