CHAPTER 8
The second law of thermodynamics: Borgnakke C, Sonntag RE. (2009) Fundamentals of Thermodynamics. Wiley, Chichester.
Sitting on cell membranes: The mitochondria are the organelles that produce energy in most eukaryotic cells. The electron transfer chain that I describe occurs within the membranes of mitochondria. In prokaryotes, the transfer chain occurs in the cellular membrane, not in an organelle.
Mitchell creatively figured: Mitchell P. (1961) The chemiosmotic hypothesis. Nature 191, 144–148.
As the protons flow: The rotation of ATP synthase is itself reducible to remarkable physical principles, in particular Brownian motion, in which the random movement of protons is used to drive its rotation in a form of ratchet motion. Many other biochemical processes tap into Brownian motion to achieve directional movement. See Oster G. (2002) Darwin’s motors: Brownian ratchets. Nature 417, 25. Like the bacterial flagellum, ATP synthase is another example of a circular wheel-like contraption in living things, albeit not for moving across surfaces, but for a rotating structure nonetheless.
The changing shape of ATP synthase: Phosphates are a chemical group with the formula PO42−.
The molecule so produced, ATP: The phosphate bonds within ATP do not release energy when they are broken elsewhere in the cell (to break bonds requires energy). Instead, the small amount of energy needed to break the phosphate off ATP is more than made up for by the energy released when that phosphate binds to water after its release. The breakage of ATP is a hydrolysis reaction, and the net effect of all the bonds broken and made releases energy. A subtlety, but nevertheless an important one.
If you think this is a trifling process: The numbers are an estimate, as they depend on many factors. But roughly, you need about 2000 kilocalories of energy each day, that is, about three moles of glucose or about 1.8 × 1024 molecules of glucose. For each molecule of glucose shunted through the electron transport chain and onward, 36 molecules of ATP can be produced, so that’s about 6.5 × 1025 molecules of ATP produced per day, or about 2.7 × 1024 per hour. Regardless of academic quibbling about the various conversions and efficiencies, the number is huge.
Or is the architecture: The conditions that gave rise to early proton gradients may have been hydrothermal vents. The early evolution of the process is discussed in Martin WF. (2012) Hydrogen, metals, bifurcating electrons, and proton gradients: The early evolution of biological energy conservation. FEBS Letters 586, 485–493.
We already know: Imkamp F, Müller V. (2002) Chemiosmotic energy conservation with Na(+) as the coupling ion during hydrogen-dependent caffeate reduction by Acetobacterium woodii. Journal of Bacteriology 184, 1947–1951.
Nevertheless, protons are: An excellent book exploring these early cellular processes and how the first gradients for energy acquisition might have formed is Lane N. (2016) The Vital Question. Profile Books, London.
No group of people: Boston PJ, Ivanov MV, McKay CP. (1992) On the possibility of chemosynthetic ecosystems in subsurface habitats on Mars. Icarus 95, 300–308.
Hydrogen gas can be ancient: The link between serpentinization and life is discussed in Okland I et al. (2012) Low temperature alteration of serpentinized ultramafic rock and implications for microbial life. Chemical Geology 318, 75–87.
Microbial communities: Spear JR, Walker JJ, McCollom TM, Pace NR. (2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proceedings of the National Academy of Sciences 102, 2555–2560.
The core molecules: Some of the proteins involved in the electron transfer chain are clearly ancient. For an early review, see Bruschi M, Guerlesquin F. (1988) Structure, function and evolution of bacterial ferredoxins. FEMS Microbiology Reviews 4, 155–175. More recent studies have investigated their function and antiquity in deep-branching microorganisms. See, for example, Iwasaki T. (2010) Iron-Sulfur World in aerobic and hyperthermoacidophilic Archaea Sulfolobus. Archaea, 842639. The notion of an “iron-sulfur world” in which these combinations of iron and sulfur atoms, perhaps in hydrothermal vent minerals, would provide the prebiotic conditions for the emergence of biochemistry and the electron transport process has been put forth by Günter Wächtershäuser, a particularly enthusiastic proponent of this version of early events. See, for example, Wächtershäuser G. (1990) The case for the chemoautotrophic origin of life in an iron-sulfur world. Origins of Life and Evolution of Biospheres 20, 173–176.
Place an electrode: This has been a growing area of investigation. See, for example, Rowe AR et al. (2015) Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism. Frontiers in Microbiology, doi.org/10.3389/fmicb.2014.00784; and Summers ZM, Gralnick JA, Bond DR. (2013) Cultivation of an obligate Fe(II)-oxidizing lithoautotrophic bacterium using electrodes. MBio 4, e00420–e00412. doi: 10.1128 /mBio.00420-12.
Elemental sulfur, thiosulfates: The role and sheer scale of biogeochemical cycles is nicely explored in Falkowski PG. (2015) Life’s Engines: How Microbes Made Earth Habitable. Princeton University Press, Princeton, NJ. For biogeochemical cycles in the marine environment, see Cotner JB, Biddanda BA. (2002) Small players, large role: Microbial influence on biogeochemical processes in pelagic aquatic ecosystems. Ecosystems 5, 105–121.
In a now seminal paper: A whole book might be written about Broda. He was a communist sympathizer suspected to have been a KGB spy, code-named Eric, who may have been involved in passing information to the Soviets about British and American nuclear research. Anything to do with energy seems to attract interesting characters. Broda E. (1977) Two kinds of lithotrophs missing in nature. Zeitschrift für allgemeine Mikrobiologie 17, 491–493.
This anaerobic ammonia oxidation: Strous M et al. (1999) Missing lithotroph identified as new planctomycete. Nature 400, 446–449.
The microbes, by using uranium: The uranium becomes more “reduced,” that is, it gains electrons as the electron acceptor. Lovley DR, Phillips EJP, Gorby YA, Landa ER. (1991) Microbial reduction of uranium. Nature 350, 413–416.
Combining sandwiches: These reactions can be used to predict the amount of energy available, allowing scientists to then go into the environment to search for the potential microbes that might make use of these energy-yielding chemicals. A good example is Rogers KL, Amend JP, Gurrieri S. (2007) Temporal changes in fluid chemistry and energy profiles in the Vulcano Island Hydrothermal System. Astrobiology 7, 905–932, which elegantly illustrates how life in extreme environments, potentially limited by energy, can be understood and predicted using the basic physics of Gibbs free energy in any given chemical reaction. Here we see how physics and the basic principles it elucidates can be used to enhance the predictive power of biological sciences.
In anaerobic habitats: Clearly where there is no energy, there can be no active life, but life also needs a basic level of energy to survive, and so for many organisms, even a little energy may be too little. The role of energy in limiting life is explored in Hoehler TM. (2004) Biological energy requirements as quantitative boundary conditions for life in the subsurface. Geobiology 2, 205–215; and Hoehler TM, Jørgensen BB. (2013) Microbial life under extreme energy limitation. Nature Reviews Microbiology 11, 83–94.
However, why did the concentrations of oxygen: Catling DC, Claire MW. (2005) How Earth’s atmosphere evolved to an oxic state. Earth and Planetary Science Letters 237, 1–20.
Giant tubeworms: Two papers that explore this fascinating symbiosis are Cavanaugh, CM, Gardiner SL, Jones ML, Jannasch HW, Waterbury JB. (1981) Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: Possible chemoautotrophic symbionts. Science 213, 340–342; and Minic Z, Hervé G. (2004) Biochemical and enzymological aspects of the symbiosis between the deep-sea tubeworm Riftia pachyptila and its bacterial endosymbiont. European Journal of Biochemistry 271, 3093–3102.
The radiation produced: Lin L-H et al. (2005) The yield and isotopic composition of radiolytic H2, a potential energy source for the deep subsurface biosphere. Geo
chimica et Cosmochimica Acta 69, 893–903.
Fungi that contained the pigment: Dadachova E et al. (2007) Ionizing radiation changes the electronic properties of melanin and enhances the growth of melanized fungi. PLoS ONE 2, e457.
In an elegant stroll: Schulze-Makuch D, Irwin LN. (2008) Life in the Universe: Expectations and Constraints. Springer, Heidelberg.
Kinetic energy: By “some protozoa,” I mean the ciliates, such as Paramecium species.
Perhaps thermal energy: Here I mean the direct use of thermal gradients. Photosynthesis using geothermally produced light (wavelengths greater than approximately 700 nanometers) has been reported in hydrothermal vents, linking thermal environments to energy acquisition. However, such organisms use conventional photosynthetic apparatus that just happens to be using nonsolar photons (Beatty JT et al. [2005] An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent. Proceedings of the National Academy of Sciences 102, 9306–9310).
CHAPTER 9
Samuel Taylor Coleridge: Samuel Taylor Coleridge. (1834) The Rime of the Ancient Mariner.
There is a lot of water on Earth: Taken from the US Geological Survey website in December 2017.
The quixotic intelligent interstellar cloud: Astrophysicist Fred Hoyle, in an intriguing science-fiction story (The Black Cloud, published by William Heinemann in 1957), describes a giant sentient cloud that enters the Solar System and accidentally blocks sunlight from reaching Earth. The sentient being expresses some surprise that there could be life on this ball of rock.
We know of no single organism: It may not be outside the capacities of synthetic biologists and chemists to make self-replicating molecules—cells, even—that will operate in other solvents. But like artificially altered genetic codes and the incorporation of novel amino acids into proteins, these laboratory fabrications may tell us very little about whether such entities would emerge under natural processes.
One of the most notable: The phase diagram of water is remarkably complex, with unusual forms of water ice occurring under high pressures and temperatures as the hydrogen-bonding networks change in their orientation. See, for example, Choukrouna M, Grasset O. (2007) Thermodynamic model for water and high-pressure ices up to 2.2 GPa and down to the metastable domain. Journal of Chemical Physics 127, 124506.
This property is strange: A gigapascal is a unit of pressure (one billion pascals). On Earth at sea level, atmospheric pressure is equivalent to 101,325 pascals.
It inhabits the undergrowth: Storey KB, Storey JM. (1984) Biochemical adaption for freezing tolerance in the wood frog, Rana sylvatica. Journal of Comparative Physiology B 155, 29–36.
Hydrolysis reactions: An old paper but one that nevertheless presents some of the reactions illustrating the reactive nature of water is Mabey W, Mill T. (1978) Critical review of hydrolysis of organic compounds in water under environmental conditions. Journal of Physical and Chemical Reference Data 7, 383–415.
By binding to the outside of proteins: An excellent review on the role of water in the cell is Ball P. (2007) Water as an active constituent in cell biology. Chemical Reviews 108, 74–108. As the author recognizes, our comprehension of how water works is changing quickly. However, the remarkably versatile and subtle roles of water in biochemistry are no longer in doubt.
This arrangement allows the genetic code: Robinson CR, Sligar SG. (1993) Molecular recognition mediated by bound water: A mechanism for star activity of the restriction endonuclease EcoRI. Journal of Molecular Biology 234, 302–306.
The ability of some proteins: Klibanov AM. (2001) Improving enzymes by using them in organic solvents. Nature 409, 241–246.
However, there the similarities: Benner SA, Ricardo A, Carrigan MA. (2004) Is there a common chemical model for life in the universe? Current Opinions in Chemical Biology 8, 672–689.
For example, it can dissolve: The properties of ammonia have been known for a long time. See, for example, Kraus CA. (1907) Solutions of metals in non-metallic solvents; I. General properties of solutions of metals in liquid ammonia. Journal of the American Chemical Society 29, 1557–1571.
We leave the oceans: A good discussion of some of these possibilities can be found in Schulze-Makuch D, Irwin LN. (2008) Life in the Universe: Expectations and Constraints. Springer, Berlin, which reviews some of the advantages and disadvantages of different solvents, but the authors conclude that no known solvent would be better than water, apart from, potentially, ammonia at low temperatures.
The optimistic temperature: For a suggestion of blimp-like creatures in the clouds of Venus, see Morowitz H, Sagan C. (1967) Life in the clouds of Venus. Nature 215, 1259–1260. For sulfate-reducing bacteria that eat sulfate compounds in the Venusian atmosphere, see Cockell CS. (1999) Life on Venus. Planetary and Space Science 47, 1487–1501. Sulfur also features in Schulze-Makuch D et al., Grinspoon DH, Abbas O, Irwin LN, Mark A, Bullock MA. (2004) A sulfur-based survival strategy for putative phototrophic life in the Venusian atmosphere. Astrobiology 4, 11–18. These thoughts are fun, and the reader should not take the authors of these papers to be expressing a genuine committed belief that Venus has life. Like many of these discussions, however, they can provide a backdrop to ask stimulating questions about our own biosphere. For example, here are just two questions that emerge from contemplating life on Venus: Can you have a persistent aerial biosphere on a planet when the surface is uninhabitable? Why don’t we observe blimp-like balloon organisms floating in Earth’s atmosphere?
In an intriguing thought experiment: Benner SA, Ricardo A, Carrigan MA. (2004) Is there a common chemical model for life in the universe? Current Opinions in Chemistry and Biology 8, 672–689.
And yet even here, they must get enough energy: This is a calculation made for Mars, but the order-of-magnitude estimate is applicable to Earth (Pavlov AA, Blinov AV, Konstantinov AN. [2002] Sterilization of Martian surface by cosmic radiation. Planetary and Space Science 50, 669–673).
Here, even a radiation-resistant: Dartnell LR, Desorgher L, Ward JM, Coates AJ. (2007) Modelling the surface and subsurface Martian radiation environment: Implications for astrobiology. Geophysical Research Letters 34, I.02207.
The formation of reactive oxygen species: Price PB, Sowers T. (2004) Temperature dependence of metabolic rates for microbial growth, maintenance, and survival. Proceedings of the National Academy of Sciences 101, 4631–4636; Lindahl T, Nyberg B. (1972) Rate of depurination of native deoxyribonucleic acid. Biochemistry 11, 3610–3618; Brinton KLF, Tsapin AI, Gilichinsky D, McDonald GD. (2002) Aspartic acid racemization and age-depth relationships for organic carbon in Siberian permafrost. Astrobiology 2, 77–82.
Indeed, for chemical reactions: Chemical disequilibria made from geologically active processes.
Rivers of methane: Lorenz R. (2008) The changing face of Titan. Physics Today 61, 34–39.
Using this chemical compound: Stevenson J, Lunine J, Clancy P. (2015) Membrane alternatives in worlds without oxygen: Creation of an azotosome. Science Advances 1, e1400067.
They proposed that by reacting hydrocarbons: McKay CP, Smith HD. (2005) Possibilities for methanogenic life in liquid methane on the surface of Titan. Icarus 178, 274–276.
These ideas have even received: Strobel DF. (2010). Molecular hydrogen in Titan’s atmosphere: Implications of the measured tropospheric and thermospheric mole fractions. Icarus 208, 878–886.
However, the presence of possible energy sources: I say “most” because impacts on Titan’s surface might generate local hydrothermal systems that warm the surface. Furthermore, a subsurface ocean on Titan might provide opportunities for prebiotic and biological processes.
Then there are the ice caps: The Kuiper Belt is a disc of objects beyond the orbit of Neptune. Although it is similar to the asteroid belt that lies between Mars and Jupiter, it is about twenty to two hundred times as massive.
Look at the reaction scheme below: See, for example, Klare G. (1988) Reviews in Modern Astronomy 1: Cosmic Chemistry. Springer, Heidelberg.
CHAPTER 10
I absolutely deny being a Trekkie: A bona fide Star Trek fan.
creature is tracked down: Tracking down an alternate life form in itself is an interesting problem that vexes astrobiologists: how do we detect life elsewhere with the minimum number of assumptions about its chemical composition? Of course, in Star Trek, the crew members merely change the settings on their tricorders, devices for scanning the world around them, to detect silicon-based life, but it is not clear how one would detect a silicon-based life form residing in rocks that average around 40 to 70 percent silicon.
So hydrogen, with one proton: Oganesson is named after Russian nuclear physicist Yuri Oganessian, who played a leading role in the discovery of the heaviest elements in the periodic table.
This principle, that electrons: Fermions are a group of subatomic particles, including the protons, which also exhibit this behavior. For the Pauli exclusion principle, see Massimi, M. (2012) Pauli’s Exclusion Principle: The Origin and Validation of a Scientific Principle. Cambridge University Press, Cambridge. This book is a good place to look at this principle in more detail.
Like the twins: More exactly, no two fermions can have identical quantum numbers, the four numbers that define its state—the principal quantum number, the angular momentum in its orbital (known as the angular momentum quantum number), the availability of orbitals (magnetic quantum number), and the spin quantum number. For particles that have a half-integer spin (such as electrons), the wave function that described its wavelike property is antisymmetrical, which means that if they are in an identical place, the two waves cancel each other out and the particles cease to exist, which is impossible. Therefore, either their spin or one of their other properties has to be different to prevent this occurrence.
The Equations of Life Page 35