New study sheds light on origins of life on Earth

[beecee]

https://phys.org/news/2022-01-life-earth.html

Addressing one of the most profoundly unanswered questions in biology, a Rutgers-led team has discovered the structures of proteins that may be responsible for the origins of life in the primordial soup of ancient Earth.

The study appears in the journal Science Advances.

The researchers explored how primitive life may have originated on our planet from simple, non-living materials. They asked what properties define life as we know it and concluded that anything alive would have needed to collect and use energy, from sources such as the Sun or hydrothermal vents.

In molecular terms, this would mean that the ability to shuffle electrons was paramount to life. Since the best elements for electron transfer are metals (think standard electrical wires) and most biological activities are carried out by proteins, the researchers decided to explore the combination of the two—that is, proteins that bind metals.

more at link..............

the paper:

https://www.science.org/doi/10.1126/sciadv.abj3984

Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer

Abstract

Biological redox reactions drive planetary biogeochemical cycles. Using a novel, structure-guided sequence analysis of proteins, we explored the patterns of evolution of enzymes responsible for these reactions. Our analysis reveals that the folds that bind transition metal–containing ligands have similar structural geometry and amino acid sequences across the full diversity of proteins. Similarity across folds reflects the availability of key transition metals over geological time and strongly suggests that transition metal–ligand binding had a small number of common peptide origins. We observe that structures central to our similarity network come primarily from oxidoreductases, suggesting that ancestral peptides may have also facilitated electron transfer reactions. Last, our results reveal that the earliest biologically functional peptides were likely available before the assembly of fully functional protein domains over 3.8 billion years ago.

Thus, life is a special, very complex form of motion of matter, but this form did not always exist, and it is not separated from inorganic nature by an impassable abyss; rather, it arose from inorganic nature as a new property in the process of evolution of the world. We must study the history of this evolution if we want to solve the problem of the origin of life. [A. I. Oparin (1)]

[Doogles31731]

Does this suggest that we should repeat those experiments involving mixtures of H20, CO2, NH3 in flasks with bursts of electricity, but this time adding a range of metallic elements such as iron (catalase), selenium (glutathione peroxidase), manganese and zinc (superoxide dismutases?

[DaviBrons]

Did I understand correctly that we are talking about what synergetics, the science of the self-organization of matter, does? Roughly speaking, this self-organization has several levels, which possibly one follows from the other: physical (four forces of interaction - primarily mutual attraction) -> chemical -> biological. In principle, you can continue -> social (unification of people for joint survival and solving various problems). But this is easier - much more difficult with the self-organization of non-intelligent matter. Perhaps someday it will be possible to derive biological self-organization from chemical, and chemical self-organization from physical.

[joigus]

On 1/14/2022 at 9:05 PM, beecee said:

https://phys.org/news/2022-01-life-earth.html

[...]

Addressing one of the most profoundly unanswered questions in biology, a Rutgers-led team has discovered the structures of proteins that may be responsible for the origins of life in the primordial soup of ancient Earth.

The study appears in the journal Science Advances.

The researchers explored how primitive life may have originated on our planet from simple, non-living materials. They asked what properties define life as we know it and concluded that anything alive would have needed to collect and use energy, from sources such as the Sun or hydrothermal vents.

In molecular terms, this would mean that the ability to shuffle electrons was paramount to life. Since the best elements for electron transfer are metals (think standard electrical wires) and most biological activities are carried out by proteins, the researchers decided to explore the combination of the two—that is, proteins that bind metals.

 

(My emphasis.)

Yes!! Very interesting. Thank you. The most important factor of life is the controlled use of electron carriers in a recyclable way (photosynthesis, ATP production by ATP-synthase.) If you take a look --schematically-- at the chemical pathways, these electron carriers always go round and round and get recycled, getting ready to carry electrons again.

I think RNA must be part of the picture too.

I'll take a look at the main salient aspects ASAP.

[CharonY]

Photosynthesis proteins as well as ATP-synthases arose a fair bit later. A common assumption is that substrate level phosphorylation was at the beginning. There are other hypotheses around which are based on how other reactions were potentially thermodynamic favourable, but i haven't looked at those for a while.

[joigus]

33 minutes ago, CharonY said:

Photosynthesis proteins as well as ATP-synthases arose a fair bit later. A common assumption is that substrate level phosphorylation was at the beginning. There are other hypotheses around which are based on how other reactions were potentially thermodynamic favourable, but i haven't looked at those for a while.

I know, I know. I didn't mean to say that these membrane proteins were there at the beginning. I just meant that the "minimum common factor for life" so to speak, is a pathway in which electron carriers (molecules that capture electrons, but not too strongly, so they can be "robbed" of them, are very mobile, etc) play the role of taking these electrons to the ultimate electron acceptor, and get recycled so as to get the cyclic pathway going.

ATP synthase and the similar membrane-protein machine in photosynthesis (I forget the name now) are big, sophisticated proton-pumping machines that must have arisen much, much later.

But the common theme is (seems to me to be): Some "light" electron acceptors act as electron carriers, while some protein in the pathway graciously takes these electrons and consummates the final oxidative reaction.

Is that picture anything like right?

Edited January 20, 2022 by joigus
minor correction

[CharonY]

Ah I see. Fundamentally redoxreactions are at the core of it. I could have said oxidative phosphorylation, right? And anaerobic fermentation is basically just a means to recycle reducing equivalents. However, they do not need to go through membranes as such. That being said, it is assumed that fermentation might have created excess of acids (as the and proton pumps may have been an early development to deal with it. These are then potentially the precursor of electron transport chains. However, this is based on student-level reading, I don't know how much these assumptions have changed in the last two or so decades. Ancestral metabolism is not my specialty.

 

[TheVat]

On 1/16/2022 at 2:02 AM, Doogles31731 said:

Does this suggest that we should repeat those experiments involving mixtures of H20, CO2, NH3 in flasks with bursts of electricity, but this time adding a range of metallic elements such as iron (catalase), selenium (glutathione peroxidase), manganese and zinc (superoxide dismutases?

I think they redid the Miller-Urey xp recently and one issue raised was about the original flask material, which was a borosilicate glass.  IIRC other flask materials didn't work nearly as well, not having silica.

The pH of the original xp was high enough (despite Pyrex's reputation for inertness) to dissolve out some of the silica(!).

Will see if I can find the article...

Here it is, in SciAm....

https://www.scientificamerican.com/podcast/episode/redo-of-a-famous-experiment-on-the-origins-of-life-reveals-critical-detail-missed-for-decades/

 

[studiot]

I would be very wary of expecting parallels between modern biological processes and primordial ones.

This is because of the large number of bio-catalysts that modern life employs for its processes.

Quote

https://www.ncbi.nlm.nih.gov/books/NBK9921/

In the absence of enzymatic catalysis, most biochemical reactions are so slow ... of different enzymes, and their activities determine which of the many .

Primordial chemical processes will not have had the benefit of these catalysts, as we would have to believe that not only did the right components come togther for the protein etc to form but also the right components for the catalyst as well. (Most such catalysts are complicated biomolecules in their own right).

 

Indeed it begs the question, which came first the catalyst or the product protein ?

Edited January 20, 2022 by studiot

[Arthur Smith]

2 hours ago, studiot said:

Indeed it begs the question, which came first the catalyst or the product protein ?

RNA is both template and catalyst.

[studiot]

11 minutes ago, Arthur Smith said:

RNA is both template and catalyst.

OK so maybe RNA is an autocatalyst.

But how did the first molecule of RNA from ?

(This is equivalent to asking did Adam have a navel)

 

Actually lots of folks have considered this question.

https://www.google.co.uk/search?hl=en-GB&source=hp&biw=&bih=&q=RNA+autocatalysis&iflsig=ALs-wAMAAAAAYenPdzZGQshq61NkRjjw0ZBSHtq2UEo0&gbv=2&oq=RNA+autocatalysis&gs_l=heirloom-hp.3...1082.5864.0.6258.17.17.0.0.0.0.306.2478.2j7j3j2.14.0....0...1ac.1.34.heirloom-hp..6.11.1842.0XdHvwMhTXo

[Arthur Smith]

1 minute ago, studiot said:

OK so maybe RNA is an autocatalyst.

No maybe. COVID is an RNA virus, storing it's genetic information in RNA. When it infects a cell the replication system it hijacks is the ribosome, the functional catalytic element is RNA. RNA World is a good hypothesis of "why not both".

[CharonY]

8 minutes ago, Arthur Smith said:

No maybe. COVID is an RNA virus, storing it's genetic information in RNA. When it infects a cell the replication system it hijacks is the ribosome, the functional catalytic element is RNA. RNA World is a good hypothesis of "why not both".

That is not the common definition of a catalyst, though. The closest is a ribozyme, which are a kind of RNA that have catalytic functions. But those that "only" code for a protein for example have not catalytic functions themselves.

 

3 hours ago, studiot said:

Indeed it begs the question, which came first the catalyst or the product protein ?

Proteins certainly came later as there is evidence that even small peptides can have catalytic functions. But as mentioned ribozymes could also have play a role. In addition, there are some who think that we are looking at the thermodynamics wrong and that at the beginning of life certain reactions may have been energetically favourable even without more complex molecules, but I don't know how strong the evidence for that currently is.

 

[Arthur Smith]

2 minutes ago, CharonY said:

That is not the common definition of a catalyst, though. The closest is a ribozyme, which are a kind of RNA that have catalytic functions. But those that "only" code for a protein for example have not catalytic functions themselves.

Ribozymes are RNA catalysts. And the ribosome is an example that has not been superseded by a protein complex. Proteins are ubiquitous in living organisms today but proteins do not self-replicate, unlike RNA. That proteins have assumed the rôle of catalyst in most metabolic processes doesn't rule out that RNA could have done both replication and catalysis in the earliest self-sustaining self-replicators. It only needed to work, the first living entities would have no competition.

[Genady]

44 minutes ago, Arthur Smith said:

Ribozymes are RNA catalysts. And the ribosome is an example that has not been superseded by a protein complex. Proteins are ubiquitous in living organisms today but proteins do not self-replicate, unlike RNA. That proteins have assumed the rôle of catalyst in most metabolic processes doesn't rule out that RNA could have done both replication and catalysis in the earliest self-sustaining self-replicators. It only needed to work, the first living entities would have no competition.

I have a question about the RNA world (the idea of which is quite attractive to me). Do we consider "first living entities" or the entire world was one living entity, without membranes?

Added: Or, each separate "pond" was a living entity?

Edited January 20, 2022 by Genady

[StringJunky]

27 minutes ago, Genady said:

I have a question about the RNA world (the idea of which is quite attractive to me). Are we consider "first living entities" or the entire world was one living entity, without membranes?

Added: Or, each separate "pond" was a living entity?

Scientific consensus sets the 'lines' for mutual communicability between scientists, as a means to differentiate areas under focus (language), but there are no lines in nature.... it is one thing. "The map is not the territory". It seems to me that there is a continuous emergent process from the  inamate object to the autonomous animate object. Stone is to life as mass is to gravity.

Edited January 20, 2022 by StringJunky

[CharonY]

2 hours ago, Arthur Smith said:

Ribozymes are RNA catalysts. And the ribosome is an example that has not been superseded by a protein complex. Proteins are ubiquitous in living organisms today but proteins do not self-replicate, unlike RNA. That proteins have assumed the rôle of catalyst in most metabolic processes doesn't rule out that RNA could have done both replication and catalysis in the earliest self-sustaining self-replicators. It only needed to work, the first living entities would have no competition.

In my original reading of your it seemed to me that were arguing that the viral RNA was also a ribozyme or somehow a catalyst, but maybe I misread. I am not disputing that RNA can have catalytic functions.

 

[Genady]

1 hour ago, StringJunky said:

Stone is to life as mass is to gravity.

I think I understand what you mean by a continuous emergent process. But could you please elaborate on this last statement?

[StringJunky]

12 hours ago, Genady said:

I think I understand what you mean by a continuous emergent process. But could you please elaborate on this last statement?

The stone represents all the elements that make life, but we are not sure as to the process, as with mass to gravity/curved spacetime.

[Genady]

2 minutes ago, StringJunky said:

The stone represents all the elements that make life, but we are not sure as to the process, as with mass to gravity/curved spacetime.

Got it.

[Arthur Smith]

15 hours ago, studiot said:

But how did the first molecule of RNA from ?

Science is not static.

https://bme.gatech.edu/bme/node/3152

Though I concede, origin-of-life research has more ideas than definitive evidence.

[studiot]

15 hours ago, Arthur Smith said:

No maybe. COVID is an RNA virus, storing it's genetic information in RNA. When it infects a cell the replication system it hijacks is the ribosome, the functional catalytic element is RNA. RNA World is a good hypothesis of "why not both".

 

15 hours ago, CharonY said:

 

 

Proteins certainly came later as there is evidence that even small peptides can have catalytic functions. But as mentioned ribozymes could also have play a role. In addition, there are some who think that we are looking at the thermodynamics wrong and that at the beginning of life certain reactions may have been energetically favourable even without more complex molecules, but I don't know how strong the evidence for that currently is.

 

 

So perhaps someone with sufficient biological knowledge might like to address my points about the chemical kinetics of the reactions that led to life and its precursor chemicals.

All I know about them is that the kinetics of these reactions are some of the most complicated known, many without a (known) closed form solution.

[Arthur Smith]

12 hours ago, CharonY said:

I am not disputing that RNA can have catalytic functions.

 

Does have. The sharp end of our (human) ribosomes is RNA.

[studiot]

2 minutes ago, Arthur Smith said:

Science is not static.

https://bme.gatech.edu/bme/node/3152

Though I concede, origin-of-life research has more ideas than definitive evidence.

Edit

Thank you for that link.

I did not appreciate the comment about Science, where did I say it was ?

[Arthur Smith]

3 minutes ago, studiot said:

So perhaps someone with sufficient biological knowledge might like to address my points about the chemical kinetics of the reactions that led to life and its precursor chemicals.

All I know about them is that the kinetics of these reactions are some of the most complicated known, many without a (known) closed form solution.

You won't get a definitive, consensus, universally accepted explanation from anyone, because there isn't one yet. Current life on Earth is all commonly descended from one remote ancestor, the last, universal common ancestor. I can't tell you much about those early organisms except there is no reason to think they were not preceded by simpler, different organisms and systems of which there is no trace. First life may have exploited other sources of energy, anaerobic chemosynthesis rather than needing light or oxygen, life may have got going in deep sea vents where chemicals emerge from the crust at high concentration in very hot water which rapidly cools on mixing. There are surfaces, holes and crevices that are potentially almost infinite in their micro-niche properties. 

There's always the possibility of a second data point. Something on Mars or further afield. Till then, speculation (based on what we know and what we can show) is available. Nick Lane is someone to google.

11 minutes ago, studiot said:

Edit

Thank you for that link.

I did not appreciate the comment about Science, where did I say it was ?

I'm an inveterate speed-reader. Apologies if I missed or misunderstood a point you were making. Please feel free to ask again or link to what I missed.