a short essay to compare and contrast the use of ionic, covalent, hydrogen, and Van der Waals interactions in living things with an example for each of how they bond together atomic and molecular structures.8 Describe the difference between an emission and absorption spectrum, explaining how they are produced by changes in electron energies. How might such spectra be used to look for gases produced by life in the atmosphere of an extrasolar planet?
Bibliography
Books
1 Colvin, J. and Larsen, J. (2013). Extreme Physics: Properties and Behavior of Matter at Extreme Conditions. Cambridge: Cambridge University Press.
2 Pavia, D.L., Lampman, G.M., and Kriz, G.S. (2000). Introduction to Spectroscopy. Fort Worth: Brooks/Cole.
3 Tabor, D. (1991). Gases, Liquids and Solids: And Other States of Matter. Cambridge: Cambridge University Press.
Papers
1 Attard, P. (1996). Patterns of hydrogen bonding in water and ice. Physics A 233: 742–753.
2 Auffinger, P., Hays, F.A., Westhof, E. et al. (2004). Halogen bonds in biological molecules. Proceedings of the National Academy of Sciences of the United States of America 101: 16789–16794.
3 Autumn, K., Sitti, M., Liang, Y.A. et al. (2002). Evidence for van der Waals adhesion in gecko setae. Proceedings of the National Academy of Sciences of the United States of America 99: 12252–12256.
4 Burrows, A.S. (2014). Spectra as windows into exoplanet atmospheres. Proceedings of the National Academy of Sciences of the United States of America 111: 12601–12609.
5 Drake, F.D. (1973). Life on a neutron star. Astronomy (December): 5.
6 Fidler, A.L., Vanacore, R.M., Chetyrkin, S.V. et al. (2014). A unique covalent bond in basement membrane is a primordial innovation for tissue evolution. Proceedings of the National Academy of Sciences of the United States of America 111: 331–336.
7 Gobre, V.V. and Tkatchenko, A. (2013). Scaling laws for van der Waals' interactions in nanostructured materials. Nature Communications 4 https://doi.org/10.1038/ncomms3341.
8 Harding, S.E., Channell, G., and Phillips-Jones, M.K. (2018). The discovery of hydrogen bonds in DNA and a re-evaluation of the 1948 Creeth two-chain model for its structure. Biochemical Society Transactions 46 (5): 1171–1182.
9 Holm, R.H., Kennepohl, P., and Solomon, E.I. (1996). Structural and functional aspects of metal sites in biology. Chemical Reviews 96: 2239–2314.
10 Horowitz, S. and Trievel, R.C. (2012). Carbon–oxygen hydrogen bonding in biological structure and function. Journal of Biological Chemistry 287: 41576–41582.
11 Jones, E.G. and Lineweaver, C.H. (2012). Using the phase diagram of liquid water to search for life. Australian Journal of Earth Science 59: 253–262.
12 Jones, E.G., Lineweaver, C.H., and Clarke, J.D. (2011). An extensive phase space for the potential Martian biosphere. Astrobiology 11: 1017–1033.
13 Lattimer, J.M. and Prakash, M. (2004). The physics of neutron stars. Science 304: 536–542.
14 Leckband, D. and Israelachvili, J. (2001). Intermolecular forces in biology. Quarterly Reviews of Biophysics 34: 105–267.
15 Raines, R.T. (1997). Nature's transitory covalent bond. Nature Structural Biology 4: 424–427.
16 Rigoldi, F., Donini, S., Redaelli, A. et al. (2018). Review: engineering of thermostable enzymes for industrial applications. APL Bioengineering 2: 011501. 2.
17 Tadmor, R. (2001). The London–van der Waals interaction energy between objects of various geometries. Journal of Physics: Condensed Matter 13: L195–L202.
4 The Molecular Structure of Life
Learning Outcomes
Understand that the basic elements required by life are carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur (CHNOPS). Other elements are used for a range of functions specific to particular types of life.
Understand why carbon is the most versatile backbone of molecules – life is “carbon-based.”
Know the characteristics of the major classes of biological macromolecules: proteins, carbohydrates, lipids, and nucleic acids.
Understand that some classes of molecules such as proteins and carbohydrates are chiral.
Understand why water is the most versatile and plausible solvent for life.
Understand some of the arguments for, and some of the limitations of, proposed alternative building block elements for life such as silicon, and alternative solvents such as ammonia.
4.1 Building Life
In Chapter 3, we saw how different bonding types allow for the association of atoms, ions, and molecules. Life assembles these units, a bit like a construction kit, into macromolecules (large molecules), which themselves form the architecture of all cells from which life is assembled.
In this chapter, we focus on the construction of living things from the atomic scale to this larger molecular scale. We explore some of the characteristics of the major groups of molecules that make up living things. We also identify and discuss common themes and principles that emerge about the construction of living things.
4.2 The Essential Elements: CHNOPS
Building from the previous chapter, we could start with a very simple question: what is the minimum set of elements that life needs to assemble molecules? The matter from which life is constructed is unsurprisingly restricted to what is in the Periodic Table, and therefore its options are not unlimited.
Furthermore, we can assume that the Periodic Table is universal. This seems a reasonable working assumption, as no astrophysicist has yet observed a place in the Universe that seems to have an entirely alien chemistry; in fact quite the contrary – as we shall see later, many elements of importance to life, such as carbon, seem to be surprisingly abundant throughout the Universe. Therefore, the observations we make about the chemistry of terrestrial life are likely to reveal important insights into the potential chemistry of life anywhere in the Universe.
If we survey the elements from which life is constructed, we find six that are found in all living things; they have often been described as the “building block” elements of life (Figure 4.1). They are C (carbon), H (hydrogen), N (nitrogen), O (oxygen), P (phosphorus), and S (sulfur). They are sometimes remembered as the odd word CHNOPS, or the variation SPONCH – take your pick.
Figure 4.1 The six ubiquitous elements of life, CHNOPS. The van
