of RNA. (a) The schematic structure and bases of a single strand of RNA. (b) The molecular structure of the RNA molecule. The key difference with DNA is the presence of the –OH group at the 2′ position of the ribose sugar in the sugar–phosphate backbone, hence the name ribonucleic acid, in comparison to deoxyribonucleic acid (DNA). RNA also uses a uracil (U) rather than a thymine (T) base.
The synthesis of RNA is similar to DNA, but the molecule is built up using triphosphate molecules that have a ribose sugar instead of deoxyribose (i.e. ATP, CTP, GTP, and TTP).
As a sneak preview, but a point of astrobiological interest, you will meet ATP again when we discuss energy harvesting in cells (Chapter 6). It is interesting that ATP is processed to dATP to make DNA, which might suggest that RNA is more primitive and was a precursor to DNA, a point that leads to suggestions that RNA was an early form of genetic information (Chapter 12). It might also suggest a deep link between energetic processes, which use ATP to store cellular energy, and information storage, in which ATP is a building block of RNA.
Discussion Point: How Different Could the Genetic Code Be?
Research has shown that “unnatural” base pairs can be incorporated into cells. For example, d5SICS and dNaM are a synthetic base pair successfully incorporated into the DNA of the microorganism Escherichia coli. This research raises the question of whether the genetic code needs to have the four bases that we find in the natural terrestrial genetic code. Are they the serendipitous result of one evolutionary path? Is it possible that we could have an entirely different set of bases? A second, and related, question is whether the fundamental structure of DNA need be the same, even if the base pairs were different. You might like to discuss what sort of molecular structure an alternative information storage system could have, bearing in mind that it must replicate and be used to code information to construct other molecules (such as proteins). What required general characteristics does this impose upon an information storage system? Does such an information storage system have to be organic? Could you imagine such a system using minerals or regular crystal structures to store the quantity of information needed to build life?
Hoshika, S., Leal, N.A., Kim, M-Y. et al. (2019). Hachimoji DNA and RNA: A genetic system with eight building blocks. Science 363: 884–887.
Malyshev, D.A., Dhami, K., Lavergne, T. et al. (2014). A semi-synthetic organism with an expanded genetic alphabet. Nature 509: 385–388.
RNA is an important part of the architecture of reading the cell's information, and we look at it further in Chapter 5 when we investigate how the genetic code is read. RNA is also found in a range of viruses. The RNA molecule, on account of its different chemistry and orientation of its bases, is generally more reactive than DNA. We will see later that on account of these properties, RNA plays a central role in some theories about the origin of life.
At this point in the book, it is worth visiting yet again that question we thought about in Chapter 3. How universal would we expect the preceding discussion to be? Must life use proteins, carbohydrates, lipids, and nucleic acids to build itself? Must all information storage molecules have the same chemistry as DNA? Must all cell membranes be made of lipids? Certainly, even in terrestrial biology we see a great deal of diversity, for example in the different lipids and sugars used to assemble macromolecules. One point of view could be that the major classes of macromolecules used by life are universal, but their details are subject to great variation depending on how a particular biochemistry evolves. What do you think?
4.10 The Solvent of Life
We now turn to another essential requirement for building life. All the molecules that have been discussed must be assembled in a liquid. Life requires a solvent for chemical reactions to occur. Chemical reactions cannot occur efficiently when a system is completely desiccated, as the reactants that we need for chemical reactions cannot easily move and interact.
This solvent must have several characteristics which include physical characteristics that allow molecules essential to biological function to be moved around rapidly enough to allow chemical reactions to occur. The substance must support the carbon-based chemistry we have been discussing, or variations on it, without destroying the molecules.
4.10.1 Water as a Solvent
One solvent that meets these needs, as life on Earth shows, is water, or H2O.
Of the characteristics that make water a particularly suitable solvent for life is its dipole moment or polarity (measured as permittivity or the dielectric constant). The dipole moment of water (6.2 × 10−30 C m [coulomb meter] or 1.85 debye) is such that the molecule readily dissolves both ions and small organic molecules (Figure 4.15). Both cations (positively charged ions such as K+, Na+, Fe2+) and anions (negatively charged ions such as Cl−) play a role in a variety of functions such as stabilizing membranes or as sources of electrons. The dissolution of ions contributes to the ability of water to act as a medium for chemical reactions that require charged species. The polarity of water also allows for the dissolution of small organic compounds, such as amino acids. This property allows water to act as a mediator of the organic polymerization reactions discussed in previous sections.
Figure 4.15 Water dissolves a range of substances, including salts, sugars, and small organic compounds such as amino acids.
The polarity of water allows water molecules to bond together through hydrogen bonding. This property accounts for the wide temperature range of water, temperatures that overlap with environmental conditions on the surface and in the subsurface of a variety of planetary bodies (obviously including Earth) such as the interior of the Jovian moon Europa or the Saturnian moon Enceladus. Without the capacity for hydrogen bonding, the small molecular weight of water would result in a much smaller range of temperature conditions in the liquid state.
Water is not merely a solvent for life; it also plays fundamental roles in biochemical reactions. For example, it can act as a proton wire, conducting protons through its hydrogen-bonded network. This has been demonstrated in bacteriorhodopsin, a molecule involved in bacterial photosynthesis. In some proteins, water is found within the active site of enzymes where more than merely being part of the solvent, the water molecules there play a role in binding to the substrate as it is aligned within the active site to take part in chemical reactions. In proteins, water plays a role in binding to the outside of molecules and contributing to the fine balance between the flexibility and rigidity of the molecules. Thus, water is very much part of the structure of life, not merely a passive solvent in which reactants move.
Other properties of water account for many of its beneficial uses as a biological solvent. Water has a high heat of vaporization (in other words, it takes quite a lot of energy to get it to vaporize), which promotes a stable liquid phase inside organisms and stabilizes temperatures within them, enhancing the ability of organisms to cope with fluctuating environmental temperature regimens. A high heat of vaporization also implies a high energy loss during evaporation, which is used by multicellular organisms to achieve evaporative cooling against high temperatures in the environment.
Perhaps one of the most discussed properties of water that has been implicated in its biological usefulness is the lower density of ice than water, which
