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Life can even use something other than amino acids. They are really inconvenient when you think about it. Fixed nitrogen is extremely rare, and there are no nit

by cyberax 5mo ago

Life can even use something other than amino acids. They are really inconvenient when you think about it. Fixed nitrogen is extremely rare, and there are no nitrogen-containing minerals other than some exotic exceptions. Amino acids are useful because they can be easily joined together and split apart (via the C-N bond). But there are other types of "molecular glues" that are viable, like sulfur or phosphorus.

adrian_b 5mo ago
Amino acids are much more likely to be involved in the appearance of life anywhere than other molecules. For instance it would be much less surprising if an alien life form used another kind of polymer to store information, instead of nucleic acids, than if it would not use amino acids. The fact that on Earth the living beings eventually used ATP and RNA appears to have been determined in great part by chance, while the use of amino acids seems to have been much more deterministic. Some of the simple amino acids are very easy to be synthesized in abiotic conditions, which is why they are ubiquitous in many celestial bodies. The advantage of amino acids is that they do not contain only one end that can be attached to other molecules, but that they contain two such ends. A molecule with only one connector would attach to another, forming a dimer, after which no further reaction is possible. A molecule with two connectors, like an amino acid that has both a carboxyl end and an amine end, can be daisy chained into a polymer of arbitrary length. This allows building complex structures. There are other molecules with two connectors, but they are much more unlikely to appear in abiotic conditions. Thioesters, i.e. a kind of organic molecules that are bound by a sulfur bridge, like you mention, appear to have been much more important when life has appeared on Earth than today, but such molecules were important as intermediates in metabolic reactions, not as structural blocks, like amino acids, and there are no known naturally-produced molecules with sulfur that could be used as easily as amino acids to make molecules with arbitrary complex shapes.
- cyberax 5mo ago
  > The fact that on Earth the living beings eventually used ATP and RNA appears to have been determined in great part by chance, while the use of amino acids seems to have been much more deterministic. It looks like on Earth the RNA was the initial replicant. RNA can be folded into complex shapes and can have catalytic properties in itself. Ribosomes that assemble proteins have RNA at the active site with proteins only providing structural framework. That's why amino acids might not end up being so universal.
  - don_esteban 5mo ago
    There is no contradiction: simple amino acids as a basic building block being coopted by replicating RNA to build more sophisticated structures. You can conceive other than nuclear-acids based replicant, using the same ubiquitous amino-acids to build a protein life not using RNA/DNA but some other encoding structure. The question is what is the chemically most likely 'other'? Also, what could be alternatives for ATP/sugars?
    - cyberax 5mo ago
      Sugars are just chains of hydrocarbons with alcohol groups, they are probably going to be ubiquitous. ATP is useful because the phosphate groups make a stable bond that nevertheless can be hydrolyzed, releasing a lot of energy. But the adenosine "backbone" of the ATP is more-or-less arbitrary. Other forms of life can use something different. Or they might use the phosphorus bonds themselves where terrestrial life uses peptide bonds. Disulfide bonds exhibit similar properties, and terrestrial life also uses them to give additional "rigity" to certain proteins. It's also likely a late addition to the genetic code, cysteine is nestled between two stop codons (it clearly used up the initially reserved block of the address space tagged for future expansion). And if you look at meteorites, sulfur compounds are _much_ more common. Sulfur chemistry also doesn't require scarce fixed nitrogen that could only be replenished by lightning before nitrogen-fixing enzymes first evolved. So I don't believe at all that exactly our RNA/amino acids are going to be universal.
      - adrian_b 5mo ago
        I also do not believe that our RNA and complex amino acids are likely to be universal. On the other hand, the simple amino acids are known to be universal, both from chemical analyses of celestial bodies and from abiotic syntheses in laboratories. In theory, sugars can be produced abiotically by the polymerization of formaldehyde. However, sugars are not very stable chemically and suitable catalysts for formaldehyde polymerization seem to be rare, because sugars are much less ubiquitous than amino acids in lifeless environments. The role of phosphorus in biology is determined entirely by the property of the phosphate anions that they can eliminate water and condense into polyphosphates, then the polyphosphates can extract water from other molecules, forcing condensation reactions, which can be used for various purposes, e.g. for building polymers. The nucleoside parts of ATP and related substances play only the role of a "handle", which can be used to control the location of the polyphosphate parts, so that they will perform their function where intended. Thus for controlling the polyphosphates other molecules may also be suitable. Disulfide bonds, which already exist in the pyrite mineral, must have had a crucial role in the origin of life. But their role is very different from that of polyphosphates, because they extract hydrogen, instead of extracting water, so they perform redox reactions, not condensation/hydrolysis reactions. Thioesters are the sulfur compounds that can play the same role as ATP, by taking part in condensation/hydrolysis reactions. There is no doubt that all the 5 elements H, C, N, O and S, which happen to be the most abundant electronegative elements in the entire Universe, must be used by any living being, since the origin of life. Whether phosphorus has also been used since the beginning, or it is a later addition, is uncertain, because thioesters could have been used originally for performing all the functions now done with phosphates like ATP. Both nitrogen and phosphorus are affected by similar availability problems. While nitrogen is too volatile and most of it would always have been stored in dinitrogen gas, which is inert, instead of being stored in easy to use ammonia or hydrogen cyanide molecules (while hydrogen cyanide and carbon monoxide are now toxic for most living beings, it is likely that they both are very important for the appearance of life), for phosphorus the problem is that most of it is stored in insoluble phosphate minerals. This must have been alleviated around the origin of life by the fact that the early oceans were much more acidic than today, so much more phosphate ions would have remained dissolved in sea water, than today. Unlike for phosphorus, there is no substitute for nitrogen in biology. The role of nitrogen in organic molecules is the same as the role of dopants in semiconductor devices. When nitrogen substitutes carbon in an organic molecule, that position in the molecule becomes positively charged, instead of being electrically neutral. These electric charges play very important roles in many chemical reactions. The poor availability of nitrogen must have been the main constraint in the growth of the early forms of life, until the development of the nitrogenase catalysts that allow the use of dinitrogen from the atmosphere. Similarly, it is likely that the earliest forms of life used carbon from carbon monoxide, whose lower availability limited growth until the development of a catalyst that reduces carbon dioxide to formic acid, which allowed the use of the more abundant carbon dioxide. Both catalysts, which are used to capture carbon dioxide and dinitrogen, appear to have used in their earliest variants molybdenum, or possibly the related tungsten. While molybdenum seems to be a later addition to the set of chemical elements used for life, iron, cobalt and nickel are all necessary for the appearance of life as catalysts, while potassium is also necessary since the beginning for maintaining the electrical neutrality of a water solution without producing solid precipitates that would cause death. The abilities to use directly carbon dioxide and dinitrogen, which are the main constituents of most planetary atmospheres, and which were also the main constituents of the early atmosphere of the Earth, must have greatly expanded the environments suitable for life, which previously must have been restricted to small neighborhoods of hydrothermal vents or sources of volcanic gases.

by cyberax 5mo ago

adrian_b 5mo ago

Amino acids are much more likely to be involved in the appearance of life anywhere than other molecules. For instance it would be much less surprising if an alien life form used another kind of polymer to store information, instead of nucleic acids, than if it would not use amino acids. The fact that on Earth the living beings eventually used ATP and RNA appears to have been determined in great part by chance, while the use of amino acids seems to have been much more deterministic. Some of the simple amino acids are very easy to be synthesized in abiotic conditions, which is why they are ubiquitous in many celestial bodies. The advantage of amino acids is that they do not contain only one end that can be attached to other molecules, but that they contain two such ends. A molecule with only one connector would attach to another, forming a dimer, after which no further reaction is possible. A molecule with two connectors, like an amino acid that has both a carboxyl end and an amine end, can be daisy chained into a polymer of arbitrary length. This allows building complex structures. There are other molecules with two connectors, but they are much more unlikely to appear in abiotic conditions. Thioesters, i.e. a kind of organic molecules that are bound by a sulfur bridge, like you mention, appear to have been much more important when life has appeared on Earth than today, but such molecules were important as intermediates in metabolic reactions, not as structural blocks, like amino acids, and there are no known naturally-produced molecules with sulfur that could be used as easily as amino acids to make molecules with arbitrary complex shapes.

cyberax 5mo ago
> The fact that on Earth the living beings eventually used ATP and RNA appears to have been determined in great part by chance, while the use of amino acids seems to have been much more deterministic. It looks like on Earth the RNA was the initial replicant. RNA can be folded into complex shapes and can have catalytic properties in itself. Ribosomes that assemble proteins have RNA at the active site with proteins only providing structural framework. That's why amino acids might not end up being so universal.
- don_esteban 5mo ago
  There is no contradiction: simple amino acids as a basic building block being coopted by replicating RNA to build more sophisticated structures. You can conceive other than nuclear-acids based replicant, using the same ubiquitous amino-acids to build a protein life not using RNA/DNA but some other encoding structure. The question is what is the chemically most likely 'other'? Also, what could be alternatives for ATP/sugars?
  - cyberax 5mo ago
    Sugars are just chains of hydrocarbons with alcohol groups, they are probably going to be ubiquitous. ATP is useful because the phosphate groups make a stable bond that nevertheless can be hydrolyzed, releasing a lot of energy. But the adenosine "backbone" of the ATP is more-or-less arbitrary. Other forms of life can use something different. Or they might use the phosphorus bonds themselves where terrestrial life uses peptide bonds. Disulfide bonds exhibit similar properties, and terrestrial life also uses them to give additional "rigity" to certain proteins. It's also likely a late addition to the genetic code, cysteine is nestled between two stop codons (it clearly used up the initially reserved block of the address space tagged for future expansion). And if you look at meteorites, sulfur compounds are _much_ more common. Sulfur chemistry also doesn't require scarce fixed nitrogen that could only be replenished by lightning before nitrogen-fixing enzymes first evolved. So I don't believe at all that exactly our RNA/amino acids are going to be universal.
    - adrian_b 5mo ago
      I also do not believe that our RNA and complex amino acids are likely to be universal. On the other hand, the simple amino acids are known to be universal, both from chemical analyses of celestial bodies and from abiotic syntheses in laboratories. In theory, sugars can be produced abiotically by the polymerization of formaldehyde. However, sugars are not very stable chemically and suitable catalysts for formaldehyde polymerization seem to be rare, because sugars are much less ubiquitous than amino acids in lifeless environments. The role of phosphorus in biology is determined entirely by the property of the phosphate anions that they can eliminate water and condense into polyphosphates, then the polyphosphates can extract water from other molecules, forcing condensation reactions, which can be used for various purposes, e.g. for building polymers. The nucleoside parts of ATP and related substances play only the role of a "handle", which can be used to control the location of the polyphosphate parts, so that they will perform their function where intended. Thus for controlling the polyphosphates other molecules may also be suitable. Disulfide bonds, which already exist in the pyrite mineral, must have had a crucial role in the origin of life. But their role is very different from that of polyphosphates, because they extract hydrogen, instead of extracting water, so they perform redox reactions, not condensation/hydrolysis reactions. Thioesters are the sulfur compounds that can play the same role as ATP, by taking part in condensation/hydrolysis reactions. There is no doubt that all the 5 elements H, C, N, O and S, which happen to be the most abundant electronegative elements in the entire Universe, must be used by any living being, since the origin of life. Whether phosphorus has also been used since the beginning, or it is a later addition, is uncertain, because thioesters could have been used originally for performing all the functions now done with phosphates like ATP. Both nitrogen and phosphorus are affected by similar availability problems. While nitrogen is too volatile and most of it would always have been stored in dinitrogen gas, which is inert, instead of being stored in easy to use ammonia or hydrogen cyanide molecules (while hydrogen cyanide and carbon monoxide are now toxic for most living beings, it is likely that they both are very important for the appearance of life), for phosphorus the problem is that most of it is stored in insoluble phosphate minerals. This must have been alleviated around the origin of life by the fact that the early oceans were much more acidic than today, so much more phosphate ions would have remained dissolved in sea water, than today. Unlike for phosphorus, there is no substitute for nitrogen in biology. The role of nitrogen in organic molecules is the same as the role of dopants in semiconductor devices. When nitrogen substitutes carbon in an organic molecule, that position in the molecule becomes positively charged, instead of being electrically neutral. These electric charges play very important roles in many chemical reactions. The poor availability of nitrogen must have been the main constraint in the growth of the early forms of life, until the development of the nitrogenase catalysts that allow the use of dinitrogen from the atmosphere. Similarly, it is likely that the earliest forms of life used carbon from carbon monoxide, whose lower availability limited growth until the development of a catalyst that reduces carbon dioxide to formic acid, which allowed the use of the more abundant carbon dioxide. Both catalysts, which are used to capture carbon dioxide and dinitrogen, appear to have used in their earliest variants molybdenum, or possibly the related tungsten. While molybdenum seems to be a later addition to the set of chemical elements used for life, iron, cobalt and nickel are all necessary for the appearance of life as catalysts, while potassium is also necessary since the beginning for maintaining the electrical neutrality of a water solution without producing solid precipitates that would cause death. The abilities to use directly carbon dioxide and dinitrogen, which are the main constituents of most planetary atmospheres, and which were also the main constituents of the early atmosphere of the Earth, must have greatly expanded the environments suitable for life, which previously must have been restricted to small neighborhoods of hydrothermal vents or sources of volcanic gases.