20.3: Formation of Organic Molecules in an Earthly Reducing Atmosphere

A prerequisite to prebiotic chemical experimentation is a source of organic molecules. Just as life requires energy (to do anything and everything), converting inorganic molecules into organic molecules requires an input of free energy. As we have seen, most living things today get free energy by oxidizing nutrients or directly from the sun by photosynthesis. Recall that all the chemical energy sustaining life today ultimately comes from the sun. But before there were cells, how did organic molecules form from inorganic precursors? Oparin and Haldane hypothesized a reducing atmosphere on the prebiotic earth, rich in inorganic molecules with reducing power (like \(\rm H_2, NH_3, CH_4\), and \(\rm H_2S\)) as well as \(\rm CO_2\) to serve as a carbon source. The predicted that the physical conditions on a prebiotic earth were:

• lots of water (oceans).
• High heat (no free \(\rm O_2\)).
• lots ionizing (e.g., X-, \(\gamma\)-) radiation from space, (no protective ozone layer).
• frequent ionizing (electrical) storms generated in an unstable atmosphere.
• volcanic and thermal vent activity.

20.3.1 Origins of Organic Molecules and a Primordial Soup

Oparin suggested that abundant sources of free energy fueled the reductive synthesis of the first organic molecules to create what he called a “primeval soup”. No doubt, he called this primeval concoction a “soup” because it would have been rich in chemical (nutrient) free energy. Harold Urey, who had already won the 1934 Nobel Prize in Chemistry for discovering deuterium, and Stanley Miller tested the prediction that, under Haldane’s and Oparin’s prebiotic earth conditions, inorganic molecules can produce the organic molecules in what became known as the primordial soup. In their classic experiment, a mix of inorganic molecules provided with an energy source was reduced to very familiar organic molecules, supporting the Oparin/Haldane proposal. Their experiment is shown below in Figure 20.4.

Figure 20.4: The Miller & Urey experiment: organic molecules seen in living things today form spontaneously in the lab under reducing conditions like those expected in a prebiotic earth atmosphere.

Miller’s earliest published data indicated the presence of several organic molecules in their ocean flask, including a few familiar metabolic organic acids (lactate, acetate, several amino acids…) as well as several highly reactive aldehydes and nitriles. The latter can interact in spontaneous chemical reactions to form organic compounds. Later analyses further revealed purines, carbohydrates, and fatty acids in the flask. Some 50 years after Miller’s experiments (and a few years after his death), some un-analyzed samples collected from those early experiments were discovered. When their contents were re-analyzed with newer, more sensitive detection techniques, they were shown to contain organic molecules not originally reported, including 23 amino acids (to read more, see Surprise Goodies in the Soup!).

Clearly, the thermodynamic and chemical conditions proposed by Oparin and Haldane did support a reductive synthesis of organic molecules. Next, these evolving chemistries would have been internalized inside semipermeable aggregates (or boundaries) destined to be a cell. Proposals for such structures are discussed below. Such events in a nutrient-rich primordial soup would likely have led to the genesis of heterotrophic cells that could use environmental nutrients for energy and growth. This implies an early evolution of fermentative pathways like glycolysis. But here’s the rub: these first cells would have quickly consumed the nutrients in the soup, quickly ending the Earth’s new vitality!

To stop life from becoming a dead-end experiment, one must propose the early evolution of autotrophs, cells that could capture free energy from inorganic molecules (chemoautotrophs) or even sunlight (photoautotrophs). As energy-rich organic nutrients in the ‘soup’ declined, autotrophs would be selected, for example photoautotrophs that could fix (i.e., reduce) \(\rm CO_2\), with \(\rm H^{-}\) ions split from water. In this way, photosynthesis would replenish carbohydrates and other nutrients in the oceans and splitting water would add \(\rm O_2\) to the atmosphere. Oxygen would have been toxic to most cells at the time, but some of those cells already had the ability to survive oxygen. These survived, evolving into cells that could respire, i.e., use oxygen to burn environmental nutrients. In fact, respiratory metabolism must have followed hard on the heels of the spread of photosynthesis. After photosynthesis emerged, sometime between 3.5 and 2.5 billion years ago (the Archaean Eon), photosynthetic and aerobic cells and organisms achieved a natural balance to become the dominant species in our oxygen-rich world.

20.3.2 The Tidal Pool Scenario for an Origin of Polymers and Replicating Chemistries

In this scenario, prebiotic organic monomers concentrate in tidal pools and polymerize in the heat of a primordial day by dehydration synthesis. This uphill reaction requires free energy. Very high temperatures (heat of baking) can link monomers by dehydration synthesis in the lab and may have formed random polymers in tidal pool sediments, as shown in Figure 20.5, which further assumes dispersal of these polymers with the ebb and flow of the tides.

Figure 20.5: Scenario for the synthesis of prebiotic polymers in tidal pools.

The catalytic properties of metals (e.g., nickel, platinum, silver, magnesium, and manganese) are exploited in the laboratories to speed up chemical reactions. Such metals were likely present in primordial ocean sediments in the early Earth’s crust, including, just as they are there today. And their catalytic properties in soil and clay aggregates have also been demonstrated. In fact, metals like magnesium and manganese are now an integral part of many enzymes, consistent with an origin of biological catalysts as prebiotic benthic minerals. Finally, some metals like magnesium (\(\rm Mg^{++}\)) readily associate with nucleotides. Before life, the microsurfaces of ocean sediments, if undisturbed, may have catalyzed the same or at least similar reactions repeatedly, leading to related sets of polymers. Consider the possibilities for RNA monomers and polymers, based on the assumption that life began in an “RNA world” (Figure 20.6). The concentration of putative organic monomers at the bottom of mineral-rich tidal pools may have accelerated polymerization reactions.

Figure 20.6: Scenario for the synthesis of redundant prebiotic nucleic acid polymers in tidal pools.

The result predicted by this scenario is the formation not only of RNA-like polymers (perhaps only short ones at first), but of H-bonded double-stranded molecules that might effectively replicate at each cycle of concentration, polymerization, and dispersal. High heat could have supported polymerization, while catalysis enhanced the fidelity of template-based replication. Of course, repeated high heat or other physical or chemical attack might degrade newly formed polymers, unless some double strands were resistant to destruction. These would accumulate at the expense of the weaker, more susceptible ones. In this way, the fittest replicated molecules would be stable in the environment. The environmental accumulation of structurally related, replicable, and stable polymers reflects a prebiotic chemical homeostasis (one of those properties of life!). For this scenario to work, prebiotic nucleosides must have been available and stable. We’ll revisit this issue shortly

349 Life Origins in a Reducing Atmosphere?

Overall, the tidal pool scenario for life origins in a reducing environment hung together nicely for many decades. But there are now challenging questions about the premise of a prebiotic reducing environment. Newer evidence suggests an Earth atmosphere that was not at all reducing, casting doubt on the idea that heterotrophs were the first cells on the planet. Recent proposals posit alternative sources of prebiotic free energy and organic molecules that look quite different from those assumed by Oparin, Haldane, Urey and Miller.