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

  • Allen P. MintonEmail author
  • Germán Rivas
Chapter

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.

Keywords

Synthetic Biology Standard Free Energy Relative Free Energy Exclude Volume Effect Macromolecular Crowding 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

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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Copyright information

© Springer Netherlands 2011

Authors and Affiliations

  1. 1.Section on Physical Biochemistry, Laboratory of Biochemistry and GeneticsNIDDK, National Institutes of HealthBethesdaUSA
  2. 2.Chemical and Physical Biology Program, Centro de Investigaciones BiológicasCSICMadridSpain

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