Isomer Ratios: Free Amino Acids

Isomers are compound with the same molecular formula but with a different structural arrangement of atoms, leading to different properties. There are several types of isomers, including structural isomers, stereoisomers, and geometric isomers. Enantiomers are a type of isomers that are non-superimposable mirror images of each other, often involving a chiral center (an atom, usually carbon, with four different substituents). By convention, one enantiomer is labeled left-handed (L) and the other is labeled right-handed (R). Earth life uses L-amino acids to form proteins. As a result, mixtures of those biological amino acids are said to have high enantiomeric excess, and sometimes, but not always, they display perfect enantiomeric excess (ee = 100%). In contrast, enantiomeric ratios in abiotic amino acid mixtures tend to be racemic (ee = 0%) or have low enantiomeric excess. This reflects abiotic reaction kinetics and thermodynamics. This distinction can serve as a signature of life.

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Definition
HIGH
LOW

Abundance in the prebiotic environment: Amino acids are abundant in a diversity of prebiotically-relevant environments such as primitive oceans, meteorites, and hydrothemal systems. This increases the likelihood that they will be incorporated into incipient biochemistries. [General]

Environments
All
eAmino acids are likely to be available in prebiotic environments such as the primeval oceans of Earth

eAmino acids are commonly found in carbonaceous chondries 

eAlkaline hydrothermal vents may be energetically a suitable environment for the synthesis and polymerization of amino acids.

 

Evolutionary forces: Enzymes catalyze reactions most effectively when interacting with homochiral substrates. Since evolutionary processes will favor biochemical economy and efficiency life will always tend to form homochiral polymers. In the case of peptides and proteins, this will lead to amino acid mixtues with enantiomeric excess. [General]

Environments
All
eEvolutionary pressures inevitably lead to homochiral biochemistries

eStereospecificity is inherent in the catalytic action of enzymes

 

Protein functionality: Functional proteins and peptides must be homochiral to ensure proper folding, stability, and biological activity. Homochirality allows consistent interactions between amino acids, enabling the formation of specific 3D structures essential for the protein's function. This results in biotic amino acid mixtures with enantiomeric excess. [General]

Environments
All
eThe longest protein that contains D-amino acids only has 42 residues, which suggests that larger, functional proteins must be built with amino acids of the same chiral form.

eThe presence of D-amino acids destabilizes the helical secondary structure of proteins

eThe beta-sheet structure of proteins has more stability when made from a single enantiomer

 

Protein functionality: There are known cases of functional proteins and peptides that are not homochiral. This suggests that life forms could exists, perhaps shortly after the origin of life, that generate amino acid mixtures with low enantiomeric excess.  [General]

Environments
All
eD-amino acid containing peptides (DAACP) have been found in biology

eThere are known cases of biologcial peptides with D-amino acid residues

eThe Protein Data Bank contains examples of peptides and proteins with D-amino acid residues

eThere are different biochemical pathways that can generate peptides and proteins with D-amino acid residues

Enzymatic specificity: Protein making machinery is optimized to work with homochiral amino acids, that is, with amino acids of the same handedness, resulting in mixtures that have enantiomeric excesses. [General]

Environments
All
eRibosomes discriminate against incorporation of D-amino acids into proteins 

eIncorporation of homochiral amino acids may be favored by reaction rates

ePeptidyl transferase specificity prevents incorporation of D-amino acids during protein synthesis

 

Enzymatic specificity: It is possible for the ribosome to use amino acids of the opposite handedness during protein synthesis, thereby lowering the enantiomeric excess of the resulting amino acid mixtures. [General]

Environments
All
While this argument is true, so far it has only been demonstrated in systems modified by humans. In addition, the resulting amino acid mixtures still display a significant enantiomeric excess in multiple aminon acids
eModified ribosomes have been engineered to permit incorporation of D-amino acids during protein synthesis

eSome D-amino acids can be incorporated into peptides, though not as efficiently as their L-counterparts

eEngineered tRNAs allow for incorporation of consecutive D-amino acids into a peptide chain

eA review of the possible mechanisms for producing D-amino acid containing peptides in living cells

 

Use of amino acids of opposite handedness in specialized roles: Not all mixtures of terrestrial biological amino acids are homochiral because some D-amino acids are crucial in specific roles such as structural support of cell walls. Thus, the existence of D-amino acids and the enzymatic processes creating them in Earth biochemistry demonstrate that biological systems can function with non-homochiral amino acid mixtures. [General]

Environments
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eD-amino acids used as neurotransmitters in mice brains demonstrate the use of biotic amino acids of the opposite handedness. 
This study focuses on mammalian systems, which are unlikely to be representative of life on other planets.

eD-amino acids used as signaling molecules in plants demonstrate the use of biotic amino acids of the opposite handedness. 
This study focuses on plants, which are unlikely to be representative of life on other planets.

eThere are spcialized enzymes that convert L-amino acids into D-amino acids for use in peptidoglycan

eBacteria produce diverse D-amino acids that modulate the synthesis of peptidoglycan in response to changing environmental conditions.

Definition
HIGH
LOW

Biologial activity: If extant life is present, it will enzymatically maintain an enantiomeric excess in the environment by the recycling of free amino acids that have racemized. [Production, Survivability]

Environments
All
eLife uses racemases to convert the non-preferred to the preferred enantiomer

 

Biological activity: If extant life is present, it may decrease the enantiomeric excess in the environment through its capability to enzymatically racemize free amino acids. [Production, Survivability]

Environments
All
It would be good to clarify whether this can still happen after the organism is dead.
eAmino acids can be racemized by biological enzyme in neutral pH condition.

Preservation under cold and dry conditions: Extremely cold and dry conditions on the surface of ocean worlds will help preserve the enantiomeric ratios of amino acids for geologic timescales. [Survivability]

Environments
Mars: Surface, Mars: Subsurface, Ocean Worlds: Enceladus Surface, Ocean Worlds: Europa Surface, Ocean Worlds: Titan Surface
eCold and dry conditions enhance the preservation of amino acids over geologic timescales 

eEnantiomeric excess in aqueous solutions is likely to be left behind and seep into the soil preserving it in high salt concentrations (e. g. evaporites).

eAmino acids can be preserved for geologically long periods in sulfate mineral matrices

 

Preservation under cold and dry conditions: Amino acids near the surface of Mars (top 2 meters) will degrade relatively fast from exposure to ionizing radiation, which may limit their detectability. [Survivability]

Environments
Mars: Surface
eExperimental results suggest serious challenges for the search of ancient amino acids and other potential organic biosignatures in the top 2 m of the martian surface.
This treatment did not cause amino acid racemization after gamma radiation exposure of the samples, which indicates that the chirality of some surviving amino acids may still be preserved.

 

Preservation in liquid water: The enantiomeric excess of amino acids within fluids will be lost over time. [Survivability]

Environments
Mars: Surface, Mars: Subsurface, Ocean Worlds: Enceladus Surface, Ocean Worlds: Enceladus Subsurface, Ocean Worlds: Europa Surface, Ocean Worlds: Europa Subsurface
This statement relies too heavily on the biochemistry of planet Earth, with its 20 amino acids. Murchison and other meteorites contain (at least) 70 identified amino acids, some of which racemize very slowly – such as isovaline which is detected with an L-excess. One should consider that life elsewhere maybe based on a (partially) different set of amino acids, some which racemize very, very slowly, if at all, under wet conditions.
eWet conditions do not preserve enantiomeric excess

eRacemization rates of bound amino acids inside and outside spores are of the order of up to tens of thousands of years.
Fast racemization rates in spores were measured for aspartic acid only, whose half life is significantly shorter than other biotic amino acids

 

Production of minor enantiomers: There can be substantial production of free amino acids of the minor enantiomer (on Earth D-amino acids) for non-enzymatic roles which can lower the overall enantiomeric ratios in biological amino acid mixtures. [Production, Survivability]

Environments
All
eD-amino acids may emerge as a consequence of an existing complex microbiome. They play an important role in cell defense, regulation, communication, biofilm formation, and survival in extreme environments.

Effects of ionizing radiation: Enantiomeric excess will be preserved under ionizing radiation over geologic timescales, even if overall amino acid levels are reduced by radiolysis [Survivability]

Environments
All
This is true for un-polarized irradiation (which is the case in the cited Evidence). But what if the amino acids are exposed to circularly polarized electromagnetic irradiation? After all, this is currently a leading hypothesis of is there an L-excess at all.
This may only be applicable to dry (and not wet) conditions.
eEnantiomeric excess of amino acids in comets can be preserved for geologic timescales

 
Definition
HIGH
LOW

Abundance in the prebiotic environment: Amino acids are abundant in a diversity of prebiotically-relevant environments such as primitive oceans, meteorites, and hydrothemal systems. This increases the likelyhood that they will be incorporated into incipient biochemistries. [General]

Environments
All
eAmino acids are likely to be available in prebiotic environments such as the primeval oceans of Earth 

eAmino acids are commonly found in carbonaceous chondries  

eAlkaline hydrothermal vents may be energetically a suitable environment for the synthesis and polymerization of amino acids. 

 

Abiotic chirality amplification: There are abiotic chemical reactions that can preferentially amplify one chiral form of amino acids. The resulting abiotic amino acid mixtures can have a relatively large enantiomeric excesses. [General]

Environments
All
eEnantiomeric enrichment of racemic alpha-amino acids occurs during sublimation in the presence of another enantiomerically enriched alpha-amino acid. 
Several aspects of the paper were not entirely clear (e.g., the difference between the uses of “recrystallization” and “crystallization”, the precise conditions of the recrystallization experiments [was an excess of enantiomeric asparagine always present?], and the nature of the “prebiotic” mixtures and the “electrical discharge” mixtures)

eCrystallization of complex organic mixtures containing a plethora of amino acids generated under prebiotic conditions can generate crystals with an excess of L or D amino acids, depending upon the conditions of crystallization. 

eEnantiomeric selection of amino acids can be achieved in amounts of up to 100% simply by recrystallizing a mixture of 12 racemic amino acids plus a four-fold excess (over the combined 12 amino acids) of racemic asparagine. 

eCrystals of high enantiomeric purity can be obtained via enantiomer-specific oriented attachment during which a racemic mixture of nano- or microcrystals undergo oriented attachment to form single crystal aggregates. 

eThis review article covers recent results suggesting various chemical models of catalysis-based mechanisms for amplifying chirality under prebiotic conditions on Earth. A theoretical example is presented for alpha-amino acids but no experimental data.

 

Enantiomeric excess in meteorites: Some abiotic amino acids found in carbonaceous chondrite meteorites have a preferential abundance of one chiral form, which can lead to amino acid mixtures with enantiomeric excess. [General]

Environments
All
eSmall L-enantiomeric excesses ranging from 1 to 9% were found in six abiotic amino acids in Murchison and Murray meteorites

eL-isovaline excesses ranging from 15.2 - 18.5% were identified in the aqueously altered Murchison and Orgueil meteorites.

eLarge L-excesses of aspartic acid and glutamic acid up to ~60% were measured in the Tagish Lake meteorite.

 

Enantiomeric excess in meteorites: Most abiotic amino acids found in carbonaceous chondrites are racemic, and the resulting amino acid mixtures have relatively low enantiomeric excess. [General]

Environments
All
eThe majority of chiral amino acids of abiotic origin in meteorites are racemic

Definition
HIGH
LOW

Preservation under cold and dry conditions: Extremely cold and dry conditions on the surface of ocean worlds will help preserve the enantiomeric ratios of amino acids for geologic timescales. [Survivability]

Environments
Mars: Surface, Mars: Subsurface, Ocean Worlds: Enceladus Surface, Ocean Worlds: Enceladus Subsurface, Ocean Worlds: Europa Surface, Ocean Worlds: Europa Subsurface, Ocean Worlds: Titan Surface, Ocean Worlds: Titan Subsurface
eEnantiomeric excess in aqueous solutions is likely to be left behind and seep into the soil preserving it in high salt concentrations (e. g. evaporites). 

eAmino acids can be preserved for geologically long periods in sulfate mineral matrices 

eAmino acids will not racemize on geologic timescales under dry conditions at temperatures <250K.

 
 

Preservation in liquid water: Enantiomeric enrichments in abiotic alpha-amino acids will not be preserved for geologic timescales in an environment under wet conditions [Survivability]

Environments
All
eIn the presence of liquid water chiral amino acids can undergo racemization in short geological timescale

 

Effects of hydrolysis during sample preparation: Hydrolysis can promote racemization of amino acids and large enantiomeric excesses can be converted into a racemic mixture of equal amounts [Survivability]

Environments
Mars: Surface, Mars: Subsurface, Ocean Worlds: Enceladus Subsurface, Ocean Worlds: Europa Subsurface, Ocean Worlds: Titan Subsurface
This is generally true, but again, AAs such as isovaline where the alpha position is blocked, need quite harsh wet conditions to racemize.
eAcid hydrolysis–induced racemization can compromise accurate determination of enantiomeric amino acid compositions

Effects of ionizing radiation: Enantiomeric enrichments in abiotic, chiral alpha-amino acids will be preserved for geologic timescales even after exposure to ionizing radiation [Survivability]

Environments
Venus, Exoplanets: Atmosphere, Exoplanets: Surface, Mars: Surface, Ocean Worlds: Enceladus Surface, Ocean Worlds: Europa Surface, Ocean Worlds: Titan Surface, Ocean Worlds: Other
That is correct, provided that the radiation is not polarized
eTwenty proteinaceous amino acids can survive in relatively large amounts a gamma-radiation dose of 14 MGy

eA fraction of the 20 proteinaceous amino acids can survive a massive radiation dose preserving also an enantiomeric enrichment.

 

Effects of ionizing radiation: Enantiomeric enrichments in some abiotic chiral alpha-amino acids will decay over geologic timescales due to exposure to ionizing radiation (i.e., radioracemization) [Survivability]

Environments
All
eIsovaline in some meteorites can undergo significant radioracemization