Miller–Urey experiment revisited

This is an interesting link to a wikipedia entry on the famous Miller-Urey experiment that looked at the generation of biomolecules from simple reactants, thought to be present on the early earth, namely ammonia, carbon monooxide, methane, hydrogen, water and also simulating the conditions of lightning.

Re-analysis of the vials used in the original experiments, using modern sensitive techniques, has shown a much richer diversity of amino acids was created than previously thought, some 22 in all, as opossed to the five originally detected.

These new results provide new evidence for the abiogenesis hypothesis (for the origin of life) that biological molecules can readily form from simple organic and inorganic reactants.

http://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment

Originally posted by Diodorus Siculus
This is an interesting link to a wikipedia entry on the famous Miller-Urey experiment that looked at the generation of biomolecules from simple reactants, thought to be present on the early earth, namely ammonia, carbon monooxide, methane, hydrogen, water and also simulating the conditions of lightning.

Re-analysis of the vials used in the orig ...[text shortened]... organic and inorganic reactants.

http://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment

I read that report, newer technology squeezing more data out of the old experiment, seems it needs to be repeated, eh.

Originally posted by Diodorus Siculus
This is an interesting link to a wikipedia entry on the famous Miller-Urey experiment that looked at the generation of biomolecules from simple reactants, thought to be present on the early earth, namely ammonia, carbon monooxide, methane, hydrogen, water and also simulating the conditions of lightning.

Re-analysis of the vials used in the orig ...[text shortened]... organic and inorganic reactants.

http://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment

Have such experiments created any hitherto undiscovered amino acids? That is, are the chemical
building blocks of life set or is it possible that lifeforms on other planets would use at least some
different amino acids than the 20+ ones used on this one?

Nemesio

I think the re-analysis using HPLC and MS is largely of historical interest as the apparatus is so famous. Of course, the work has been repeated and expanded upon. The thick organic haze discovered on present day Titan is one such spur to a series of experiments:
http://www.pnas.org/content/103/48/18035.short

Originally posted by Nemesio
Have such experiments created any hitherto undiscovered amino acids? That is, are the chemical
building blocks of life set or is it possible that lifeforms on other planets would use at least some
different amino acids than the 20+ ones used on this one?

Nemesio

No new amino acids to my knowledge which is not surprising but I always thought there were 20 amino acids known on earth, but two new ones have been discovered relatively recently, that are also genetically encoded so now 22 is the count so far:
http://researchnews.osu.edu/archive/aminosyn.htm
The famous Murchison meteorite also has a few "unnatural" amino acids, like isovaline, so it will be interesting when we do finally find life outside of earth what the code is and as you say, what amino acids they have, but I bet it's very, very similar to our own archea.

I am continually surprised and baffled why this experiment is not done extremely often and done in many laboratories all over the world. It seems to me to be an experiment that is so “obviously” of immense scientific interest.

The most “obvious” experiment to do here in my view is to repeat the experiment but try to make it more closely simulate the actual conditions that existed then by, for example, adding some ground-up igneous rock (because that might produce some interesting surface chemistry) and add some hydrogen sulphide (which would have been released from volcanoes) and create some turbulence in the water and make some of the sparks of electricity actually enter the water itself (because lighting must occasionally strike the oceans) etc.

Also should check for any signs that some of the amino acids have linked up together to form chains etc.

Originally posted by Andrew Hamilton
I am continually surprised and baffled why this experiment is not done extremely often and done in many laboratories all over the world. It seems to me to be an experiment that is so “obviously” of immense scientific interest.

The most “obvious” experiment to do here in my view is to repeat the experiment but try to make it more closely simulate ...[text shortened]... uld check for any signs that some of the amino acids have linked up together to form chains etc.

Erm, they do but it has moved on somewhat as the conditions in the classic Miller-Urey experiment were too optimistic. Astrobiology is a journal dedicated to this kind of work. A sample abstract is below.

The catalytic potential of cosmic dust: implications for prebiotic chemistry in the solar nebula and other protoplanetary systems.
Hill HG, Nuth JA.

International Space University, Strasbourg Central Campus, Illkirch-Graffenstaden, France.

The synthesis of important prebiotic molecules is fundamentally reliant on basic starting ingredients: water, organic species [e.g., methane (CH(4))], and reduced nitrogen compounds [e.g., ammonia (NH(3)), methyl cyanide (CH(3)CN) etc.]. However, modern studies conclude that the primordial Earth's atmosphere was too rich in CO, CO(2), and water to permit efficient synthesis of such reduced molecules as envisioned by the classic Miller-Urey experiment. Other proposed sources of terrestrial nitrogen reduction, like those within submarine vent systems, also seem to be inadequate sources of chemically reduced C-H-O-N compounds. Here, we demonstrate that nebular dust analogs have impressive catalytic properties for synthesizing prebiotic molecules. Using a catalyst analogous to nebular iron silicate condensate, at temperatures ranging from 500K to 900K, we catalyzed both the Fischer-Tropsch conversion of CO and H(2) to methane and water, and the corresponding Haber-Bosch synthesis of ammonia from N(2) and H(2). Remarkably, when CO, N(2), and H(2) were allowed to react simultaneously, these syntheses also yielded nitrogen-containing organics such as methyl amine (CH(3)NH(2)), acetonitrile (CH(3)CN), and N-methyl methylene imine (H(3)CNCH(2)). A fundamental consequence of this work for astrobiology is the potential for a natural chemical pathway to produce complex chemical building blocks of life throughout our own Solar System and beyond.

Originally posted by Andrew Hamilton
I am continually surprised and baffled why this experiment is not done extremely often and done in many laboratories all over the world. It seems to me to be an experiment that is so “obviously” of immense scientific interest.

The most “obvious” experiment to do here in my view is to repeat the experiment but try to make it more closely simulate ...[text shortened]... uld check for any signs that some of the amino acids have linked up together to form chains etc.

Abiogenesis, or the origin of life from inanimate matter, centres on the RNA world hypothesis. Specifically, even if amino acids polymerise into oligo- and polypeptides without an error-prone self-replication system no evolution or inheritance is possible so a nucleic acid-based model for the early origin of life is necessary and has evidence to support it. The ability of RNA in modern cells to serve as both a messenger (mRNA) of the DNA genetic code allied with it's enzymatic roles (previously thought only to be carried out be proteins) suggest this remarkable molecule, in particular ribosomal RNA, is the evolutionary remnant of the RNA world.

RNA enzymes, or ribozymes, are essential components of the ribosome, which is vital for protein synthesis and directed evolution in the lab has created ribozymes with a variety of activities. It has also been suggested that amino acids may have initially been complexed with RNA molecules as co-factors enhancing or diversifying their enzymatic capabilities, before evolving to the more complex peptides. mRNA may have evolved from such RNA molecules, and tRNA from RNA molecules which had catalyzed amino acid transfer to them. It is fascinating that research on the origins of life on this planet have come so far and so quickly.

Originally posted by Diodorus Siculus
Abiogenesis, or the origin of life from inanimate matter, centres on the RNA world hypothesis. Specifically, even if amino acids polymerise into oligo- and polypeptides without an error-prone self-replication system no evolution or inheritance is possible so a nucleic acid-based model for the early origin of life is necessary and has evidence to sup ascinating that research on the origins of life on this planet have come so far and so quickly.

I have heard of the hypothesis that DNA evolved from RNA and originally all microbes had only RNA and no actual DNA -given the fact that many modern-day viruses are “RNA viruses” ( http://en.wikipedia.org/wiki/Positive-sense_ssRNA_virus ) and manage just fine with all the genetic information within them stored in only RNA with no DNA, I think this is a perfectly plausible and reasonable hypothesis!

Originally posted by Nemesio
Have such experiments created any hitherto undiscovered amino acids? That is, are the chemical
building blocks of life set or is it possible that lifeforms on other planets would use at least some
different amino acids than the 20+ ones used on this one?

Nemesio

An amino acid is just and amine group and a carboxylate group linked by a carbon, with that middle carbon often having other groups. You could conceivably substitute any group on that carbon, and still have an amino acid. It's just two dozen or so of those are ever used by living things.

Interesting thread.

Originally posted by convect
An amino acid is just and amine group and a carboxylate group linked by a carbon, with that middle carbon often having other groups. You could conceivably substitute any group on that carbon, and still have an amino acid. It's just two dozen or so of those are ever used by living things.

Interesting thread.

……It's just two dozen or so of those are ever used by living things. ..…

That is what I thought until recently somebody pointed out this at:

http://en.wikipedia.org/wiki/Amino_acid

“Hundreds of types of non-protein amino acids have been found in nature and they have multiple functions in living organisms.”

-but note the words “non-protein” in the above; when people usually talk about “amino acids” they are usually only referring to the few that are found in proteins.

Originally posted by Andrew Hamilton
[b]……It's just two dozen or so of those are ever used by living things. ..…

That is what I thought until recently somebody pointed out this at:

http://en.wikipedia.org/wiki/Amino_acid

“Hundreds of types of non-protein amino acids have been found in nature and they have multiple functions in living organisms.”

-but note the words “non- ...[text shortened]... talk about “amino acids” they are usually only referring to the few that are found in proteins.[/b]

Also like neutrinos amino acids are almost exclusively left handed. The two functional groups described above, rotate around the central "chiral" carbon and so can have one of two forms (Pasteur started all this handedness work I think, looking at crystals of tartaric acid). The reason for this homochirality is not known, though there is a pretty wild theory, called the Bonner hypothesis, that proposes that circularly polarised light in space (say from a neutron star) could lead to left handed amino acids, which would explain the left handed amino acid enrichment in meteorites and in the known 20 odd "natural" ones in lifeforms on Earth. Racemic is the word for a mix of both forms which was seen in the M-U experiment (they didn't have a neutron star handy in the lab presumably!).

What did the Miller–Urey experiment show?

That aminoacids can be produced spontaneously in an well defined environment?
or
That life began in an environment like the one in the experiment?

What have we learned from the experiment?

Originally posted by Diodorus Siculus
Also like neutrinos amino acids are almost exclusively left handed. The two functional groups described above, rotate around the central "chiral" carbon and so can have one of two forms (Pasteur started all this handedness work I think, looking at crystals of tartaric acid). The reason for this homochirality is not known, though there is a pretty wi seen in the M-U experiment (they didn't have a neutron star handy in the lab presumably!).

I have formed my own theory why amino acids are almost exclusively left handed in proteins in all living things -and this is it:

The very first microbe used both left-handed and right-handed amino acids from its natural environment and there was NO bias for the spontaneous formation of left-handed amino acids from right-handed amino acids in the environment! They formed in equal proportions.

But, this meant the protein molecules that were formed in that first microbe where a bit misshaped and in a bit of a mess because the left-handed and right-handed amino acids where all jumbled up along the peptide chains in a totally random and haphazard fashion. This would have meant that those proteins didn’t do their job very well because the function of a protein is largely controlled by the shape of the molecule. So it would be of survival advantage for the microbe to only use amino acids of the same handiness.

But then evolution had an effect: a chance mutation made one of those microbes tend to select ONLY left-handed amino acids for protein synthesis. The mutation could have just as easily made it select right-handed acids for protein synthesis in which case all amino acids today would be right-handed amino acids and we all be asking ourselves “why are they all right-handed? -I mean, what is so special about right-handed ones as opposed to left-handed ones?” -and the answer would be there is nothing special about it at all.

After that mutation, that microbe would have had a big competitive edge over all others thus natural selection would have allowed them to spread and eventually eliminated all the others by competition for finite space and energy sources etc and perhaps before any of the others had a chance to mutate to use right-handed amino acids hence this is why all amino acids used in life today are left-handed.

Originally posted by Andrew Hamilton
I have formed my own theory why amino acids are almost exclusively left handed in proteins in all living things -and this is it:

The very first microbe used both left-handed and right-handed amino acids from its natural environment and there was NO bias for the spontaneous formation of left-handed amino acids from right-handed amino acids in the e ...[text shortened]... e right-handed amino acids hence this is why all amino acids used in life today are left-handed.

Yes, I agree it was probably an accident that was subsequently perpetuated in all progeny, however, D-amino acids do however exist as tetrapeptides in the NAG-NAM cell wall of bacteria:
http://en.wikipedia.org/wiki/Peptidoglycan
This may be of interest to you too Mr. Hamilton:
http://sandwalk.blogspot.com/2008/05/amino-acids-and-racemization-problem.html