Skip to main content

In Vitro Versus In Vivo: Concepts and Consequences

  • Chapter
  • First Online:
Book cover ENZYMES: Catalysis, Kinetics and Mechanisms

Abstract

Biochemists enjoy the freedom to purify and study enzymes in isolation, saturate an enzyme with its substrate, trap/remove the products, and also provide optimal pH, ionic strength, etc. On the other hand, cell extracts are by their very nature “dirty enzymes”; intact cells and organisms are “dirtier” still. The cell by design is greatly constrained to provide a consensus medium to simultaneously support hundreds of diverse enzyme-catalyzed reactions. Only some of these enzymes may be operating under optimal conditions at any time. The context for an enzyme to function in vivo is very different from the well-defined conditions deliberately set up for its study in vitro. And classical biochemistry is founded on several assumptions valid in dilute aqueous solutions. These assumptions are often extended without question to the cellular milieu. But the cell interior is far away from being an ideal solution. The key features that differentiate the state of affairs in vivo from that in vitro are cataloged below.

(The biochemist’s word) may not be the last in the description of life, but without his help the last word will never be said.

Sir Gowland Hopkins

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Albe KR, Butler MH, Wright BE (1990) Cellular concentrations of enzymes and their substrates. J Theor Biol 143:163–195

    Article  CAS  Google Scholar 

  • Banani SF, Lee HO, Hyman AA, Rosen MK (2017) Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Molec Cell Biol 18:285–298

    Article  CAS  Google Scholar 

  • Benner SA (1989) Enzyme kinetics and molecular evolution. Chem Rev 89:789–806

    Article  CAS  Google Scholar 

  • Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 5:593–599

    Article  CAS  Google Scholar 

  • Burbaum JJ, Raines RT, Albery WJ, Knowles JR (1989) Evolutionary optimization of the catalytic effectiveness of an enzyme. Biochemistry 28:9293–9305

    Article  CAS  Google Scholar 

  • Castellana M, Wilson MZ, Xu Y, Joshi P, Cristea IM, Rabinowitz JD, Gitai Z, Wingreen NS (2014) Enzyme clustering accelerates processing of intermediates through metabolic channeling. Nat Biotechnol 32:1011–1018

    Article  CAS  Google Scholar 

  • Dang L, White DW, Gross S, Bennett BD, Bittinger MA, Driggers EM, Fantin VR, Jang HG, Jin S, Keenan MC, Marks KM, Prins RM, Ward PS, Yen KE, Liau LM, Rabinowitz JD, Cantley LC, Thompson CB, Vander Heiden MG, Su SM (2009) Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462:739–744

    Article  CAS  Google Scholar 

  • Dave K, Punekar NS (2015) Expression of lactate dehydrogenase in Aspergillus niger for L-lactic acid production. PLoS One 10(12):e0145459

    Article  CAS  Google Scholar 

  • Dobzhansky T (1973) Nothing in biology makes sense except in the light of evolution. Am Biol Teach 35:125–129

    Article  Google Scholar 

  • Ellis RJ (2001) Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci 26:597–604

    Article  CAS  Google Scholar 

  • Fischbach MA, Walsh CT (2006) Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 106:3468–3496

    Article  CAS  Google Scholar 

  • Halling PJ (1989) Do the laws of chemistry apply to living cells? Trends Biochem Sci 14:313–353

    Article  Google Scholar 

  • Hardt SL (1979) Rates of diffusion controlled reactions in one, two and three dimensions. Biophys Chem 10:239–243

    Article  CAS  Google Scholar 

  • Hasinoff BB (1984) Kinetics of carbonic anhydrase catalysis in solvents of increased viscosity: a partially diffusion controlled reaction. Arch Biochem Biophys 233:676–681

    Article  CAS  Google Scholar 

  • Knowles JR, Albery WJ (1977) Perfection in enzyme catalysis: the energetics of trisoephosphate isomerase. Acc Chem Res 10:105–111

    Article  CAS  Google Scholar 

  • Kornberg A (2000) Ten commandments: lessons from the enzymology of DNA replication. J Bacteriol 182:3613–3618

    Article  CAS  Google Scholar 

  • Kornberg A (2003) Ten Commandments of enzymology, amended. Trends Biochem Sci 28:515–517

    Article  CAS  Google Scholar 

  • Luby-Phelps K (2000) Cryo-architecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area. Int Rev Cytol 192:189–221

    Article  CAS  Google Scholar 

  • Mathews CK (1993) The cell – a bag of enzymes or a network of channels? J Bacteriol 175:6377–6381

    Article  CAS  Google Scholar 

  • Milo R, Phillips R (2016) Cell biology by the numbers. Garland Science, Taylor & Francis Group, LLC, New York

    Google Scholar 

  • Perham RN (2000) Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu Rev Biochem 69:961–1004

    Article  CAS  Google Scholar 

  • Sanyal N, Arentson BW, Luo M, Tanner JJ, Becker DF (2015) First evidence for substrate channeling between proline catabolic enzymes. J Biol Chem 290:2225–2234

    Article  CAS  Google Scholar 

  • Savageau MA (1992) Critique of the enzymologist’s test tube. In: Fundamentals of medical cell biology, vol 3A, chemistry of the living cell. Elsevier, Amsterdam

    Google Scholar 

  • Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasic’ I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P (2013) A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes. FEBS Lett 587:2832–2841

    Article  CAS  Google Scholar 

  • Srere PA (1967) Enzyme concentrations in tissues. Science 158:936–937

    Article  CAS  Google Scholar 

  • Srere PA (1970) Enzyme concentrations in tissue II. Biochem Med 4:43–46

    Article  CAS  Google Scholar 

  • Srere PA (1984) Why are enzymes so big? Trends Biochem Sci 9:387–390

    Article  CAS  Google Scholar 

  • Srivastava DK, Bernhard SA (1986) Enzyme-enzyme interactions and the regulation of metabolic reaction pathways. Curr Top Cell Regul 28:1–68

    Article  CAS  Google Scholar 

  • Storey KB (2005) Functional metabolism: regulation and adaptation. Wiley, Hoboken (First three chapters, in particular)

    Google Scholar 

  • van Eunen K, Bouwman J, Daran-Lapujade P, Postmus J, Canelas AB, Mensonides FIC, Orij R, Tuzun I, van den Brink J, Smits GJ, van Gulik WM, Brul S, Heijnen JJ, de Winde JH, Teixeira de Mattos MJ, Kettner C, Nielsen J, Westerhoff HV, Bakker BM (2010) Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J 277:749–760

    Article  CAS  Google Scholar 

  • Verkman AS (2002) Solute and macromolecule diffusion in cellular aqueous compartments. Trends Biochem Sci 27:27–33

    Article  CAS  Google Scholar 

  • Weeks A, Lund L, Raushel FM (2006) Tunneling of intermediates in enzyme-catalyzed reactions. Curr Opin Chem Biol 10:465–472

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Punekar, N.S. (2018). In Vitro Versus In Vivo: Concepts and Consequences. In: ENZYMES: Catalysis, Kinetics and Mechanisms. Springer, Singapore. https://doi.org/10.1007/978-981-13-0785-0_38

Download citation

Publish with us

Policies and ethics