The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry

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 pKa and their applicati...

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Autor principal:	Todd P. Silverstein
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	acidity pH aqueous solution acid catalysis enzyme catalysis proton transfer Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/bf4ce441c42744fbbec2ec053f3f3c29
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spelling	oai:doaj.org-article:bf4ce441c42744fbbec2ec053f3f3c292021-12-01T05:50:03ZThe Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry2296-889X10.3389/fmolb.2021.764099https://doaj.org/article/bf4ce441c42744fbbec2ec053f3f3c292021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmolb.2021.764099/fullhttps://doaj.org/toc/2296-889XThe 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 pKa 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.Todd P. SilversteinFrontiers Media S.A.articleaciditypHaqueous solutionacid catalysisenzyme catalysisproton transferBiology (General)QH301-705.5ENFrontiers in Molecular Biosciences, Vol 8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	acidity pH aqueous solution acid catalysis enzyme catalysis proton transfer Biology (General) QH301-705.5
spellingShingle	acidity pH aqueous solution acid catalysis enzyme catalysis proton transfer Biology (General) QH301-705.5 Todd P. Silverstein The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry
description	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 pKa 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.
format	article
author	Todd P. Silverstein
author_facet	Todd P. Silverstein
author_sort	Todd P. Silverstein
title	The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry
title_short	The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry
title_full	The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry
title_fullStr	The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry
title_full_unstemmed	The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry
title_sort	proton in biochemistry: impacts on bioenergetics, biophysical chemistry, and bioorganic chemistry
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/bf4ce441c42744fbbec2ec053f3f3c29
work_keys_str_mv	AT toddpsilverstein theprotoninbiochemistryimpactsonbioenergeticsbiophysicalchemistryandbioorganicchemistry AT toddpsilverstein protoninbiochemistryimpactsonbioenergeticsbiophysicalchemistryandbioorganicchemistry
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The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry

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