The Chemical Origins of Life

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$50,000 Reward: "The Origin-of-Life Prize" will be awarded for proposing a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life. To win, the explanation must be consistent with empirical biochemical, kinetic, and thermodynamic concepts as further delineated herein, and be published in a well-respected, peer-reviewed science journal(s). http://lifeorigin.org/rul_desc.htm

“The atmosphere of the young Earth was rich in ammonia and methane. Such conditions, while toxic to plants and animals, were cozy for archaeans. Archaea represent remnants of once-thriving communities that dominated the world when it was young. Molecular fossils of Archaea in the form of isoprenoid residues were first reported from the Messel oil shale of Germany. Material from the shale was dissolved and analyzed using a combination of chromatography and mass spectrometry. These processes produce a "chemical fingerprint". The fingerprint of the Messel shale included isoprene compounds identical to those found in some archaeans. Based on the geologic history of the Messel are, the most likely culprits are archaeal methanogens (methane-producers). Since their discovery in the Messel shales, isoprene compounds indicative of ancient Archaea have been found in numerous other localities, including Mesozoic, Paleozoic, and Precambrian sediments. Their chemical traces have even been found in sediments from the Isua district of west Greenland, the oldest known sediments on Earth at about 3.8 billion years old.” http://www.ucmp.berkeley.edu/archaea/archaeafr.html

The Origin of the Universe occurred ~15 bya and led to the following sequence of events: condensation and accretion of chemicals > planetissimals > protoplanets > planets (molten earth) > reducing atmosphere > primordial earth with organic molecules (N2, H2O, CO2, CO, CH4, NH3) > macromolecule polymers produced through dehydration reactions (removal of -H or -OH) (condensation and polymerization of organic mix occurred by smashing against hot rocks, sand and clay - catalytic surfaces) > amino acids + heat > polypeptide precursors of proteins and polynucleotide precursors of DNA > nucleic acids > protocells/protobionts (microspherical coacervates) > progenotes (RNA world was a primitive self-replicating system) > cenancestors (DNA world) > prokaryotes > eukaryotes.

Comparison of protein sequences to the genomes of several prokaryotes establish the origin of life at about 4.1 bya and the origin of methanogens to be 3.8 - 4.1 bya.See: “Genomic timescale of procaryotic evolution,” by Battistuzzi, et al., Evolutionary Biology, 2004; 4: 44

RNA was the first self-replicating polymer and is supported by the fact that catalytic RNA is found in cells living today. As replicating RNA polymers formed into colloidal suspensions, they were encapsulated with a natural aqueous solution in a two-layered outer lipid membrane. This protected and stabilized the aggregate internal environment from the hostile external environment. RNA and protein molecules then interact in template assisted ligation and cleavage for replication. This is the origin of the RNA World. If RNA formed on clay, then the molecular structure of the clay served as a template to build the RNA molecule. Nucleic Acids then formed and mutated to control metabolism and reproduction

Source: http://www.star.ucl.ac.uk/~rhdt/diploma/lecture_4/

The Catalytic Function of RNA
Source: http://www-micro.msb.le.ac.uk/109/Origins.html

 

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Metabolism in Coacervates: Redox Reaction and Polymerization
Source: http://www.science.siu.edu/microbiology/micr425/425Notes/14-OriginLife.html

What are Coacervates, Proteinoid Microspheres, and Liposomes?
See: http://fig.cox.miami.edu/~cmallery/150/life/protobionts.htm

Do It Yourself: How to Create Coacervates in the Lab
See: http://www.indiana.edu/~ensiweb/lessons/coac.lab.pdf

Liposomes have a lipid bilayer separating proteins from the environment and can easily be formed by simply dropping a small amount of oil in water. They behave dynamically by engulfing smaller liposomes then splitting into two smaller liposomes ad infinitum. Coacervates are liposomes with enzymes in the lipid bilayer for chemical exchanges.

RNA replication: Tom Cech (1980s) showed that ribozymes can edit introns from RNA. These short RNA polymers can copy RNA as a template (like clay). This establishes a form of heredity, but no retention or evolution. However, autocatalytic short RNA began to fold into three dimensional structures. At this point the phenotype is the same as the genotype. RNA-amino acid interactions led to proteins and some of these proteins acted as enzymes to help stabilize the RNA replication. The first step toward translation was the transferring of molecules held in proximity to the replicating RNA. The RNA configurations then led to positive selections.
Synthesis of Purines: “Adenine is a pentamer of hydrogen cyanide. On the primitive earth a tetramer of HCN probably formed by successive condensations. This then rearranged under the influence of ultraviolet light to form one ring. A fifth HCN then condensed with this precursor to form the second ring. When HCN is heated in solution with NH3 a black tar is formed together with adenine as the major soluble aromatic product…. Smaller amounts of guanine and other purine derivatives are also formed…. Inorganic polyphosphates would have been present in primeval times (formed by volcanic heat from phosphates for example). Polyphosphates can react with many organic molecules to give organic phosphates. Amino acids give two possible products. Acyl phosphates have the phosphate group attached to the carboxyl group of the amino acid (NH2CHRCO-OPO3H2) Phosphoramidates have it attached to the amino group of the amino acid (H2O3P-NH-CHR-COOH). Heating or irradiation will then give polypeptides. Modern life uses acyl phosphate derivatives during protein synthesis. However, laboratory synthesis of DNA uses phosphoramidates. Analogous reactions can give AMP from adenine and polynucleotides can then form by polymerization.
Biological information is passed on by template-specific polymerization of nucleotides. A mixture of polyphosphate, purine and pyrimidines will produce random nucleic acid chains if ribose or deoxyribose is included. One problem, not yet solved is that life uses 3', 5' linked nucleic acid whereas primeval type syntheses give RNA molecules with a mixture of linkages, but mostly 2', 5'. (Deoxyribose has no 2'-OH so cannot give 2', 5' links). When an RNA template is incubated with a mixture of nucleotides, plus a primeval condensing agent, a complementary piece of RNA is synthesized. This nonenzymatic reaction is catalyzed by lead ions, with an error rate of about 1 wrong base in 10. With zinc ions, a great improvement is seen and lengths of up to 40 bases are produce with an error rate of about 1 in 200. All modern day RNA and DNA polymerases contain zinc. If a 3', 5' linked RNA template is used about 75% of the newly formed RNA is 3', 5' linked. However, this does not surmount the problem that the original formation of RNA type polymers favors the non-biological 2', 5' linkage very heavily. It is thought that RNA probably provided the first informational molecule and that DNA is a later invention designed to store information in a more stable and more accurate form.”
See: http://www.science.siu.edu/microbiology/micr425/425Notes/14-OriginLife.html