# Structural Biochemistry/Pyrite Theory

The predominant theory of the origin of biomolecules, such as lipids, DNA/RNA, and carbohydrates, is that there existed an autocatalytic carbon dioxide fixation cycle, specifically the reductive citrate cycle. Researchers have proposed that the reducing power from this archaic reductive citrate cycle came from pyrite, an iron sulfide with the formula FeS$_2$. The theory contends that through pyrite mediated reduction-oxidation reactions, carbon fixing and condensation were able to occur and give rise to a variety of biomolecules. The underlying reaction that generates pyrite from ferrous ions and hydrogen sulfide is as follows:
                                           FeS + H$_2$S --> FeS$_2$ + 2 H$^+$ + 2 e$^-$

### Speculation for an Energy Source

The Miller-Urey experiment determined that moleculues can spontaneously combine and form organic molecules in primordial Earth conditions.
It was thought that evolution, from a chemical standpoint, was simply one archaic autocatalytic reaction branching out to numerous different reactions, using different substrates and generating different products over the course of billions of years. The primordial Earth did not have biomolecules; thus, reactions were not catalyzed by enzymes. Inorganic catalysts must have been used for reactions to take place.
Researchers proposed that in the chemoautotrophic origin of life model, the starting material for all biomolecules and organic molecules was carbon dioxide. Because carbon dioxide is in a fully oxidized state, all reactions involving carbon dioxide must have been reductive, and a reducing agent must have been necessary. The reducing agent must have fit the following criteria:
- had to be strong enough to reduce carbon dioxide in order for a reaction to occur - must have been readily available in the environment of primordial Earth - must be somehow connected to today's known biochemistry - must remain stable even after going through many reactions
Following these criteria, researchers determined that a very plausible molecule was pyrite.

### Pyrite

It is known that pyrite has a standard potential of -620 mV, which is enough for all biochemical reducing reactions. It is readily available under anaerobic conditions, which is consistent with the atmosphere of primordial Earth. It is a deep heat sink, meaning that it is thermodynamically stable and is able to undergo many redox reactions; even hot, concentrated hydrochloric acid cannot dissolve it.
Structurally, the surface of a pyrite crystal is cationic. This serves as the reaction site for its redox reactions, as the carbon fixation products are usually anionic. The positively charged surface of the pyrite crystal electrostatically bonds to the products of carbon fixation. Having a method to bond reactants to the surface of pyrite allows for process for attachment and detachment for pyrite's reagents. Furthermore, as polymers are constructed and anionic charge accumulates, the positively charged surface stabilizes the polymer and allows for larger polymers to form, giving rise to more complexity in biomolecules. It was observed that as increasing amounts of anionic lipids gathered on the surface of pyrite, a membrane will automatically develop.
It was originally believed that pyrite could only be formed by the following reaction:
                                              FeS + S ---> FeS$_2$
The generally accepted method of forming pyrite was not consistent with the method that the researchers had proposed. However, the researchers were able to experimentally determine another method of generating pyrite under anaerobic conditions, mimicking primordial Earth:
                                              FeS + H$_2$S --> FeS$_2$ + H$_2$
By discovering this reaction, researchers were able to determine that protons could serve as the reducing agent to generate pyrite. By proving that pyrite could be generated and was a possible energy source for primordial biomolecular reactions, researchers were able to explain why hydrogenases have an iron-sulfur core -- because they originated as pyrite.

### Autocatalytic Carbon Fixation

Researchers proposed that FeS / H$_2$S was the sole reducing agent in all archaic biomolecular reactions, taking the place of the nonexistent hydrogenase enzymes. It was proved that the most important step in modern carbon fixation, the reductive step, could run without its specific enzyme, TPP. This is the reductive step of carbon fixation, catalyzed by TPP:
                         CH$_3$-COSR + CO$_2$ --> CH$_3$-CO-COOH
It was shown that TPP could be replaced by an iron-sulfur complex and a reducing agent, and the reaction would still take place, suggesting that FeS / H$_2$S provides enough reducing power for carbon fixation reactions and the inorganic iron-sulfur clusters that are needed for the reaction.
By analyzing the mechanism for the conversion of the amino acid glycine to acetyl-CoA, researchers were able to determine an analogous primordial reaction and determine how new carbon-containing molecules were generated from pre-existing carbon-containing molecules. It was determined and tested that aqueous FeS / H$_2$S can reduce oxaloacetate to succinate, phenylpyruvate to phenylpropionate, and mercaptoacetate to acetate.
The mechanism of pyrite reactions remains unknown, but it is suggested that an FeS molecule strips a $^-$SCR$_3$ molecule of its sulfur, generating FeS$_2$ and a $^-$CR$_3$ carbanion. This carbanion can readily attack other molecules, as it is a very strong molecule, generating new carbon-carbon bonds. Carbon fixation and the Claissen condensation are two possible routes that the generated carbanion can take.
FeS / H$_2$S is not found in today's metabolic cycles because NADH has replaced it as the reducing agent. With pyrite, oxaloacetate was able to be directly converted to malate; however, with NADH, it is converted to malate, and then converted to succinate. Thus, today's metabolic carbon fixation cycles do not encorporate FeS / H$_2$S.
Thus, it can be seen that pyrites are able to reduce molecules for all biochemical reactions and activate groups to promote condensation and carbon fixing.

### Biomolecular Pathways
##### Lipid Pathways

As lipids accumulate onto the pyrite surface, the surface becomes very hydrophobic due to the long side chains of lipids. The equilibrium is thus shifted to favor carbon dioxide condensation. As it was previously determined that FeS / H$_2$S reduces carbonyl groups, the following reactions are considered:
                      R-CH$_2$CO- + H$_2$S --> R-CH=C(SH)- + H$_2$O
                      R-CH=C(SH)- + FeS --> R-CH=CH- + FeS$_2$
This general reaction of carbonyls with FeS / H$_2$S produces an olefin. By having 2-ketoglutarate as the reactant:
                      HOOC-CH$_2$-CH$_2$-CO-COOH --> HOOC - CH$_2$-CH=CH-COOH
Glutaconic acid is generated. Glutaconic acid is the vinyl form of malonic acid, which is the key molecule in malonic ester synthesis. Through further reactions, a fatty acid lipid can be formed. This reaction is important, as it demonstrates that malonyl-thioester, necessary for fatty acid lipid biosynthesis, can be synthesized without the use of an enzyme or ATP. This gives credibility to the pyrite theory of biosynthesis.

##### Tetrapyrrol Pathways

Many products have nitrogen in them, such as amino acids and DNA/RNA bases. Thus, it must be determined what the source of the ammonia starting material is. It was shown that ammonia could be obtained by reducing nitrate with FeS / H$_2$S, and nitrate can be produced by discharges of nitrogen, water, and carbon dioxide. The proposed mechanism of how nitrogen is incorporated into biomolecular products is that ammonia units will react with biomolecules on pyrite's surface site. It is postulated that this would give rise to amino acids and nitrogenous bases.
It was assumed that the primordial catalysts were not selective molecules, suggesting that other molecules could enter and leave pathways at any given moment. This can give rise to a variety of products, and explain how various structures form. For example, tetrapyrrol rings, which have 8 methyl groups, form when an alanine replaces glycine in a reaction.

### References

* 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 Wächtershäuser, G. "The cradle chemistry of life: On the origin of natural products in a pyrite-pulled chemo- autotrophic origin of life". Pure & Appl. Chem., Vol. 65, No. 6, pp. 1343-1348, 1993.