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Biochemical Reactions in the Crowded and Confined Physiological Environment: Physical Chemistry Meets Synthetic Biology

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Abstract

Proteins and nucleic acids constitute at least 20–30% of the total mass (and volume) of all living organisms without exception. Although local composition may vary widely with location within a given cell and between cells, it is evident that much of the chemistry of life – as opposed to laboratory biochemistry – takes place within media containing a substantial volume fraction of macromolecules. These media are termed “crowded” or “volume-occupied”, rather than “concentrated”, as no single macromolecular species need be concentrated. Moreover, many biological compartments do not consist of a continuous fluid phase, but rather a series of small interstitial elements of fluid, or “pores”, bounded by membranes or other relatively immobile structural elements such as cytoskeletal filaments. Such interstitial volume elements might be likened to the holes in a sponge, except that the characteristic sizes of the “holes” are of the order of tens of nanometers. The soluble macromolecules within these pores are termed “confined” to reflect the discontinuous nature of the fluid phase and the small dimensions of the pores.

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Notes

  1. 1.

    The apparent equilibrium constant, defined as a function of the concentrations of solute species, is distinguished from the thermodynamic equilibrium constant, which is defined as a function of the thermodynamic activities of solute species. The relations presented in this section describe the effect of background interactions upon the apparent equilibrium constant for the selected reaction

  2. 2.

    Free energy changes denoted by ΔF may refer to either Gibbs or Helmholtz free energies since the relationships described here hold equally in constant pressure and constant volume systems

  3. 3.

    Predicted effects of macromolecular confinement on association equilibria have not yet been tested

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Acknowledgements

Research conducted in A.P.M.’s laboratory is supported by the Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health. The author thanks Peter McPhie (NIH) for reviewing drafts of this Commentary.

Research in GR lab is funded by the Spanish Ministry of Science and Innovation (grant BIO2008-04478-C03-03), the Madrid Government (COMBACT_CM), and the EU (HEALTH-F3-2009-223431).

We are grateful to Company of Biologists Ltd., which allowed the reproduction of the full article (Minton 2006).

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Authors and Affiliations

  1. Section on Physical Biochemistry, Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, MD, USA

    Allen P. Minton

  2. Chemical and Physical Biology Program, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain

    Germán Rivas

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  1. Allen P. Minton
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  2. Germán Rivas
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Correspondence to Allen P. Minton .

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  1. Dipto. Biologia, Università Roma Tre, Viale Guglielmo Marconi 446, Roma, 00146, Italy

    Pier Luigi Luisi

  2. , Biology Department, University of Roma Tre, Viale Guglielmo Marconi 446, Rome, 00146, Italy

    Pasquale Stano

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Minton, A.P., Rivas, G. (2011). Biochemical Reactions in the Crowded and Confined Physiological Environment: Physical Chemistry Meets Synthetic Biology. In: Luisi, P., Stano, P. (eds) The Minimal Cell. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9944-0_5

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