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The Composition and Architecture of the Cell

In chapter 1, we have seen how phospholipids can cooperatively assemble to form membrane structures, which resemble the membranes of biological cells. Now, let us take a look at the composition and organization of the cell, which will allow us to put the physics in its biological context. Some of the terms and concepts introduced in this chapter (e.g., proteins, cell membrane, etc.) will be dealt with in more details later on in this book, while others (such as those concerning the structure and function of cellular organelles, biochemistry of the cell, etc.) are explained in many excellent books that are available on molecular and cellular biology (e.g., Alberts et al., 2002; Lodish et al., 2004; Berg et al., 2002). The reader should therefore be aware that by no means do we intend in this section to provide a comprehensive review of subjects normally covered by cell biology and biochemistry textbooks. Instead, herein the biological information is reduced to its bare essentials, and it will be introduced and used only insofar as it can help the progression towards understanding of the biophysics concepts and principles presented in this book.

Broadly speaking, there are two classes of living systems: viruses and uni- or multi-cellular organisms. Of these, only cellular organisms present the two main distinguishing features of a living system, self-reproduction and metabolism, viruses not being endowed with their own metabolism. Both deoxyribonucleic-based (DNA) viruses and ribonucleic-based (RNA) viruses rely on the cellular metabolism of the host cell, in order to self-multiply.

Section 2.1 is concerned with a brief description of the organization of biological cells, which is considered to be the fundamental morphological and functional unit of living matter. Section 2.2 will provide a description of protein structure, folding and misfolding, while section 2.3 will discuss the DNA structure and replication (multiplication).

Keywords

Double Helix Nuclear Overhauser Effect Helix Axis Deoxyribose Nucleic Acid International Human Genome Sequencing Consortium 
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.

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References

  1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K and Walter, P. (2002) Molecular Biology of the Cell, 4th ed., Garland Science/Taylor & Francis, New YorkGoogle Scholar
  2. Anfinsen, C. B. (1973) Principles that govern the folding of protein chains, Science, 181: 223CrossRefADSGoogle Scholar
  3. Baker, D. (2000) A surprising simplicity to protein folding, Nature, 405: 39CrossRefADSGoogle Scholar
  4. Berg, J. M., Tymoczo, J. L. and Stryer, L. (2002) Biochemistry, 5th ed., W. H. Freeman, New YorkGoogle Scholar
  5. Clementi, C. and Plotkin, S. S. (2006) The effects of nonnative interactions on protein folding rates: Theory and simulation, Prot. Sci., 13: 1750CrossRefGoogle Scholar
  6. Dobson, C. M. (2002) Getting out of shape, Nature, 418: 730CrossRefADSGoogle Scholar
  7. Drenth, J. (1994) Principles of X-Ray Crystallography, Springer, New YorkGoogle Scholar
  8. Eisenberg, D. (2003) The discovery of the α-helix and β-sheet, the principal structural features of proteins, Proc. Natl. Acad. Sci. USA, 100: 11207CrossRefADSGoogle Scholar
  9. Fenn, J. B. (2002) Electrospray ionization mass spectrometry: How it all began, J. Biomol. Tech., 13: 101Google Scholar
  10. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome, Nature, 431: 931Google Scholar
  11. Kline, A. D., Braun, W. and Wütrich, K. (1988) Determination of the complete three-dimensional structure of the α-amylase inhibitor tendamistat in aqueous solution by nuclear magnetic resonance and distance geometry, J. Mol. Biol., 204: 675CrossRefGoogle Scholar
  12. Lodish, H., Berk, A., Matsudaira, P., Kaiser, C. K., Krieger, M., Scott, M. P., Zipursky, S. L. and Darnell, J. (2004) Molecular Cell Biology, 5th ed., W. H. Freeman, New YorkGoogle Scholar
  13. Malacinschi, G. M. (2003) Essentials of Molecular Biology, 4th ed., Jones and Bartlett, Boston, MA/LondonGoogle Scholar
  14. Maddox, B. (2003) Rosalind Franklin: The Dark Lady of DNA, Harper Collins, New YorkGoogle Scholar
  15. Martini, F. H. (2004) Fundamentals of Anatomy & Physiology, 7th ed., Benjamin Cummings, San FranciscoGoogle Scholar
  16. Mirny, L. and Shaknovich, E. (2001) Protein folding theory: from lattice to all-atom models, Annu. Rev. Biophys. Biomol. Struct., 30: 361CrossRefGoogle Scholar
  17. Moreland, J. L., Gramada, A., Buzko, O. V., Zhang, Q. and Bourne, P. E. (2005) The Molecular Biology Toolkit (mbt): A modular platform for developing molecular visualization applications, BMC Bioinformatics, 6: 21CrossRefGoogle Scholar
  18. Neutze, R., Wouts, R., van der Spoel, D., Weckert, E. and Hajdu, J. (2000) Nature 406: 752CrossRefADSGoogle Scholar
  19. Normille, D. (2006) Japanese latecomer joins race to build a hard X-ray laser, Science 314: 751CrossRefGoogle Scholar
  20. Onuchic, J. N. and Wolynes, P. G. (2004) Theory of protein folding, Curr. Opin. Struct. Biol., 14: 70CrossRefGoogle Scholar
  21. Pande, V. S. (2003) Meeting halfway on the bridge between protein folding theory and experiment, Proc. Natl. Acad. Sci. USA, 100: 3555CrossRefADSGoogle Scholar
  22. Rose, G. D., Fleming, P. J. Banavar, J. R. and Maritan, A. (2006) A backbone-based theory of protein folding, Proc. Natl. Acad. Sci. USA, 103: 16623CrossRefADSGoogle Scholar
  23. Saven, J. G., Wang, J. and Wolynes, P. G. (1994) Kinetics of protein folding: The dynamics of globally connected rough energy landscapes with biases, J. Chem. Phys., 101: 11037CrossRefADSGoogle Scholar
  24. Shneerson, V. L., Ourmazd, A. and Saldin, D. K. (2007) to be published in Acta. Cryst. (personal communication by D. K. Saldin)Google Scholar
  25. Schmidt, M., Pahl, R., Srajer, V., Anderson, S., Ren, Z., Ihee, H., Rajagopal, S. and Moffat, K. (2004) Protein kinetics: structures of intermediates and reaction mechanism from time-resolved x-ray data, Proc. Natl. Acad. Sci. USA, 101: 4799CrossRefADSGoogle Scholar
  26. Schrödinger, E. (1992) What Is Life?: The Physical Aspect of the Living Cell With Mind and Matter and Autobiographical Sketches, Cambridge University Press, CambridgeGoogle Scholar
  27. Serdyuk, I. N., Zaccai, N. R. and Zaccai, J. (2007) Methods in Molecular Biophysics. Structure, Dynamics, Function, Cambridge University Press, Cambridge/New York/MelbourneGoogle Scholar
  28. Spence, J. C. H., Schmidt, K., Wu, J. S., Hembree, G., Weierstall, U., Doak, B. and Fromme, P. (2005) Diffraction and imaging from a beam of laser-aligned proteins: resolution limits, Acta Cryst. A, 61: 237CrossRefGoogle Scholar
  29. Svedberg, T., Pedersen, K. O. (1940) The Ultracentrifuge, Clarendon, OxfordGoogle Scholar
  30. Walter, F., Boron, E. L. and Boulpaep, M. D. (2004) Medical Physiology: A Cellular and Molecular Approach, Saunders/Elsevier, PhiladelphiaGoogle Scholar
  31. Watson, J. D. and Crick, F. H. C. (1953) Molecular structure of nucleic acids. A structure for the deoxyribose nucleic acid. Nature, 171: 737CrossRefADSGoogle Scholar
  32. Williamson, M. P., Havel, T. F. and Wütrich, K. (1985) Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry, J. Mol. Biol., 182: 295CrossRefGoogle Scholar
  33. Wütrich, K. (2001) The way to NMR structures of proteins, Nature, 8: 923Google Scholar

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