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The Molecules of Life

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Bioinformatics

Part of the book series: Computational Biology ((COBO,volume 21))

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Abstract

This chapter complements the preceding Chap. 10 by being devoted to the molecules found within living organisms. Water, due to its ubiquity and yet unusual properties, is given detailed coverage. The rest of the chapter covers DNA, RNA, proteins, polysaccharides and lipids.

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Notes

  1. 1.

    See Ramsden and Grätzel (1986).

  2. 2.

    For polymers confined by their congeners, a given chain can slowly escape from its tube by Brownian motion: The mobility \(\mu \) of the whole chain N monomers long is \(\mu _1/N\), where \(\mu _1\) is the mobility of one monomer. Hence, from the Einstein relation \(D_\mathrm{tube} = \mu _1 k_B T/N\) and the relaxation time (to which viscosity is proportional) for tube length L (\({\sim }N\)) to be lost and created anew, \(\tau _\mathrm{tube} \sim L^2/D = NL^2/(\mu _1 k_B T) \sim N^3\), in contrast to small molecules not undergoing reptation, for which \(\tau \sim N\).

  3. 3.

    Including heterochromatin formation.

  4. 4.

    See Sinanoǧlu (1981).

  5. 5.

    See Fernández and Cendra (1996).

  6. 6.

    See Zamyatnin et al. (2006).

  7. 7.

    Rocco et al. (1987) describe this for fibronectin.

  8. 8.

    Another kind of Ramachandran plot is used to represent the structure of an entire polypeptide chain, by plotting the actual values of \(\psi \) versus \(\phi \) in the folded structure of each amino acid.

  9. 9.

    As shown in Fig. 11.6, some residues can also participate in hydrogen bonding, but the backbone peptide H-bonds (or potential H-bond donors and acceptors) are of course more numerous and, hence, more significant.

  10. 10.

    The dehydron concept is due to A. Fernández. See, for example, Fernández and Scott (2003) and Fernández et al. (2002, 2003).

  11. 11.

    Empirically, a certain threshold density of dehydrons per unit area should be exceeded for a surface to qualify as sticky.

  12. 12.

    For some of the problems associated with the production of recombinant proteins, see Protein production and purification, Nature Methods 5 (2008) 135–146.

  13. 13.

    Multiple isomorphous replacement—MIR—whereby a few heavy atoms are introduced into the protein, which is then remeasured, is used to determine the diffraction phases. The heavy atoms should not, of course, induce any changes in the protein structure.

  14. 14.

    See Dwek and Butters (2002) for an overview.

  15. 15.

    See also “Symbols for specifying the confirmation of polysaccharide chains”, Eur. J. Biochem. 131 (1983) 5–7, or Pure Appl. Chem. 55 (1983) 1269–1272.

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Authors and Affiliations

  1. The University of Buckingham, Buckingham, UK

    Jeremy Ramsden

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  1. Jeremy Ramsden
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Correspondence to Jeremy Ramsden .

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Ramsden, J. (2015). The Molecules of Life. In: Bioinformatics. Computational Biology, vol 21. Springer, London. https://doi.org/10.1007/978-1-4471-6702-0_11

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  • DOI: https://doi.org/10.1007/978-1-4471-6702-0_11

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