To account for the origin of life on our earth requires solving several problems:
- How the organic molecules that define life, e.g. amino acids, nucleotides, were created;
- How these were assembled into macromolecules, e.g. proteins and nucleic acids, — a process requiring catalysts;
- How these were able to reproduce themselves;
- How these were assembled into a system delimited from its surroundings (i.e., a cell).
A number of theories address each of these problems.
As for the first, three scenarios have been proposed: organic molecules
- were synthesized from inorganic compounds in the atmosphere
- rained down on earth from outer space
- were synthesized at hydrothermal vents on the ocean floor
Stanley Miller, a graduate student in biochemistry, built the apparatus shown here. He filled it with - water (H2O
- methane (CH4)
- ammonia (NH3) and
- hydrogen (H2)
- but no oxygen
He hypothesized that this mixture resembled the atmosphere of the early earth. (Some are not so sure.) The mixture was kept circulating by continuously boiling and then condensing the water.
The gases passed through a chamber containing two electrodes with a spark passing between them.
At the end of a week, Miller used paper chromatography to show that the flask now contained several amino acids as well as some other organic molecules.
In the years since Miller's work, many variants of his procedure have been tried. Virtually all the small molecules that are associated with life have been formed:
- 17 of the 20 amino acids used in protein synthesis, and
- all the purines and pyrimidines used in nucleic acid synthesis.
- But abiotic synthesis of ribose — and thus of nucleosides — has been much more difficult.
One difficulty with the primeval soup theory is that it is now thought that the atmosphere of the early earth was not rich in methane and ammonia — essential ingredients in Miller's experiments.
| Representative amino acids found in the Murchison meteorite. Six of the amino acids (blue) are found in all living things, but the others (yellow) are not normally found in living matter here on earth. The same amino acids are produced in discharge experiments like Miller's. |
|---|
| Glycine |
Glutamic acid |
| Alanine |
Isovaline |
| Valine |
Norvaline |
| Proline |
N-methylalanine |
| Aspartic acid |
N-ethylglycine |
This meteorite, that fell near Murchison, Australia on 28 September 1969, turned out to contain a variety of organic molecules including:
- purines and pyrimidines
- polyols — compounds with hydroxyl groups on a backbone of 3 to 6 carbons such as glycerol and glyceric acid. Sugars are polyols.
- the amino acids listed here. The amino acids and their relative proportions were quite similar to the products formed in Miller's experiments.
The question is: were these molecules simply terrestrial contaminants that got into the meteorite after it fell to earth.
Probably not:
- Some of the samples were collected on the same day it fell and subsequently handled with great care to avoid contamination.
- The polyols contained the isotopes carbon-13 and hydrogen-2 (deuterium) in greater amounts than found here on earth.
- The samples lacked certain amino acids that are found in all earthly proteins.
- Only L amino acids occur in earthly proteins, but the amino acids in the meteorite contain both D and L forms (although L forms were slightly more prevalent).
This meteorite arrived here from Mars. It contained not only a variety of organic molecules, including polycyclic aromatic hydrocarbons, but — some claim — evidence of microorganisms as well.
Furthermore, there is evidence that its interior never rose about 40° C during its fiery trip through the earth's atmosphere. Live bacteria could easily survive such a trip.
Astronomers, using infrared spectroscopy, have identified a variety of organic molecules in interstellar space, including
- methane (CH4),
- methanol (CH3OH),
- formaldehyde (HCHO),
- cyanoacetylene (HC3N) (which in spark-discharge experiments is a precursor to the pyrimidine cytosine).
- polycyclic aromatic hydrocarbons
- as well as such inorganic building blocks as carbon dioxide (CO2), carbon monoxide (CO), ammonia (NH3), hydrogen sulfide (H2S), and hydrogen cyanide (HCN).
There have been several reports of producing amino acids and other organic molecules by taking a mixture of molecules known to be present in interstellar space such as:
- ammonia (NH3)
- carbon monoxide (CO)
- methanol (CH3OH) and
- water (H2O)
- hydrogen cyanide (HCN)
and exposing it to
- a temperature close to that of space (near absolute zero)
- intense ultraviolet (uv) radiation.
Whether or not the molecules that formed terrestrial life arrived here from space, there is little doubt that organic matter continuously rains down on the earth (estimated at 30 tons per day).
Some deep-sea hydrothermal vents discharge copious amounts of hydrogen, hydrogen sulfide, and carbon dioxide at temperatures around 100°C. (These are not "black smokers".) These gases bubble up through chambers rich in iron sulfides (FeS, FeS2). These can catalyze the formation of simple organic molecules like acetate. (And life today depends on enzymes that have Fe and S atoms in their active sites.)
Another problem is how polymers — the basis of life itself — could be assembled.
- In solution, hydrolysis of a growing polymer would soon limit the size it could reach.
- Abiotic synthesis produces a mixture of L and D enantiomers. Each inhibits the polymerization of the other. (So, for example, the presence of D amino acids inhibits the polymerization of L amino acids (the ones that make up proteins here on earth).
This has led to a theory that early polymers were assembled on solid, mineral surfaces that protected them from degradation, and in the laboratory polypeptides and polynucleotides (RNA molecules) containing about ~50 units have been synthesized on mineral (e.g., clay) surfaces.
All metabolism depends on enzymes and, until recently, every enzyme has turned out to be a protein.
But proteins are synthesized from information encoded in DNA and translated into mRNA.
So here is a chicken-and-egg dilemma. The synthesis of DNA and RNA requires proteins. So - proteins cannot be made without nucleic acids and
- nucleic acids cannot be made without proteins.
The discovery that certain RNA molecules have enzymatic activity provides a possible solution.
These RNA molecules — called ribozymes — incorporate both the features required of life:
- storage of information
- the ability to act as catalysts
While no ribozyme in nature has yet been found that can replicate itself, ribozymes have been synthesized in the laboratory that can catalyze the assembly of short oligonucleotides into exact complements of themselves. The ribozyme serves as both
- the template on which short lengths of RNA ("oligonucleotides" are assembled following the rules of base pairing and
- the catalyst for covalently linking these oligonucleotides.
(The figure is based on the work of Green and Szostak, Science 258:1910, 1992.)
In principal, the minimal functions of life might have begun with RNA and only later did
- proteins take over the catalytic machinery of metabolism and
- DNA take over as the repository of the genetic code.
Several other bits of evidence support this notion of an original "RNA world":
- Many of the cofactors that play so many roles in life are based on ribose; for example:
- In the cell, all deoxyribonucleotides are synthesized from ribonucleotide precursors.
- Many bacteria control the transcription and/or translation of certain genes with RNA molecules (Link to "riboswitches") , not protein molecules.
Perhaps the earliest form of reproduction was a simple fission of the growing aggregate into two parts — each with identical metabolic and genetic systems intact.
To function, the machinery of life must be separated from its surroundings — some form of extracellular fluid (ECF). This function is provided by the plasma membrane.
Today's plasma membranes are made of a double layer of phospholipids. They are only permeable to small, uncharged molecules like H2O, CO2, and O2. Specialized transmembrane transporters are needed for ions, hydrophilic, and charged organic molecules (e.g., amino acids and nucleotides) to pass into and out of the cell.
However, the same Szostak lab that produced the finding described above reported in the 3 July 2008 issue of Nature that fatty acids, fatty alcohols, and monoglycerides — all molecules that can be synthesized under prebiotic conditions — can also form lipid bilayers and these can spontaneously assemble into enclosed vesicles.
Unlike phospholipid vesicles, these
- admit from the external medium charged molecules like nucleotides
- admit from the external medium hydrophilic molecules like ribose
- grow by self-assembly
- are impermeable to, and thus retain, polymers like oligonucleotides.
These workers loaded their synthetic vesicles with a short single strand of deoxyguanosine (dC) structured to provide a template for its replication.
When the vesicles were placed in a medium containing (chemically modified) dG, these nucleotides entered the vesicles and assembled into a strand of Gs complementary to the template strand of Cs.
Here, then, is a simple system that is a plausible model for the creation of the first cells from the primeval "soup" of organic molecules.
The 3 kingdoms of contemporary life — archaea, bacteria, and eukaryotes — all share many similarities of their metabolic and genetic systems [Link]. Presumably these were present in an organism (or organisms) that were ancestral to these groups: the "LUCA". Although there are not enough data at present to describe LUCA, comparative genomics and proteomics reveal a closer relationship between archaea and eukaryotes than either shares with the bacteria. (Except, of course, for the mitochondria and chloroplasts that eukaryotes gained later from bacterial endosymbionts [Link].)
16 July 2008