Antibodies & B Cell Development PDF

All righty, so last class we left off just the very basics of the antibodies if you haven't seen the canvas course yet I did shift I was gonna do B cell development But I think like we did with T cells doing the receptors first made more sense to see the structure because then we can say When those...

All righty, so last class we left off just the very basics of the antibodies if you haven't seen the canvas course yet I did shift I was gonna do B cell development But I think like we did with T cells doing the receptors first made more sense to see the structure because then we can say When those receptors being rearranged the B cell development So at this point we are going to move into antibodies and I'm calling them antibodies even though obviously you guys all know They are bound to B cells. They are the B cell receptor They're only considered antibodies when they are soluble free-floating, which is what these guys are So that's what we're gonna pick up once we finish the anatomy today So like I mentioned last class I still expect you to know what primary and secondary lymphoid organs are even if we don't you know going to in-depth about thymus We've already spent enough time doing that. There's no point So we'll spend a little bit more time going through the bone marrow this the module and obviously lymph nodes and spleen Especially as they pertain to B cells Specifically you guys know tertiary still exists and the barrier tissue is pretty much the mucosal surfaces Which you guys also know In case you forgot this image, this is where all of them are We know the primaries are in red so thymus and bone marrow But most of our focus is going to be again on that bone marrow specifically with B cells since that's where they stay to develop Bless you. Everyone go get your flu and flu shots and COVID shots Things are things and if you're eligible for RSV and pneumococcus and all the different ones just get all of them Everything is circulated like all the professors like I'm out today. I got something. I'm like, oh dear god I'm gonna hide in my office for a week or longer So yes, it's it's coming. It's happening soon All of the secondary lymphoid organs are in yellow. You guys need the adenoid tonsils pyres patches I'm not going to go super in-depth with that As long as you guys know what the primary and secondary are with a focus on the bone marrow since that is what we are Focusing on that is the most important. So I did say limited in spleen I would review it just some of the areas because again You might still see something from that. There is no draw it to know it on the bone marrow But we will go through stuff in class and again just another image showing the primary lymphoid organs You guys know the thymus is one of them. We're getting a breeze right past that and focus on the bone marrow here You know already since we've covered it a lot is soft Spongy tissue that has many blood vessels in it and it's found in the center of most bones As you guys know yellow is fatty and it contains some stem cells that can contribute to cartilage fat or bone and some more of Structural cells there in the structural precursors, but all of our immune cells come from your red bone marrow Which is your blood stem cells and your matter poetic stem cells there and that's where we see that hematopoiesis and the split into the different varieties And so hematopoiesis of the red blood cells and platelets occurs primarily in the red bone marrow in adults and then as we age So think about it You have certain bone areas with certain and like our thymus rest in peace as we get older We actually do lose some of our bone marrow and it does tend to you know focus hematopoiesis on certain areas of the body So our larger bones and in this case, it's going to be our skull our sternum Our ribs our vertebrae and our pelvis a great question earlier that was asked is like is that why they do? Bone marrow transplants from your femur or your hip and yes It's because we see especially in adults a lot more bone marrow in those areas and the focus on that so that makes sense also Easy access you have to go through a little less muscle if you go through the back of the hip But that's why we go through those areas when we are doing bone marrow transplants, too Because as we get older, it's restricting to certain areas our B cells which are created there from that pneumatic Letting stem cell precursor continue to stay there as they go through their education and mature This is where they undergo their positive and negative selection And in case you're curious what it looks like here You got the yellow marrow kind of you know scattered throughout but in the red marrow we have that spongy bone here Notice there are a lot of blood vessels It's innervated all throughout because think about it your blood brings oxygen other nutrients to it And if this is the nursery where all of your baby cells are developing We'd want our nutrients to go there and our oxygen and things like that And so that's why we have tons of blood vessels scattered throughout Because it helps bring blood through and also how the cells can leave when they hypothetically go straight out to blood like red blood cells Or if they need to use those blood vessel pathways to get to the thymus to start developing further as T cells Uh bone marrow if you see the abbreviation BM and immuno it specifically means bone marrow in micro It means bowel movement so do keep that distinct between both semesters We're gonna be talking about a bone marrow for this one So it does contain contact connective tissue because think about it needs structural cells to help control it We talked about those being the particular cells. It does have blood vessels We talked about the nutrients there as well as some fat and nutrients there including the hematopoietic stem cells inside to help support as well We need that vasculature again to bring nutrients in and provide exit and entryways for various cell types to get in and out of the bone Marrow as needed cells committed to the B cell lineage remain within the B the bone marrow For further development with the exception of B1 which is pretty much as soon as they're created they sneak out So it's like if someone showed up to BMS masters on day one orientation showed up printed out a diploma and left Didn't go through any of the education said there a BMS From MUW com didn't actually go through it versus you guys the conventional B2 who are still sitting here halfway through the semester tediously going through all these steps and details And so when we talk about B cell development, it is organized based on the structure of their heavy and light chain Rearrangement and surface expression. So as we start going through, you know The bone marrow and then stages of development within the bone marrow They're organized based on when we see various heavy and light chains, which is what we're gonna start talking about today For the next pretty much two classes before moving into the actual steps and stages of development here So I'm just key Anatomy for you guys. It's mostly definitions for this one again You guys can't from a you know pathological standpoint. You see a couple cartoon images That's not enough for you guys to truly be able to define what it is some or identify it based on a picture So definitions are key for these guys here Medullary cavity in general is the hollow part of the bone that contains the bone marrow If you talk about a reticular cell we talked about those with the thymus They are structural cells are kind of the nannies of the area They provide provide foundational support and just kind of structure as the cells kind of move along as they go through development here They also help synthesize collagen and reticular fibers It again also help provide the structure of that bone marrow that allows the immune cells to move around because they're not like free- floating And they're like it's like if you had a gigantic Rope course and you're pulling yourself along the rope course That's kind of how these cells are moving through the reticular fibers and the reticular cells It also helps regulate hematopoiesis as well, and then are part of those you'll niche I jumped down so and those you'll niche here by definition complex structure with a stem cells progenitor cells your stromal cells Which are your reticular cells growth factors and extracellular matrix again those reticular fibers and support help participate in the regular regulation of hematopoiesis because again, it's the structural foundation and You separate and yet it is from the vascular niche because as we talked about it There's blood vessels scattered throughout so it's like the blood vessels are within and scattered inside of that endos do niche However, if we were specifically just talking about all the blood vessels in the blood vessel vessels network We refer to that specifically as the vascular niche So like on this picture, I wouldn't show you this picture But if I did all these blood vessels here if I said this general area we're referring to that vascular niche But notice here these are basically the yeah, it's looking through an image here These are the blood vessels quite cut through the side And so you can see that it's scattered and innervated pretty much throughout because again, you need oxygen nutrients You know if you've got a parasitic worm infection and we're sending out cytokines to tell the bone marrow to make more eosinophils You need blood vessels for the cytokines to get through and let the bone marrow know We need more eosinophils and to start producing more eosinophils And so just scattered throughout are going to be your reticular cells and within those are going to be your hematopoietic Prescursors and eventually your B cells as they kind of go through the development Unlike thymus which kind of had that nice tour of the whole tissue as the cells developed. There are no separate Locations really that would go through bone marrow development They're kind of just in the bone marrow in that industrial niche as they're developing So it's not gonna be like oh is it in the you know Corticomagillary junction. No, it's pretty much just in there within the bone marrow, which is nice but it is a good comparing contrast because You know, you do have separate regions of the thymus that T cells are going through as they develop Meanwhile B cells are just in the bone marrow So it is showing that when they leave the bone marrow They are carried in the blood to lymph nodes spleen and pyres patches shown in pink here as well as other secondary lymphoid Tissues so we could add in tonsils adenoids all the other ones in the upper respiratory tract here In order to show that that's how they move from there So they'll leave in the blood vessels and they'll travel If you guys remember that term for the blood vessel that innervates most secondary lymphoid tissues, it's a three-letter abbreviation HEV they also use the HEV to exit out into those lymphoid tissues We'll talk about that a lot more when we actually do talk about B cells moving From bone marrow to lymphoid tissues to encounter their antigen So they do get into the blood highway and travel to various secondary lymphoid tissues in order To look for their antigen and see if they can encounter what they've been trained for I would say pyres patches are fair game by identification But you guys know secondary lymphoid tissue is secondary lymphoid tissue at this point You're also scientists from last class is Astrid Fegraeus. She was one of the early PhDs She was the first to discover that plasma cells function to produce antibodies and so for this discovery She was awarded the Jubilee Prize by the Swedish Society of Medicine in 1950 She's also the first professor of immunology in Sweden because again it is still a very novel field here And she contributed to the production of the Swedish polio vaccine because again we use Antibodies and etc all kinds of fun stuff as we're making vaccines as we're making treatments and therapeutics all kinds of fun Stuff just heavily involved in immunology wonderful person unfortunately died. unfortunately died. Oh God She died before most of all were born, okay Who's that we figured out who in the class is like was anybody born in the 90s in this class? like was anybody born in the 90s in this class? Oh? Thank God, okay I'm slowly moving it was like my first year teaching there were enough students where I was like, okay, we're within a few years Moving farther and farther along and I'm like You're born in 2000. Oh God you were born after September 11th. How is that not a thing? That's a key metric in my lifetime key metric that it was I mean like signific Katrina and 9-11 key growing time points for me, and I'm like I or I'm sorry yeah He said to rub it in a little bit. Yes. I was in fourth grade You are close enough Do you remember like do you remember something was different that day or like did they tell y'all? You guys are listening to history right now. This is important You remember it. Yeah, like as long as people remember it. I'm like we're reaching the point where you're like what? You guys probably remember Katrina because you guys have been little a little like Katrina Well now you guys know hurricanes not that you guys get anything up this far But they have if you do your residencies or fellowships down in Florida Guarantee you will see them You can also do oh fun fact when you do rotations here you have electives your fourth year You are always welcome to go down and do a rotation in cities that you want to just visit So, you know plan one in Miami plan one in New Orleans have an eight-week vacation there while you're doing work If you really want to trauma, that's the place to be for trauma though Okay, so today's lecture Let's see, and of course, we're now on the trend where if I include a student's dog picture They're not here that day unless Evan specifically said my dog is gonna be in this I do not want to be here today So this is Evan's dog. He's clearly a great doggy daddy because this is I don't know if it's a birthday treat or just I hope it's just because cuz that's a very cute dog who did look at this look at this face I think they did something bad and I really want to know the story of this face here. But anyway, uh I didn't include the notes on this one. I think he said that he likes to eat socks So that's very useful information We don't have any more true homework until module four. So great job. So great job. You guys you've completed that office hours Are you know our normal scheduling and since we don't really have any exam anytime soon? have any exam anytime soon? It's in like two weeks though In case you're following along in our textbook Case you're following along in our textbook These are the orders we're now going in because it makes a little bit more sense to go kind of how your textbook structured They do talk about antibody development first So that's the order we're going through as well I'm gonna talk about B cell development and then their effector functions, which is pretty much antibody mediated immunity And so that's the new structure going through. This is my favorite video and I hope the sound is I know her I'm actually in one of her science music videos. You have to go find it now Don't let me tell you what had went down now was two bands away from getting bro whole barbershop, bro Right like compliment. They put gauze. It's just like a white night. I'm so nice a baby Let me make it tasty macrophages. They be looking they might eat it up They might fight and can't have to kill us make it hate us going night-night neutralize a pocket shot We play it in the high light blue and it is together like this white rice scary little germs run away cuz it's Right night. Everybody asking me. What's the vaccine? Check up for the right nucleic acids and proteins. Check up for the right nucleic acids and proteins. We make it just to build up here that doesn't mean It's a great way of knowing like Forbes 30 under 30 but For those paying attention What immunoglobulin molecule? What immunoglobulin molecule? Did she not mention? Igd Igd and why you think she might not have mentioned that one We still really fully know what it does based on the slides we showed earlier We do know that it does help with mast cells and basophils But as of right now again, Igd is one of the ones that really I'm not gonna say let's get rid of it because it probably has a useful function But we don't really know what that is just yet. And so science is still kind of figuring that one out So the primary ones are m g a and e and so today we're gonna go through a lot of the different structures Yes pictures are fair game That is why I include the structure function role and appearance So we're gonna go through a lot of the different structures In this or various combinations of you could get a picture where it's just the molecule Or you could have a picture with a description, especially if they're very similar and you can't really tell the difference There would have to be some additional information, but a lot of them are different enough That you can visualize the difference. This is a really cool You know, we love images scanning electron micrograph of who can guess which immunoglobulin molecule? IgM because it is the pentameric little star shaped form here and it's one of the first immunoglobulin molecules produced In the immune system here and as we know just that basic fun fact plasma cells are what secrete the antibody of the same antigen specificity As that of the antigen receptor or the b cell receptor of the cell that it differentiated from Which is why we create those plasma cells specifically from that cell why we care so much about that clonal expansion because You know, why are we expanding b cells and plasma cells for tetanus if we have coped? Not going to help you that much. So it is important that we have that specific b cell to respond here So this is just showing you a resting b cell, which means it's not really active. It's kind of be like you're naive It hasn't encountered its antigen yet versus here It's showing it binding on to a bacteria here which can help stimulate it whether it's through this or it's through t cells Telling a b cell it's time to start fighting and differentiating That can trigger it to differentiate into plasma cells Which are then responsible for secreting and cutting it all off their surface To release it out where it can then bind on to the various bacteria here overall They are composed antibody specifically and those b cell receptors are composed of polypeptides with variable and constant regions So this is very similar to that t cell receptor concept that we talk about here And again to reiterate this home I don't know i'm going to keep continuing to say this because it is such a key piece of information That b cell receptor is the surface bound Immunoglobulin it will eventually be called an antibody When the cell differentiates into a plasma cell and it is secreted off the surface But we refrain and keep that term antibody bless you for that secreted Immunoglobulin molecule when it's not attached to a cell versus when we talk about b cell receptor It's what's still bound onto the surface of that b cell And so here it's showing you the structure of them. And so these pictures are similar It's just using different colors here to highlight different portions between the two pictures here So at the very top here that n termini, that's the antigen binding site It's a tippy top and it's what binds on to the bacteria like that picture that we just looked at and so Immunoglobulin molecules are made up of heavy and light chains. These are different From our t cell receptors because again when we talked about how t cell receptor kind of just looks like this one portion of it this one fab fragment B cell receptors and antibodies are a little bit larger in general So the c termini is what's attached onto the surface of the cell The n termini is basically where the antigen binding sites are The light chains are the short small molecules on the outside. That's why they're called light. They're smaller They're lighter and the heavy chains are the ones that are actually bound to the surface of the cell They are larger therefore They are heavier and that's why they get the name heavy and light chain here The two halves and even the light chain attached to the heavy chain are held together by disulfide bonds Those are the little black lines shown here And here and the different immunoglobulin molecules do differ In the number of disulfide bonds holding them together where you will see those pictures in the future You do have generic carbohydrates on them. I'm not going to go into detail on those guys Just know that if you see this little turquoise hexagon, it is the carbohydrates bound on the surface It's also how we help differentiate the different types of immunoglobulin molecules here Now if we were just to look at a different view At the very top is that antigen binding site again that n termini portion But it's the outermost portion of those immunoglobulin molecules that are the variable regions Because they have more diversity at the top because again, that's where they are binding on to those You know antigens and the pathogens the constant regions are all at the bottom and pretty much again They're constant. They're conserved across You know different types of molecules and again, they're the stable like stability that kind of hold it there. It's the heavy The constant region of the light chain that attaches to the constant region of the heavy chain and keeps that attached there with a disulfide bond We'll also talk about hinge region. They do kind of differ in their hinge regions But in general like if my body was An immunoglobulin molecule i've got like one y here or like one arm there and then my body is like the constant region Hinges it can be in various ways. It's how they bend So the arms can kind of move and branch out and get wider or closer together It's like cheerleading or you know bend over here But typically anywhere you'll have those bends available and we'll talk about which ones can bend in different ways Those are known as your hinge region specifically here The carbohydrate was admitted from this lower picture for simplicity, but they do have it on So these are the very basic images just to teach you the foundational concepts of them We will go into more examples and details as we go on here So how we create these different molecules and it's kind of cool because we can use this kind of how they figured out the structure Of immunoglobulin molecules as they were going through it specifically here But we can use a protease which is an enzyme that breaks down proteins to actually cleave Here the hinge of each heavy chain So it kind of cuts if we imagine proteases as molecular scissors cut right here and right here And it will actually break down those dulcide disulfide bonds there in order to create three pieces You will end up with a fab fragment Another fab fragment and an fc or the constant the f constant region. That's where you get fc here When it is bound on together, so if we were describing the anatomy now, you'd still have two fab fragments and an fc Region we use the term region when it's attached because it's still a piece of something It's a chunk of something versus if we cut it We'll just call it fc fragment because if you think about a fragment, it's a piece Of something that is a nitpicky definition that I would flag Because it is important to know that if it's bound together and attached, you know a combined immunoglobulin molecules two fab fragments with An fc region, but when it's separated it's two fab fragments and one fc Fragment here specifically too you guys remember the definition of the fragment with antigen binding or fab That's a proteolytic fragment of igg specifically. That's a proteolytic fragment of igg specifically. It's just showing that this one Igg is only used for most examples, but we can also see that with the other immunoglobulin molecules Igg for simplicity's sake is kind of used as like The standard like example of what things should look like even though you have it pretty much all of them here But it consists of the light chain and amino terminal half of the heavy chain held together by a disulfide bond So for like there will be questions about this for the exam So for the exam if I were to give you this verbatim definition i'm looking for fragment with antigen binding If I were to say hey, we're going through the steps. We use a protease we cleave an iga A monomeric ig into different pieces what would be included? You could still say two fab fragments in an fc fragment Because igg is again used as that You know standard patient kind of almost but it's you know It applies to pretty much all the different immunoglobulin molecules when they're found in their monomeric form Does that make sense? Does that make sense? Does everyone understand what i'm saying? There can be different presentations of it But I do not want you to get the question wrong because you think it only applies to igg the definition just happened to use Igg but all immunoglobulin molecules like iga technically igd if I wanted to mess with it I could add protease and cleave it up a little bit more and you'd still have Two fab fragments in an fc fragment. Yes, collect Yes So the reason they teach it is basically to teach you the structure of it overall Um, but I think it's more of a tribute to history because it's how we figured out how immunoglobulin molecules are actually structured Is by scientists who went in the lab and they were like, well, we have this molecule But how is it put together? How is it created? You know using specific proteases that break specific disulfide bonds Allowed us to know that it was disulfide bonds holding it together and knowing that like the constant region is made up of all of this is because they were able to separate the different pieces and then further break them down to kind of Understand so it's still taught as a foundational like you need to know the structure of it But in terms of relevance like is this actually really going to help be that much probably not in medicine But it is a nice, you know hats off to the people who spent time figuring this out and doing these experiments Um, so unfortunately, it's one of those things that still kept in touch and they will apparently still quiz you on that in the med school Even though to be completely honest, it's really not that relevant With the exception of knowing that like a fab fragment is kind of the equivalent similarity of T cell receptor That's kind of the only like important takeaway of it. Yes Is there something holding the fc chains together? Is there something holding what too? I'm sorry. The fc chains together. Yes, you will have bonds there, too It's not shown on this one, but you will also have disulfide bonds holding it together, too Um that can also be cleaved more going through it here Also, just by definition again, these guys are definitions That would be like literally regurgitation of the definition or you know I give you the definition ask you what the definition word is So fc fragment is that proteolytic fragment of an antibody that consists of the carboxy terminal halves of the two heavy chains Disulfide bonded to each other by the residual hinge region. So it does say the disulfide bonds holding them together kind of shown there It was called fc because it was the most readily crystallized. I forgot about that fact. That's another thing. That's not really relevant but Hats off to the people who figured that one out. Uh, and so when we talk about again, it's intact immunoglobul. You can get a In a difficult question You can make an educated guess on whether the immunoglobulin molecule is still whole or not Whether we use the term fc region or fragment So that is where it's critical because if I say fc region it's implying it is still an attached whole Immunoglobulin molecule if it says it says fc fragment like the word fragment sounds it's a piece So that is an important distinction there, too In talking about the hinge region It is cool, too And again, it contributes to like it's how they figured out they get bound together and how they can kind of bend with those hinge regions And the disulfide bonds because the more flexible an immunoglobulin molecule is at the surface It allows it to bind to various things and they can be things that are farther away So, you know imagine some with a shorter wingspan You know or has you know frozen shoulder if you ever heard of that with sports You have enough scar tissue built up. You can't really move your arms around You can't really reach as far to get something on the top shelf If you can't really bend your arms as much and so the more flexibility you have in that hinge region The better it is for the immune system because like it's showing here you could reach really far away Or what if you grab a bacteria over here and it's got a buddy over there and you really want it too You can bend and grab it. And so in general ones that are a little bit more flexible Can one would argue can have a little bit better superiority in helping the immune system function here And so there are a lot of different arrangements and like we talked about what you're reading like This angle or this angle or this or like the canadian flag Signallers on the mountains. I was wildly obsessed with that as a child in case you've never heard of them They used to signal with flags. There's a whole language you could do with flags who knew These are the different molecules. I'm introducing the basics right now There are sub types of igg that we will act actually talk about a little bit more in the future But for right now again, we're easing into the various ones and again, notice how they mostly keep that standard patient You know igg shape, but we do have some differences between them like notice here Igm is a slightly longer heavy chain ige also has a slightly longer heavy chain here So where we get the names again, I mentioned last class. We don't call them by the greek alphabet letters here However, their chains are named based on the greek letters So igg comes because the heavy chain is known as gamma Igm Gets the name igm because it comes from mu. It's heavy chain here. Both of these guys are known as mu heavy chains Igd same thing you guys should know recognize delta and gamma at least mu is the new one You guys know alpha and beta too or alpha and epsilon But alpha here is the heavy chain that makes up iga And epsilon is the heavy chain that makes up ig and again notice they have differences in disulfide bonds This one because it's a tinier like harder to picture It does show a little black dots to show you have disulfide bonds here It showed it more diagonally here, but you do have disulfide bonds again connecting the light chain to the heavy chain Same thing here. They did diagonal to show it. These guys are a little bit different. It's horizontal here Um again diagonal on this one and there I notice again how there are differences like this has two disulfide bonds holding it together It also contributes if you think about the structure, you know If you have two ropes tying something together versus one, which you think is going to be a little bit stronger Two ropes, yeah, so some can be broken apart a little bit more easily than others And so that does contribute over all the different things too And so there are differences in the length of the heavy chain sea regions Locations of the disulfide bonds and the presence of a hinge region, which we will elaborate So this really doesn't have as much of a hinge here either same with ig You need this kind of extra space here because again That's the part where you can wiggle a little bit more if it's bound directly on you're a little bit more structured and stable In that way i'd say you know igm and ig kind of have more, you know frozen shoulder They can't move as much here And so they get their name based on this so say I gave you a picture of a generic Immunoglobulin molecule and I said it has the presence of a mute chain You can tell me which immunoglobulin molecule it is which would be Igm yep, and if I gave you it has heavy chain alpha IgA same thing. So epsilon gamma you guys can make those educated guesses. So definitely be careful when you're going through the exam I'll give you the information somewhere hidden. There will be an epsilon or an alpha, you know, especially if it's a picture That's generic doesn't give you enough information There will be typically a greek letter to let you know Which one it is or i'll say, you know, it's one of the ones that has four You know chunks of constant which would be igm and ig since they are a little bit longer here So when we talk about it when they are membrane bound, they are all monomers, which means they exist in a singular form here A monomer is a single mono one When they are soluble, so they're secreted. They're considered antibodies IgD IgE and IgG are the only ones that exist as monomers IgA can form both monomers and dimers if you remember that picture from before it's like two y's Thank you epsilon for this one It's two y's next to each other because their butts get attached And you have double the cool thing about that is it means now If one molecule has one binding site and two binding sites if you have two of those together, how many total do you have? Four you have four binding sites because if we stuck two of these together You have one two and on this other side imagine there was one there three and four Same with igm IgM can form a pentamer. So when we stick five of those guys together kind of bound by the butts they're all sticking out And it technically has two binding sites per molecule and you have five of them. How many total binding sites do you have? Ten ten binding sites five times two is ten So that's why we talked about that earlier With immunoglobulin molecules. Here's another protein shape that people definitely spent a lot of time figuring this one out here, too Again, it's using igg as your standard patient, but it can be applied to pretty much the other ones, too Just keep in mind some of them have different numbers of constant regions They are folded up in chains here and they're from similar shaped Immunoglobulin domains and they are folded into compact and stable protein domains giving you this nice structure here And it's showing you here that heavy chain of one heavy chain of the other and it's showing those light chain here in the pink And again, notice it did point out the other thing to know if you have subscript letters So if I see v in a subscript h do you think that's the variable region of the heavy chain or the light chain? Heavy chain here versus if I said v l it's the variable region of the Light chain if I showed you like a c and an l Is that a variable region or a constant region? Constant or isn't found on the light chain or the heavy chain? So it's very important especially with this exam that you pay close attention to stuff like that because that can make a huge Difference that if i'm asking if it's on a heavy chain or light chain, it'll be given it'll be there It's just important to go back and look for that extra piece of information like hey you absorbed it's v it's variable You jumped to the rest of the question But you missed that it mentioned that it was out on the heavy chain versus the light chain that can make a difference So just be very careful as we're going through it. It will be clean cut It's not like i'm gonna make like a size two font h It will be obvious and present, but it's important to know They also number the constants from top to bottom. So from farthest away to the cell to the bottom So if I talk about ch one i'm talking about the constant heavy region that's the top Like towards the antigen binding site up here and then it goes down. So one two three So if I was looking at this picture here, I'd count constant one two three One two three four make sense They count from top to bottom So that's the structure on there and again It's just showing you a lot of different presentations of the same thing Just so you guys get comfortable with the structure function things like that like that outer portion. We have those little binding grooves That's again where we have the antigen binding sites at that very top here Just so there's no confusion. We will talk about cdr again. The cdr is the same as hvr or hv Um, they're basically the same hv and hvr. So if I said cdr who remembers what that is See, it will at least what it stands for Complementarity determining region And then hvr or hv is hyper variable And so the antigen binding sites that very tippy top here is formed from that hyper variable region It just means at that very tip top you're going to have More variations because again, that's where the antigen binding at the very top you want more diversity there because that's how you get that Wide range and repertoire of the different types of binding sites so we can have a binding site for Covid alpha the first string we ever saw and then the new one that came out They just gave it a new name like last week forgot what it's called But they tried to make it sound cool and it's really not that cool I think it's like hec or something. I don't know they threw a new abbreviation And we have a new strain circulating and so it's you know mutated It's deviated enough that because we have a lot of variability there We want immunoglobulin molecules with more variability at the surface To be specialized for the new subtypes that we're seeing here, too And so this hyper variable region at the top is made up of you know more mutations hyper more mutations hyper variable here In both the heavy And the light chains so say we kept you know the heavy chains in the same variability here But we added a new light chain with new variability that creates the whole it changes the whole surface and the whole like shape Of what can bind on it and again? That's what gives us such a broad diversity of the immunoglobulin molecules and antibodies of our immune system overall Don't memorize this chart over here. It's just showing you that people have done experiments to figure out What spots in the genome they actually have the most? Variations and the most mutations that occur which is pretty cool and so similarly to what we saw With the t cell receptors we talked about how they had cdr1 2 and 3 same thing here They refer to it more as hyper variable regions. They call it hv1 2 and 3, but it is synonymous. It is the same And so the hyper variable regions are in loops at one end of the domain structure Which is basically that antigen binding site at the top so here again? It's just showing you the experiment that they did to figure out Which places and as you can see there are mutations pretty much that could occur anywhere these can be point mutations They can be shifts. They can be all different types of things, but they had three specific locations that provided the most variability So they argue that's the most critical for the diversity that we see with immunoglobulin molecules here And so again, this is specifically looking at our light chain variability here A definition of that if we were talking about it It's the ratio of the number of different amino acids found at that position because as you guys know for biochem you guys have Gone through like you mix the letters up and you get an amino acid and there's a chart that you can use to You know a u with a ug is start. It's been a long time since i've done that one. Um b ug right start But anyway, you could change the g to something else a ua and it's an entirely different amino acid So that's what they're talking about here But the definition is the ratio of the number of different amino acids found at that specific genetic position To the frequency of the most common amino acid at that position. So that's kind of how they figured out the math on this chart here The maximum they could possibly have is 400 So the square of 20 because that's a total number of amino acids we have just in the system of science And that's why people are like, well, how do we know like what our bodies are going to see? Because we have a limited number of amino acids that are also found in the rest of the world It's not like we you don't have alien particles that are yet with other, you know, amino acid molecular structures It's conserved at least across all species earth things like that And because of that we can do math to calculate and figure out what's there here The minimum value is at least one which is nice You can't really have zero or you wouldn't have a functioning immunoglobulin molecule But with this one here, they do have those three hyper variable regions again It's the same thing as saying cdr1 two and three just with b cells. They call them hb1 two and three. They are synonymous They're flanked on either side, but what's in its framework region So this is slightly new but as it sounds framework provides stability So on either side of a hyper variable region You just have a framework which kind of holds it together and it's a stable there So it's pointed in yellow framework one two three and four and you have your hyper variable or cdr One two and three and again, it's showing that loop of where they would occur here It's at that very surface of the protein. So again That antigen binding site at the top you'd find three on the heavy chain and you'd find three on the light chain on both sides So again just different presentations of that and again It's looking at the tippy top portion here just kind of zoomed in just to show you where those loops are But again, it provides that variability So the nice thing about this is it highlighted in red consistently across where they did the science experiments Where they've actually seen those loops occur at the surface And then the very tippy top of the antigen binding site is where you're going to see that variability and again It can occur both on heavy and light chains here So again, it is the same thing as your complementarity determining region. So again same picture as before They are in, you know numbered loops one two and three and so You know They are the definition of the hyper variable region but short region of high diversity in that amino acid sequence That we see with amino globulins. I underlined and bolded that because that's what we're talking about right now And your t cell receptors chain and as you guys know hv1 is the same as cdr1 Etc here too. And so the only reason reiterate they are synonymous Unfortunately for whatever reason b cells really like using hyper variable more And t cells really use when cdr is more and just in common language. They are exactly the same here Um, but in asking about differences between oh, wait, I gave the way the answer. Never mind Sorry, that was a pop. It was supposed to be popways. There's really no difference between the two. Uh, and so That's just the important part to note There's supposed to be a trick question, but there really is no difference between the two so that you Absorb the information. Hopefully just go back and review this question in like 48 hours when you've maybe forgotten and you need to review that So again, just looking at generic shapes here because they are very similar So that kind of led us into what it looks like So what we see with an immunoglobulin molecule has a little bit more detail than what we talked about that t cell receptor Because if we just look at this fab fragment here That fab fragment is what a t cell receptor looks like. So again, it's showing you they have similar parts They have the antigen binding sites at the top here They have variable regions shown here that highlight top portion of it and they have constant regions The only difference is you know These guys have slightly longer constant regions and they're separated by heavy And light chains and so one t cell receptor kind of just looks like one fab fragment. Does that make sense? It's just showing you similar portions. So if I were to like copy this out and overlay it over this It's basically similar you have the variable and you have the constant at the bottom so I could overlay it here you'd still have variable at the top that antigen binding site at the very top and then The constant regions the only difference is We have two of those we have two fab fragments and then a constant additional constant So it's a slightly larger molecule overall And it's made up of more than just your t cell receptor Everyone fairly comfortable with that Again, the pictures are nice, but if you don't get the pictures and you don't get the colors at first It can be a little confusing But if you have any questions about that, let me know but again they still have to be bound via that transmembrane region into the cell membrane so that they are attached to the surface because we're talking about B cell receptors at this point here Antigen binding sites do vary in their shape and their physical properties. You know again based on those hyper variable regions here We have a couple different types of multivalent antigen. So multivalent antigen means like say you get a bacteria You know bacteria doesn't just have one protein on its surface. It could have cell wall proteins It could have capsule proteins It could have a tail all different types of things to it That make it unique and so because of that there's lots of different antigen found on the surface of bacteria And so as a consequence of that we can have a lot of different types of antibody molecules or immunoglobulin molecules Finding onto the different ones. So say we get infected, you know with a bacteria that has You know a little finger like projections from the surface and we also have Like little fimbriae and we also have you know a cell wall We could have a b cell with an antigen or an antibody b cell receptor on the surface that recognizes cell wall proteins That could start proliferating, but we could also have a b cell receptor that recognizes capsule proteins So we can have a lot of different cells proliferating too as long as they're finding their specific antigen that they're supposed to respond to So the picture take away here and again the shapes match up. You're not going to put a triangle in a circle You're not going to put a square In a circle too and so it's showing here that we have lots of different antibodies that can bind to different types of antigen So even on one bacteria You can have many different antibodies from different b cells binding on Because it's recognizing different types of antigen on the surface here Which is pretty cool because again You can have a stronger immune response because you've got more, you know Antibodies binding on and helping to protect body Or you can have bacteria that have a lot of the same antigens on their surface Which is great the clones from that one b cell can just make a lot of eventual antibodies and produce and bind on to the exact same square That everyone comfortable with that. It's just showing the different shapes that you can have, you know antigen That's the same or repeated epitope It's the exact same. It's the same little rectangle on the surface in which case the same antibodies are going to be binding on and recognizing that Versus If we have an epitope or an antigen with a lot of different epitopes on the surface Bacteria with a lot of different antigens on the surface we can have antibodies from different b cells bind on and recognize it That's just the very basic. It seems complicated. It's very simple Obviously epitopes combine in a lot of different shapes. Each one is different So it can bind on it's just showing an example of a circle or you know pocket screws extended surfaces here Even knobs which would protrude out and so it's just showing you that it's different shapes that they bind onto but again The shapes are fitting to the correct Like hole for the shapes of squares and squares rectangles and rectangles things like that. You guys didn't have that like nerve-wracking game Forgot what it was called where it's like it's timed It pops in your face if you don't get it, right? But you have all the different shapes and you have to quickly put them in this like they have an x and they have a Trial oh my god, that's where my anxiety started In case anyone was wondering my parents gave it to me Um, but yeah, you it was timed and you had to put the shapes as fast as possible little plastic shapes in there And if you had all the pieces in there It held the game in place and it didn't pop in your face And if you didn't do it the whole game popped and flung all the pieces in your face It was a I probably still have it somewhere. Ooh wildly traumatic experience But the concept is here you want to put the triangles with the triangles circles with circles the shapes fit They know what they bind on to they'll bounce around and they're like hey this handshake doesn't feel right I'm gonna go shake somebody else's hand until it finds its proper epitope here And so that's all it's showing is this takeaway from this picture It can bind lots of different things to just make sure that it fits in the right room in the right spot I need to know Oh my god, you can buy it on oh This is so dangerous You can buy it on ebay What if I have one for class and you guys have to play it now, you'll know how anxious Anxious. Oh my god. They have it. Let's see. We're gonna we're gonna pause class We're not we don't have that many slides actually we'll do we got two more slides and we'll watch the video the other key takeaway from this one too Because of the binding sites and we know they kind of have like three grooves at the surface We can bind epitopes where they have linear which means they're right next to each other like all three pieces line up in the right holes here Or we can have what's known as discontinuous where maybe it binds on to you know One protein epitope here and another one from a different portion of you know Whatever's on the surface And so the point is it can be things that are directly adjacent to each other And so a linear epitope of a pro by definition of a protein antigen is formed from contiguous The word I under I underlined it because on the exam, I guarantee you one student will say do you mean continuous? They are slightly different things continuous does mean it's continuing on a line contiguous means they're directly adjacent to each other So it is a word I do mean to say contiguous but linear is basically meaning that yes, technically these are continuing on but they are directly adjacent to each other So linear is contiguous discontinuous like this whole chain is continuing on But they are formed from amino acids from different parts of the polypeptide And so notice how like not all pieces bound on but they still have enough to potentially bind on and pick up things That's why cross- reactivity is so important because even though we have slightly different covid strains now There are still some polypeptides that will at least bind to certain spots of you know, covid antibodies and provide some protection there You're also a scientist with shift peli He is the director of harvard's immunology phd program And he has made fundamental discoveries of immune cells called b lymphocytes and the treatment our novel treatments of b cell leukemias He studies how autoimmune cells can go rogue in autoimmune diseases like systemic sclerosis and ig4 related disease In patients with genetic disorders of the immune system and in covid 19 since we're seeing a lot more autoimmune after covid. He also wrote One of uh abbess's textbook is what they use in the med school here. It's very heavy duty immunology and I don't like it It's a lot of stuff Um, but it's what they use. He's also one of the authors on that one So just in case you were wondering you might see his name So now we're going to watch a youtube video You're more than welcome to pack up and leave but like you guys this traumatic game and now i'm going to find it I'm going to literally buy it for this class I'm, so gonna buy it Have you guys played it before besides ellen? Oh god, they have the 80s commercial. I don't want to watch that This is customize and save with liberty mutual customize And it was time when you didn't put them in the right Push the plunger down at the timer I think they traumatized my parents. They traumatized me I'm gonna find it and traumatize my kids It's like jack in the box but no one's gonna pop it so much you know, it's coming in that means it works All right, well you guys have a very lovely weekend And I will see you on monday My goal is to try to get ahead on class hopefully, but I also have a ton of cbl to finish grading