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  • richardmitnick 2:47 pm on August 31, 2018 Permalink | Reply
    Tags: A Tiny Protein Like This May Have Kick-Started Life On Earth, Ambidoxin, Amino Acids, , , , , Computer modeling, Ferredoxins, , Peptides, , Redox catalysis, , Rutgers' Environmental Biophysics and Molecular Ecology Laboratory   

    From Rutgers University via Forbes: “A Tiny Protein Like This May Have Kick-Started Life On Earth” 

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    From Rutgers University

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    Forbes

    Aug 31, 2018
    Fiona McMillan

    1
    Ambidoxin is a synthetic small protein that wraps around a metal core composed of iron and sulfur. Vikas Nanda/Rutgers University-New Brunswick

    Researchers have reverse engineered a simple protein that may have helped kick start life on Earth.

    Their findings, published in the Journal of the American Chemical Society, provide strong new evidence that simple protein catalysts could have contributed to the development of life.

    A few decades ago, a chemist named Günter Wächtershäuser put forward a theory that life most likely began on volcanic rocks in the ocean that were rich in iron, sulfur and a variety of other minerals and elements useful for the kind of chemistry needed for simple life forms to emerge. He and others went on to surmise that this process would have been helped along by peptides — which are short proteins — that would have been capable of functioning as catalysts.

    A catalyst is anything that can speed up or increase the likelihood of a chemical reaction. Protein catalysts, or enzymes, are able to achieve this by bringing the reactants together in close proximity, and sometimes by also bringing other factors into the mix that help the reaction along, such as a metal ion, a water molecule, or some other type of molecule that gets things moving. In this way, enzymes are like really good party hosts.

    Of course, modern enzymes are often big bulky things comprising hundreds of amino acids. There are 20 amino acids to choose from, so countless combinations are possible. These big, complex enzymes are able fold into a stunning variety of elaborate shapes, enabling them to capture and hold reactants, and carry out reactions. They’re absolutely critical to the function of both simple and complex cellular life; we literally couldn’t live without them.

    However, such complex molecules took billions of years to evolve. Wächtershäuser and others have proposed that the earliest peptides would have had much simpler structures — perhaps just 10 or 20 amino acids — with just enough chemical complexity to enable them to carry out basic primordial chemistry.

    Yet exactly what such peptides may have looked like has been a mystery.

    3
    Underwater sulfur chimneys at Northwest Eifuku volcano. Life may have begun on volcanic underwater rocks like these.Credit: Pacific Ring of Fire 2004 Expedition. NOAA Office of Ocean Exploration; Dr. Bob Embley, NOAA PMEL, Chief Scientist; Public domain image

    Now Vikas Nanda and his colleagues at Rutgers University have used computer modeling to find out just how simple a peptide can get while still retaining the ability to function as a catalyst.

    In so doing, they have designed a peptide only 12 amino acids long that is able to wrap around a cluster of iron and sulfur atoms, which closely resemble iron-sulfur clusters that would have been found in ancient oceans.

    Interestingly, the peptide, which they named ambidoxin, doesn’t need the full variety of 20 amino acids available to modern proteins — it only requires two types of amino acid. Given its simplicity, the researchers suggest such a structure could have evolved spontaneously under the right conditions.

    Importantly, ambidoxin is able to carry out simple oxidation-reduction chemistry, also known as redox catalysis. Essentially it is able to be charged and discharged without falling apart, effectively enabling it to shuttle electrons from one place to another.

    “Modern proteins called ferredoxins do this, shuttling electrons around the cell to promote metabolism,” says senior author Paul G. Falkowski, who leads Rutgers’ Environmental Biophysics and Molecular Ecology Laboratory.

    “A primordial peptide like the one we studied may have served a similar function in the origins of life,” he says.

    By shuttling electrons around, ambidoxin (or something like it) may have contributed to early metabolic cycles, and could have served as a precursor to longer, more complex enzymes.

    See the full article here .


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    • stewarthoughblog 6:08 pm on August 31, 2018 Permalink | Reply

      How to get this straight? Ambidoxin is a synthetic molecule? It took intelligent designers to reverse engineer a simple protein? A totally open system of underwater volcanic rocks supposed was the source for this molecular development? Protein enzymes also had to form to “capture, hold and carry out reactions? the complex molecular enzymes took billions of years to “evolve, when evolution only occurs to living reproductive organisms that did not exist yet? Regardless of this obstacle, the 10-20 amino acids proposed to make its simpler for the formation of the molecule must be homochiral, a condition that no naturalistic process can accomplish. Which “2 amino acids?” Only the simplest can form naturalistically.

      There is no way the full article can rectify the absurd propositions in this article. This is intellectually insulting in its preposterous and nonscientific speculation.

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    • richardmitnick 1:12 pm on September 1, 2018 Permalink | Reply

      • stewarthoughblog 6:42 pm on September 1, 2018 Permalink | Reply

        Thank you for the reply and illumination of astrobiology.net’s beliefs. Nothing in their article answers the questions I posed.

        I can only offer my questions to them for serious response, as the astrobiology profession is motivated to pursue any and all aspects of potential life generation from a naturalistic worldview that is motivated to posit any and all mechanisms for the potential creation, development and sustaining of life. More cynically, their paycheck and funding depends on serious investigation and support of naturalistic processes, regardless of their viability.

        The second to last para of the article reveals an ostensible reliance on “evolution” for the formation of abiotic pre-assemblages of molecules that logically advocate abiogenetic assembly results. This, despite the well established disavowal by evolutionists of any evolution within abiogenesis. The astrobiologists are not so ideologically dogmatic if some origin of life milestone can be attained through evolutionary processes.

        Thank you. Regards.

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  • richardmitnick 7:32 am on August 10, 2015 Permalink | Reply
    Tags: Amino Acids, ,   

    From Cosmos: “Why the building blocks in our cells turned to the left” 

    Cosmos Magazine bloc

    COSMOS

    10 Aug 2015
    Viviane Richter

    1
    Crystals of glycine, the simplest amino acid. Delivered by meteorites, did amino acids from space seed life on Earth?Credit: JERZY GUBERNATOR / Getty Image

    Deep down, all right handers are lefties – at least when it comes to their amino acids. These are the building blocks of life on Earth and like most molecules, they can exist in right- or left-handed mirror image orientations. But life’s chemistry only works with lefties. Yasuhiro Oba and colleagues at Japan’s Hokkaido University now offer a novel reason for why that is: left-handed biology originated in space. They published their findings in Chemical Physics Letters in July.

    When amino acids are cooked up in the lab, they come in left or right-handed mirror image forms. And just as your left and right hand are functionally the same, they can never be superimposed on the same space. And that matters when two amino acids try to hook up to make proteins and conduct the chemistry of life. Just as you can’t pull your right glove on to your left hand, a left and right amino acid protein simply can’t get together.

    2
    Credit: Cosmos Magazine

    It’s never a problem because living systems always exclude right-handed amino acids and make exclusively left-handed proteins. But it didn’t have to be that way. When life first emerged, why did it choose left and not right? “That question has a lot of answers,” says Steven Benner, a chemist at the Foundation for Applied Molecular Evolution in Florida – but none of these ‘answers’ has yet been proved.

    We know amino acids can hitch a ride through space on comets and meteorites, and some scientists suspect these amino-acid-laden meteorites kicked off life on Earth. The Murchison meteorite that crashed near Melbourne in 1969, for example, carried more than 15 different amino acids. But with only a few exceptions, the amino acids found on such meteorites are evenly divided between left and right.

    However, four billion years ago, when life first stirred on Earth, the Universe contained a higher density of dusty star-forming galaxies. These dust grains – smaller than a thousandth of the width of a human hair – could have been a microscopic platform letting amino acids react and pick their side. Could the amino acid cocktail that smashed into Earth during this dustier era have contained more left-handed molecules than right?

    Yes, says the Hokkaido team. Oba and his colleagues considered the smallest and simplest amino acid, glycine. Uniquely among amino acids, glycine is symmetrical and has no handedness. But it can be forced into left or right-handedness if one of its hydrogen atoms is knocked out and replaced with the slightly heavier deuterium atom.

    Oba and his team asked whether this hydrogen-deuterium switch could take place in space – specifically, within dusty star-forming clouds. They are rich in deuterium but so cold that some scientists question whether any chemistry could take place there. To find out, Oba built a special chamber to mimic these conditions – a near vacuum cooled to about 10 ˚C above absolute zero. Inside, the researchers bombarded glycine with deuterium atoms, then weighed the sample to see if any deuterium had stuck. Sure enough, the sample was slightly heavier, confirming it is possible to make the glycine “handed”. Moreover they showed that the glycine appeared to “pick a side”. Just which side that was, they can’t yet say because the sample was too small. But the team may soon find out, as they plan to scale up the experiment.

    3
    Inside their reactor, the researchers recreated the icy, near-vacuum conditions of deep spaceCredit: Yasuhiro Oba

    For now, Benner isn’t convinced amino acids from space tipped life toward left-handedness. He believes biology picked left by chance. It would only take a small amount to tip the balance and give left-handed life a crucial early numbers advantage, he says. Malcolm Walter, an astrobiologist at the Australian Centre for Astrobiology at the University of New South Wales agrees. He also doubts we’ll ever come up with a definitive answer for why biology decided to be a lefty. “It’s going to remain speculative for a very long time – if not forever!”

    See the full article here.

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