Archive for the ‘light’ Category
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
towards James Clerk Maxwell 5: a bit about light
Canto: Our last piece in this Maxwell series dealt with the apparently irrelevant matter of Newton’s laws of motion…
Jacinta: But not irrelevant in that Newton was so seminal to the foundation of, and mathematisation of, modern physics, and he set the course…
Canto: Yes and we’ll have to go back to his work on gravity to really get a feel for the maths side of things I think.
Jacinta: No doubt, but in keeping with our disorganised approach to out topic I’m going to fast forward to give a partial account of Maxwell himself, before he did his major work. Maxwell was clearly indefatigably curious about the physical world even in childhood. He was conducting various chemical, electrical and magnetic experiments at home and later at the University of Edinburgh, from his early teens, and writing papers – the first at the age of fourteen – which were accepted by the Royal Society of Edinburgh, though he was considered too young to present them himself.
Canto: But we’re going to focus here on his focus on light, since we’ve been going on mostly about electricity and magnetism thus far. Light, and its wave properties, is something we’re going to have to get our heads around as we approach Maxwell’s work from various angles, and it’s horribly mathematical.
Jacinta: Yes, the properties of polarised light were among Maxwell’s earliest and most abiding areas of interest and research, so we need to understand what that’s all about.
Canto: Okay, here’s a simple definition of the term ‘polarisation’. It’s ‘a property applying to transverse waves that specifies the geometrical orientation of the oscillations’. That’s from Wikipedia.
Jacinta: That’s not simple. Do you understand that?
Canto: No, not yet. So waves are generally of two types, transverse and longitudinal. A moving wave oscillates. That’s the up-and-down movement you might see on a graph. In a transverse wave, the oscillations are at right angles to the movement of the wave. Light waves are transverse waves apparently, as opposed to sound waves, which are longitudinal – in which the wave oscillates, or vibrates, in the direction of propagation. That doesn’t make immediate sense to me, but for now we’ll focus on transverse light waves and polarisation. A light wave, we now know, is an electromagnetic wave, but don’t worry about that for now. Let me try to explain unpolarised light. The light from the sun is unpolarised, as is your bedroom light or that from a struck match. The light waves from these sources are vibrating in a multitude of directions – every direction, you might say. Polarised light is light that we can get to vibrate on a single plane, or in some other specific way..- .
Jacinta: So how do we polarise light is presumably the question. And why do we call it polarised?
Canto: I don’t know why it’s called polarised, but it’s light that’s controlled in a specific way, for example by filtration. The filter might be a horizontal grid or a vertical grid. Let me quote two sentences from one of many explaining sites, and we’ll drill down into them:
Natural sunlight and almost every other form of artificial illumination transmits light waves whose electric field vectors vibrate in all perpendicular planes with respect to the direction of propagation. When the electric field vectors are restricted to a single plane by filtration, then the light is said to be polarized with respect to the direction of propagation and all waves vibrate in the same plane.
So electric field vectors (and we know that vectors have something to do with directionality, I think) are directions of a field, maybe. And a ‘field’ here is an area of electric charge – the area in which that charge has an influence, say on other charges. It was Michael Faraday who apparently came up with this idea of an electric field, which weakens in proportion to distance, in the same manner as gravity. A field is not actually a force, but more a region of potential force.
Jacinta: It seems we might have to start at the beginning with light, which is a huge fundamental force or energy, which has been speculated on and researched for millennia. I’ve just been exploring the tip of that particular iceberg, and it makes me think about how particular forces or phenomena, which are kind of universal with regard to humans on our modern earth, are taken for granted until they aren’t. Think for example of gravity, which wasn’t even a thing before Newton came along, it was just ‘natural’ that things fell down to earth. And think of air, which many people still think of as ’empty’. Light is another of those phenomena, but it’s been explored for longer than the others because it’s much more variable and multi-faceted, at least at first glance haha.. Darkness, half-light, firelight, shadow effects, the behaviour of light in water, rainbows and other tricks of light would’ve challenged the curious from the beginning, so it’s not surprising that theories of light and optics go back such a long way.
Canto: Yes and the horror of it – for some – is that mathematics is key to understanding so much of it – especially trigonometry. But returning to those electric field vectors – and maybe we’ll go back to the beginning with light in the future, – in a light wave, the oscillations are the electric and magnetic fields, pointing in all directions perpendicular to the wave’s propagation.
Jacinta: Yes, I get that, and polarised light limits all those perpendicular directions, or perpendicular planes, to one, by filtration, or maybe some other means.
Canto: Right, but notice I spoke of electric and magnetic fields, which is why light is described as an electromagnetic wave. It should also be pointed out that we tend to call them light waves only in the part of the spectrum visible to humans, but physics deals with all electromagnetic waves. Our eyes, and it’s different for many other species, detect light from a very small part of the entire wave, or electromagnetic, spectrum. Wavelengths of less than about 380 nanometres (even less when we’re young) at the ‘ultraviolet’ end, and of more than about 750 nm at the long ‘infrared’ end, form the visible spectrum for humans. Beyond UV light we have x-rays and then gamma rays, and beyond the infrared we have microwaves and then radio waves.
Jacinta: I wonder if Maxwell knew about all this in his day.
Canto: We’ll no doubt find out…
References
https://en.wikipedia.org/wiki/Transverse_wave
https://www.physicsclassroom.com/class/light/Lesson-1/Polarization