Posts Tagged ‘oxygen’
oxidised by hydrogen escape…? Chasing the origins of life…
first life? something tiny and green?
I’ve been intrigued and mystified by this phrase (among many others) in Oliver Morton’s book on photosynthesis, the chemistry of which I’m really struggling with. I first read the book a decade or so ago, and in this second reading I’m really beginning to understand how little I’ve understood about the process so central to life on Earth. So, as I too often do, I’ll start with AI (never lies):
Oxidation by hydrogen escape is a planetary process where light hydrogen atoms permanently drift into space from a planet’s upper atmosphere. Because hydrogen is lost, leftover oxygen atoms and other heavy molecules chemically bind to crust and mantle rocks. This leaves the planet’s surface and interior permanently oxidized over geologic time…
I don’t fully understand this. Light hydrogen atoms are also known as protium, which is the most common and lightest isotope of hydrogen (AI again). It’s just a proton in a nucleus. So this drifting off of light hydrogen in an atmosphere, leaving oxygen, etc behind, suggests that the atmosphere must have contained water vapour, inter alia?
So there are further explanations. Ultraviolet sunlight breaks apart water vapour in the upper atmosphere, as well as methane CH4), The hydrogen, being light and fast-moving, escapes the atmosphere, while the heavier elements, such as oxygen, drop down to the planetary surface, and, for example react with iron in the crust.
So what’s with this oxidising thing? It’s a bonding in particular with iron and manganese and appears to have a connection with the Great Oxidation Event (GOE). According to Science Direct, ‘oxygenic photosynthesis appears to be necessary for an oxygen-rich atmosphere like Earth’s’. Are there other kinds of photosynthesis? Apparently so – anoxygenic photosynthesis is used by some bacteria, with hydrogen sulphide being the likely electron donor, but let’s not get side-tracked…
Atmospheric oxygen today is at around 21% concentration, and this is known as PAL, the present atmospheric level by volume. The GOE has been calculated as a 200 million-year transformation occurring about 2.4 billion years ago, bringing about a relatively rapid rise in atmospheric O2…
So, our atmosphere is layered: nearest the ground and rising about 12 kilometres is the troposphere, and above that is the stratosphere (up to 50 kms), then the mesosphere (85), the thermosphere (600) and finally the exosphere, where it thins out into space and where satellites are mostly situated. But to complicate matters we also have the homosphere, and at its upper boundary the turbopause. This ‘sphere’ is so called due to its more or less uniformity. To quote AI it’s ‘the lower layer of the atmosphere where constant mixing by wind and turbulence keeps the chemical composition uniform’.
So when did our atmosphere stabilise, assuming it ever has? Again, I find this is divided into periods, the first one being ‘primordial outgassing’, some 4.5 to 4 billion years go, ‘As early Earth cooled, volcanic outgassing created a thick, toxic precursor atmosphere mostly made of water vapour, carbon dioxide, and nitrogen’. And the Smithsonian Environmental Research Centre goes on, re the Archaean Eon, during which:
methane droplets in the air shrouded the young Earth in a global haze. There was no oxygen gas on Earth. Oxygen was only in compounds such as water. Complex chemical reactions in the young oceans transformed carbon-containing molecules into simple, living cells that did not need oxygen to live. Instead they made energy out of sulphur and other elements.
It also points out that in this early phase of our planet’s life the sun was only around three quarters as bright as it is now – it has gotten brighter over time. The Earth was prevented from freezing over by the greenhouse gases, mostly CO2 and CH4 (methane). But over time, cyanobacteria began to flourish in the oceans, and they were photosynthesising, making free oxygen gas from CO2, H2O and the sun’s light, and so creating something like the atmosphere we know today.
So what exactly are cyanobacteria and why did they come to exist, and then flourish? As to when – likely not before 3 billion years ago, at least not in great numbers. As to where – in the oceans, which were more plentiful, a ‘water world’, according to you know what. And as to how, that’s of course more complex and uncertain. AI gives this not-so-satisfactory explanation:
- Ancestral Microbes: Early Earth had an anoxic (oxygen-free) atmosphere filled with methane and carbon dioxide.
- New Biochemistry: Single-celled anaerobic bacteria in the oceans evolved specialised cell membrane structures.
- Splitting Water: These organisms harnessed sunlight to split water molecules (H2O) and carbon dioxide into sugars for energy.
- Oxygen Waste: The process released oxygen gas (O2) as a waste product, which built up over time and triggered the [GOE]
So, it’s all about ‘ancestral microbes’ and ‘anaerobic [meaning ‘sans oxygen’] bacteria’. So, the ‘life from non-life’ problem presumably remains unsolved. Understandable, I suppose.
References
https://www.sciencedirect.com/science/article/pii/S0009254113003513
https://en.wikipedia.org/wiki/Anoxygenic_photosynthesis
https://arxiv.org/html/2512.09844v1
the photosynthesis challenge
c’est bien simple…
So I wrote last time about my non-career in science, with a promise to myself that I might try to get my head around photosynthesis. So, years ago I read Oliver Morton’s fiendishly difficult book, Eating the Sun, and all I clearly remembered about it was that there were two types, simply named type 1 and type 2, and that the processes are very very very complex, and took decades to unravel. And a feeling that it was all over my head. Or that one had to be there, in those labs, or chatting at science conferences with the experts, as Morton no doubt was, to have a chance of getting my dull head around it all. And yet, never say never…
So I’m rereading Morton’s book (published in 2007 – has more been nailed down about the processes since?), having nothing better to do – and that isn’t meant as an insult – and I’m currently about a quarter of the way through. What I note is that Morton intermixes the undeniably complex science with interesting character sketches of the major researchers and theorists, and descriptions of the mostly mid-twentieth century background of war and conflict (at least in this early part of the book). My aim here though is self-education, so I’ll be focussing entirely on the science as far as I can grapple with it. So there will be no names, just a lot of ‘this breakthrough led to a new avenue of research’, etc.
So, photosynthesis is about using sunlight as sustenance. Of course, water is also required, and CO2. The devil’s in the detail, and there’s an awful lot of it..
So, where to begin. Chlorophyll, I suppose. That’s the green pigment in the chloroplasts of plants and algae. They absorb light, mostly from the sun. But what does this mean? And how did we come to know this?
Chloophyll is green because the green area of the light spectrum is reflected, while blue and red light is trapped, mostly. So, though plants ‘eat’ sunlight, they don’t eat the green part of that light, which is fascinatingly counter-intuitive.
As to these chloroplasts, these key sub-cellular elements in plants and algae, they’re a product of endosymbiosis, the colonisation of eukaryotic cells by earlier microbes – bacteria or their ancestors. Mitochondria, the engines of ATP through oxidative phosphorylation (wateva), are another such product.
Which brings me to photophosphorylation in plants, as useful and interesting a starting point as any. This process, originally called photosynthetic phosphorylation, might be expected to be carried out by mitochondria in plants, as it is in mammals, but plant biologists noted that ‘the leaf cells with the greatest number of chloroplasts – the cells that do the bulk of the photosynthesis – contain remarkably few mitochondria’ (Morton, p76).
Phosphorylating, as I understand it, involves adding a phosphate to ADP (adenosine diphosphate) to create adenosine triphosphate (ATP), the principal ‘energy molecule’. Another such molecule is NADPH (Nicotinamide Adenine Dinucleotide Phosphate), of which more later, perhaps. They are both important in plants, and are key to what became known as the Calvin-Benson cycle, a set of chemical reactions (independent of light) within chloroplasts as a part of photosynthesis. These reactions convert CO2 from the atmosphere into sugars for energy.
There are apparently two main stages to photosynthesis, the light-dependent stage and the light-independent stage (aka the Calvin-Benson cycle, or even the Calvin-Benson-Bassham cycle). The light-dependent stage occurs inside the thylakoid membranes of the chloroplasts. Here’s Wikipedia:
Thylakoids are membrane-bound compartments inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis. Thylakoids consist of a thylakoid membrane surrounding a thylakoid lumen. Chloroplast thylakoids frequently form stacks of disks referred to as grana (singular: granum). Grana are connected by intergranal or stromal thylakoids, which join granum stacks together as a single functional compartment.
In thylakoid membranes, chlorophyll pigments are found in packets called quantasomes. Each quantasome contains 230 to 250 chlorophyll molecules.
So that’s something about thylakoid structure. Now to function. Or maybe not – it’s all so complex. The thylakoid proteome (set of individual proteins) consists of at least 335 protein types, of which 89 are in the lumen or central cavity. At this stage it’s calculated that about 42% of these proteins are involved in photosynthesis.
Jumping away from all this, it’s important to note that for us mammals, the essential value of photosynthesis is that it creates, or releases, oxygen. Think of the great oxygenation event, mainly involving oceanic cyanobacteria, ‘about 2.4 billion years ago, shortly after the end of the Archaean’, according to Morton (p175). So how does that oxygenising aspect of photosynthesis work?
But I was going to write about the light-dependent part of photosynthesis, requiring sunlight and water. It’s called photosystem 1, and Wikipedia calls it ‘a vital membrane protein complex that uses light energy to transfer electrons from plastocyanin to ferredoxin, producing NADPH and helping generate ATP.’ So, digging slightly deeper, plastocyanin is ‘a small copper-containing protein that acts as a mobile electron carrier in the photosynthetic electron transport chain of plants, green algae and cyanobacteria’, and ferredoxins are ‘small iron-sulphur proteins that act as electron carriers in a wide variety of biological redox reactions’.
Now, NADPH is, of course, ‘the reduced form of nicotinamide adenine dinucleotide phosphate’ which acts as ‘a key electron donor and energy carrier’ in various processes, including photosynthesis. So, my guess is that these movements of electrons create chemical changes, and a moment’s research tells me that’s what redox reactions are all about. In oxidation, electrons are lost, which takes the oxidation number up (the substance is oxidised), and in reduction they’re gained, which takes it down, and the substance is reduced.
In oxidation, electrons are lost, which takes the oxidation number up (the substance is oxidised), and in reduction they’re gained, which takes it down, and the substance is reduced.
Ok so that’s enough for now, there’s so much more to explore – rubisco, the z scheme… I cannot help but feel that it’s not light yet, but it’s getting there, to non-paraphrase Dylan….
References
Oliver Morton, Eating the Sun, 2007
a little about the chemistry of water and its presence on Earth
So I now know, following my previous post, a little more than I did about how water’s formed from molecular hydrogen and oxygen – you have to break the molecular bonds and create new ones for H2O, and that requires activation energy, I think. But I need to explore all of this further, and I want to do so in the context of a fascinating question, which I’m hoping is related – why is there so much water on Earth’s surface?
When Earth was first formed, from planetesimals energetically colliding together, generating lots of heat (which may have helped with the creation of H2O, but not in liquid form??) there just doesn’t seem to have been a place for water, which would’ve evaporated into space, wouldn’t it? Presumably the still-forming, virtually molten Earth had no atmosphere.
The most common theory put out for Earth’s water is bombardment in the early days by meteors of a certain type, carbonaceous chondrites. These meteors were formed further out from the sun, where water would have frozen. Carbonaceous chondrites are known to contain the same ratio of heavy water to ‘normal’ water as we find on Earth. Heavy water is formed with deuterium, an isotope of hydrogen containing a neutron as well as the usual proton. Obviously there had to have been plenty of these collisions over a long period to create our oceans. Comets have been largely ruled out because, of the comets we’ve examined, the deuterium/hydrogen ratio is about double that of the chondrites, though some have argued that those comets may be atypical. Also there’s some evidence that the D/H ratio of terrestrial water has changed over time.
So there are still plenty of unknowns about the history of Earth’s water. Some argue that volcanism, along with other internal sources, was wholly or partly responsible – water vapour is one of the gases produced in eruptions, which then condensed and fell as rain. Investigation of moon rocks has revealed a D/H ratio similar to that of chondrites, and also that of Earth (yes, there’s H2O on the moon, in various forms). This suggests that, since it has become clear that the Moon and Earth are of a piece, water has been there on both from the earliest times. Water ice detected in the asteroid belt and elsewhere in the solar system provides further evidence of the abundance of this hardy little molecule, which enriches the hypotheses of researchers.
But I’m still mystified by how water is formed from molecular, or diatomic, hydrogen and oxygen. It occurs to me, thanks to Salman Khan, that having a look at the structural formulae of these molecules, as well as investigating ‘activation energy’, might help. I’ve filched the ‘Lewis structure’ of water from Wikipedia.
It shows that hydrogen atoms are joined to oxygen by a single bond, the sharing of a pair of electrons. They’re called polar covalent bonds, as described in my last post on the topic. H2 also binds the two hydrogen atoms with a single covalent bond, while O2 is bound in a double covalent bond. (If you’re looking for a really comprehensive breakdown of the electrochemical structure of water, I recommend this site).
So, to produce water, you need enough activation energy to break the bonds of H2 and O2 and create the bonds that form H2O. Interestingly, I’m currently reading The Emerald Planet, which gives an example of the kind of activation energy required. The Tunguska event, an asteroid visitation in the Siberian tundra in 1908, was energetic enough to rip apart the bonds of molecular nitrogen and oxygen in the surrounding atmosphere, leaving atomic nitrogen and oxygen to bond into nitric oxide. But let’s have a closer look at activation energy.
So, according to Wikipedia:
In chemistry and physics, activation energy is the energy which must be available to a chemical or nuclear system with potential reactants to result in: a chemical reaction, nuclear reaction, or various other physical phenomena.
This stuff gets complicated and mathematical very quickly, but activation energy (Ea) is measured in either joules (or kilojoules) per mole or kilocalories per mole. A mole, as I’ve learned from Khan, is the number of atoms there are in 12g of carbon-12. So what? Well, that’s just a way of translating atomic mass units (amu) to grams (one gram equals one mole of amu).
The point is though that we can measure the activation energy, which, in the case of molecular reactions, is going to be more than the measurable change between the initial and final conditions. Activation energy destabilises the molecules, bringing about a transition state in which usually stable bonds break down, freeing the molecules to create new bonds – something that is happening throughout our bodies at every moment. When molecular oxygen is combined with molecular hydrogen in a confined space, all that’s required is the heat from a lit match to start things off. This absorption of energy is called an endothermic reaction. Molecules near the fire break down into atoms, which recombine into water molecules, a reaction which releases a lot of energy, creating a chain of reactions until all the molecules are similarly recombined. From this you can imagine how water could have been created in abundance during the fiery early period of our solar system’s evolution.
I’ll end with more on the structure of water, for my education.
As a liquid, water has a structure in which the H-O-H angle is about 106°. It’s a polarised molecule, with the negative charge on the oxygen being around 70% of an electron’s negative charge, which is neutralised by a corresponding positive charge shared by the two hydrogen atoms. These values can change according to energy levels and environment. As opposite charges attract, different water molecules attract each other when their H atoms are oriented to other O atoms. The British Chemistry professor Martin Chaplin puts it better than I could:
This attraction is particularly strong when the O-H bond from one water molecule points directly at a nearby oxygen atom in another water molecule, that is, when the three atoms O-H O are in a straight line. This is called ‘hydrogen bonding’ as the hydrogen atoms appear to hold on to both O atoms. This attraction between neighboring water molecules, together with the high-density of molecules due to their small size, produces a great cohesive effect within liquid water that is responsible for water’s liquid nature at ambient temperatures.
We’re all very grateful for that nature.