Cooperative binding & Allostery - Hemoglobin pt 1

Hemoglobin’s the reason your blood can take oxygen from your lungs to your toe & the Bohr effect helps hemoglobin know when & when not to let go! I hope it wouldn’t bore you if I discuss the Bohr effect - it’s the reason the hemoglobin in your blood chooses whether to oxygen bind or eject! Yawning? Then you’re taking in oxygen which hemoglobin will take to tissues in need, those with lots of CO₂ but little O₂. And it’s thanks to the Bohr effect that this molecular magic it can do!
note: I accidentally say negative cooperativity would have a negative Hill coefficient, but I meant it would have a Hill coefficient less than 1 (but positive). Sorry!!!
blog form (originally posted a couple years ago, but I’m busy with some very non-boring stuff): bit.ly/bohreffect
The textbook-y explanation, and then a deeper, bumblier look. The Bohr effect describes how low pH (acidity) lowers the affinity of hemoglobin for oxygen, making hemoglobin more likely to offload oxygen in areas of low pH, which for reasons I’ll get into, tissues in need of oxygen tend to have. So how does it work? Well first, what is hemoglobin?
Hemoglobin is this protein in your blood that picks up oxygen from your lungs and takes it all the way to your toes. We’ve talked about it a lot in terms of when it doesn’t work - like in sickle cell disease where mutations cause it to clump up and block blood vessels, cutting off circulation to tissues and organs, and causing pain and organ damage. bit.ly/sicklece...
But we haven’t talked much about hemoglobin when it does work. So that’s what I want to tell you about today - how hemoglobin “knows” when to take or give up oxygen - and how we know how it “knows.” It’s a really cool protein - it has 4 subunits which can each take an oxygen and they work as a team so that one binding makes it easier for the others to bind and one letting go makes it easier for the others to let go. This is called cooperativity - and we’ll talk more about what causes it in a bit. But this kind of take-all or dump-all approach with respect to oxygen means that it has to be tightly regulated so that it doesn’t all get dumped too soon. And the hemoglobin doesn’t just retake what it dumps. And, as we’ll see, the Bohr effect helps with both of these.
Often “respiration” is used to describe breathing, but biochemists often talk about respiration in terms of the processes that take place in your cells to use the oxygen (O₂) you get when you breath to make energy. The basic idea of cellular respiration is that you breathe in oxygen, combine it with breakdown products of things like glucose (blood sugar) to make the energy storage molecule ATP, and generate carbon dioxide (CO₂) that you breathe out as a waste product in the process. That has to occur in cells all throughout your body. So oxygen has to be able to get to all of those cells. And you have CO₂ being produced in all of those cells. But you only have oxygen entering your body in one place - your lungs.
Your lungs might not seem that big, but they use their allocated space wisely. They have a branching structure with the branches ending in tiny grape-like parts called alveoli which are covered with tiny little blood vessels called capillaries. They’re tiny in terms of diameter, but huge in terms of surface area, so they can let lots of oxygen in. It’s an easy route for free oxygen to get in - it just has to diffuse through the cell membrane, which is easy for it because it’s so small. Diffusion’s basically just random molecule moving - it leads to a net movement of molecules from where they’re more cramped (areas of high concentration) to places where they’re less cramped (areas of low concentration) until the concentration is equal everywhere. The molecules still move around randomly but because their movement is random, for each molecule “moving left” there’s another one “moving right” so there’s no net movement and no net change in concentration anywhere once a system reaches equilibrium.
When it comes to reporting concentrations of gases, people frequently talk in terms of partial pressures. The “partial” comes from the fact that when you have a gas or a mixture of gases, the total pressure is proportional to the number of gas molecules, not their identity (e.g. either 1000 CO₂ gas molecules OR 1000 O₂ gas molecules would produce the same pressure). So, instead of counting individual gas molecules, you can get information about how many gas molecules there are by measuring the pressure. And since the identity of the gas doesn’t matter, you can add the pressure contribution of different gases (their partial pressures) together to get the total pressure (e.g. a mixture of 1000 CO₂ gas molecules AND 1000 O₂ gas molecules TOGETHER would have a total pressure proportional to 2000 gas molecules).
finished in comments

[@krishanuchoudhury7943]

I just love your way of teaching and making others understand🎉😊

[@thebumblingbiochemist]

Thanks so much! I'm so happy it helps you understand!

[@krishanuchoudhury7943]

Actually I have a query I have some difficulties in understanding some topics of Lehninger should I use both Voet&Voet along with Lehninger!

[@thebumblingbiochemist]

If that helps!

[@thebumblingbiochemist]

So, when we talk about a higher partial pressure of oxygen, that means that there’s a higher concentration of oxygen. So places where there’s a lot of oxygen available (like your lungs when you breathe in) have high partial pressure of oxygen, whereas places where there’s not a lot of oxygen available (like your toes) have low partial pressures of oxygen. Why care? The concentration of oxygen determines how likely a hemoglobin is to bump into an oxygen atom, and the affinity of hemoglobin for oxygen determines how likely the oxygen is to “stick” to the hemoglobin and stay stuck if that encounter occurs. If the affinity is low, you’ll need a lot of bump-intos in order to get all the hemoglobin subunits bound to oxygen (full saturation). It’s kinda like buying a lot of lottery scratchers where the odds of any ticket being a winner are really low. But if the affinity is high (each scratcher has a high chance of being a winner) you don’t need as high of an oxygen concentration to reach the same saturation level (you reach the same prize total with fewer scratchers). So you can make an “oxyhemoglobin dissociation curve” plotting the partial pressure of oxygen (pO₂) (in mmHg or torr or atm) on the x-axis against the hemoglobin saturation on the y-axis. The less affinity hemoglobin has for oxygen, the less likely it is to bind it if it bumps into it. So it needs to have more “bumping into it“ encounters, so it requires higher pO₂ to reach the same amount of saturation, say 50% (this is referred to as the P50 value, with normal P50 being ~27 mmHg). So things that make hemoglobin want to unload instead of reload give you a rightward shift, whereas things that make hemoglobin want to hold on tighter give you a leftward shift. And the curve you’re shifting is sigmoidal (S-shaped), which is a sign of cooperative binding. Remember how I said hemoglobin has 4 subunits (typically 2 copies of a β globin subunit & 2 copies of an α globin subunit)? Each of those subunits is a separate protein chain. And they bind each other, but they also each bind a non-protein molecule called heme. more on that here: bit.ly/hemeahprnai But basically, heme is this ring-full thing that binds iron. And that iron can bind oxygen. And each globin subunit has one, so each complete hemoglobin can bind up to four oxygens. And they bind “cooperatively” - basically this means that, instead of each subunit just doing its own thing as if the others didn’t exist, binding of oxygen at one site affects how much the other sites want to bind oxygen. And, in the case of hemoglobin, the cooperativity is positive - binding of oxygen to one site makes the other sites more likely to bind oxygen (more on why later). And this makes it so that you don’t need there to be a ton of oxygen for hemoglobin to take all it can get. But it’s reversible binding, so it also means that if one site lets go of its oxygen, the rest quickly follow, kinda like an all-or-nothing take or dump. This gives you the sigmoidal (S-shaped) curve. So how to keep it from dumping it all too soon? And from just retaking what it dumps? It could - if it can find oxygen again (molecules like to diffuse away remember) which is one of the reasons why places like the lungs, where there’s plenty of oxygen to easily find (high partial pressures of oxygen) have mostly oxygen-holding hemoglobin. But you need more control than just that or else oxygen wouldn’t be released until your tissues were majorly oxygen-deprived. So we need a way to shift the curve in different tissues based on their oxygen needs. And this requires changing the affinity, not just the oxygen concentration. And this is where the Bohr effect comes in, shifting the curve to the right (favoring release at lower oxygen concentrations) in the tissues that need oxygen. It’s able to do this because it’s not just that those tissues have less oxygen - they also have more CO₂. Because - in addition to not having as easy an oxygen supply, the reason they have less oxygen is because they’ve used what they’ve gotten. And when they use it, they make CO₂. And CO₂ doesn’t just wait around doing nothing - a protein enzyme (reaction mediator/speed-upper) called carbonic anhydrase takes it, and water (another byproduct of respiration) and combines them to make carbonic acid, H₂CO₃. And this takes us to an aside about acids. An acid (in one definition) is a molecule that can donate a proton (H⁺). Atoms are the basic units of elements (hydrogen, carbon, oxygen, etc.) and they’re made up of smaller parts called protons (positively-charged), neutrons (neutral), & electrons (negatively-charged). The protons and neutrons gang up in a dense central nucleus & the electrons are more free to roam around in an “electron cloud” surrounding the nucleus. Atoms can share pairs of electrons to form strong covalent bonds. But sometimes they don’t share fairly - oxygen, for example, is a major electron hog (highly electronegative) so it pulls shared electrons closer to itself. And poor little hydrogen, which only has a single positive proton to pull back with, doesn’t stand much of a chance, so sometimes it “breaks off” leaving its electron behind, and thus that hydrogen is now just a single proton without an electron to balance it, so it has a positive charge, H⁺. These “break-offs” (more technically called “deprotonations” or “proton dissociations”) can happen in a lot of different molecules and, as a result, you can get lots of free protons wandering around. And when you have such a scenario we call something “acidic.” Not many protons and we call something “basic” or “alkaline” (pH of 7 is typically where we draw the line). pH? How’d you sneak in? pH is a measure of how many free protons there are in a solution. But it’s an inverse log, so the higher the concentration of protons (more acidic), the lower the pH and vice versa - the lower the concentration of protons (less acidic/more basic) the higher the pH. The log part just makes it so that the numbers we’re dealing with are smaller - because even in a basic solution, there are a lot of proton break-offs. One such place it can occur is that carbonic acid we made from the CO₂. H₂CO₃ can “dissociate” into its “conjugate base” bicarbonate, HCO₃⁻. It’s called a conjugate base because, having lost a proton, it can now act as a base, which is something that then accept a proton. So, the process is reversible H₂CO₃ ⇌ H⁺ + HCO₃⁻ That protonation/deprotonation doesn’t require any enzymatic help or anything, so how does it determine which direction to go? Concentrate on the concentrations! At the extreme, if you have no H₂CO₃, you can only go left, but if you have a lot of H₂CO₃, the reaction is driven to the right. And what determines how much H₂CO₃ there is? The CO₂ it’s made from! (produced during cellular respiration) CO₂ + H₂O ⇌ H₂CO₃ So overall you have CO₂ + H₂O ⇌ H₂CO₃ ⇌ H⁺ + HCO₃⁻ So, the more cellular respiration (energy-making), the more CO₂ & H₂O. And the more of those, the more H₂CO₃ you make. And the more H₂CO₃ there is, the more protons you produce. And the more protons there are, the more acidic the solution (lower the pH). But pH is just a measurement - it tells us about how many protons are on the loose, but not what they then do… Once that proton is released from carbonic acid, or any other acid, it can seek out new binding partners. And, when it spies hemoglobin, it likes what it sees… Which is a good thing because, for one thing, if it didn’t find a new partner your blood would get super acidic. By binding protons, hemoglobin is able to serve as a pH buffer, keeping the pH from dropping too low. But, binding the proton has another effect - it causes hemoglobin to like oxygen less (it lowers the oxygen affinity). So it gives up its oxygen - right where you want it to - the tissues that have spent most of their oxygen. And, still proton-bound and thus not wanting oxygen, it doesn’t just grab that oxygen right back. You might be wondering - how does a single proton do all that?! I know I was… So I looked into what was happening at the structural level - and I think it’s really cool - it involves protein shape-shifting (conformational change). A protein gets its shape (structure) from a combination of factors, at the heart of which is the “primary structure” - which is the sequence of amino acids (protein letters). Those letters have generic parts that let them link together and unique parts (side chains or “R groups”) that stick off like charms from a charm bracelet - except that some of the charms like some of the other charms but want to avoid others - some like water, some don’t - so the protein tries to fold up to accommodate them all, but it’s restricted - the protein backbone can only rotate certain ways, some of the chains are big & bulky, etc. So each protein, with its unique sequence of amino acids will settle on some 3-D shape. But if some other molecule comes to interact with them, they can “shape-shift” a bit because they now have new preferences to take into consideration.

[@thebumblingbiochemist]

This “shape-shifting” is more formally referred to as a conformational change, with the different shapes being called conformations. They can be subtle, like just a few amino acids rotating a little. Or they can be dramatic, like whole sections of the protein shifting hinge-like. Since the amino acids are linked up, a “small” change in one place - like a single proton latching on to a single charm - even far away from the place where the exciting stuff happens (e.g. the oxygen-binding sites) can cause a sort of “ripple effect” that can lead to changes in those other sites that change what goes on there. We call this “allosteric regulation” Hemoglobin has 2 main shapes - a taut state (T) and a relaxed state (R). The taut (T) state is the one that’s proton-bound and oxygen-lacking (deoxyhemoglobin). And the relaxed (R) state is the one that likes oxygen (and when it binds oxygen we can refer to the oxygen-bound form as oxyhemoglobin). In the pics you can see some figures I made from crystal structures of deoxyhemoglobin (PDB ID 2hhb) representing the T state and oxyhemoglobin (PDB ID 1hho) representing the R state. In the T state, the subunits are connected more tightly because they have additional inter-sbunit “salt bridges.” When you hear “salt” you might think of table salt, which is NaCl. Like any salt, it’s a “neutralized” thing that it has a positive part (Na⁺) and a negative part (Cl⁻) connected through an “ionic bond” (a strong, full-charge-based attraction). Proteins can also have positive and negative parts because certain amino acid side chains can be positively or negatively charged depending on the pH and thus their protonation state. The amino acids Aspartate (Asp, D) and Glutamate (Glu, E) tend to be negatively-charged at physiological (bodily) pH, whereas Lysine (Lys, K) & Arginine (Arg, R) are almost always positively-charged. Histidine (His, H) can also be positively-charged, but it’s more “give or take-y” at normal pH. It’s kinda on the borderline and if pH decreases (maybe because of that CO₂ thing…) there are more protons to take, so it will and you get a positively-charged His. Which can then form one of those ionic bonds with a negatively-charged amino acid - like Asp. This happens at the interfaces of the hemoglobin subunit - the last (C-terminal) residue of the β chain is a His (β His146). And when it’s protonated, it forms a salt bridge with another amino acid (β Asp94). Those are in the same chain, but it has the effect of shifting His so that it can interact with an Asp in the neighboring α chain too (α Lys40). This interaction is through the β chain’s “tail” - the free C terminus. The “C” in C terminus stands for “carboxyl” and it refers to the carboxylic acid (COOH) group, which, at bodily pH is typically in its conjugate base, “carboxylate” form, COO⁻. So you have another negative charge, which is now near that positively-charged Lys, so you get an interchain salt bridge (β His146 to α Lys40) in addition to the intrachain one (β His146 to β Asp94). And this stabilizes the “T state” that has a lower affinity for oxygen. But at higher pH, His is neutral, so it can’t form that intrachain salt bridge that swings it into position to form that interchain salt bridge, so hemoglobin “relaxes” into the R state. And that R state is the one that likes to bind oxygen. So, we now have a structural biochemical explanation for the Bohr effect - at lower pH, there are more protons available to find & bind hemoglobin, so oxygen-less hemoglobin is in its taut form (T), which doesn’t like oxygen as much. And, there’s less free oxygen available even if it wanted to bind. As a result, you get a net offloading of oxygen into tissues that, thanks to lots of CO₂ from spending the oxygen they got before, are acidic and have low partial pressures of oxygen. Conversely, in the lungs, where there’s plenty of oxygen and you can just breathe out CO₂ without having to worry about it acidifying things so the pH is lower, free hemoglobin is less likely to be in the T form and, if it is, there’s enough O₂ to have enough bumping into its so that even though it has a lower affinity, it will eventually bind - and when it does you get a shift to the relaxed (R) form, where it’s happy to take up oxygen. And thanks to the positive cooperativity, the other sites follow suit - the cooperativity comes in part because, when oxygen binds, it tugs on the heme a little causing it to “de-pucker,” so you get one of those allosteric ripple-effect shape-shift that encourages binding of oxygen at the other sites. Even though I’m focusing today mainly on when all “goes right” with hemoglobin, there are times when, even if the hemoglobin itself is structurally sound - no mutations or anything - the Bohr effect can “go wrong”… This is because it’s based on there being more CO₂ where you need oxygen in order to get the needed acidity for the His to protonate and those salt bridges to form and stabilize the T state that promotes the unloading of oxygen. But if there’s not enough CO₂ (hypocapnia), the pH won’t be lowered. This can happen when you hyperventilate - you’re really just making things worse for yourself because you’re exhaling CO₂ without taking in enough O₂ to compensate. So you’re reducing the pH-lowering Bohr-effect-ing power that makes hemoglobin want to give up oxygen where it’s needed. And you’re not taking in much oxygen to be able to give up even if it wanted to. The reason people tell you to breathe into a paper bag is because it forces you to rebreathe in that CO₂. In addition to panic-induced hyperventilation, which hopefully won’t last long, chronic hyperventilation can occur in patients with asthma, cystic fibrosis, etc. that make it hard to get enough oxygen - in order to get enough oxygen they have to expel CO₂ faster than they go through it, so they can have chronic hypocapnia. Hypocapnia refers to lower than usual (hypo) amounts of CO₂, whereas hypercapnia refers to higher levels of CO₂, which leads to acidification (acidemia), which gives you a right-shift in the oxygen dissociation curve (more likely to give it up). There are other ways that hemoglobin is regulated, including via a molecule called 2,3-Bisphosphoglyceric acid (2-3-BPG), which binds hemoglobin and causes a right-ward shift. It’s produced during glycolysis (the initial, non-oxygen-requiring) part of the sugar breakdown pathway. So if you have increased glycolysis under hypoxic (low-oxygen) conditions, you make more 2-3-BPG without making a lot of CO₂, but you still get a right-shift (phew!) Also, don’t confuse carbon dioxide (CO₂) with carbon monoxide (CO). CO₂ (indirectly, through the Bohr effect) causes hemoglobin to release oxygen. But CO directly prevents oxygen from binding in the first place - it binds in oxygen’s “parking spot” in an almost irreversible fashion - it binds ~200x tighter, so order to get it to leave you have to use super high oxygen concentrations to compete it out - so patients with CO poisoning are treated with hyperbaric oxygen therapy where they’re given 100% oxygen. CO also stabilizes the R form, so it’s happy to bind oxygen at non-CO bound sites, but less happy to ever give it up, and it doesn’t cooperate with cooperativity, so you get a left shift in the dissociation curve and a reduction in sigmoidal shape. link to English translation of first description of Bohr effect - straight from the (translated) mouth of Bohr himself: bit.ly/2OGB6Wh                                                more about all sorts of things: #365DaysOfScience All (with topics listed) 👉 bit.ly/2OllAB0 or search blog: thebumblingbiochemist.com