Atoms, Electrons, and Change
Faraday's ... demonstrations appealed directly to the minds of his audience because they touched their senses directly. ... A century and a half later, when we feel compelled to explain reactions in terms of atoms, we are more remote from the tangible. Yet this change of focus from the reality of visible form to the unfamiliarity of atoms is the necessary price to pay if we are to penetrate the surface of change... It is through the atomic, and below that the subatomic, that the tangible becomes explicable. (p. 9)
When chemists heat a reaction mixture, their purpose is to lever reactants over the energy barrier that prevent immediate reaction, and these barriers are consequences of quantum mechanics. (p. 10)
Comment: Not only in micro scales the energy barrier is important, but also in macro scales. This is what fixed cost is all about.
Thus in one reaction a single electron ... may need to be hustled away from a molecule before that molecule has time to react in an inappropriate way that, if allowed, would show itself as disease. A particular atom may need to be removed from one point of a molecule a billionth of a second before another is attached if the reaction is to run a particular course and the cell is not to die. (p. 10)
One of the great journeys of the world is the one in which carbon steps from an inorganic existence, as carbon dioxide, to an organic one, as glucose. This step is photosynthesis, in which green plants utilize the energy provided by the sun and, by plucking carbon dioxide from the air, convert it into carbohydrate. Photosynthesis is the reaction that lies at the head of the food chain, for in capturing the energy from the sun and trapping it as an elaborate form of matter, it generates a primary fuel. ¡ With the reaction of photosynthesis, it is a vibrant green globe thronged with life that is supported by the pyramid of consumption that projects upward from its carbohydrate base and culminates currently in carnivores. Through photosynthesis, the sun coils the spring of all our activities. (p. 204)
By virtue of the energy a photon can bring, light drives the most widespread of all chemical reactions on earth. Photosynthesis operates on a colossal scale. Each year, a hundred trillion kilograms of carbon are captured from the air and turned into carbohydrate. The energy stored in this way each year is about 1018 kilojoules, which is about 30 times the global consumption. ¡ Priestly recognized another of the crucial contributions of this reaction to our habitat when he identified oxygen as a by-product of photosynthesis and realized that a plant ¡°could restore air which has been injured by the burning of candles.¡± Today we recognize the importance of photosynthesis to the cleansing of our atmosphere of the injuries that we inflict on it now that we have moved beyond mere candles.
Yet photosynthesis was not always the method by which solar energy was captured, and the stumbling into it by organisms had a greater environmental impact than any of humanity¡¯s current puny meddlings. Before the onset of photosynthesis there was little oxygen in the atmosphere --- what there was had been released from the earth¡¯s crust and the impact of solar radiation on the water that had out of volcanoes. But once photosynthesis begin, there was a sudden outpouring of its byproduct, oxygen.
Almost all the oxygen in our atmosphere is the polluting effluent (from the viewpoint of the dominant lifeforms of the time) of the biological power stations found in green vegetation. The Great Oxygenation of the atmosphere brought in its train the possibility that life could lift up its roots and become mobile; thus animals emerged. Since animals hunt and are hunted, they must be able to respond immediately to tactical variability, and as a result intelligence evolved. Thus not only do we persist on account of photosynthesis, but our origin can be traced back to the onset of that reaction. (p. 211)
The stumbling of organisms into discovering the
water-splitting reaction led to an extraordinary outburst of evolutionary
activity. Hitherto, anoxygenetic photosynthetic
bacteria had clutched at organic acids and simple inorganic compounds for their
hydrogen atoms (and, as we shall see, the electrons that are essential to photosynthesis).
But these compounds are rare, and so the niches that could support life were scarece. Then suddenly, about three billion years ago, an
organism hit upon
water as the source of hydrogen and electrons. That organism was
the
There were two prices to pay for this adventurous opportunism. One was the onset of an extraordinary wave of global pollution, when the fecundity of the newly thriving novel organisms transformed the atmosphere by generating vast quantities of the deadly gas oxygen from the water that had been split. We can tell the moment of the Great Oxygenation, for the earth rusted, and many of our oxide ores date from that era. The other price concerned the organism themselves, for the decomposition products of water --- the intermediates produced on its progress toward becoming oxygen --- are intensely dangerous and, if allowed to react with the other substances in the cell, could kill it. (p. 215)
Comments: From H2S to H2O is from low fixed cost to high fixed cost. It exhibits the common patterns involved in this evolution. First, the market size has to be larger. Second, the byproduct, O2 is more lethal. Third, pollution becomes more global.
It turns out, however, that nature appears to have made a design fault in the Calvin cycle in an overhasty adoption of rubisco as the enzyme. The fault arises because rubisco was developed early in the history of photosynthesis, when carbon dioxide was abundant in the atmosphere and there was very little oxygen. The particular fault that has become apparent is that rubisco also catalyzes a reaction that competes with the linking of carbon dioxide to RuBP. In the competing reaction, oxygen, not carbon dioxide, is added to RuBP to form one three-carbon molecule and one two-carbon molecule:
This reaction is particularly important now that oxygen is so abundant. A series of reactions seek to repair the damage by managing to convert two of the two-carbon molecules into a three-carbon molecule plus one one-carbon molecule; but that one-carbon molecule is carbon dioxide! Thus, rubisco had defeated the whole elaborate network of reactions by taking oxygen and converting it into carbon dioxide --- the very opposite of what the chloroplast aims to achieve. This unwelcome path, the analog of respiration in animals (but without the beneficial production of ATP that occurs in animal respiration), is called ¡°photorespiration.¡± Under normal conditions, as much as half the carbon fixed by photosynthesis may be burned away to carbon dioxide by photorespiration. The problem is particularly severe in tropical plants because the rate of photorespiration increases more rapidly with temperature than does that of the carbon-fixing reaction, and so in hot climates the net rate of photosynthesis may be low.
This serious fault can perhaps be repaired by genetic engineering. IF photorespiration were to be successfully suppressed, the engineered plant would be able to process carbon dioxide significantly more efficiently, thus resulting in greater crop yields even in temperate climates. Such studies are currently in progress. Nature has itself recognized the fault and has experimented with the evolution of an alternative pathway, known as the C4 pathway, or the Hatch-Slack pathway, after the Australian plant physiologist M.D. Hatch and C. R. Slack, who established it. In C4 plants, the carbon dioxide molecule is linked to a three-carbon molecule to give a four-carbon intermediate. This four-carbon intermediate, which is formed outside the chloroplast in the mesophyll of the leaf, breaks down into carbon dioxide in the region of chloroplast, and that carbon dioxide enters the Calvin cycle. The C4 cycle makes heavier demand on the energy production of the cells involved, because whereas C3 plants need three ATP molecules to fix one carbon dioxide molecule, a C4 plant needs four. However, the advantage of the C4 pathway is that photorespiration in such plants is nearly completely absent. This is because C4 pathway leads to a very high local concentration of carbon dioxide in the region where the Calvin cycle is taking place, so that the carbon-fixing reaction becomes dominant. In effect, the C4 pathway recreates the microenvironment within the leaf that is similar to the carbon-dioxide-rich environment in which rubisco originally developed. Overall, therefore, the process may be more efficient even though it takes heavier demands of ATP.
The provision of carbon dioxide by this mechanism also helps the plant to make more efficient use of sunlight. In tropical regions, the supply of carbon dioxide limits the rate at which photosynthesis can occur, but the C4 mechanism helps to pump the meager supply to the exact location it is needed. The contribution of the C4 pathway can be quite substantial, for the net photosynthetic rates of C4 grasses such as corn and sugarcane can exceed by a factor of two or three the rates of C3 grasses such as rye, oats and rice.
The role of the C4 pathway is apparent in lawns, which in cooler climates consist of C3 grasses, such as creeping bent. However, in the heat of summer, the C4 grasses like crabgrass with their broader, paler leaves, may overwhelm the darker, finer C3 grasses as the more efficient C4 pathway delivers carbon dioxide to the Calvin cycle. (P. 226)