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What are the energetics of protein digestion during which the enzyme pepsin is "activated" (whatever that means) by HCl? I've looked and been unable to find anything like a chemical equation that includes an energy term.

Of course, pepsin, being an enzyme, is not used up in that sought-for equation. Is HCl used up? If so, what are the products? How and in what form is the chlorine removed, assuming the HCl is consumed in the equation?

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This is well-explained on the Wikipedia page for pepsin. You are misinterpreting the use of the word activated. The protein is secreted by chief cells in the gastric glands in the form of pepsinogen, an inactive pro- form which has an extra ~40 amino acids at its N-terminus (the propeptide). The propeptide binds at the catalytic site of the enzyme and keeps it inactive. At low pH (this is where the HCl comes in - HCl secreted by parietal cells of the gastric glands acidifies the stomach) the protein is able to cleave off its own propeptide, making it fully active.

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So it would appear that the HCl is consumed in a chemical equation that looks something like: pepsinogen + HCl => pepsin + ?Cl + ?Joules Moreover, the HCl apparently isn't substantially involved in digesting the protein directly (say, by hydrolyzing it). Furthermore, pepsin isn't consumed in the chemical equations for digestion (it being an enzyme) so much as it is lost due to normal mechanical effects. So my question really reduces to filling in the '?' in the prior equation. –  James Bowery Nov 15 '13 at 6:20
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The HCl isn't really involved in the reaction at all, except in the sense that it drives the pH down. There may be some binding and/or release of protons during the autocatalytic process. I haven't been able to find anything about the free energy change that accompanies the reaction. Of course the entropy will increase (1 molecule > 2 molecules), so it is even possible that the enthalpy term (your ?joules I assume) would be positive. –  Alan Boyd Nov 15 '13 at 16:44
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