the origin of life

=biology =chemistry =biochemistry

 

 

How did life start? This question has quite a bit of prior work, which Wikipedia has a summary of. Still, I know a bit about biochemistry, and thought I'd explain my views on it.

 

 

significance

 

Does this question matter? Why would someone study it? Here are some reasons:

 

1) Understanding important things about the universe is a goal in itself.

2) It's good practice for biochemistry.

3) It can explain some things about biology, such as why DNA uses the structure it does.

4) Understanding abiogenesis provides information about the likelyhood of extraterrestrial life and about what it would be like.

5) Space aliens aren't currently visible, which means that information about the probabilities of intelligent life emerging provides information about the probabilities of "filters".

 

 

panspermia

 

Did life originate on Earth, or were some microorganisms carried from elsewhere? The latter hypothesis is panspermia.

It's possible for a large meteor impact to eject some rocks into space. That's the standard hypothesis for where Luna came from.

The existence of interstellar asteroids (and rogue planets) shows that ejection from a solar system is possible, but most of them were ejected early on in the life of a solar system, before orbits stabilized. Escaping a solar system requires a lot of energy and is generally quite difficult.

It's possible for microbes to survive space. It's possible for an asteroid to happen to hit a habitable planet. It's possible for microbes to survive reentry inside an asteroid.

All the necessary steps are theoretically possible, but they're collectively extremely unlikely. I think that a planet that forms (non-intelligent) life would spread it to far less than 1 planet on average, probably <0.01 on average. So, it's very likely that life originated on Earth.

There's another argument against panspermia: the "oxygen catastrophe". Photosynthetic life from another planet would presumably already have adapted to the presence of oxygen.

 

 

backwards from current life

 

Current life requires:

- DNA replication with DNA polymerase
- DNA to RNA with RNA polymerase
- RNA to proteins with ribosomes
- amino acid synthesis (by at least some organisms)
- ATP production using H+ or Na+ gradients with ATP synthase

 

DNA polymerase, RNA polymerase, ribosomes, and ATP synthase are all very complex. Any of them forming spontaneously is implausible.

Photosynthesis requires a way to produce an ion gradient from light. The simplest approach is creating a gradient across the cell membrane with a single-protein light-driven ion pump, such as bacteriorhodopsin.

The Purple Earth hypothesis is that early photosynthesis used retinal, but retinal is produced by oxidative cleavage of carotenoids using oxygen, which wasn't available before photosynthesis was developed. I agree that early photosynthesis used something other than chlorophyll, but I don't think it was retinal.

DNA is more stable than RNA, but it's possible for life to only use RNA. Producing DNA involves an extra step, with a diol dehydratase and reduction, so RNA probably came first.

RNA can sometimes catalyze reactions, and ribozymes are (rarely) used by current organisms.

Ribosomes are complex. Early life using only ribozymes is the RNA world hypothesis, which avoids the need for ribosomes and amino acid production. I think that hypothesis is correct.

Some RNA polymerase ribozymes have been discovered that produce RNA from triphosphorylated ribonucleosides. Thermodynamically, diphosphate would be sufficient, but catalyzing reactions is easier with triphosphate.

Speaking of ribonucleoside triphosphates, ATP and GTP, which are universally used by life to carry energy, are ribonucleoside triphosphates.

 

 

forwards from chemistry

 

If you look at the homepage of this website, you'll see a chemical reaction: formamide to purine. I chose that to represent organic chemistry and emergent complexity, but it's also probably related to the origin of life.

Hydrogen cyanide (HCN) can form from methane and ammonia at high temperatures. UV light or lightning in an atmosphere containing methane and ammonia can also form HCN.

In an atmosphere of methane and CO2, lightning can produce formaldehyde.

HCN can by hydrated to formamide. Hydrolysis of formamide produces ammonium formate. Heating formamide, ammonium formate, and formaldehyde can produce nucleobases.

Formaldehyde can produce sugars in the formose reaction. However, under the conditions where sugars are made from formaldehyde, they're also quickly destroyed, as this paper notes. Instead of accumulation of 5 or 6 carbon sugars happening, tar is produced. This paper has an answer: 5-carbon sugars form complexes with borate, which stabilizes them, resulting in accumulation of ribose produced from formaldehyde. It also suggests a specific geology that seems reasonable.

 

 

proposed route

 

Here's how I think early life developed:

 

1) An atmosphere with CO2, methane, and ammonia forms.
2) Lightning and UV produce HCN, formaldehyde, and small amounts of glycolaldehyde.
3) HCN in water is hydrated to formamide and ammonium formate.
4) In the presence of borate and initiated by glycolaldehyde, formaldehyde forms ribose complexed with borate.
5) Formamide and ammonium formate solutions are concentrated by evaporation, and heated by geothermal heat, forming nucleobases.
6) Nucleobases condense with ribose to form nucleosides.
7) Corrosion of iron phosphide, perhaps from meteorites, creates inorganic polyphosphate and some nucleotides with cyclic phosphate bonds.
8) Purine nucleotides with cyclic phosphate bonds polymerize, forming RNA oligomers.
9) Some of the RNA oligomers happen to be ribozymes that catalyze triphosphorylation of nucleosides using inorganic polyphosphate, and RNA polymerase ribozymes that produce RNA from triphosphorylated ribonucleosides.
10) Wind spreads droplets containing ribozymes.
11) Mutations during RNA replication create new ribozymes.
12a) Cell membranes, DNA, and ribosomes are developed in some order.
12b) Growth involving substrate-level phosphorylation from sulfur oxidation, probably using nitrate and adenylyl-sulfate reductase.
13) ATP synthase is developed, using a cell membrane proton gradient.
14a) Photosynthesis using a light-driven H+ pump protein.
14b) An oxygen-sensitive CO2 fixation method is developed, probably the Wood-Ljungdahl pathway.
15) Growth of photosynthetic microbes causes the Great Oxidation Event.
16) CO2 fixation using the reverse citric acid cycle displaces the (oxygen-sensitive) Wood-Ljungdahl pathway.
17) The Calvin cycle is developed.

 

If this is correct, then ATP and GTP go all the way back to the origin of life.

 

 

possible variations

 

What aspects of abiogenesis were necessary? What differences from life on Earth could extraterrestrial life (hereafter "EL") reasonably have?

Could EL be based on silicon instead of carbon? No, silicon compounds don't support the necessary chemical reactions.

Could EL use arsenic instead of phosphorus? No, arsenate esters aren't stable enough.

Would EL use the same nucleobases as DNA and RNA? If EL originated from formamide condensation, then I think EL genetic material would contain purine and pyrimidine nucleobases, but some minor structural variations of nucleobases are possible. If there's some other route, then EL genetic material would probably be very different.

If EL uses the same nucleobases, then it would probably use nucleoside triphosphates to carry energy, which would likely be ATP and GTP, but the roles of ATP and GTP could easily be reversed.

Would EL use 2-amino acids for enzymes? I think so.

- Esters are much less stable than amides, and have much weaker self-interactions.
- Aminotransferases would convert between 3-amino acids and 3-keto acids, which spontaneously decarboxylate.
- 4-amino acids would be hard to make, too big for good proteins, and tend to form 5-membered rings.
- 5-amino acids would be hard to make, too big for good proteins, and tend to form 6-membered rings.
- 6-amino acids and higher would be much too big and very hard to make.

 

Would EL use the same amino acids? I think amino acids would be mostly the same but have some differences.

I think these would definitely be used: glycine, alanine, serine, aspartate, glutamate.

I think phenylalanine and tyrosine would probably be used by EL, produced via the shikimate pathway. Some sort of amino acid containing a benzene ring would definitely be used, and the shikimate pathway seems like the easiest way to make that.

Imidazole and thiazole are needed for the active sites of some enzymes. Histidine is logical as an amino acid containing imidazole, but maybe a cofactor like thiamine could be used instead.

Would EL ribosomes use the same basic mechanism of codon-tagged amino acids? Yes, I think so.

Would EL codons be the same? No, codons are arbitrary.

Would cellulose be used by EL? I think so; it's the strongest thing you can reasonably make out of sugars.

Would EL plants use the Calvin cycle? I think the chance of that is <50%. There are several CO2 fixation mechanisms in microorganisms, but they require higher CO2 concentrations than the Calvin cycle. Still, there are more-efficient possibilities that work at low CO2 concentrations; here's an example.