In my last post I talked about the role of molecules within cells. I noted that they are like timing belts. However, I left open the mechanism by which these timing belts are transported into cell and taken out, when transformed into waste.
In this post, I’m going to talk about the transport of oxygen into cells. The topic is at the same time familiar to me but has a lot of unknowns. I’ll try my best to manage not to be too wrong.
Two of the most important things about oxygen transport that I have knowledge over both relate to shape. First is the diameter of heme and second is the overall shape and dimensions of red blood cells. Heme is the molecule contained in hemoglobin that binds oxygen. Oxygen, naturally, is what drives metabolism.
Heme
The basic structure of heme is a porphyrin core: the same as with chlorophyll. And porphyrin is a molecule I’m very familiar with, as I’ve both synthesized porphyrin compounds and done photochemistry with it. Both porphyrin and heme have an absorption peak of ca. 420 nm, called a soret peak. In the post about chlorophyll I remarked that this peak reflects the size of a ring of light (not a single photon, though) that is absorbed by the collection of molecules. We saw that in the case of chlorophyll, you do see rods of the molecules, but you also need enzymes mixed with the chlorophyll molecules to capture the energy of the light captured by the rod.
In the case of heme, it isn’t too different. Heme is trapped inside a protein hemoglobin, with a ratio of four hemes to hemoglobin (in mammals). It makes up 96 % of the dry weight of red blood cells, or erythrocytes. At first glance the red color of porphyrin and red blood cells seems to be caused by individual molecules, as the four hemes makes up roughly 3.8 weight percent of the total mass of hemoglobin (heme = 616.487 g/mol, hemoglobin = 65248 g/mol). Also, it doesn’t help that heme is rather scattered in hemoglobin, so it seems extra odd that there would be an aggregate effect of a cluster of hundreds of nanometers long.
Hemoglobin
In this paper researchers cut a red blood cell open to see how the cytoskeletal protein spectrin is distributed. In the paper, the distribution of spectrin is clearly visible, but hemoglobin itself does not seem to reveal clear structure. For now, I’m forced to own up to my ignorance. The heme molecules must be somehow connected to each other, but I have no idea how. This almost 50-year-old paper says that there is an absence of heme-heme interactions in hemoglobin. However, as each heme binds an oxygen molecule, it is possible that is the oxygen molecule that somehow connects neighboring hemes. Possibly it is not useful to think of the capture of light in terms of spherical shells, as in the explanation of hydrogen lines, but more like fractal antenna, used in cell phones. My hunch is that the shape of hemoglobin is exactly what is required to enable the capture and release of oxygen.
While it’s also likely that the supramolecular structure is connected via the rest of the hemoglobin, all of the absorption peaks seen in the hemoglobin spectrum should correspond to these ‘fractal antenna’. That is, somehow all of the absorption peaks correspond to interconnected supramolecular structures. I just don’t know how.
Next, we compare deoxygenated (oxygen-free) hemoglobin with oxygenated hemoglobin and observe one clear distinction. This is the absorption peak at around 760 nm in the deoxygenated hemoglobin. Curiously, this is the same peak as that of oxygen. While I’m by no means the first person to note this, this correlation does not mean as much if one does not consider it to represent a physical structure. But if we consider oxygen to be composed of loops of 760 nm in diameter, what we can assume to happen in the oxygenation of hemoglobin in the lungs is that the supramolecular structure of hemoglobin physically captures a loop of oxygen. In this process, the iron of heme incorporates an oxygen molecule into it, and the supramolecular peak disappears.
UV-Vis spectra of hemoglobin and oxygen
So, we have no idea what the fractal antenna of heme in hemoglobin in red blood cells looks like, but we have a clue that it exists from the binding of oxygen. Slightly dissatisfactory, but much better than nothing.
Next, we’ll look at the shape of the whole red blood cell. Why does it look the way it does: like a miniature beanbag chair? The common answer is to increase surface area. While not exactly wrong, the good next question is how does this shape form. The width of the red blood cell is ~7500 nm, whereas the peak of black body radiation at 37 °C is ~9350 nm. If we fit a red blood cell between two spheres of 9350 nm, we see that the fit is quite snug. The smallest diameter in the center corresponds to the diameter of oxygen and the diameter of the toroidal section is 2600 nm is pretty close to the diameter of water vapor. I couldn’t say whether the matching of the shape is at least in part by coincidence, but it certainly is something to think about.
Red blood cell fitted between two spheres with a diameter of black body radiation at 37 °C
Next, I must talk about the elephant in the room, which is the monster of an equation describing the intensity of black body radiation. This is Planck’s law:
which is quite a mouthful. You can try to figure it out by reading the Wikipedia page of black body radiation, but honestly, it’s not at all intuitive. However, you can increase the intuitiveness by considering that it involves Planck spheres, each with the speed of c, and their number proportional to the cube of the diameter λ of the quantum state and involves the emission of rings with a diameter of λ and a speed of c. So if we rewrite the equation as a function of λ instead of ν (ν = c/λ), we get
We’re not fully in the clear yet. The Boltzmann constant has to be still explained, but at least it remains constant. Then we have the curious case of temperature, T. The definition of temperature is quite unsatisfying. Wikipedia says: “Temperature is a physical quantity that expresses the hotness of matter or radiation.” The International System of Units, or SI, says that the thermodynamic temperature is defined by the mean average kinetic energy, E, of an individual particle, or
Next, we need to describe kinetic energy. Kinetic energy, as we might remember from high school physics, is:
So
or
or conversely
Here we see that the temperature is the rotational component of the speed of the Planck spheres in orbit. Or here I see. It might take a bit of getting used to, if you haven’t been thinking about for long.
But why the complex equation? It goes to show that if you know your mathematics, you can figure things out much before you know what’s really going on. It’s important to note that none of the preceding mathematics are wrong.
But if the maximum intensity of black body radiation is not the same as the maximum wavelength of radiation, then where do these larger rings of light come from? The most honest answer is that I don’t know yet. But if I had to hazard a guess, I think it’s a phenomenon of smaller rings of light fusing into larger rings. As the rings are being emitted from the object at a specific temperature, the probability of rings fusing once is higher than them fusing several times. This way the long tail is just probabilities.
And the curious thing is that the additional rotational energy isn’t about the increase of speed of the Planck spheres, but about the orbital being physically stretched to allow a larger rotational component. The Planck spheres at the z axis (this confusingly representing both the rotating supramolecular shell, as well as the molecular orbital) are moving tangentially to the orbital, whereas the further from the z axis the Planck spheres get, the higher their rotational component. To get more energy to the system, you must introduce more Planck spheres to the system. And even to maintain their rotation, and equal amount of energy needs to be absorbed as is emitted as black body radiation. As to why the previous mathematical description would also apply, when this proposed explanation seems so different, all I can say is that there is no inherent reason for why they couldn’t both be true. The concept of energy has always been rather vague, apart from E = mc², which is in complete agreement of the addition of more matter into a quantum state when it is sped up.
But honestly, what I’ve written here should again be taken with a generous pinch of salt. It’s not that I think I’m wrong. It just that many of the ideas I have are so new that errors can remain. Possibly even large ones. The biggest question is my interpretation of the wavelength of peak for the black body radiation. I've plotted the equation above and used two different black body radiation calculators, and all of them give slightly different results. This is apparently at least in part to do with whether one deals in Watt space or photon space. However, even if the numbers are slightly off, this shouldn't change the overall conclusions.
Comentarios