Archive for the ‘ATP’ 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
stuff on the immune system and that recent pandemic: 1 – how to get lost in a single cell
got that?
Canto: So, looking way back to the Covid-19 year or two, which we survived (and I’m wondering if the virus has too), have we retained what we’ve learned from all those Medcram videos we watched, and from the various ‘vaccine hesitant’ characters we encountered…
Jacinta: One of whom was a nurse as I recall, but I must say, mind like a sieve, I don’t feel I’ve retained much, so we’re reading Nobel Prize-winning immunologist Peter Doherty’s An insider’s plague year, to help us set down some info and promote our lifelong learning.
Canto: So what’s the difference between a drug and a vaccine, Doherty asks, noting that even experienced journalists confuse the two. Drug of course is a broad term, for anything chemical used to treat people, by pill, injection, bottle, patch or suppository. At the beginning of his ‘plague journal’ Doherty mentions two drugs I recall from our Medcram viewings, hydroxychloraquine, an anti-malarial, and remdesivir, ‘an experimental anti-Ebola drug’.
Jacinta: Yes, hydroxychloraquine was touted early on in the year (2020) as being of some use. A USA site, Drugbank online, said this:
Chloroquine and hydroxychloroquine are both being investigated for the treatment of SARS-CoV-2
followed by this:
The FDA emergency use authorization for hydroxychloroquine and chloroquine in the treatment of COVID-19 was revoked on 15 June 2020.
Remdesivir seems to have been somewhat more effective in reducing symptoms, as was seen earlier in treating MERS-CoV sufferers. It received the FDA’s authorisation just a few weeks before the other drug’s authorisation was revoked.
Canto: The word drug features in the USA’s FDA (Food and Drug Administration), while in Australia we have the TGA (Therapeutic Goods Administration), and therapeutic is simply medicalese for drug. The first of these tended to be natural remedies such as quinine, a useful anti-malarial extracted from Cinchona tree bark. Tonic water has quinine in it, hence the name. Another natural anti-malarial is artemisinin, from sweet wormwood. These ingredients, extracted and purified, have been extremely important in combatting the biggest killer disease in the global south.
Jacinta: In treating SARS-CoV2, remdesivir was the only effective antiviral in the first 12 months, apart from – monoclonal antibodies. I’ve heard of them, now I’m going to try and explain them. I’ll start with this quote from the Mayo Clinic:
Monoclonal antibodies are laboratory-produced molecules engineered to serve as substitute antibodies that can restore, enhance, modify or mimic the immune system’s attack on cells that aren’t wanted, such as cancer cells.
Antibodies (aka immunoglobulin, of which there are 5 types) are Y-shaped proteins that can bind to specific antigens (the foreign nasties) via a lock-and-key mechanism. Monoclonal antibodies, as mentioned above, have been particularly effective in some cancer treatments.
Canto: Well, only this month our TGA has posted an update on the decreased effectiveness of monoclonal antibodies against emerging SARS-CoV2 variants:
emerging data show that anti-spike protein monoclonal antibodies demonstrate a significant decrease in their in-vitro neutralising activities against many newer circulating SARS-CoV-2 variants, particularly Omicron and its subvariants.
Jacinta: Mmm. So let’s go on with our very basic training in immunology. So it’s the organs of the lymphatic system – the lymph nodes, the thymus, the spleen and the bone marrow – that produce or harbour and further develop our immune cells. Now, these immune cells come in different types with different names, such as phagocytes, which are a type of white blood cell (WBC)…
Canto: Yes, this immune system stuff might require dozens or hundreds of posts. Phagocytes can be ‘professional’ or non-professional’ depending on effectiveness. The professionals include neutrophils, macrophages, mast cells, dendritic cells and monocytes – all WBCs. They’re all more or less good at detecting antigens. And I believe these WBCs form what’s called the innate, rather than adaptive, immune system.
Jacinta: So getting back to the SARS-CoV2 Betacoronavirus – we’ll be jumping around a lot in these posts, methinks – it has this thing called a spike protein on its outer coat, and this protein has a receptor-binding domain (RBD) with binds to the angiotensin-converting enzyme (ACE) receptor, or ACE2 receptor. ACE2 receptors exist throughout the body but the principal pathway for this virus involves the epithelial cells at the base of the lungs and in the blood vessels. So I’m reading a Nature article, referenced below, entitled ‘Mechanisms of SARS-CoV-2 entry into cells’, and I want to frame this stuff in my own words to understand it. Apparently ACE2 is the receptor for other Betacoronaviruses and Alphacoronaviruses, so immunologists and virologists are pretty familiar with it.
Canto: Yes, and there’s all this terminology – for example a virion is the whole viral particle – not just the DNA or RNA core and its proteins but the external envelope – everything that allows it to exist extra-cellularly. So a coronavirus virion is made up of nucleocapsid and other proteins, including the spike proteins that facilitate entry into potential host cells via the ACE2 receptors.
Jacinta: So let’s focus for now on the nucleocapsid (N) protein. Another Nature article, with multiple authors, has this title: ‘The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA’, which sounds ominous. And the article starts with a problem:
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood.
Yes, especially by me. I get that these N proteins bind and ‘package’ the RNA, but I don’t get ‘phase separation’…
Canto: Phase separation is a key biological concept, it seems, but complex, and probably something that requires lab work to fully comprehend. Here’s a quote from ScienceDirect that might help:
Many biological macromolecules, such as proteins and nucleic acids, exert their biological functions by forming phase-separated condensates, and phase separation is closely related to various human diseases. Gene transcriptional regulation is an indispensable part of gene expression and normal function in cells. Its abnormal regulation often causes the occurrence of different diseases. In recent years, the occurrence of phase separation during transcriptional regulation has become an area of intense research.
It sounds like problems with phase separation may lead to irregular transcription, or vice versa, resulting in variants, mutations and such, but I’m guessing.
Jacinta: So reading further into the ScienceDirect article, you’re right, it’s near impossible to understand this stuff just through reading – you surely need to see it happening in cells. And cells, such as our own, are effing complex. Here’s another (long) quote to prove it:
In cells, which are the basic unit of the structure and function of organisms, the need for various components to perform their corresponding functions at the correct time and space is a problem that cells continuously need to solve. To this end, cells have evolved a set of organelles, including membrane-encapsulated organelles (such as mitochondria, nuclei, lysosomes, the Golgi apparatus, and endoplasmic reticulum) and membrane-less organelles (such as nucleoli, Cajal bodies, stress granules, P bodies, U bodies, and signaling bodies) …. Membrane-encapsulated organelles enclose specific proteins, nucleic acids and other substances to perform their functions within a particular space. Still, how other types of membrane-less organelles form and exert their biological functions has eluded investigators for many years. In recent years, it has been discovered that different intracellular biological macromolecules assemble and separate from each other to form liquid-like structures called “biomolecular condensates”….
and it goes on. It’s dauntingly complex, but I must say I wish I was 40 years younger and working in this fascinating field. To work out more precisely the processes involved and then to be able to manipulate them…
Canto: Homo deus indeed.
Jacinta: Femo deus if you don’t mind, and that’s not even a recognised term. I just can’t wait for the 31st century.
Canto: Well let’s just stay in the shallows and say a few words about these membraned and unmembraned intracellular organelles. Mitochondria we know a bit about, the ATP-yielding (making?) organelles that existed separately eons ago as prokaryotes…
Jacinta: Thank the indefatigable iconoclast Lynn Margulis for presenting this argument, and endosymbiosis in general, against vociferous mostly male opposition…
Canto: Lysosomes are the ‘digestive system’ of the cell, containing enzymes that break down the polymeric structures of proteins, lipids, nucleic acids and carbohydrates. They vary greatly in size depending on the digestive tasks they work on. The Golgi apparatus or complex is, unsurprisingly, a complex organelle that packages proteins to be sent out into the intracellular or intercellular world – nuff said. The endoplasmic reticulum has two sub-units, rough and smooth. They’re kind of attached to the nuclear membrane of the cell, the smooth further out than the rough. It’s involved in transportation and protein folding, let’s say no more.
Jacinta: So now to the membrane-less organelles – but it looks like phase transition as a subject for analysis is about how these organelles transition from dormant to active states or how they transition from one task to another. Anyway, just a few words to introduce these organelles. Nucleoli are defined briefly as ‘small dense spherical structures in the nucleus of a cell during interphase’. They also appear to segregate in unexpected ways as cells divide – again something about phase transition. Cajal bodies are often associated with nucleoli and are involved in the processing of some RNA molecules. They appear to have other roles that aren’t yet fully understood. Stress granules are these changeable, dynamic, liquid-solid entities made from RNP (ribonucleoprotein). P bodies are somewhat similar, as are U bodies, named for being ‘uridine-rich’, whatever that may mean. In any case P and U bodies appear to act co-operatively. Signalling bodies, according to Khan Academy:
A signaling molecule is released by one cell, then travels through the bloodstream to bind to receptors on a distant target cell elsewhere in the body.
Canto: Okay, that’s enough terminology, and we won’t do all the references as nobody reads this stuff anyway.
Jacinta: Fine, we’re having fun, though it may take till doomsday to get our heads around this stuff. Wish I could afford a lab, and all its equipment….
References
Peter Doherty, An insider’s plague year, 2021
https://go.drugbank.com/drugs/DB01611
https://www.nejm.org/doi/full/10.1056/nejmoa2007764
https://www.tga.gov.au/news/news/update-effectiveness-monoclonal-antibodies-against-covid-variants
Abiogenesis – LUCA, gradients, amino acids, chemical evolution, ATP and the RNA world
Jacinta: So now we’re thinking of the Earth 4 billion years BP, with an atmosphere we’re not quite sure of, and we want to explore the what and when of the first life forms. Haven’t we talked about this before?
Canto: Yeah we talked about the RNA world and viroids and abiogenesis, the gap between chemistry and biology, inter alia. This time we’re going to look more closely at the hunt for the earliest living things, and the environments they might’ve lived in.
Jacinta: And it started with one, it must have. LUA, or LUCA, the last universal common ancestor. Or the first, after a number of not-quite LUCAs, failed or only partially successful attempts. And finding LUCA would be much tougher than finding a viroid in a haystack, because you’re searching through an immensity of space and time.
Canto: But we’re much closer to finding it than in the past because we know so much more about what is common to all life forms.
Jacinta: Yes so are we looking definitely at the first DNA-based life form or are we probing the RNA world again?
Canto: I think we’ll set aside the world of viroids and viruses for now, because we want to look at the ancestor of all independently-existing life forms, and they’re all DNA-based. And we also know that LUCA used ATP. So now I’m going to quote from an essay by Michael Le Page in the volume of the New Scientist Collection called ‘Origin, Evolution, Extinction’:
How did LUCA make its ATP? Anyone designing life from scratch would probably make ATP using chemical reactions inside the cell. But that’s not how it is done. Instead energy from food or sunlight is used to power a protein ‘pump’ that shunts hydrogen ions – protons – out of the cell. This creates a difference in proton concentration, or a gradient, across the cell membrane. Protons then flow back into the cell through another protein embedded in the membrane, which uses the energy to produce ATP.
Jacinta: You understand that?
Canto: Sort of.
Jacinta: ‘Energy from food or sunlight is used..’ that’s a bit of a leap. What food? The food we eat is organic, made from living or formerly living stuff, but LUCA is the first living thing, its food must be purely chemical, not biological.
Canto: Of course, not a problem. I believe the microbes at hydrothermal vents live largely on hydrogen sulphide, and of course sunlight is energy for photosynthesising oganisms such as cyanobacteria.
Jacinta: Okay, so your simplest living organisms, or the simplest ones we know, get their energy by chemosynthesis, or photosynthesis. Its energy, or fuel, not food.
Canto: Semantics.
Jacinta: But there are other problems with this quote re abiogenesis. For example, it’s talking about pre-existent cells and cell membranes. So assuming that cells had to precede ATP.
Canto: No, he’s telling us how cells make ATP today. So we have to find, or synthesise, all the essential ingredients that make up the most basic life forms that we know – cell membranes, proteins, ATP and the like. And people are working towards this.
Jacinta: Yes and first of all they created these ‘building blocks of life’, as they always like to call them, amino acids, in the Miller-Urey experiments, since replicated many times over, but what exactly are nucleic acids? Are they the same things as nucleic acids?
Canto: Amino acids are about the simplest forms of organic compounds. It’s probably better to call them the building blocks of proteins. There are many different kinds, but generally each contain amine and carboxyl groups, that’s -NH2 and -COOH, together with a side chain, called an R group, which determines the type of amino acid. There’s a whole complicated lot of them and you could easily spend a whole lifetime fruitfully studying them. They’re important in cell structure and transport, all sorts of things. We’ve not only been able to create amino acids, but to combine them together into longer peptide chains. And we’ve also found large quantities of amino acids in meteorites such as the Murchison – as well as simple sugars and nitrogenous bases. In fact I think we’re gradually firming up the life-came from-space hypothesis.
Jacinta: But amino acids and proteins aren’t living entities, no matter how significant they are to living entities. We’ve never found living entities in space or beyond Earth. Your quote above suggests some of what we need. A boundary between outside and inside, a lipid or phospho-lipid boundary as I’ve heard it called, which must be semi-permeable to allow chemicals in on a very selective basis, as food or fuel.
Canto: I believe fatty acids formed the first membranes, not phospho-lipids. That’s important because we’ve found that fatty acids, which are made up of carbon, hydrogen and oxygen atoms joined together in a regular way, aren’t just built inside cells. There’s a very interesting video called What is Chemical Evolution?, produced by the Center for Chemical Evolution in the USA, that tells about this. Experimenters have heated up carbon monoxide and hydrogen along with many minerals common in the Earth’s crust and produced various carbon compounds including fatty acids. Obviously this could have and can still happen naturally on Earth, for example in the hot regions maybe below or certainly within the crust. It’s been found that large concentrations of fatty acids aggregate in warm water, creating a stable, ball-like configuration. This has to do with the attraction between the oxygen-carrying heads of fatty acids and the water molecules, and the repulsion of the carbon-carrying tails. The tails are forced together into a ball due to this repulsion, as the video shows.
fatty acids, with hydrophobic and hydrophilic ends, aggregating in solution
Jacinta: Yes it’s an intriguing video, and I’m almost feeling converted, especially as it goes further than aggregation due to these essentially electrical forces, but tries to find ways in which chemical structures evolve, so it tries to create a bridge between one type of evolution and another – the natural-selection type of evolution that operates upon reproducing organisms via mutation and selection, and the type of evolution that builds more complex and varied chemical structures from simpler compounds.
Canto: Yes but it’s not just the video that’s doing it, it’s the whole discipline or sub-branch of science called chemical evolution.
Jacinta: That’s right, it’s opening a window into that grey area between life and non-life and showing there’s a kind of space in our knowledge there that it would be exciting to try and fill, through observation and experimentation and testable hypotheses and the like. So the video, or the discipline, suggests that in chemical evolution, the highly complex process of reproduction through mitosis in eukaryotic cells or binary fission in prokaryotes is replaced by repetitive production, a simpler process that only takes place under certain limited conditions.
Canto: So under the right conditions the balls of fatty acids grow in number and themselves accumulate to form skins, and further forces – I think they’re hydrostatic forces – can cause the edges of these skins to fuse together to create ‘containers’, like vesicles inside cells.
Jacinta: So we’re talking about the creation of membranes, impermeable or semi-permeable, that can provide a safe haven for, whatever…
Canto: Yes, and at the end of the video, other self-assembling systems, such as proto-RNA, are intriguingly mentioned, so we might want to find out what’s known about that.
Jacinta: I think we’ll be doing a lot of reading and posting on this subject. I find it really fascinating. These limited conditions I mentioned – limited on today’s Earth surface, but not so much four billion years ago, include a reducing atmosphere lacking in free oxygen, and high temperatures, as well as a gradient – both a temperature gradient and a sort of molecular or chemical gradient, from more reducing to more oxidising you might say. These conditions exist today at hydrothermal vents, where archaebacteria are found, so researchers are naturally very interested in such environments, and in trying to replicate or simulate them.
Canto: And they’re interested in the boundary between chemical and biological evolution, and reproduction. There are so many interesting lines of inquiry, with RNA, with cell membranes….
Jacinta: Researchers are particularly interested in alkaline thermal vents, where alkaline fluids well up from beneath the sea floor at high temperatures. When this fluid hits the ocean water, minerals precipitate out and gradually create porous chimneys up to 60 metres high. They would’ve been rich in iron and sulphide, good for catalysing complex organic reactions, according to Le Page. The temperature gradients created would’ve favoured organic compounds and would’ve likely encouraged the building of complexity, so they may have been the sites in which the RNA world began, if it ever did.
a hydrothermal vent off the coast of New Zealand. Image from NOAA
Canto: So I think we should pursue this further. There are a lot of researchers homing in on this area, so I suspect further progress will be made soon.
Jacinta: Yes, we need to explore the exploitation of proton gradients, the development of proton pumps and the production of ATP, leaky membranes and a whole lot of other fun stuff.
Canto: I think we need to get our heads around ATP and its production too, because that looks pretty damn complex.
Jacinta: Next time maybe.