Classic 'life chemistry' experiment still excites.

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Classic 'life chemistry' experiment still excites.

#1  Postby trubble76 » Mar 24, 2011 10:06 am

Foul-smelling hydrogen sulphide may have been an important precursor in the chemistry that eventually led to life on Earth, a new study suggests.

Modern analyses of samples archived from 1950s experiments indicate the gas can, under the right conditions, play a role in reactions that produce some of the building blocks of biology - amino acids, which combine to make proteins.

The findings are based on the work of Stanley Miller who famously tried to replicate the chemical "primordial soup" from which life may have emerged.


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Re: Classic 'life chemistry' experiment still excites.

#2  Postby The Hanging Monkey » Mar 25, 2011 10:15 am

Interesting article, it's great that these samples are going to be analysed using modern techniques.
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Re: Classic 'life chemistry' experiment still excites.

#3  Postby rainbow » Jun 12, 2011 12:02 pm

Dead end.
Proteins can't replicate, and so weren't involved in the first life form.
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Re: Classic 'life chemistry' experiment still excites.

#4  Postby campermon » Jun 12, 2011 12:21 pm

rainbow wrote:Dead end.
Proteins can't replicate, and so weren't involved in the first life form.


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

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Re: Classic 'life chemistry' experiment still excites.

#5  Postby rainbow » Jun 12, 2011 12:35 pm

Prions don't replicate. They cause other proteins to fold in a particular shape, and this effect can cause further protein misfolding.
Not quite the same thing as replication.
....still a dead end I'm afraid.
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Re: Classic 'life chemistry' experiment still excites.

#6  Postby campermon » Jun 12, 2011 12:54 pm

rainbow wrote:Prions don't replicate. They cause other proteins to fold in a particular shape, and this effect can cause further protein misfolding.
Not quite the same thing as replication.
....still a dead end I'm afraid.


Aye! Prions 'cheat' in their replication.

I'm sure that I've read about self assembling proteins from somewhere......

Any biochemists on the thread?

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Re: Classic 'life chemistry' experiment still excites.

#7  Postby rainbow » Jun 13, 2011 9:39 am

campermon wrote:Aye! Prions 'cheat' in their replication.

...only if strawmen can construct themselves.
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Re: Classic 'life chemistry' experiment still excites.

#8  Postby kathreeds » Jun 21, 2011 5:41 pm

rainbow wrote:Dead end.
Proteins can't replicate, and so weren't involved in the first life form.



Now, certain proteins are essential for the replication of DNA. So the question arises, if DNA cannot replicate without these proteins, what DNA was use to make these proteins themselves?
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Re: Classic 'life chemistry' experiment still excites.

#9  Postby trubble76 » Jun 21, 2011 6:50 pm

kathreeds wrote:
rainbow wrote:Dead end.
Proteins can't replicate, and so weren't involved in the first life form.



Now, certain proteins are essential for the replication of DNA. So the question arises, if DNA cannot replicate without these proteins, what DNA was use to make these proteins themselves?


That assumes DNA is the only tool capable of creating something that does that job.
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Re: Classic 'life chemistry' experiment still excites.

#10  Postby Rumraket » Jun 21, 2011 6:59 pm

kathreeds wrote:
rainbow wrote:Dead end.
Proteins can't replicate, and so weren't involved in the first life form.



Now, certain proteins are essential for the replication of DNA. So the question arises, if DNA cannot replicate without these proteins, what DNA was use to make these proteins themselves?

The answer to that question would be RNA, since RNA can both serve as the information storing molecule and as an enzyme. Certain strings of RNA have been found which can replicate themselves.

Self-Sustained Replication of an RNA Enzyme
Tracey A. Lincoln and Gerald F. Joyce
http://www.sciencemag.org/content/323/5 ... 9.abstract

ABSTRACT

An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other's synthesis from a total of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo self-sustained exponential amplification in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about 1 hour and can be continued indefinitely. Populations of various cross-replicating enzymes were constructed and allowed to compete for a common pool of substrates, during which recombinant replicators arose and grew to dominate the population. These replicating RNA enzymes can serve as an experimental model of a genetic system. Many such model systems could be constructed, allowing different selective outcomes to be related to the underlying properties of the genetic system.
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Re: Classic 'life chemistry' experiment still excites.

#11  Postby rainbow » Jun 22, 2011 8:04 am

Rumraket wrote:The answer to that question would be RNA, since RNA can both serve as the information storing molecule and as an enzyme.

Yes, possibly.
RNA is NOT made from protein, and was not formed in the Miller experiment.
The experiment was therefore a dead end, and can't be linked to the RNA-first hypothesis of Abiogenesis.
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Re: Classic 'life chemistry' experiment still excites.

#12  Postby Rumraket » Jun 22, 2011 10:14 am

rainbow wrote:
Rumraket wrote:The answer to that question would be RNA, since RNA can both serve as the information storing molecule and as an enzyme.

Yes, possibly.
RNA is NOT made from protein, and was not formed in the Miller experiment.
The experiment was therefore a dead end, and can't be linked to the RNA-first hypothesis of Abiogenesis.

It's not really clear what you mean by "linked" to the RNA-first hypothesis.

I think it would be more correct to say that the experiment didn't show how life can arise from prebiotic chemistry. I still think aminoacids are important for the subsequent evolution of the first life-form, however you define it. Simple dipeptides are an important aspect in the evolution of the genetic code, for example, and this obviously requires aminoacids to be present in the environment. Their presence may even be important in terms of serving as catalysts for other prebiotically relevant reactions.

I think it's a mistake to think of the origin of life as the origin of some single specific molecule(or type of molecule), like ribonucleotides. The picture that emerges from the field of origins of life research seems a lot more muddled to me, than this compartmentalized type thinking where things happen in discreet "steps". I used to think along those lines myself earlier but it's really not how chemistry works of course.
In any given naturally ocurring chemical synthesis, a whole host of compounds are produced and they all play some sort of role in the subsequent behavior of that chemical system. The constituents of modern organisms, like lipids, proteins, sugars and nucleotides, probably were all somehow present in the first life-form in much simpler versions, serving very different functions.

Today proteins still serve as catalysts in the form of large complex enzymes. But many proteins have specific catalytic regions/cores that only function in the presense of specific metal catalysts. These catalytic regions show very high degrees of conservation through all of life and serve as a hint to the environments from which they evolved. In the exact same way the catalytic core of the Ribosome, peptidyl-transferase, is made of RNA, not protein and serves as a powerful indication for a past where much of the chemistry of life was done by RNA.

In this respect, the first "enzymes" could have been very simple dipeptides catalyzed by metal ions seeping up from hydrothermal cracks in the ocean floot. The funny thing is, in almost all prebiotic synthesis expriments, amino acids are ubiquitous in some version or another. While they would neither serve as a gentic system, nor be linked into complex enzymes to begin with, they could still easily play a role in the chemistry that ultimately leads to a form of life.

Some papers that discuss the roles of these small precursors and metal catalysts:
http://www.biology-direct.com/content/4/1/26
http://www.biology-direct.com/content/4/1/27
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Re: Classic 'life chemistry' experiment still excites.

#13  Postby rainbow » Jun 22, 2011 10:57 am

Rumraket wrote:
rainbow wrote:
Rumraket wrote: Simple dipeptides are an important aspect in the evolution of the genetic code, for example, and this obviously requires aminoacids to be present in the environment. Their presence may even be important in terms of serving as catalysts for other prebiotically relevant reactions.

Maybe, though it hasn't been demonstrated. On the other hand, organic compounds can act as catalysts, and inorganic compounds can act as catalysts - so the role if any of amino-acids is not established.
Miller-Urey has another problem. The simple organic compounds are produced in the atmosphere, and would be dispersed at a low concentration of the vast prebiotic ocean.
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Re: Classic 'life chemistry' experiment still excites.

#14  Postby Rumraket » Jun 22, 2011 11:31 am

rainbow wrote:
Rumraket wrote:
rainbow wrote:

Maybe, though it hasn't been demonstrated. On the other hand, organic compounds can act as catalysts, and inorganic compounds can act as catalysts - so the role if any of amino-acids is not established.
Miller-Urey has another problem. The simple organic compounds are produced in the atmosphere, and would be dispersed at a low concentration of the vast prebiotic ocean.

Sure, but I wasn't thinking specifically about spark-discharge experiments in gases. Only the possible role of amino acids, whatever the nature of their source.

There are plenty of papers on the synthesis of amino acids under hydrothermal conditions. Here are two random ones I dug up quickly:
http://www.sciencedirect.com/science/article/pii/0016703794902887
http://www.sciencedirect.com/science/article/pii/0032063393E0043C
And indeed experiments that demonstrale polymerization of amino acids into peptides, under hydrothermal conditions:
http://www.springerlink.com/content/h534w723kl061293/
Followed by experiments on the type of amino-acid catalyzed chemical evolution I spoke about earlier:
http://marsh.cms.udel.edu/mast634/Refs/HydrothermalVentChemistry.pdf
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