Amino Acids: Origin of the canonical twenty amino acids required for life

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Amino acid synthesis requires solutions to four key biochemical problems

1. Nitrogen fixation
Nitrogen is an essential component of amino acids. Earth has an abundant supply of nitrogen, but it is primarily in the form of atmospheric nitrogen gas (N2), a remarkably inert molecule. Thus, a fundamental problem for biological systems is to obtain nitrogen in a more usable form. This problem is solved by certain microorganisms capable of reducing the inert N = N triple-bond molecule of nitrogen gas to two molecules of ammonia in one of the most amazing reactions in biochemistry. Nitrogen in the form of ammonia is the source of nitrogen for all the amino acids. The carbon backbones come from the glycolytic pathway, the pentose phosphate pathway, or the citric acid cycle.

2. Selection of the 20 canonical bioactive amino acids
Why are 20 amino acids used to make proteins ( in some rare cases, 22) ? Why not more or less ? And why especially the ones that are used amongst hundreds available? In a progression of the first papers published in 2006, which gave a rather shy or vague explanation, in 2017, the new findings are nothing short than astounding. In January 2017, the paper : Frozen, but no accident – why the 20 standard amino acids were selected, reported:

" Amino acids were selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets. Factors to take into account when assessing why a particular amino acid might be used include its component atoms, functional groups, biosynthetic cost, use in a protein core or on the surface, solubility and stability. Applying these criteria to the 20 standard amino acids, and considering some other simple alternatives that are not used, we find that there are excellent reasons for the selection of every amino acid. Rather than being a frozen accident, the set of amino acids selected appears to be near ideal. Why the particular 20 amino acids were selected to be encoded by the Genetic Code remains a puzzle."

3. Homochirality
In amino acid production, we encounter an important problem in biosynthesis—namely, stereochemical control. Because all amino acids except glycine are chiral, biosynthetic pathways must generate the correct isomer with high fidelity. In each of the 19 pathways for the generation of chiral amino acids, the stereochemistry at the a -carbon atom is established by a transamination reaction that includes pyridoxal phosphate (PLP) by transaminase enzymes, which however were not extant on a prebiotic earth, which creates an unpenetrable origin of life problem. One of the greatest challenges of modern science is to understand the origin of the homochirality of life: why are most essential biological building blocks present in only one handedness, such as L-amino acids and D-sugars ?

4. Amino acid synthesis regulation
Biosynthetic pathways are often highly regulated such that building blocks are synthesized only when supplies are low. Very often, a high concentration of the final product of a pathway inhibits the activity of allosteric enzymes ( enzymes that use cofactors ) that function early in the pathway to control the committed step. These enzymes are similar in functional properties to aspartate transcarbamoylase and its regulators. Feedback and allosteric mechanisms ensure that all 20 amino acids are maintained in sufficient amounts for protein synthesis and other processes.

Otangelo

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Glycine:
Phosphoglycerate dehydrogenase
http://en.wikipedia.org/wiki/Phosphoglycerate_dehydrogenase
Phosphoserine transaminase
http://en.wikipedia.org/wiki/Phosphoserine_transaminase
Phosphoserine phosphatase
http://en.wikipedia.org/wiki/Phosphoserine_phosphatase
Serine hydroxymethyltransferase
http://en.wikipedia.org/wiki/Serine_hydroxymethyltransferase

Valine
Acetolactate synthase enzyme
http://www.ebi.ac.uk/interpro/entry/IPR004789
Acetohydroxy acid isomeroreductase
http://www.ebi.ac.uk/interpro/entry/IPR013023
Dihydroxy-acid dehydratase
http://en.wikipedia.org/wiki/Dihydroxy-acid_dehydratase

Leucine and Isoleucine
Acetolactate synthase
https://en.wikipedia.org/wiki/Acetolactate_synthase
2-isopropylmalate synthase
https://en.wikipedia.org/wiki/2-isopropylmalate_synthase
3-Isopropylmalate dehydratase
https://en.wikipedia.org/wiki/3-Isopropylmalate_dehydratase
3-Isopropylmalate dehydrogenase
https://en.wikipedia.org/wiki/3-Isopropylmalate_dehydrogenase
Transaminase
https://en.wikipedia.org/wiki/Transaminase

Otangelo

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Tryptophan and the riddle of making amino acids by hypercomplex enzymatic reactions

https://reasonandscience.catsboard.com/t1740p25-amino-acids-origin-of-the-canonical-twenty-amino-acids-required-for-life#6700

If you can't make a brick, you can't make a house. Naturalistic scenarios are all based on ad-hoc anecdotal pseudo-scientific claims. Without having the right twenty left-handed amino acids, life essential proteins cannot be made, nor protein complexes, nor biological cells. The pathway of tryptophan synthesis is perhaps the most thoroughly studied of any biosynthetic sequence, particularly in terms of its genetic organization and expression.

Never, in any simulated Origin of Life experiment, the amino acid Tryptophan was synthesized. Why? The biosynthesis pathway to make tryptophan is the most biochemically expensive and most complicated process of all life essential amino acid pathways, and tightly regulated. Glucose feeds the Glycolysis pathway, which utilizes nine enzymatic steps and enzymes to produce a subproduct, which enters the Shikimake pathway, which uses another seven enzymes, to make chorismate, which enters the Tryptophan biosynthesis pathway, and after another five steps and enzymes, finally produces Tryptophan. So, in total, 21 enzymes.

Some enzymes in the pathway are highly sophisticated, veritable multienzyme nanomachines, like a paper called the bacterial tryptophan synthase, which channels the substrates through a long interconnecting tunnel with a clear logic: the substrate is not lost from the enzyme complex and diluted in the surrounding milieu. This phenomenon of direct transfer of enzyme-bound metabolic intermediates, or tunnelling, increases the efficiency of the overall pathway by preventing loss and dilution of the intermediate. Smart, hah ??!!

You can have a closer look at the entire pathway to make tryptophan here:
https://reasonandscience.catsboard.com/t1740-origin-of-the-canonical-twenty-amino-acids-required-for-life#5939

Now let me tell you why this is so relevant. Tryptophan is the substrate, used to make one of the most important electron carriers used in life: NAD:

Nicotinamide adenine dinucleotide (NAD) in origin of life scenarios
https://reasonandscience.catsboard.com/t2708-nicotinamide-adenine-dinucleotide-nad-in-origin-of-life-scenarios#6060

NAD is pivotal for cell life, first as a reusable redox coenzyme for energy production, second as a consumable substrate in enzymatic reactions regulating crucial biological processes, including gene expression, DNA repair, cell death and lifespan, calcium signaling, glucose homeostasis, and circadian rhythms.  (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components. It is also the driving force of most biosynthetic enzymatic reactions, including those responsible for the biosynthesis of all major cell components, such as DNA and lipids. The consumption of NADP+ is connected to the consumption of NAD+ and to the regulation of various major biological activities such as DNA repair, gene expression, apoptosis, nitrogen fixation, and calcium homeostasis.  (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components.

Free-living bacteria synthesize tryptophan (Trp), which is an essential amino acid for mammals, some plants, and lower eukaryotes. The Trp synthesis pathway appears to be highly conserved, and the enzymes needed to synthesize tryptophan are widely distributed across the three domains of life. This pathway is one of three that compose aromatic amino acids from chorismate. As another point of distinction, the Trp pathway is the most biochemically expensive of the amino acid pathways, and for this reason, it is expected to be tightly regulated.

Tryptophan (Trp) biosynthesis is a biologically expensive, complicated process. In fact, the products of four other pathways are essential contributors to carbon or nitrogen during tryptophan formation. Thus, the principal pathway precursor, chorismate, is also the precursor of the other aromatic amino acids, phenylalanine and tyrosine, as well as serving as the precursor of aminobenzoic acid and several other metabolites.

Chorismate biosynthesis occurs via the shikimate pathway:

1. DAHP synthase
2. 3-dehydroquinate synthase
3. 5-Dehydroquinate Synthetase
4. Shikimate dehydrogenase
5. Shikimate kinase
6. 3-enolpyruvylshikimate-5-phosphate synthase
7. Chorismate synthase

The Aromatic Amino Acids Are Synthesized from Chorismate
Indeed, chorismate is common to the synthesis of cellular compounds having benzene rings, including these amino acids, the fat-soluble vitamins E and K, folic acid, and coenzyme Q and plastoquinone (the two quinones necessary to electron transport during respiration and photosynthesis, respectively). Lignin, a polymer of nine-carbon aromatic units, is also a derivative of chorismate. Lignin and related compounds can account for as much as 35% of the dry weight of higher plants; clearly, enormous amounts of carbon pass through the chorismate biosynthetic pathway.

Enzymes and reactions in the Tryptophan biosynthesis pathway:
Tryptophan is synthesized in five steps from chorismate. Each step requires a specific enzyme activity. The four intermediates between chorismate and tryptophan serve no function other than as precursors of tryptophan.

That means, these enzymes have no other purpose, and could not have been co-opted from other synthesis pathways. Their exclusive and necessity in intermediate stages make them irreducible, and the pathway as a whole is irreducibly complex.

6. Anthranilate synthase
7. Anthranilate phosphoribosyltransferase
8. Phosphoribosylanthranilate isomerase
9. Indole-3-glycerol-phosphate synthase
10 + 11. Tryptophan synthase

Origin of Tryptophan biosynthesis and abiotic scenarios
Aromatic amino acid biosynthesis proceeds via a long series of reactions, most of them concerned with the formation of the aromatic ring before branching into the specific routes to phenylalanine, tyrosine, and tryptophan. Chorismate, the common intermediate of the three aromatic amino acids, is derived in eight steps from erythrose-4-phosphate and phosphoenolpyruvate.

How Structure Arose in the Primordial Soup
Tryptophan, in comparison, has a complex structure and is comparatively rare in the protein code, like a Y or Z, leading scientists to theorize that it was one of the latest additions to the code. 6

How Structure Arose in the Primordial Soup
May 19, 2015
In research published online in March in the Journal of Molecular Evolution, Fournier showed that the last chemical letter added to the code was a molecule called tryptophan 2

Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code.1
2015 Mar 20
The genetic code was likely complete in its current form by the time of the last universal common ancestor (LUCA). Several scenarios have been proposed for explaining the code’s pre-LUCA emergence and expansion, and the relative order of the appearance of amino acids used in translation. One co-evolutionary model of genetic code expansion proposes that at least some amino acids were added to the code by the ancient divergence of aminoacyl-tRNA synthetase (aaRS) families.

It is important to remark that secular science puts the origin and appearance of amino acids prior to LUCA. That said, it's clear that any allusion to evolution is prohibited by the fact that there was no evolution prior to DNA replication.

1. https://www.ncbi.nlm.nih.gov/pubmed/25791872
2. https://www.scientificamerican.com/article/how-structure-arose-in-the-primordial-soup/
3. http://2009.igem.org/wiki/images/a/a7/The_tryptophan_biosynthetic_pathway.pdf
4. http://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/18486479
5. Origins of Life on the Earth and in the Cosmos SECOND EDITION, page 117
6. https://www.scientificamerican.com/article/how-structure-arose-in-the-primordial-soup/
7. https://www.nature.com/scitable/topicpage/an-evolutionary-perspective-on-amino-acids-14568445
8. https://en.wikipedia.org/wiki/Tryptophan

Otangelo · 29 Tryptophan Thu 6 Feb 2020 - 19:47

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Tryptophan

Enzymes and reactions in the Tryptophan biosynthesis pathway:

Tryptophan is synthesized in five steps from chorismate. Each step requires a specific enzyme activity. The four intermediates between chorismate and tryptophan serve no function other than as precursors of tryptophan. these enzymes have no other purpose, and could not have been co-opted from other synthesis pathways. Their exclusive and necessity in intermediate stages make them irreducible, and the pathway as a whole is irreducibly complex.Enzymes and reactions in the Tryptophan biosynthesis pathway:

1. DAHP synthase
2. 3-dehydroquinate synthase
3. 5-Dehydroquinate Synthetase
4. Shikimate dehydrogenase
5. Shikimate kinase
6. 3-enolpyruvylshikimate-5-phosphate synthase
7. Chorismate synthase8. Anthranilate synthase
9. Anthranilate phosphoribosyltransferase
10. Phosphoribosylanthranilate isomerase
11. Indole-3-glycerol-phosphate synthase
12 + 11. Tryptophan synthase

The bacterial tryptophan synthases are multienzyme nanomachines that catalyze the last two steps in L-tryptophan biosynthesis. 4

Aromatic amino acid biosynthesis proceeds via a long series of reactions, most of them concerned with the formation of the aromatic ring before branching into the specific routes to phenylalanine, tyrosine, and tryptophan. Chorismate, the common intermediate of the three aromatic amino acids, is derived in eight steps from erythrose-4-phosphate and phosphoenolpyruvate.

It is important to remark that secular science puts the origin and appearance of amino acids prior to LUCA. That said, it's clear that any allusion to evolution is prohibited by the fact that there was no evolution prior to DNA replication.

1. https://www.ncbi.nlm.nih.gov/pubmed/25791872
2. https://www.scientificamerican.com/article/how-structure-arose-in-the-primordial-soup/
3. http://2009.igem.org/wiki/images/a/a7/The_tryptophan_biosynthetic_pathway.pdf
4. http://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/18486479
5. Origins of Life on the Earth and in the Cosmos SECOND EDITION, page 117
6. https://www.scientificamerican.com/article/how-structure-arose-in-the-primordial-soup/
7. https://www.nature.com/scitable/topicpage/an-evolutionary-perspective-on-amino-acids-14568445
8. https://en.wikipedia.org/wiki/Tryptophan

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Scientists find biology's optimal 'molecular alphabet' may be preordained

https://phys.org/news/2019-09-scientists-biology-optimal-molecular-alphabet.html?fbclid=IwAR18uckj_nrJ1p6B8Gi7n3QRW-WoAnEi3RH57SrOXxoj6yvjx5CkofkWqAY

There are millions of possible types of amino acids that could be found on Earth or elsewhere in the universe, each with its own distinctive chemical properties. Indeed, scientists have found these unique chemical properties are what give biological proteins, the large molecules that do much of life's catalysis, their own unique capabilities. The team had previously measured how the CAA set compares to random sets of amino acids and found that only about 1 in a billion random sets had chemical properties as unusually distributed as those of the CAAs.

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Dimas A. M. Zaia A Few Experimental Suggestions Using Minerals to Obtain Peptides with a High Concentration of L-Amino Acids and Protein Amino Acids 10 December 2020

The peptides/proteins of all living beings on our planet are mostly made up of 19 L-amino acids and glycine, an achiral amino acid. Arising from endogenous and exogenous sources, the seas of the prebiotic Earth could have contained a huge diversity of biomolecules (including amino acids), and precursors of biomolecules.

My comment: Agreed. There is NO REASON or function whatsoever that molecules could have benefitted from, by performing a selection of amino acids used in life.

Thus, how were these amino acids selected from the huge number of available amino acids and other molecules? What were the peptides of prebiotic Earth made up of? How were these peptides synthesized? Minerals have been considered for this task, since they can preconcentrate amino acids from dilute solutions, catalyze their polymerization, and even make the chiral selection of them.

My comment: How could mineral select the chiral form of amino acids? I have never seen a science paper solving that issue.

However, until now, this problem has only been studied in compartmentalized experiments. There are separate experiments showing that minerals preconcentrate amino acids by adsorption or catalyze their polymerization

My comment: The polymerization would/could have occurred by binding one amino acid to another at any of the possible binding sites, like on the side chain.

or separate L-amino acids from D-amino acids. Based on the [GADV]-protein world hypothesis, as well as the relative abundance of amino acids on prebiotic Earth obtained by Zaia, several experiments are suggested. The main goal of these experiments is to show that using minerals it is possible, at least, to obtain peptides whose composition includes a high quantity of L-amino acids and protein amino acids (PAAs). These experiments should be performed using hydrothermal environments and wet/dry cycles. In addition, for hydrothermal environment experiments, it is very important to use one of the suggested artificial seawaters, and for wet/dry environments, it is important to perform the experiments in distilled water and diluted salt solutions.

My comment: The only problem is that distilled water was not the medium in the prebiotic earth....

Finally, from these experiments, we suggest that, without an RNA world or even a pre genetic world, a small peptide set could emerge that better resembles modern proteins.

https://www.mdpi.com/2073-8994/12/12/2046

Otangelo · Jan 13, 2014

The 20 standard amino acids - as general reasons for choosing side chains, we can now consider the 20 individually.

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Is the prebiotic origin of amino acids by natural means plausible?

https://reasonandscience.catsboard.com/t1740p25-amino-acids-origin-of-the-canonical-twenty-amino-acids-required-for-life#9379

Chemical evolution of amino acids and proteins ? Impossible !!
https://www.youtube.com/watch?v=1L1MfGrtk0A

Chemical evolution of amino acids and proteins ? Impossible !!
https://reasonandscience.catsboard.com/t2887-chemical-evolution-of-amino-acids-and-proteins-impossible

Amino acids are monomers. (A monomer is a molecule that can react together with other monomer molecules to form a larger polymer chain or three-dimensional network 49) They are one of the principal components that make up proteins. 22 amino acids encode proteins. 20 in the standard genetic code and another 2 (selenocysteine, which is an essential amino acid component in selenoproteins, which are involved in a variety of cellular and metabolic processes 43 and pyrrolysine are restricted to a very small number of organisms and proteins. 42 )

Scitable gives us a short description of AAs:
Chemically, an amino acid is a molecule that has a carboxylic acid group 38 (COOH) and an amino group 39 (NH2) that are each attached/bonded to a central carbon atom, also called the α carbon. Each of the 20 amino acids has a specific side chain, known as an R group, that is also attached to the α carbon. 40 and a hydrogen atom. The R groups, 41 the variable group or the side-chain, have a variety of shapes, sizes, charges, and reactivities. This allows amino acids to be grouped according to the chemical properties of their side chains. For example, some amino acids have polar side chains that are soluble in water; examples include serine, threonine, and asparagine. Other amino acids avoid water and are called hydrophobic, such as isoleucine, phenylalanine, and valine. The amino acid cysteine has a chemically reactive side chain that can form bonds with another cysteine. 23

Amino Acids: Origin of the canonical twenty amino acids required for life - Page 2 Aminoa10

A single amino acid – the subunit monomer of polypeptides and proteins.
NH2 is the amine group and the blue -COOH is the carboxylic acid group. The green R is a side-chain that is different for each of the 20 or so amino acids found in proteins.Attribution: Marc T. Facciotti (own work)

Alpha-amino acids are monomer units that are bonded ( polymerized ) and linked to polymer strands via a head-to-tail linkage that can fold ( depending on the sequence ) into complex functional 3D shapes. Once folded, often as a joint venture with other polymer strands, they form secondary, tertiary, and quaternary structures and catalytic pockets where in many cases complex metal clusters perform the catalytic reaction where the manufacturing of a compound takes place.

Origin of the proteinogenic ( protein creating ) amino acids used in life
There are many hypotheses about how the amino acids used in life could have originated. They are divided into terrestrial, and extraterrestrial origin. Terrestrial proposals are Spark discharge, Irradiation (UV, X-ray, etc.), Shock heating, and hydrothermal vents. Extraterrestrial amino acids have been observed in various types of carbonaceous chondrites, comets, and micrometeorites. Norio Kitadai and colleagues gave a good overview in their scientific paper: Origins of building blocks of life: A review from 2017 54 As we will see, none of them withstand scrutiny. Wherever one looks, there are problems.

Extraterrestrial origins
Norio Kitadai et al. 2017:

To date, over 80 kinds of amino acids have been identified in carbonaceous chondrites, including 12 protein-amino acids of Ala, Asp, Glu, Gly, Ile, Leu, Phe, Pro, Ser, Thr, Tyr, and Val.

Amongst the problems is that these amino acids come always in mixtures with non-proteinogenic aa's, and they are all chirally mixed ( L and R-handed chiral form)

Panspermia
One hypothesis is that amino acids amongst other biofriendly molecules were made in space, and delivered to our planet by meteorites, comets, interplanetary dust particles, etc. It is called panspermia ( seeds everywhere in the universe ). There are good reasons to reject the idea. Nir Goldman and colleagues published an article in Nature magazine on the subject in 2010. They wrote:

Delivery of prebiotic compounds to early Earth from an impacting comet is thought to be an unlikely mechanism for the origins of life because of unfavorable chemical conditions on the planet and the high heat from impact. 5

Hugh Ross pointed out what seems to be one of the main problems:
What happens to comets and their supply of these molecules when they pass through Earth’s atmosphere and when they strike the planetary surface presents a big problem. Calculations and measurements show that both events generate so much heat (atmosphere passage generates 500°+ Centigrade while the collision generates 1,000°+ Centigrade) that they break down the molecules into components useless for forming the building blocks of life molecules. In 1974, comet 81P Wild passed within 500,000 miles of Jupiter, which caused the comet to be perturbed into orbiting within the inner solar system. This new orbit enabled NASA to send the Stardust Spacecraft to the comet in 2004 to recover samples, which were returned to Earth and analyzed for organic molecules. The only amino acid indisputably detected in the sample was glycine at an abundance level of just 20 trillionths of a mol per cubic centimeter. 7

Amino acids found in meteorites are racemic, that is, they come in right-handed, and left-handed helicity. Life uses 100% left-handed AAs. [url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919777/#:~:text=Analyses of pieces of the,alanine%2C suggesting minimal terrestrial biological]10[/url]

Recently a new discovery made the rounds. Yasuhiro Oba and colleagues reported in Nature Communications:
the detection of nucleobases in three carbonaceous meteorites using state-of-the-art analytical techniques optimized for small-scale quantification of nucleobases down to the range of parts per trillion (ppt). 8

Liz Kruesi reported in an article in science news about the finding:
Space rocks that fell to Earth within the last century contain the five bases that store information in DNA and RNA. These “nucleobases” — adenine, guanine, cytosine, thymine and uracil — combine with sugars and phosphates to make up the genetic code of all life on Earth. The discovery adds to evidence that suggests life’s precursors originally came from space, the researchers say. Scientists have detected bits of adenine, guanine and other organic compounds in meteorites since the 1960s Researchers have also seen hints of uracil, but cytosine and thymine remained elusive, until now. “We’ve completed the set of all the bases found in DNA and RNA and life on Earth, and they’re present in meteorites,” says astrochemist Daniel Glavin of NASA’s Goddard Space Flight Center in Greenbelt, Md. 9

but here comes the cold shower from the same article:

In the new analysis, the researchers measured more than a dozen other life-related compounds, including isomers of the nucleobases.

That means the anthropogenic nucleobases are mixed with other isomeric molecules, not used in living cells. That raises the question, of how those used in life could have been joined, concentrated, selected and sorted out from those not used in life.

And PIERAZZO and colleagues wrote in the paper: Amino acid survival in large cometary impacts:
It is clear that there are substantial uncertainties in estimates for both exogenous and endogenous sources of organics, as well as the dominant sinks. All of the likely mechanisms described here lead to extremely low global concentrations of amino acids, emphasizing the need for substantial concentration mechanisms4r for altogether different approaches to the problem of prebiotic chemical synthesis. 6

This is what Stanley Miller had to say in an interview that was conducted in October, 1996
The amount of useful compounds you are going to get from meteorites is very small. The dust and comets may provide a little more. Comets contain a lot of hydrogen cyanide, a compound central to prebiotic synthesis of amino acids as well as purines. Some HCN came into the atmosphere from comets. Whether it survived impact, and how much, are open to discussion. I'm skeptical that you are going to get more than a few percent of organic compounds from comets and dust. It ultimately doesn't make much difference where it comes from. I happen to think prebiotic synthesis happened on the Earth, but I admit I could be wrong. There is another part of the story. In 1969 a carbonaceous meteorite fell in Murchison Australia. It turned out the meteorite had high concentrations of amino acids, about 100 ppm, and they were the same kind of amino acids you get in prebiotic experiments like mine. This discovery made it plausible that similar processes could have happened on primitive Earth, on an asteroid, or for that matter, anywhere else the proper conditions exist. 20

What about the synthesis of amino acids in hydrothermal vents?
Hugh Ross and Fazale Rana explain:
Laboratory experiments simulating a hot, chemically harsh environment modeled after deepsea hydrothermal vents indicate that amino acids, peptides, and other biomoleculars can form under such conditions. However, a team led by Stanley Miller has found that at 660 °F (350 °C), a temperature that the vents can and do reach, the amino acid half-life in a water environment is only a few minutes. (In other words, half the amino acids break down in just a few minutes.) At 480 °F (250 °C) the half-life of sugars measures in seconds. For a nucleobase to function as a building block for DNA or RNA it must be joined to a sugar. For polypeptides (chains of amino acids linked together by peptide bonds but with much lower molecular weight than proteins) the half-life is anywhere from a few minutes to a few hours. 21

Punam Dalai and colleagues inform:
The thermal and chemical gradients at hydrothermal vents on the Earth’s surface may have played an important role in thermodynamically favorable reactions for organic synthesis. These reactions may have been catalyzed by transition metal–sulfide minerals such as pyrite. However, destructive free radicals are also generated photo catalytically at the surface of these sulfides and at the surfaces of the ultramafic minerals that constitute peridotite and komatiite. 58

The Miller-Urey experiment
Miller and Urey performed the legendary in vitro spark-discharge experiments in 1953, attempting to produce amino acids under primitive earth conditions. 13 With that experiment, only a few weeks distant from Watson and Crick discovering the DNA structure, the modern era in the study of the Origin of life began. The hope was that this experiment would pave the road to finding naturalistic answers to life's origins. It has widely been heralded as evidence for the origin of the set of amino acids used in life, and based on it, many claim even today that abiogenesis did become a plausible explanation for the origin of life. After 50 years, in 2003 Jeffrey L. Bada and Antonio Lazcano commemorated the Miller-Urey experiment in an article published in Science magazine. They wrote:

But is the “prebiotic soup” theory a reasonable explanation for the emergence of life? Contemporary geoscientists tend to doubt that the primitive atmosphere had the highly reducing composition used by Miller in 1953. 14

Miller himself pointed out that:
There is no agreement on the composition of the primitive atmosphere; opinions vary from strongly reducing (CH4 + N2, NH3 + H2O, or CO2 + H2 + N2) to neutral (CO2 + N2 + H2O) 53

We don't know what the conditions were, so every laboratory experiment is flawed from the get-go. Nobody knows the influencing conditions, like geological, temperature, electromagnetic radiation, etc. contributing to the Physico-chemical complexity of the earth influencing biochemical processes. There are several other fatal flaws. There is always a team of researchers, that tweak and fine-tune the experiment towards the desired outcome. On prebiotic earth, there was no such thing.

Consider what the researchers had to do to set up the experiment: Jeffrey L. Bada and colleagues explained:
Numerous steps in the protocol described here are critical for conducting Miller-Urey type experiments safely and correctly. First, all glassware and sample handling tools that will come in contact with the reaction flask or sample need to be sterilized. Sterilization is achieved by thoroughly rinsing the items in question with ultrapure water and then wrapping them in aluminum foil, prior to pyrolyzing at 500 °C in air for at least 3 hr. Once the equipment has been pyrolyzed and while preparing samples for analysis, care must be taken to avoid organic contamination. The risk of contamination can be minimized by wearing nitrile gloves, a laboratory coat, and protective eyewear. Be sure to work with samples away from one's body as common sources of contamination include fingerprints, skin, hair, and exhaled breath. Avoid contact with wet gloves and do not use any latex or Nylon materials. 19
This is just the first step. Bada continues: There are many additional notes worth keeping in mind when carrying out various steps in the protocol outlined here.

You know where this goes. This has nothing to do with what happened on early earth. There were no test drives multiple times, trial and error to get to optimal conditions. Get a bit of atmospheric pressure here, change the gas composition a bit there. Change the electromagnetic radiation or the temperature variations. There are basically innumerable possibilities of different atmospheric conditions, and having the just-right atmosphere depends on many different factors. One can resort to the number of possible earth-like candidates in the universe and claim, that one by chance could have the right conditions. While nobody knows the odds, some scientific papers have calculated numbers that are far from what could be considered a reasonably probable chance 12 In 2008, after Miller's death, Adam P. Johnson and colleagues reexamined the boxes containing the dried residues from the apparatus from the second ( the volcanic experiment ) in 1953. 15 Miller identified five different amino acids, plus several unknowns in the extracts from this apparatus. Johnson et al. however, identified 22 amino acids and five amines. Several were not identified previously in Miller’s experiments. In 2011, the same researchers extended their analysis of Miller’s old flacons to include those from a spark-discharge experiment made in 1958. They reported:

The samples contained a large assortment of amino acids and amines, including numerous sulfur amino acids. This mixture might have been prominent on a regional scale (for example, near volcanoes), where these gases may have played a vital role in the localized synthesis of some of the first terrestrial organic compounds. 16

A survey from the U.S.Government informed that:
Ninety-nine percent of the gas molecules emitted during a volcanic eruption are water vapor (H2O), carbon dioxide (CO2), and sulfur dioxide (SO2). The remaining one percent is comprised of small amounts of hydrogen sulfide, carbon monoxide, hydrogen chloride, hydrogen fluoride, and other minor gas species. [url=https://www.usgs.gov/faqs/what-gases-are-emitted-kilauea-and-other-active-volcanoes#:~:text=Ninety%2Dnine percent of the,and other minor gas species.]17[/url]

This composition is not conducive to producing amino acids on early earth. Unless the emissions were different, supposedly 3,9 Gya ago. Were they?

The gases released into the atmosphere by high-temperature volcanic eruptions have been dominated by H2O, CO2, and SO2 since at least 3600 Ma, and probably since at least ∼3900 Ma. Mantle-derived volcanic gases that entered the atmosphere from high-temperature volcanism would have provided low, but not zero, yields of prebiotic molecules during that interval. 18

Carol Turse informed in a science paper from 2013 that:
Variations of Miller’s experiments, some completed by Miller himself, have been completed that include aspects of hydrothermal vents, neutral atmospheres, reducing H2S atmospheres, as well as volcanic conditions In each of these variations amino acids or organic precursors of amino acids are produced at some level. 51

but the following proteinogenic amino acids were never produced in any of the experiments: Cysteine, Histidine, Lysine, Asparagine, Pyrrolysine, Proline, Glutamine, Arginine, Threonine, Selenocysteine, Tryptophan, Tyrosine 52

Homochirality
The DNA and RNA ribose backbone has to be in right-handed chiral form. (Chirality is from Greek and means handedness). Amino acids, left-handed. Phospholipids, right-handed. That is essential for life, and its origin in biological systems demands an explanation. In nature, carbon compounds come in mixed chiral forms. In the cell, the complex protein machinery fabrics the materials in the right enantiomeric form, as life requires. Change Laura Tan and Rob Stadler bring it succinctly to the point. They write in: The Stairway To Life:

In all living systems, homochirality is produced and maintained by enzymes, which are themselves composed of homochiral amino acids that were specified through homochiral DNA and produced via homochiral messenger RNA, homochiral ribosomal RNA, and homochiral transfer RNA. No one has ever found a plausible abiotic explanation for how life could have become exclusively homochiral.

In order for proteins to fold into functional 3D structures, the building blocks that make them, amino acids, must be chiral. As Wikibooks explains:
A tetrahedral carbon atom with four distinct groups is called asymetric, or chiral. The ability of a molecule to rotate plane-polarized light to the left, L (levorotary) or right, D (dextrorotary) gives it its optical and stereochemical fingerprint. 50

Biologically synthesized amino acids, for instance, occur exclusively in their lefthanded (levorotatory L) form, while the sugar backbone of nucleic acids, ribose, are all right-handed (dextrorotatory D), and phospholipid glycerol headgroups of archaea and bacteria exclusively homochiral. (Bacteria and eukarya have membranes comprised of phospholipids with backbones of left-handed configurational stereochemistry, whereas archaea contain backbones of right-handed stereochemistry). Amino acids are not the same as their mirror image, analogously a left shoe will not fit properly on one's right foot no matter how someone rotates it.

Daniel P. Glavin and colleagues elucidated in a scientific paper from 2020:
The observed homochirality in all life on Earth, that is, the predominance of “left-handed” or l-amino acids and “right-handed” or d-sugars, is a unique property of life that is crucial for molecular recognition, enzymatic function, information storage, and structure and is thought to be a prerequisite for the origin or early evolution of life. 32

Racemic, mixed proteins are non-functional. If a chemist cooks up a bunch of amino acids or their precursor molecules in a laboratory, the result will always be a racemic mixture of left and right. Proteins made by mixtures of left and right-handed amino acids do not form well-defined tertiary and quaternary protein structures. Ribose must have been in its right-handed form for the first RNA molecules to be useful for functional structures, which cannot occur with random mixtures of right and left-handed nucleotides. Chemical reactions starting from racemic mixtures result always in mixed, nonchiral systems. The chemistry explaining how exclusive left-handed and right-handed molecules could have been formed is one of the biggest open questions, a profound mystery, persisting for over 150 years since Lous Pasteur discovered the right and left-handed chiral form (levorotatory and the dextrorotatory form) in chemistry. Hypotheses on the origin of homochirality in the living world can be classified into two major types: biotic and abiotic. The abiotic appearance of chiral materials hence leads to deeper questions. How can symmetry be originated in a universe that is not governed by physical laws that convey this symmetry? Scientists do not know how the right-handed amino acids and left-handed sugars and either exclusively right-handed or left-handed backbones of phospholipids could have been instantiated prebiotically by accident. Since there was no prebiotic natural selection, the only alternative to conscious choice is an unguided random non-designed coincidence. Homochirality had to arise for amino acids and sugars and phospholipids simultaneously. Life uses its complex molecular machinery to instantiate just the right or lefthanded molecules.

Benjamin List and David MacMillan were awarded the Nobel Prize in Chemistry in 2021. A science news article quoted them:

“Why in the world is biology single-handed? Why do we have this preference in nature? We don’t know,” List said. “This handedness is transferred in the catalytic reaction onto the substrates so that you get more of these handed molecules. It’s a great gift, I would say, that nature provides these molecules for us.”

“Chirality, for me, is the most interesting question in physics and chemistry and maybe even in biology,” Felser says, adding that today’s announcement could be “inspiring for the younger generations to look more for symmetry violations in nature”. 34

Homochirality, its origin a scientifically longstanding unresolved issue
Donna G. Blackmond explains in her paper published in 2010:
There is one general feature of the molecules constituting all known living systems on Earth, and in particular of biopolymers, which needs to be explained within the problem of origins: their homochirality. Most molecules of life are homochiral, that is, they possess the same handedness or chirality. Homochirality of biological molecules is a signature of life. The chirality or sense of handedness of the amino acid molecules is an important problem.
Figure above shows two versions, or enantiomers, of the amino acid alanine. Each contains exactly the same number of elements with the same types of chemical bonds, and yet they are the mirror image of each other. A molecule that is not superimposable on its mirror image is chiral. When a molecule with a definite sense of handedness reacts chemically with one that is symmetric (or otherwise does not have a particular handedness), the left- and right-handed amino acids have similar properties. Likewise, the chemical properties of an interaction between two left-handed molecules or two right-handed molecules are the same. However, neither of these interactions is the same as when left- and right-handed molecules are interacting with each other. Hence, the handedness of biological molecules such as amino acids or nucleotides plays a role in their functionality.

“Symmetry breaking” is the term used to describe the occurrence of an imbalance between left and right enantiomeric molecules. This imbalance is traditionally measured in terms of the enantiomeric excess, or ee, where ee are concentrations of the right and left-hand molecules, respectively. Proposals for how an imbalance might have come about may be classified as either terrestrial or extraterrestrial, and then subdivided into either random or deterministic (sometimes called “de facto” and “de lege” respectively). A trivial example is that any collection of an odd number of enantiomeric molecules has, by definition, broken symmetry. Fluctuations in the physical and chemical environment could result in transient fluctuations in the relative numbers of left- and right-handed molecules. However, any small imbalance created in this way should average out as the racemic state unless some process intervenes to sustain and amplify it. Thus, whether or not the imbalance in enantiomers came about by chance, arising on earth or elsewhere, an amplification mechanism remains the key to increasing enantiomeric excess and ultimately to approaching the homochiral state. 22

Amino Acids: Origin of the canonical twenty amino acids required for life - Page 2 6FjIcEc

Amino Acids: Origin of the canonical twenty amino acids required for life - Page 2 6FjIcEc

The two mirror-image enantiomers of the amino acid alanine

A. G. CAIRNS-SMITH exposes the problem in his book: Seven clues to the origin of life, on page 40:
A particularly clear case is in the universal choice of only 'left-handed' amino acids for making proteins, when, as far as one can see, 'right-handed' ones would have been just as good. Let me clarify this.
Molecules that are at all complex are usually not superposable on their mirror images. There is nothing particularly strange about this: it is true of most objects. Your right hand, for example, is a left hand in the mirror. It is only rather symmetrical objects that do not have 'right-handed' and 'left-handed' versions. When two or more objects have to be fitted together in some way their 'handedness' begins to matter. If it is a left hand it must go with a left glove. If a nut has a right-hand screw, then so must its bolt. In the same sort of way the socket on an enzyme will generally be fussy about the 'handedness' of a molecule that is to fit it. If the socket is 'left-handed' then only the 'left-handed' molecule will do. So there has to be this kind of discrimination in biochemistry, as in human engineering, when 'right-handed' and 'left-handed' objects are being dealt with. And it is perhaps not surprising that the amino acids for proteins should have a uniform 'handedness'. There could be a good reason for that, as there is good reason to stick to only one 'handedness' for nuts and bolts. But whether, in such cases, to choose left or right, that is pure convention. It could be decided by the toss of a coin. 24

A. G. CAIRNS-SMITH genetic takeover, page53
It is commonly believed that proteins of a sort or nucleic acids of a sort (or both) would have been necessary for the making of those first systems that could evolve under natural selection and so take off from the launching platform provided by prevital chemical processes. We have already come to a major difficulty here: Much of the point of protein and the whole point of nucleic acid would seem to be lost unless these molecules have appropriate secondary/tertiary structures, and that is only possible with chirally defined units. As we saw, the ‘abiotic‘ way of circumventing this problem (by prevital resolution of enantiomers) seems hopelessly inadequate, and ‘biotic’ mechanisms depend on efficient machinery already in action. 25

Sean Henahan interviewed Dr. Stanley L. Miller in 1998. To the question: What about the even balance of L and D (left and right oriented) amino acids seen in your experiment, unlike the preponderance of L seen in nature? How have you dealt with that question?, Miller answered:

All of these pre-biotic experiments yield a racemic mixture, that is, equal amounts of D and L forms of the compounds. Indeed, if you're results are not racemic, you immediately suspect contamination. The question is how did one form get selected. In my opinion, the selection comes close to or slightly after the origin of life. There is no way in my opinion that you are going to sort out the D and L amino acids in separate pools. My opinion or working hypothesis is that the first replicated molecule had effectively no asymmetric carbon. 30

Some claim that the problem of the origin of chiral molecules has been solved (May 2022), but as far as the scientific literature illucidates, that is not the case. Following are a few quotes:
Homochirality is a common feature of amino acids and carbohydrates, and its origin is still unknown. (September 24, 2020) 26
The origin of homochirality in L-amino acid in proteins is one of the mysteries of the evolution of life. (30 November 2018) 27
How L-chiral proteins emerged from demi-chiral mixtures is unknown.The lack of understanding of the origins of the breaking of demi-chirality found in the molecules of life on Earth is a long-standing problem (December 26, 2019) 28
How homochirality concerning biopolymers (DNA/RNA/proteins) could have originally occurred (i.e., arisen from a non-life chemical world, which tended to be chirality-symmetric) is a long-standing scientific puzzle.
(January 8, 2020) 29

Why only left-handed, and not right-handed amino acids?
Apparently, there is no deeper functional reason or justification that makes it necessary that they are left, rather than right-handed, which are no less stable and no more reactive 45. All they need is to be pure, that is, not mixed with left-handed ones.

Viviane Richter wrote an article for cosmosmagazine in 2015:

It didn’t have to be that way. When life first emerged, why did it choose left and not right? Steve Benner believes biology picked left by chance. 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!” 44

From prebiotic to biotic chirality determination
The formation of the left-handedness of amino acids is performed in cells by a group of enzymes called aminotransferase through a transaminase reaction. The transamination reaction involves the transfer of an amino group for example by one of these enzymes, Aspartate Transaminase AST 37 from a donor, like an aspartate amino acid, to the carbon atom of an alpha-keto acid 35, the acceptor, so that once the alpha-keto acid ring receives that amino group it will be converted into a glutamate amino acid ( the product). An example of an alpha-keto acid is an alpha-ketoglutarate ( Alpha-ketoglutarate (AKG) is a key molecule in the Krebs cycle [ or tricarboxylic acid TCA ] cycle determining the overall rate of the citric acid cycle of the organism. 36) By losing the amino group, the aspartate amino acid is transformed into oxaloacetate. And by receiving an amino group, alpha-ketoglutarate is being transformed into glutamate. In order to perform this reaction, AST requires pyridoxal 5′ phosphate (P5P) as an essential cofactor for maximum enzyme activity. P5P is the active metabolite of vitamin B6, therefore it is a reduced vitamin B6 ( it is used in hundreds of enzymes ) P5P serves as a molecular shuttle for ammonia and electrons between the amino donor and the amino acceptor. 18 different proteinogenic amino acids can be used as the starting point of the reaction. The reaction can be an anabolic reaction to make amino acids or catabolic to make waste products, like nitrogenous waste urea, and released from the body as a toxic product. Aspartate aminotransferase (AST) has high specificity to operate with alpha-ketoglutarate.

This is a complex process. The literature on ASTs spans approximately 60 years, and much fundamental mechanistic information on PLP-dependent reactions has been gained from its study. 47 but even in 2019 it was still not fully understood despite being "one of the most studied enzymes of this category" 46

Aspartate Aminotransferase
Since left-handedness is life-essential, AST is a key metabolic enzyme, and its origin has to be ancient and be part of the minimal proteome and enzymatic setup of the first life forms. It is found in bacterial to eukaryotic species.

The authors, Mei Han, and colleagues, reported in a scientific paper from 2021:
Aspartate Aminotransferase is present in all of the free-living organisms AST is a much-conserved enzyme found in both prokaryotes and eukaryotes and is closely linked to purine’s biosynthesis salvage pathway as well as the glycolytic and oxidative phosphorylation pathways. 48

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1. Craig Venter: Life: What A Concept! 2008
2. A. G. Cairns-Smith: Genetic Takeover: And the Mineral Origins of Life
3. Robert M. Hazen: Fundamentals of Geobiology 2012
4. Fred Hoyle: The Intelligent Universe   1983
5. Nir Goldman: Synthesis of glycine-containing complexes in impacts of comets on early Earth 12 September 2010
6. PIERAZZO  Amino acid survival in large cometary impacts 1999
7. Hugh Ross: Could Impacts Jump-Start the Origin of Life? November 8, 2010
8.Yasuhiro Oba: Identifying the wide diversity of extraterrestrial purine and pyrimidine nucleobases in carbonaceous meteorites 26 April 2022
9. About Liz Kruesi: All of the bases in DNA and RNA have now been found in meteorites
10. Jamie E. Elsila: Meteoritic Amino Acids: Diversity in Compositions Reflects Parent Body Histories 2016 Jun 22
11. E A Martell: Radionuclide-induced evolution of DNA and the origin of life
12. Brian C. Lacki: THE LOG LOG PRIOR FOR THE FREQUENCY OF EXTRATERRESTRIAL INTELLIGENCES September 21, 2016
13. Stanley L. Miller A Production of Amino Acids Under Possible Primitive Earth Conditions May 15, 1953
14. JEFFREY L. BADA: Prebiotic Soup--Revisiting the Miller Experiment
15. ADAM P. JOHNSON: The Miller Volcanic Spark Discharge Experiment 17 Oct 2008
16. Eric T. Parker: Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment March 21, 2011
17. [url=https://www.usgs.gov/faqs/what-gases-are-emitted-kilauea-and-other-active-volcanoes#:~:text=Ninety%2Dnine percent of the,and other minor gas species.]What gases are emitted by Kīlauea and other active volcanoes? [/url]
18. J W Delano: Redox history of the Earth's interior since approximately 3900 Ma: implications for prebiotic molecules Aug-Oct 2001
19. Eric T. Parker: Conducting Miller-Urey Experiments 2014 Jan 21
20. Dr. Stanley L. Miller: From Primordial Soup to the Prebiotic Beach An interview with exobiology pioneer
21. Hugh Ross, Fazale Rana, Origins of Life, page 73
22. Donna G. Blackmond: The Origin of Biological Homochirality 2010 May; 2
23. https://www.nature.com/scitable/definition/amino-acid-115/
24. A. G. CAIRNS-SMITH Seven clues to the origin of life, page 58
25. A. G. CAIRNS-SMITH genetic takeover 1988
26. Shubin Liu: Homochirality Originates from the Handedness of Helices September 24, 2020
27. Tadashi Ando: Principles of chemical geometry underlying chiral selectivity in RNA minihelix aminoacylation 30 November 2018
28. Jeffrey Skolnick: On the possible origin of protein homochirality, structure, and biochemical function December 26, 2019
29. Yong Chen: The origin of biological homochirality along with the origin of life January 8, 2020
30. From Primordial Soup to the Prebiotic Beach An interview with exobiology pioneer, Dr. Stanley L. Miller,
31. Change Laura Tan, Rob Stadler: The Stairway To Life: An Origin-Of-Life Reality Check March 13, 2020
32. Daniel P. Glavin: The Search for Chiral Asymmetry as a Potential Biosignature in our Solar System November 19, 2019
33.
34. Davide Castelvecchi: ‘Elegant’ catalysts that tell left from right scoop chemistry Nobel 06 October 2021
35. About: Keto acid:
36. Nan Wu: Alpha-Ketoglutarate: Physiological Functions and Applications 2016 Jan 24
37. Daniel Nelson: Amino Group: Definition And Examples  2, November 2019
38. What is Carboxylic Acid?
39. Introduction to Amines – Compounds Containing Nitrogen
40. alpha carbon:
41. [url=http://www.chem.ucla.edu/~harding/IGOC/R/r_group.html#:~:text=R group%3A An abbreviation for,halogens%2C oxygen%2C or nitrogen.]R-group: [/url]
42. Guillaume Borrel: Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette
43. Rare, but essential – the amino acid selenocysteine June 19, 2017
44. Viviane Richter [url= Why]https://cosmosmagazine.com/science/biology/why-the-building-blocks-in-our-cells-turned-to-the-left/]Why building blocks in our cells turned left[/url] 10 August 2015
45. https://www.scripps.edu/newsandviews/e_20040920/onpress.html
46. Kumari Soniya: Transimination Reaction at the Active Site of Aspartate Aminotransferase: A Proton Hopping Mechanism through Pyridoxal 5′-Phosphate
47. Michael D. Toney: [url= Aspartate]https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3946379/]Aspartate Aminotransferase: an old dog teaches new tricks [/url]2013 Oct 9.
48. Mei Han: l-Aspartate: An Essential Metabolite for Plant Growth and Stress Acclimation 2021 Apr; 26
49. Amino acids :https://bio.libretexts.org/Courses/University_of_California_Davis/BIS_2A%3A_Introductory_Biology_(Easlon)/Readings/04.3%3A_Amino_Acids
50. https://en.wikibooks.org/wiki/Structural_Biochemistry/Volume_5#Modified_Amino_Acids
51. Carol Turse: Simulations of Prebiotic Chemistry under Post-Impact Conditions on Titan 2013 Dec 17
52. Miller–Urey experiment https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment
53. Stanley L. Miller: [url= Prebiotic]https://global.oup.com/us/companion.websites/fdscontent/uscompanion/us/pdf/Rigoutsos/I-SampleChap.pdf]Prebiotic Chemistry on the Primitive Earth[/url] 2006
54. Norio Kitadai: Origins of building blocks of life: A review 29 July 2017
55. STANLEY L. MILLER AND HAROLD C. UREY: Organic Compound Synthesis on the Primitive Earth: Several questions about the origin of life have been answered, but much remains to be studied 31 Jul 1959
56. Jessica Wimmer and William Martin: Likely energy source behind first life on Earth found ‘hiding in plain sight’ January 19, 2022
57. Leslie E Orgel †: The Implausibility of Metabolic Cycles on the Prebiotic Earth  January 22, 2008
58. Punam Dalai: [url=https://pubs.geoscienceworld.org/msa/eleme

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Soo Yeon Jeong and colleagues described the enzyme in a scientific paper from 2019: L-aspartate aminotransferase (AST) is highly conserved across species and plays essential roles in varied metabolic pathways. It also regulates the cellular level of amino acids by catalyzing amino acid degradation and biosynthesis. AST generally forms a homodimer consisting of two active sites in the vicinity of subunit interfaces; these active sites bind to its cofactor PLP and substrate independently. Each subunit is composed of three parts: large domain, small domain, and N-terminal arm. The active site is situated in the cavity formed by two large domains and one small domain. 17

Proteopedia informs: It is a homodimer that is 413 amino acids long and serves a critical role in amino acid and carbohydrate metabolism 18

This is an enzyme that operates based on high specificity. Soo Yeon Jeong reported in the conclusion remarks even: "We observed the mode of intercommunication during catalytic reactions between two protomers of the dimer." There are several life-essential enzymes, that operate based on intrinsic signaling and communication ( ribosomes, aminoacyl tRNA synthetases) which indicates the high sophistication of these enzymes. pyridoxal 5′ phosphate is furthermore an integral part of the enzymatic reaction, which indicates interdependence. It performs various key functions. Considering this all together, it is remarkable evidence of an intelligently designed setup.

How were the 20 proteinogenic amino acids selected on early earth?
Science is absolutely clueless about how and why specifically this collection of amino acids is incorporated into the genetic code to make proteins. Why 20, and not more or less? ( in some rare cases, 22) considering that many different ones could have been chosen? Stanly Miller wrote in the science paper from 1981: Reasons for the Occurrence of the Twenty Coded Protein Amino Acids:

There are only twenty amino acids that are coded for in protein synthesis, along with about 120 that occur by post-translational modifications. Yet there are over 300 naturally-occurring amino acids known, and thousands of amino acids are possible. The question then is - why were these particular 20 amino acids selected during the process that led to the origin of the most primitive organism and during the early stages of Darwinian evolution. Why Are beta, gamma and theta Amino Acids absent? The selection of a-amino acids for protein synthesis and the exclusion of the beta, gamma, and theta amino acids raises two questions. First, why does protein synthesis use only one type of amino acid and not a mixture of various α, β, γ, δ… acids? Second, why were the a-amino acids selected? The present ribosomal peptidyl transferase has specificity for only a-amino acids. Compounds with a more remote amino group reportedly do not function in the peptidyl transferase reaction. The ribosomal peptidyl transferase has a specificity for L-a-amino acids, which may account for the use of a single optical isomer in protein amino acids. The chemical basis for the selection of a-amino acids can be understood by considering the deleterious properties that beta, theta, and gamma-amino acids give to peptides or have for protein synthesis. 1

Amino Acids: Origin of the canonical twenty amino acids required for life - Page 2 Beta_a10

The question is not only why not more or less were selected and are incorporated in the amino acid "alphabet", but also how they could/would have been selected from a prebiotic soup, ponds, puddles, or even the archaean ocean?
The ribosome core that performs the polymerization, or catenation of amino acids, joining one amino acid monomer to another, the ribosomal peptidyl transferase center, only incorporates alpha-amino acids, as Joongoo Lee and colleagues explain in a scientific article from 2020:

Ribosome-mediated polymerization of backbone-extended monomers into polypeptides is challenging due to their poor compatibility with the translation apparatus, which evolved to use α-L-amino acids. Moreover, mechanisms to acylate (or charge) these monomers to transfer RNAs (tRNAs) to make aminoacyl-tRNA substrates is a bottleneck. The shape, physiochemical, and dynamic properties of the ribosome have been evolved to work with canonical α-amino acids 11

There are no physical requirements that dictate, that the ribosome should/could not be constructed capable to incorporate β, γ, δ… amino acids. Indeed, scientists work on polymer engineering, designing ribosomes that use an expanded amino acid alphabet. A 3D printer uses specifically designed polyester filaments to be fed with, that can process them, and print various objects based on the software information that dictates the product form. If someone tries to use raw materials that are inadequate, the printer will not be able to perform the job it was designed for. The ribosome is a molecular 3D nano printer, as Jan Mrazek and colleagues elucidate in a science paper published in 2014

Structural and functional evidence point to a model of vault assembly whereby the polyribosome acts like a 3D nanoprinter to direct the ordered translation and assembly of the multi-subunit vault homopolymer, a process which we refer to as polyribosome templating. 12 where the reaction center is also specifically adjusted to perform its reaction with the specific set of α-amino acids.

The materials that the machine is fed with, and the machine itself have both to be designed from scratch, in order to function properly. One cannot operate with the adequacy of the other. There is a clear interdependence that indicates that the amino acid alphabet was selected to work with the ribosome as we know it.

From Georga Tech: The preference for the incorporation of the biological amino acids over non-biological counterparts also adds to possible explanations for why life selected for just 20 amino acids when 500 occurred naturally on the Hadean Earth. “Our idea is that life started with the many building blocks that were there and selected a subset of them, but we don’t know how much was selected on the basis of pure chemistry or how many biological processes did the selecting. Looking at this study, it appears today’s biology may reflect these early prebiotic chemical reactions more than we had thought,” said Loren Williams, professor in Georgia Tech’s School of Chemistry and Biochemistry 4

The authors mention 500 supposedly extant on early earth. Maybe they got that number from a scientific article about nonribosomal peptides (NRPs) which coincides with that number of 500. Areski Flissi and colleagues write:

Secondary metabolites (nonribosomal peptides) are produced by bacteria and fungi. In fact, >500 different building blocks, called monomers, are observed in these peptides, such as derivatives of the proteinogenic amino acids, rare amino acids, fatty acids or carbohydrates. In addition, various types of bonds connect their monomers such as disulfide or phenolic bonds. Some monomers can connect with up to five other monomers, making cycles or branches in the structure of the NRPs. 5

Stuart A. Kauffman (2018) gives us an entirely different perspective. He wrote on page 22, in the section Discussion: Using the PubChem dataset and the Murchison meteorite mass spectroscopy data we could reconstruct the time evolution and managed to calculate the time of birth of amino acids, which is about 165 million years after the start of evolution. ( They mean after the Big Bang) a mere blink of an eye in cosmological terms. All this puts the Miller-Urey experiment in a very different perspective. the results suggest that the main ingredients of life, such as amino acids, nucleotides and other key molecules came into existence very early, about 8-9 billion years before life. 6

Why should the number of possible amino acids on early earth be restricted to 500? In fact, as Allison Soult, a chemist from the University of Kentucky wrote: Any ( large ) number of amino acids can possibly be imagined.  7

Steven Benner goes along with the same reasoning (2008): Conceptually, the number of compounds in gas clouds, meteorites, Titan, and laboratory simulations of early Earth is enormous, too many for any but a super-human imagination to start puzzling over. Each of those n compounds (where n is a large number) can react with any of the other compounds (for the mathematically inclined, this gives n 2 reactions). Of course, each of these n 2 products can react further. Thus, any useful scientific method must begin by constraining the enormity of possibilities that observations present to focus the minds of us mortal scientists. 19

This number is defacto limitless. The universe should theoretically be able to produce an infinite number of different amino acids. The AA R sidechains can have any isomer combination. They can come right-handed, or left-handed, with one or two functional groups, with cyclic (cyclobutane, cyclopentane, and cyclohexane) and/or branched structures, they can come amphoteric, aliphatic, aromatic, polar, uncharged, positively and negatively charged, and so on. Furthermore: A carbon atom bonded to a functional group, like carbonyl, is known as the α carbon atom. The second is β (α, β, γ, δ…) and so on, according to the Greek alphabetical order. It is conceivable that the protein alphabet would be made of β peptides. There is nothing that physically constrains or limits amino acids to have different configurations. In fact, we do know bioactive peptides that use β-amino acids do form polymer sequences 3 Every synthetic chemist will confirm this. There is also no plausible reason why only hydrogen, carbon, nitrogen, oxygen, and sulfur should/could be used in a pool of 118 elements extant in the universe. If the number of possible AA combinations to form a set is limitless, then the chance of selecting randomly a specific set of AAs for specific functions is practically zero. It would have never happened by non-designed means.

Science Daily reported in 2018, claiming that quantum chemistry supposedly solved the mystery of why there are these 20 amino acids in the genetic code. They wrote: "The newer amino acids had become systematically softer, i.e., more readily reactive or prone to undergo chemical changes. The transition from the dead chemistry out there in space to our own biochemistry here today was marked by an increase in softness and thus an enhanced reactivity of the building blocks." 14 The pertinent follow-up question then is: Why the soft amino acids were added to the toolbox in the first place? What exactly were these readily reactive amino acids supposed to react with?
They answered: " At least some of the new amino acids, especially methionine, tryptophan, and selenocysteine, were added as a consequence of the increase in the levels of oxygen in the biosphere. This oxygen promoted the formation of toxic free radicals, which exposes modern organisms and cells to massive oxidative stress. The new amino acids underwent chemical reactions with the free radicals and thus scavenged them in an efficient manner. The oxidized new amino acids, in turn, were easily repairable after oxidation, but they protected other and more valuable biological structures, which are not repairable, from oxygen-induced damage. Hence, the new amino acids provided the remote ancestors of all living cells with a very real survival advantage that allowed them to be successful in the more oxidizing, "brave" new world on Earth. "With this in view, we could characterize oxygen as the author adding the very final touch to the genetic code"

There are several problems with this hypothesis.
1. if the prebiotic atmosphere were oxygenated, organic molecules like RNA and DNA would have been susceptible to thermal oxidation and photo-oxidation and would have readily been destroyed.
2. Twelve of the proteinogenic amino acids were never produced in any lab experiment 15
3. there was no selection process extant to sort out those amino acids best suited and used in life. ( those used are better than 2 million possible alternative amino acid "alphabets"
4. There was no concentration process to collect the amino acids at one specific assembly site.
5. There was no enantiomer selection process
6. They would have disintegrated, rather than complexified
7. There was no process to purify them.

John Maynard Smith, a British biologist wrote in The Major Transitions in Evolution in 1997: Why does life use twenty amino acids and four nucleotide bases? It would be far simpler to employ, say, sixteen amino acids and package the four bases into doublets rather than triplets. Easier still would be to have just two bases and use a binary code, like a computer. If a simpler system had evolved, it is hard to see how the more complicated triplet code would ever take over. The answer could be a case of “It was a good idea at the time.” A good idea of whom? If the code evolved at a very early stage in the history of life, perhaps even during its prebiotic phase, the numbers four and twenty may have been the best way to go for chemical reasons relevant at that stage. Life simply got stuck with these numbers thereafter, their original purpose lost. Or perhaps the use of four and twenty is the optimum way to do it. There is an advantage in life’s employing many varieties of amino acid, because they can be strung together in more ways to offer a wider selection of proteins. But there is also a price: with increasing numbers of amino acids, the risk of translation errors grows. With too many amino acids around, there would be a greater likelihood that the wrong one would be hooked onto the protein chain. So maybe twenty is a good compromise. Do random chemical reactions have knowledge to arrive at a optimal conclusion or a " good compromise"? 16

No, of course, chemical reactions have no knowledge, no know-how, no foresight, no goals.

Optimality of the amino acid set that is used to encode proteins
Gayle K. Philip (2011): The last universal common ancestor of contemporary biology (LUCA) used a precise set of 20 amino acids as a standard alphabet with which to build genetically encoded protein polymers. Many alternatives were also available, which highlights the question: what factors led biological evolution on our planet to define its standard alphabet? Here, we demonstrate unambiguous support that the standard set of 20 amino acids represents the possible spectra of size, charge, and hydrophobicity more broadly and more evenly than can be explained by chance alone. 2

We know that conscious intelligent agents with foresight are able to conceptualize and visualize apriori, a system of building blocks, like Lego bricks, that have a set of properties that optimally perform a specific function or/and task, that is intended to be achieved, and subsequently, we know that intelligent agents can physically instantiate the physical 3D object previously conceptualized.

Lego bricks in their present form were launched in 1958. The interlocking principle with its tubes makes it unique and offers unlimited building possibilities. It's just a matter of getting the imagination going – and letting a wealth of creative ideas emerge through play. 8

Amino acids are analogous to Lego bricks. Bricks to build a house are made with the right stability, size, materials, and capacity of isolation for maintaining adequate narrow-range temperatures inside a house. Glass is made with transparency to serve as windows. (Rare earth) Metals, plastic, rubber, etc. are made to serve as building blocks of complex machines. A mix of atoms will never by itself organize to become the building blocks of a higher-order complex integrated system based on functional, well-integrated, and matching sub-parts. But that is precisely what nature needs in order to complexify into the integrated systems-level organization of cells and multicellularity. We know about the limited range of unguided random processes. And we know the infinite range of engineering solutions that capable intelligent agents can instantiate.

Gayle K. Philip continues: We performed three specific tests: we compared (in terms of coverage) (i) the full set of 20 genetically encoded amino acids for size, charge, and hydrophobicity with equivalent values calculated for a sample of 1 million alternative sets (each also comprising 20 members) results showed that the standard alphabet exhibits better coverage (i.e., greater breadth and greater evenness) than any random set for each of size, charge, and hydrophobicity, and for all combinations thereof. Results indicate that life genetically encodes a highly unusual subset of amino acids relative to any random sample of what was prebiotically plausible. A maximum of 0.03% random sets out-performed the standard amino acid alphabet in two properties, while no single random set exhibited greater coverage in all three properties simultaneously. These results combine to present a strong indication that the standard amino acid alphabet, taken as a set, exhibits strongly nonrandom properties. Random chance would be highly unlikely to represent the chemical space of possible amino acids with such breadth and evenness in charge, size, and hydrophobicity (properties that define what protein structures and functions can be built). It is remarkable that such a simple starting point for analysis yields such clear results.

If the set does exhibit nonrandom properties, and random chance is highly unlikely, where does that optimality come from? It cannot be due to physical necessity. Matter has not the necessity to instantiate, to sort out a set of building blocks for distant goals. Evolution and natural selection is a hopelessly inadequate mechanism that was not at play at that stage. The only option left is intelligent design.

Melissa Ilardo (2015) : We compared the encoded amino acid alphabet to random sets of amino acids. We drew 10^8 random sets of 20 amino acids from our library of 1913 structures and compared their coverage of three chemical properties: size, charge, and hydrophobicity, to the standard amino acid alphabet. We measured how often the random sets demonstrated better coverage of chemistry space in one or more, two or more, or all three properties. In doing so, we found that better sets were extremely rare. In fact, when examining all three properties simultaneously, we detected only six sets with better coverage out of the 10^8 possibilities tested. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set. 9

That's pretty impressive and remarkable. That means, that only one in 16 million sets is better suited for the task. The most recent paper to be mentioned was written by Andrew J. Doig in 2016. He wrote:

Why the particular 20 amino acids were selected to be encoded by the Genetic Code remains a puzzle. They were selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets. Factors to take into account when assessing why a particular amino acid might be used include its component atoms, functional groups, biosynthetic cost, use in a protein core or on the surface, solubility and stability. Applying these criteria to the 20 standard amino acids, and considering some other simple alternatives that are not used, we find that there are excellent reasons for the selection of every amino acid. Rather than being a frozen accident, the set of amino acids selected appears to be near ideal.10 The last sentence is noteworthy: "the set of amino acids selected appears to be near ideal." It remains a puzzle as so many other things in biology that find no answer by the ones that build their inferences on a constraint set of possible explanations, where an intelligent causal agency is excluded a priori. Selecting things for specific goals is a conscious process, that requires intelligence. Attributes, that chance alone lacks, but an intelligent creator can employ to create life.

Biosynthetic cost: Protein synthesis takes a major share of the energy resources of a cell. Leu costs only 1 ATP, but its isomer Ile costs 11. Why would life ever, therefore, use Ile instead of Leu, if they have the same properties? Larger is not necessarily more expensive; Asn and Asp cost more in ATP than their larger alternatives Gln and Glu, and large Tyr costs only two ATP, compared to 15 for small Cys. The high cost of sulfur-containing amino acids is notable.

This is indeed completely counterintuitive and does not conform with naturalistic predictions.

Burial and surface: Proteins have close-packed cores with the same density as organic solids and side chains fixed into a single conformation. A solid core is essential to stabilize proteins and to form a rigid structure with well-defined binding sites. Nonpolar side chains have therefore been selected to stabilize close-packed hydrophobic cores. Conversely, proteins are dissolved in water, so other side chains are used on a protein surface to keep them soluble in an aqueous environment.

The problem here is that molecules and an arrangement of correctly selected varieties of amino acids would bear no function until life began. Functional subunits of proteins, or even fully operating proteins on their own would only have a function after life began, and the cells intrinsic operations were on the go. It is as if molecules had the inherent drive to contribute to life to have a first go, which of course is absurd. The only rational alternative is that a powerful creator had the foresight, and knew which arrangement and selection of amino acids would fit and work to make life possible.

Which amino acids came first? It is plausible that the first proteins used a subset of the 20 and a simplified Genetic Code, with the first amino acids acquired from the environment.

Why is plausible? It is not only not plausible, but plain and clearly impossible. The genetic code could not emerge gradually, and there is no known explanation for how it emerged. The author also ignores that the whole process of protein synthesis requires all parts in the process fully operational right from the beginning. A gradual development by evolutionary selective forces is highly unlikely.

Energetics of protein folding: Folded proteins are stabilized by hydrogen bonding, removal of nonpolar groups from water (hydrophobic effect), van der Waals forces, salt bridges, and disulfide bonds. Folding is opposed by loss of conformational entropy, where rotation around bonds is restricted, and introduction of strain. These forces are well balanced so that the overall free energy changes for all the steps in protein folding are close to zero.

Foresight and superior knowledge would be required to know how to get a protein fold that bears function, and where the forces are outbalanced naturally to get an overall energy homeostatic state close to zero. In the most recent Christopher Mayer-Bacon (2021): Three fundamental physicochemical properties of size, charge, and hydrophobicity have received the most attention to date in identifying how the standard amino acid alphabet appears most clearly unusual. The standard amino acid alphabet appears more evenly distributed across a broader range of values than can reasonably be explained by chance. This model indicates a probability of approximately one in two million that an amino acid set would exhibit better coverage by chance 13

How is ammonium introduced to synthesize amino acids?

Unsolved issues about the origin of amino acids on early earth:
How did unguided nondesigned coincidence select the right amino acids amongst over 300 ( known, but the number is theoretically limitless ) that occur naturally on earth? All life on Earth uses the same 20 ( in some cases, 22 genetically encoded) amino acids to construct its proteins even though this represents a small subset of the amino acids available in nature?
How would twenty amino acids be selected (+2) and not more or less to make proteins?
How was the concomitant synthesis of undesired or irrelevant by-products avoided?
How were bifunctional monomers, that is, molecules with two functional groups so they combine with two others selected, and unfunctional monomers (with only one functional group) sorted out?
How were β, γ, δ… amino acids sorted out?
How did a prebiotic synthesis of biological amino acids avoid the concomitant synthesis of undesired or irrelevant by-products?
How could achiral precursors of amino acids have produced and concentrated only left-handed amino acids? ( The homochirality problem )?
How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
How did ammonia (NH3), the precursor for amino acid synthesis, accumulate on prebiotic earth, if the lifetime of ammonia would be short because of its photochemical dissociation?
How could prebiotic events have delivered organosulfur compounds required in a few amino acids used in life, if in nature sulfur exists only in its most oxidized form (sulfate or SO4), and only some unique groups of procaryotes mediate the reduction of SO4 to its most reduced state (sulfide or H2S)?
How did a prebiotic synthesis of biological amino acids avoid the concomitant synthesis of undesired or irrelevant by-products?
How did the transition from prebiotic enantiomer selection to the enzymatic reaction of transamination occur that had to be extant when cellular self-replication and life began?
How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
How did nature select the set of amino acids which appears to be near-optimal in regard to size, charge, and hydrophobicity more broadly and more evenly than in 16 million alternative sets?
How did natural events have foreknowledge that the selected amino acids are best suited to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins?
How did Amino acid synthesis regulation emerge? Biosynthetic pathways are often highly regulated such that building blocks are synthesized only when supplies are low.
How did the transition from prebiotic synthesis to the synthesis through metabolic pathways of amino acids occur? A minimum of 112 enzymes is required to synthesize the 20 (+2) amino acids used in proteins.

1. S L Miller: Reasons for the occurrence of the twenty coded protein amino acids 1981
2. Gayle K. Philip: Did evolution select a nonrandom 2011 Mar 24
3. Chiara Cabrele: Peptides Containing β-Amino Acid Patterns: Challenges and Successes in Medicinal Chemistry September 10, 2014
4. Pre-Life Building Blocks Spontaneously Align in Evolutionary Experiment
5. Areski Flissi: Norine: update of the nonribosomal peptide resource
6. Stuart A. Kauffman: Theory of chemical evolution of molecule compositions in the universe, in the Miller-Urey experiment and the mass distribution of interstellar and intergalactic molecules  30 Nov 2019
7. LibreTexts: Amino Acids
8. https://web.archive.org/web/20150905173143/http://www.lego.com/en-us/aboutus/lego-group/the_lego_history
9. Melissa Ilardo: Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids 24 March 2015
10. Andrew J. Doig: Frozen, but no accident – why the 20 standard amino acids were selected 2 December 2016
11. Joongoo Lee: Ribosome-mediated polymerization of long chain carbon and cyclic amino acids into peptides in vitro 27 August 2020
12. Jan Mrazek: Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles 2014 Oct 30
13. Christopher Mayer-Bacon: Evolution as a Guide to Designing xeno Amino Acid Alphabets 10 March 2021
14. Quantum chemistry solves mystery why there are these 20 amino acids in the genetic code February 1, 2018
15. Miller–Urey experiment
16. John Maynard Smith: The Major Transitions in Evolution 1997
17. Soo Yeon Jeong: Crystal structure of L-aspartate aminotransferase from Schizosaccharomyces pombe August 29, 2019
18. https://proteopedia.org/wiki/index.php/Aspartate_Aminotransferase#cite_note-AST_Structure-3
19. Benner SA  Life, the universe and the scientific method. (2009)

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The problem of the prebiotic origin of amino acids
1. Amino acids are of a very specific complex functional composition and made by cells in extremely sophisticated orchestrated metabolic pathways, which were not extant on the early earth. If abiogenesis were true, these biomolecules had to be prebiotically available and naturally occurring ( in non-enzyme-catalyzed ways by natural means ) and then somehow join in an organized way. Twelve of the proteinogenic amino acids were never produced in sufficient concentrations in any lab experiment. There was no selection process extant to sort out those amino acids best suited and used in life, amongst those that were not useful. There was potentially an unlimited number of different possible amino acid compositions extant prebiotically. (The amino acids alphabet used in life is more optimal and robust than 2 million tested alternative amino acid "alphabets")
2. There was no concentration process to collect the amino acids at one specific assembly site. There was no enantiomer selection process ( the homochirality problem). Amino acids would have disintegrated, rather than complexified There was no process to purify them.
3. Taken together, all these problems make an unguided origin of Amino Acids extremely unlikely. Making things for a specific purpose, for a distant goal, requires goal-directedness. We know that a) unguided random purposeless events are unlikely to the extreme to make specific purposeful elementary components to build large integrated macromolecular systems, and b) intelligence has goal-directedness. Bricks do not form from clay by themselves, and then line up to make walls. Someone made them.

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Serine Synthesis:

Phosphoserine phosphatase (EC 3.1.3.3)
Phosphoserine aminotransferase (EC 2.6.1.52)
Glycine Synthesis:
3. Serine hydroxymethyltransferase (EC 2.1.2.1)

Cysteine Metabolism:
4. Serine O-acetyltransferase (EC 2.3.1.30)

Cysteine synthase (EC 2.5.1.47)
Methionine adenosyltransferase (EC 2.5.1.6)
S-Adenosylhomocysteine hydrolase (EC 3.3.1.1)
Cystathionine gamma-synthase (EC 2.5.1.48)
Alanine Metabolism:
9. Aspartate 4-decarboxylase (EC 4.1.1.12)

Alanine transaminase (EC 2.6.1.2)
Alanine-glyoxylate transaminase (EC 2.6.1.44)
Alanine dehydrogenase (EC 1.4.1.1)
Alanine racemase (EC 5.1.1.1)
Valine biosynthesis:
14. Acetolactate synthase (EC 2.2.1.6)

Acetohydroxy acid isomeroreductase (EC 1.1.1.86)
Dihydroxyacid dehydratase (EC 4.2.1.9)
Branched-chain amino acid aminotransferase (EC 2.6.1.42)

Leucine Biosynthesis in Bacteria:

Acetolactate synthase (EC 2.2.1.6)
Acetohydroxy acid isomeroreductase (EC 1.1.1.86)
Dihydroxy-acid dehydratase (EC 4.2.1.9)
3-isopropylmalate synthase (EC 2.3.3.13)
3-isopropylmalate dehydratase (EC 4.2.1.33)
3-isopropylmalate dehydrogenase (EC 1.1.1.85)
Branched-chain amino acid aminotransferase (EC 2.6.1.42)
Isoleucine Metabolism:
8. Threonine deaminase (EC 4.3.1.19)

3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11)
3-isopropylmalate dehydratase (EC 4.2.1.33) (Note: This enzyme is listed twice since it's also involved in leucine biosynthesis)
3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Note: This enzyme is also involved in leucine biosynthesis)
Histidine Synthesis:
12. Phosphoribosylamine--glycine ligase (EC 6.3.4.13)

Phosphoribosylformylglycinamidine synthase (EC 6.3.5.3)
Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1)
AIR carboxylase (EC 4.1.1.21)
Phosphoribosylformimino-5-amino-1-(5-phosphoribosyl)imidazolecarboxamide isomerase (EC 5.3.1.16)
Imidazoleglycerol-phosphate synthase (EC 4.1.3.15)
Imidazoleglycerol-phosphate hydrolase (EC 3.13.1.5)
Histidinol-phosphate aminotransferase (EC 2.6.1.9)
Histidinol-phosphate phosphatase (EC 3.1.3.15)
Histidinol dehydrogenase (EC 1.1.1.23)
Histidine ammonia-lyase (EC 4.3.1.3)
Phenylalanine/Tyrosine Synthesis:
23. Chorismate mutase (EC 5.4.99.5)

For Tyrosine synthesis:
24. Prephenate dehydrogenase (EC 1.3.1.12)

4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (Noted for completeness)
For Phenylalanine synthesis:
27. Prephenate aminotransferase (EC 2.6.1.78)

Arogenate dehydratase (EC 4.2.1.91)

Tryptophan Synthesis:

Chorismate pyruvate-lyase (EC 4.2.99.21)
Anthranilate phosphoribosyltransferase (EC 2.4.2.18)
Phosphoribosylanthranilate isomerase (EC 5.3.1.24)
Indole-3-glycerol-phosphate synthase (EC 4.1.1.48)
Tryptophan synthase (EC 4.2.1.20)
Aspartate Metabolism:
6. Aspartate transaminase (EC 2.6.1.1)

Aspartate carbamoyltransferase (EC 2.1.3.2)
Aspartokinase (EC 2.7.2.4)
Adenylosuccinate synthase (EC 6.3.4.4)
Asparagine Metabolism:
10. Asparagine synthetase (EC 6.3.5.4)

Asparaginase (EC 3.5.1.1)
Asparagine aminotransferase (EC 2.6.1.14)
Methionine Metabolism:
13. Homoserine dehydrogenase (EC 1.1.1.3)

O-succinylhomoserine (thiol)-lyase (EC 2.5.1.48)
Cystathionine beta-lyase (EC 4.4.1. Cool

Methionine synthase (EC 2.1.1.13)
Methylthiotransferase (EC 2.8.4.4)
Lysine Biosynthesis:
18. Dihydrodipicolinate synthase (EC 4.2.1.52)

Dihydrodipicolinate reductase (EC 1.3.1.26)
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117)
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase (EC 2.3.1.89)
Diaminopimelate reductase (EC 1.3.1.26)
Diaminopimelate epimerase (EC 5.1.1.7)
Diaminopimelate decarboxylase (EC 4.1.1.20)

Threonine Biosynthesis (from Aspartate):

Aspartokinase (EC 2.7.2.4)
Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)
Homoserine dehydrogenase (EC 1.1.1.3)
Homoserine kinase (EC 2.7.1.39)
Threonine synthase (EC 4.2.3.1)
Glutamine/Glutamate Synthesis:

Glutamate dehydrogenase (NAD+) (EC 1.4.1.2)
Glutamate dehydrogenase (NADP+) (EC 1.4.1.4)
Glutamate 5-kinase (EC 2.7.2.11)
Glutamine synthetase (EC 6.3.1.2)
Glutamine-dependent NAD+ synthetase (EC 6.3.5.1)
Arginine/Ornithine Synthesis:

N-acetylglutamate synthase (EC 2.3.1.1)
N-acetylglutamate kinase (EC 2.7.2. Cool

N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38 )
Acetylornithine aminotransferase (EC 2.6.1.11)
Ornithine carbamoyltransferase (EC 2.1.3.3)
Argininosuccinate synthase (EC 6.3.4.5)
Argininosuccinate lyase (EC 4.3.2.1)
Arginine and Proline Metabolism in Prokaryotes:

Ornithine carbamoyltransferase (EC 2.1.3.3)
Ornithine decarboxylase (EC 4.1.1.17)
Acetylornithine deacetylase (EC 3.5.1.16)
Proline dehydrogenase (EC 1.5.5.2)
Pyrroline-5-carboxylate reductase (EC 1.5.1.2)

The list you provided is a comprehensive overview of various enzymes involved in amino acid metabolism. However, when considering the Last Universal Common Ancestor (LUCA) or simple bacteria resembling LUCA, it's important to understand that our understanding of LUCA is largely hypothetical. LUCA is not a specific organism we've observed, but rather an inferred ancestral entity reconstructed from comparative genomics and molecular phylogenetics.

Serine, Glycine, and Cysteine Metabolism: The enzymes you listed for the biosynthesis of serine, glycine, and cysteine are indeed ancient. For instance, serine is synthesized from 3-phosphoglycerate, an intermediate in glycolysis, highlighting its antiquity.

Alanine Metabolism: The enzymes for alanine metabolism, including transaminases, are expected to be ancient, as alanine is a simple amino acid and its synthesis and degradation tie into central metabolism.

Branched-chain Amino Acids (Valine, Leucine, Isoleucine): The synthesis pathways for these amino acids are interconnected, and while they involve several steps, they tie back to pyruvate and other central metabolites.

Histidine Synthesis: The synthesis of histidine is complex and whether LUCA had the full pathway is a matter of debate. However, it's plausible that some of the pathway, if not all, existed in early organisms.

Phenylalanine/Tyrosine Synthesis: The synthesis of these aromatic amino acids is tied to the shikimate pathway, which is ancient and leads to the synthesis of chorismate, a precursor for both amino acids.

Tryptophan Synthesis: Like phenylalanine and tyrosine, tryptophan synthesis also starts with chorismate.

Aspartate Family (Aspartate, Asparagine, Methionine, Threonine, Lysine): These amino acids are derived from aspartate, which is directly formed from oxaloacetate, an intermediate in the TCA cycle. This family is believed to be ancient.

Glutamate Family (Glutamate, Glutamine, Arginine, Proline): Glutamate is synthesized from alpha-ketoglutarate, another TCA cycle intermediate, making its synthesis pathway ancient.

It's worth noting that while the pathways themselves may be ancient, some specific enzymes or isoforms might be later evolutionary additions or innovations. Additionally, the actual presence of these pathways in simple bacteria resembling LUCA depends on the specific bacterium in question.

Overall, while the list you provided seems generally appropriate for ancient metabolic pathways, pinning down the exact biochemistry of LUCA is a challenging endeavor due to the deep time scales involved and the lack of direct evidence.

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Serine Synthesis (3 enzymes):
Phosphoserine phosphatase (EC 3.1.3.3)
Phosphoserine aminotransferase (EC 2.6.1.52)
Serine hydroxymethyltransferase (EC 2.1.2.1)

Cysteine Metabolism (6 enzymes):
Serine O-acetyltransferase (EC 2.3.1.30)
Cysteine synthase (EC 2.5.1.47)
Methionine adenosyltransferase (EC 2.5.1.6)
S-Adenosylhomocysteine hydrolase (EC 3.3.1.1)
Cystathionine gamma-synthase (EC 2.5.1.48)

Alanine Metabolism (5 enzymes):
Aspartate 4-decarboxylase (EC 4.1.1.12)
Alanine transaminase (EC 2.6.1.2)
Alanine-glyoxylate transaminase (EC 2.6.1.44)
Alanine dehydrogenase (EC 1.4.1.1)
Alanine racemase (EC 5.1.1.1)

Valine biosynthesis (4 enzymes):
Acetolactate synthase (EC 2.2.1.6)
Acetohydroxy acid isomeroreductase (EC 1.1.1.86)
Dihydroxyacid dehydratase (EC 4.2.1.9)
Branched-chain amino acid aminotransferase (EC 2.6.1.42)

Leucine Biosynthesis in Bacteria (7 enzymes):
Acetolactate synthase (EC 2.2.1.6)
Acetohydroxy acid isomeroreductase (EC 1.1.1.86)
Dihydroxy-acid dehydratase (EC 4.2.1.9)
3-isopropylmalate synthase (EC 2.3.3.13)
3-isopropylmalate dehydratase (EC 4.2.1.33)
3-isopropylmalate dehydrogenase (EC 1.1.1.85)
Branched-chain amino acid aminotransferase (EC 2.6.1.42)

Isoleucine Metabolism (6 enzymes):
Threonine deaminase (EC 4.3.1.19)
3-methyl-2-oxobutanoate hydroxymethyltransferase (EC 2.1.2.11)
3-isopropylmalate dehydratase (EC 4.2.1.33)
3-isopropylmalate dehydrogenase (EC 1.1.1.85)

Histidine Synthesis (10 enzymes):
Phosphoribosylamine--glycine ligase (EC 6.3.4.13)
Phosphoribosylformylglycinamidine synthase (EC 6.3.5.3)
Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1)
AIR carboxylase (EC 4.1.1.21)
Phosphoribosylformimino-5-amino-1-(5-phosphoribosyl)imidazolecarboxamide isomerase (EC 5.3.1.16)
Imidazoleglycerol-phosphate synthase (EC 4.1.3.15)
Imidazoleglycerol-phosphate hydrolase (EC 3.13.1.5)
Histidinol-phosphate aminotransferase (EC 2.6.1.9)
Histidinol-phosphate phosphatase (EC 3.1.3.15)
Histidinol dehydrogenase (EC 1.1.1.23)

Phenylalanine/Tyrosine Synthesis (6 enzymes):
Chorismate mutase (EC 5.4.99.5)
Prephenate dehydrogenase (EC 1.3.1.12)
4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
Prephenate aminotransferase (EC 2.6.1.78)
Arogenate dehydratase (EC 4.2.1.91)
Homogentisate 1,2-dioxygenase (EC 1.13.11.5)

Tryptophan Synthesis (5 enzymes):
Chorismate pyruvate-lyase (EC 4.2.99.21)
Anthranilate phosphoribosyltransferase (EC 2.4.2.18)
Phosphoribosylanthranilate isomerase (EC 5.3.1.24)
Indole-3-glycerol-phosphate synthase (EC 4.1.1.48)
Tryptophan synthase (EC 4.2.1.20)

Aspartate Metabolism (4 enzymes):
Aspartate transaminase (EC 2.6.1.1)
Aspartate carbamoyltransferase (EC 2.1.3.2)
Aspartokinase (EC 2.7.2.4)
Adenylosuccinate synthase (EC 6.3.4.4)

Asparagine Metabolism (3 enzymes):
Asparagine synthetase (EC 6.3.5.4)
Asparaginase (EC 3.5.1.1)
Asparagine aminotransferase (EC 2.6.1.14)

Methionine Metabolism (5 enzymes):
Homoserine dehydrogenase (EC 1.1.1.3)
O-succinylhomoserine (thiol)-lyase (EC 2.5.1.48 )
Cystathionine beta-lyase (EC 4.4.1.8 )
Methionine synthase (EC 2.1.1.13)
Methylthiotransferase (EC 2.8.4.4)

Cysteine Metabolism (3 enzymes):
Serine acetyltransferase (EC 2.3.1.30)
O-acetylserine(thiol)-lyase (EC 2.5.1.47)
Cystathionine beta-synthase (EC 4.2.1.22)

Threonine Metabolism (3 enzymes):
Threonine dehydratase (EC 4.3.1.19)
Homoserine kinase (EC 2.7.1.39)
Threonine synthase (EC 4.2.3.1)

Isoleucine/Valine Synthesis (6 enzymes):
Acetolactate synthase (EC 2.2.1.6)
Keto-acid reductoisomerase (EC 1.1.1.86)
Dihydroxy-acid dehydratase (EC 4.2.1.9)
Alpha-isopropylmalate synthase (EC 2.3.3.13)
Alpha-isopropylmalate isomerase (EC 4.2.1.33)
Branched-chain amino acid aminotransferase (EC 2.6.1.42)

Lysine Synthesis (9 enzymes):
Aspartokinase (EC 2.7.2.4)
Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)
Dihydrodipicolinate synthase (EC 4.2.1.52)
Dihydrodipicolinate reductase (EC 1.3.1.26)
Tetrahydrodipicolinate acylase (EC 3.5.1.18)
N-succinyldiaminopimelate aminotransferase (EC 2.6.1.17)
N-succinyldiaminopimelate desuccinylase (EC 3.5.1.18)
Diaminopimelate decarboxylase (EC 4.1.1.20)
Diaminopimelate epimerase (EC 5.1.1.7)

Proline Synthesis (3 enzymes):
Glutamate 5-kinase (EC 2.7.2.11)
Glutamyl-phosphate reductase (EC 1.2.1.41)
Pyrroline-5-carboxylate reductase (EC 1.5.1.2)

Arginine Synthesis (8 enzymes):
Argininosuccinate synthase (EC 6.3.4.5)
Argininosuccinate lyase (EC 4.3.2.1)
Arginine decarboxylase (EC 4.1.1.19)
Agmatinase (EC 3.5.3.11)
SpeB (EC 3.5.3.10)
Ornithine carbamoyltransferase (EC 2.1.3.3)
Arginase (EC 3.5.3.1)
N-acetylglutamate synthase (EC 2.3.1.1)

Alanine Metabolism (2 enzymes):
Alanine transaminase (EC 2.6.1.2)
Alanine-glyoxylate transaminase (EC 2.6.1.44)

Serine Metabolism (3 enzymes):
Phosphoglycerate dehydrogenase (EC 1.1.1.95)
Phosphoserine aminotransferase (EC 2.6.1.52)
Phosphoserine phosphatase (EC 3.1.3.3)

Glycine Metabolism (4 enzymes):
Glycine hydroxymethyltransferase (EC 2.1.2.1)
Glycine cleavage system (EC 1.4.4.2, 1.8.1.4, 2.1.2.10)
Serine hydroxymethyltransferase (EC 2.1.2.1)
Glycine N-methyltransferase (EC 2.1.1.20)

Glutamate Metabolism (4 enzymes):
Glutamate dehydrogenase (EC 1.4.1.3)
Glutamine synthetase (EC 6.3.1.2)
Glutamate synthase (EC 1.4.1.13)
Glutaminase (EC 3.5.1.2)

Glutamine Metabolism (2 enzymes):
Glutamine synthetase (EC 6.3.1.2)
Glutaminase (EC 3.5.1.2)

Otangelo

Otangelo

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Lost City’ seabed rocks hold clues to Earth’s first amino acids

‘James Urquhart 2018-11-14

The amino acid tryptophan has been detected deep beneath the seafloor. Its discoverers believe it wasn’t life that created this chemical but geochemical processes. The finding supports the idea that alkaline deep-sea hydrothermal systems could have provided ideal conditions for producing the organic molecules necessary to kick-start life on Earth.

Amino acids are integral to life as the building blocks of all proteins, as well as enabling crucial biological functions in their own right. However, this throws up a ‘chicken and egg’ conundrum: if amino acids are required for – and made by – life then how did life get started without them?

Amino acids have been discovered on meteorites suggesting an extra-terrestrial abiotic source of the compounds. Meanwhile, experiments and theoretical calculations have shown that amino acids could have been synthesised abiotically on Earth under the right conditions. But no one has ever found a naturally occurring non-living mechanism for their production.

Source:

2018, Springer Nature Limited Optical microscopy image of a sample of serpentinite where the abiotically produce tryptophan was discovered. Image also show olivine (Ol) and magnetite (Mag), with the green arrow showing orientation of sample

Now, Bénédicte Ménez at Paris Diderot University, France and her colleagues have identified the amino acid tryptophan – and other organic molecules – preserved in rock samples taken from almost 175m below the mid-Atlanic ocean floor at the Lost City hydrothermal field. Ruling out biological sources and contamination, the researchers suggest these chemicals formed from interactions between seawater and mantle-derived rocks called serpentinites, which would have been abundant in the prebiotic Earth’s crust.

‘The first building blocks of life must first have been produced abiotically, so it is very exciting to have evidence for the production of amino acids in serpentinised peridotites,’ comments Andrew McCaig, who investigates hydrothermal systems at the University of Leeds, UK, and was not involved in the study.

To analyse the core samples, the team combined three high resolution imaging techniques that all pointed to tryptophan inside a network of clay nanopores. Although amino acids have been detected in fluids at the Lost City site before, their source was unknown. The team are confident that the tryptophan they identified was abiotic in origin because they found no evidence of biomarkers or other amino acids which would suggest a biological source.

Deep-sea synthesis

The researchers propose that the tryptophan could have been synthesised in the nanopores of the iron-rich clay when it formed during hydrothermal alteration of serpentinites. The team also detected indole, which is an intermediate organic compound in the synthesis of tryptophan via Friedel–Crafts-type reactions, and indicates the nanopore network may have acted as a confined microreactor to promote this reaction, while the iron-rich clay helped catalyse it and subsequently aided its preservation.

‘Hydrothermal alteration of mantle rocks never ceases to amaze me,’ says Frieder Klein, a geochemist at Woods Hole Oceanographic Institution, US. ‘This remarkable study corroborates the idea that hydrothermal systems, which likely existed throughout most of Earth’s history and possibly elsewhere in the solar system, have the potential for the abiotic synthesis of amino acids and possibly even more complex organic compounds.’

However, not everyone is convinced. ‘The spectroscopic evidence for the detection of tryptophan in this work is not terribly strong and so it seems very unlikely to me,’ says Jim Cleaves, who investigates geochemistry and the origin of life at the Tokyo Institute of Technology, Japan. He explains that some of the fluorescence spectra peaks do not match up very well, suggesting that the data could similarly fit other compounds. ‘Even if tryptophan was conclusively detected, it seems plausible there has been fluid flow within these samples providing an avenue for biological contamination.’

Jeffrey Bada, who investigates the geochemistry of amino acids at the Scripps Institution of Oceanography, US, agrees. ‘The supposed tryptophan smells like an artefact to me,’ he says. What’s more he questions its relevance to the origin of life. ‘Tryptophan is not an amino acid commonly thought to be part of the prebiotic compound inventory on the early Earth and elsewhere. It has only one codon in DNA, which has been interpreted as indicating it was a late addition.’

However, although tryptophan may not have been one of the original amino acids required for life to emerge, Ménez and colleagues argue that amino acids can act as biochemical precursors that catalyse the synthesis of sugars, aldehydes and nucleotide intermediates.

Challenges in Explaining Life's Origin from Seabed Amino Acids

1. Single Amino Acid Detection: Only tryptophan was identified:
- How representative is this of prebiotic amino acid synthesis?
- What about the other 19 proteinogenic amino acids?

2. Spectroscopic Evidence Concerns: Some experts question the data's reliability:
- How conclusive is the spectroscopic evidence for tryptophan?
- Could the data fit other compounds?

3. Contamination Possibility: Biological contamination hasn't been ruled out:
- How can we be certain the tryptophan isn't from fluid flow contamination?
- What methods could definitively prove abiotic origin?

4. Evolutionary Relevance: Tryptophan may be a late addition to life:
- How relevant is tryptophan to early life if it was incorporated later?
- What explains its single codon in DNA if it was an early amino acid?

5. Prebiotic Plausibility: Tryptophan isn't typically considered prebiotic:
- Why focus on tryptophan instead of simpler, more likely prebiotic amino acids?
- How does this align with other prebiotic chemistry theories?

6. Reaction Specificity: The proposed synthesis is complex:
- How likely are Friedel-Crafts reactions in this environment?
- What about side reactions or unwanted products?

7. Catalytic Role of Clay: Clay's role in synthesis and preservation is proposed:
- How specific is this catalysis to tryptophan?
- Could it produce a variety of organic compounds, complicating the picture?

8. Quantity and Concentration: Amount of tryptophan produced is unclear:
- Is the quantity sufficient to be relevant for prebiotic chemistry?
- How could it accumulate to useful concentrations?

9. Environmental Conditions: Deep-sea vents differ from early Earth surface:
- How would these molecules reach the surface?
- Are deep-sea conditions relevant to origin of life theories?

10. From Precursors to Life: Leap from amino acids to life remains unexplained:
- How would tryptophan lead to more complex biomolecules?
- What about the development of genetic code and metabolism?

While this discovery is intriguing, it doesn't resolve fundamental questions about life's origin. The leap from abiotic amino acid synthesis to self-replicating systems remains a significant challenge. Further research is needed to address these issues and strengthen the connection between deep-sea chemistry and the emergence of life.

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Amino Acids: Origin of the canonical twenty amino acids required for life

26 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Sat 27 Oct 2018 - 0:49

Otangelo

27 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Thu 13 Dec 2018 - 21:19

Otangelo

28 Tryptophan and the riddle of making amino acids by hypercomplex enzymatic reactions Mon 18 Mar 2019 - 15:57

Otangelo

29 Tryptophan Thu 6 Feb 2020 - 19:47

Otangelo

30 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Sat 22 Feb 2020 - 3:33

Otangelo

31 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Sat 27 Feb 2021 - 15:05

Otangelo

32 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Sat 13 Mar 2021 - 15:55

Otangelo

The 20 standard amino acids - as general reasons for choosing side chains, we can now consider the 20 individually.

Aspartic, Glutamic acid

Lysine, Arginine

Histidine

[size=13]Lysine, Arginine[/size]

Alanine

Valine, Leucine, Isoleucine, Phenylalaline

Methione

Cysteine

Proline

Tryptophan

33 Is the prebiotic origin of amino acids by natural means plausible? Fri 15 Jul 2022 - 20:43

Otangelo

34 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Fri 15 Jul 2022 - 20:44

Otangelo

35 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Fri 15 Jul 2022 - 20:44

Otangelo

36 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Sat 3 Sep 2022 - 20:41

Otangelo

37 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Sat 23 Sep 2023 - 20:25

Otangelo

38 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Sat 23 Sep 2023 - 21:11

Otangelo

39 Re: Amino Acids: Origin of the canonical twenty amino acids required for life Tue 13 Aug 2024 - 16:36

Otangelo

40 Re: Amino Acids: Origin of the canonical twenty amino acids required for life

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