Archive for the ‘carbon’ Category
abiogenesis is heavy, man
So, once more into the breach, let’s try and have fun with abiogenesis. It supposedly starts with organic compounds, generally considered as carbon-based, though I’ve heard tell of the possibility of silicon-based life – presumably you want to start with an element that combines readily with others, and those elements, but carbon in particular, fit the bill. Hydrocarbons, the simplest of which is methane (CH4), are an obvious example. However, as far as I’m aware, we haven’t been able to bridge the gap between non-life and life, inanimate and animate, chemistry and biology, in any clear-cut way in our laboratories and experiments. Membranes, self-replications, chains, autocatalysis are all more or less required, but nobody seems to have any clear idea of how and when it all started here. There may have been a few starts that then ended, until one didn’t. Here’s a bit from Wikipedia:
Life functions through the chemistry of carbon and water, and builds on four chemical families: lipids for cell membranes, carbohydrates for chemical energy storage and structural composition, amino acids for protein metabolism, and the nucleic acids DNA and RNA for heredity. A theory of abiogenesis must explain the origins and interactions of these classes of molecules.
Sounds like hard work, especially the genetic stuff. So I’ll start with amino acids, since I don’t have a clue… We get them from food, essentially, but what is food but living stuff, organic stuff, and so goes the circle. But let’s keep going. They were first discovered/identified in the early 1800s, the first being asparagine, from asparagus, in 1806. Apparently our bodies need twenty types of these carbon-based molecules, strings of which, or chains of which, form proteins. Of those twenty, eleven can be made by our bodies, and are labeled non-essential, while the other nine, the essential ones, must be obtained by food. All in all they’re important for brain chemistry, hormone production, and for maintenance and repair of muscle, skin and organ tissues.
But how did amino acids come to be? And what’s the difference between L and D types of amino acids? Apparently they’re like the mirror image of each other which makes me think of chirality which I barely understand. Britannica starts one of its articles with this:
The question of why organisms on Earth consist of L-amino acids instead of D-amino acids is still an unresolved riddle. Some scientists have long suggested that a substantial fraction of the organic compounds that were the precursors to amino acids—and perhaps some amino acids themselves—on early Earth may have been derived from comet and meteorite impacts. One such organic-rich meteorite impact occurred on September 28, 1969, over Murchison, Victoria, Australia.
… which is interesting but doesn’t help much, though it’s certainly a cause for wonder. Anyway, the video referenced below tells me that of the 20 amino acids that build proteins in our body, 19 are chiral. Then one particular amino acid, alanine, is focussed on, as it’s one of the simplest enantiomers – pairs of molecules that are mirror images of each other, and so un-super-imposable.
So this molecular biology is about life-sustaining molecules but not quite organisms, and nobody knows precisely how complex molecules become organisms – otherwise we’d be having fun creating new life forms, and only gods are allowed to have that kind of fun.
So we haven’t made life yet, but we’re getting there?
I’ve heard of course of an RNA world that might have preceded the DNA one, so let’s go there for a while. Nucleotides, nucleic acids, nucleosides, nucleobases and such all have to be understood and connected together to make sense of it all. So from here on in it will be attempted definition after attempted definition, with further attempts to connect them all together.
So what about prebiotic synthesis? Or, to quote another video referenced below, ‘location… where can we find the satisfactory chemistry required to make bioactive molecules? And what were these first biomolecules? We must surely need water and carbon – that’s what life as we know it requires, at a minimum. Then there’s nitrogen, key to building proteins (amino acids being nitrogen-based), and RNA and DNA for ‘information’. And phosphorous, essential for building many biomolecules, ATP for cellular energy, and phospholipids for cell membranes. Also referenced are amphiphiles (never heard of them) for forming primitive cells. They’re made from phospholipids so I’m not sure of the difference, just as I’m not sure of the difference between lipids and fatty acids – and did somebody mention tryptophan…? You need largely to be there in the labs being educated by the experts, and observing and experimenting.
The discovery in quite recent times of hydrothermal deep ocean vents and the chemo-synthesised, sunlight-free ecosystems they support, has added fuel, such as hydrogen sulphide, to the quest for the earliest life forms. But, to quote Phy the Neutrophil:
In an alkaline vent environment, the conditions for chemistry heavily disfavour the formation of cells. While hydrothermal vents do have the chemistry to make long-chain fatty acids, the harsh salty environment of the ocean is going to make it very difficult for these proto-membranes to form.
Mr Phy likes the Darwinian idea of a warm little pond, but also recognises that this too has its problems. In any case, some kind of cell or capsule formation, however or wherever it may have evolved, would be a major advance. Creating an enclosed micro-environment is likely to speed up the process of effective chemical development, and Mr Phy goes into much detail on this, and its alternatives, but of course I’m not strong on biochemistry, so proton gradients haven’t triggered my neurons.
But I must soldier on. AI has this to say on proton energetics:
All life uses proton gradients across membranes to drive energy production via ATP synthase. Because building proton pumps requires pre-existing energy, scientists propose that life began in alkaline hydrothermal vents, where natural geological pH gradients across inorganic pores provided the first proton-motive force before biological pumps evolved.
Adenosine triphosphate (ATP) , which I know is associated with mitochondria in humans, and is always called the ‘energy molecule’, or the energy storage molecule, as Wikipedia puts it, relies on this ATP synthase enzyme, which catalyses ATP using ADP (adenosine diphosphate) and inorganic phosphate. It gets very complicated with protons being pushed along an electrochemical gradient so that ATP can be stored by cells for future use.
Of course the evolution of ATP synthase, like so much in the make-up of the earliest life forms, is obscurely ancient, but well worth exploring as it appears to be central to all life. Wikipedia goes into hellish detail about it all, which is impressive and exhausting. I’m not sure if I can go on…
References
https://en.wikipedia.org/wiki/D-Amino_acid
https://www.britannica.com/science/amino-acid/Amino-acids-and-the-origin-of-life-on-Earth