Abstract
The proton is the smallest atomic particle, and in aqueous solution it is the smallest hydrated ion, having only two waters in its first hydration shell. In this article we survey key aspects of the proton in chemistry and biochemistry, starting with the definitions of pH and pK a and their application inside biological cells. This includes an exploration of pH in nanoscale spaces, distinguishing between bulk and interfacial phases. We survey the Eigen and Zundel models of the structure of the hydrated proton, and how these can be used to explain: a) the behavior of protons at the water-hydrophobic interface, and b) the extraordinarily high mobility of protons in bulk water via Grotthuss hopping, and inside proteins via proton wires. Lastly, we survey key aspects of the effect of proton concentration and proton transfer on biochemical reactions including ligand binding and enzyme catalysis, as well as pH effects on biochemical thermodynamics, including the Chemiosmotic Theory. We find, for example, that the spontaneity of ATP hydrolysis at pH ≥ 7 is not due to any inherent property of ATP (or ADP or phosphate), but rather to the low concentration of H+. Additionally, we show that acidification due to fermentation does not derive from the organic acid waste products, but rather from the proton produced by ATP hydrolysis.
Highlights
For such a tiny particle, the proton1 certainly packs a wallop
It is so important that most laboratories in the world routinely measure its concentration, and many compounds are judged by their ability to release it into solution
In our discussion of biochemical thermodynamics and kinetics we survey of the effects of pH on
Summary
For such a tiny particle, the proton certainly packs a wallop. It is so important that most laboratories in the world routinely measure its concentration (i.e., pH), and many compounds are judged by their ability to release it into solution. A nearby positive side chain destabilizes the protonated form of the weak acid and stabilizes the conjugate base form, which makes the acid more acidic, raising its Ka (lower pKa); a nearby negative side chain does the opposite As we see, these effects can alter the pKa of a protein side chain by up to ±5 units from its nominal value in water. The equilibrium constant for the reaction in Eq 10 must be 1 because products and reactants are identical, so pKa (H+(aq)) 0 We often see this value as −1.74 in the organic chemistry literature, but again, this value is incorrect, due to the mistaken use of the molar concentration of water, 55.3 M, rather than its activity, 1 (Meister et al, 2014) (Silverstein and Heller, 2017). We will further expand on these two types of reactions in our discussion below
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