Antibody Structure and Diversity: Videos & Practice Problems

Antibodies, or immunoglobulins, are Y-shaped proteins produced by B cells, consisting of two heavy and two light chains. They bind specifically to antigens at their antigen-binding sites, which are formed through variable regions that undergo VDJ recombination, allowing for immense diversity. This process, along with somatic hypermutation and class switching, enables B cells to adapt and produce various antibody classes (IgM, IgD, IgA, IgE, IgG) tailored for different immune responses. The strength of antigen-antibody interactions relies on non-covalent bonds formed between these regions.

Antibody Structure

Hi. In this video, I'm going to be talking about antibody structure and variety. So first, let's focus on antibody structure. We know antibodies are proteins created by B cells; they mark the pathogen for destruction, but what's their structure? First, antibodies are also called immunoglobulin. So if you ever see immunoglobulin or you see IG, they are talking about antibodies. The structure of an antibody looks like a Y. It has 4 chains, 2 of them are light, and 2 of them are heavy, based on the size; obviously, heavy is bigger and light is smaller. Both the light and heavy chains can interact with the antigen where the antibody binds to the antigen. B cells produce a ton of antibodies. When activated, they can secrete around 5,000 of these per second, and these are very specific with each B cell producing only one type of antibody. Here you see the Y. It looks exactly like a Y. You see the 2 heavy chains, the bigger ones here and here, and then you see the 2 light chains here and here. You also see that the yellow region here, this is going to be the antigen-binding site, so there's a portion on the heavy chain and a portion on the light chain, and this recognizes different antigens. They are very specific though, so you can see that the yellow antigen binding site is only going to bind the yellow antigen, and not any of these other colors up here. That's what it looks like.

Now there are multiple classes of antibodies. There are 5 classes based on the heavy chain. Here they are, IgM, IgD, IgA, IgE, and IgG. Immunoglobulin M, essentially your antibody M, is located in different locations. You see that IgM and IgD aren't secreted; they are actually located in the plasma membrane, where A, E, and G are secreted. You also see that they have different functions; they are activated different places and secreted in different places. IgM and IgD are usually present before the activation. They are sort of the initial responders to different antigens, and once they activate the B cell, you get a switch to different antibodies that can then be secreted in tears or in blood, or even be passed to the fetus in the case of IgG. They all have different functions. Interestingly, if any of you have allergies, you can blame the IgE antibody for that, which I definitely do.

Now, there are 2 different types of heavy chains, and there are also 2 types of light chains, but we're not really going to talk about them. They are virtually indistinguishable, but their expression doesn't really matter as they are just indistinguishable. Antibodies work by binding antigens in their antigen-binding site. Of course, the strength of this interaction is going to be dependent on bonds, and the antibody makes non-covalent bonds with the antigen by using the light and heavy chains to make those connections with the antigen. On each of the light and heavy chains, there are 2 regions. There are constant regions, which are going to be the same sequence for the same class of antibody. All of the IgMs have the same constant sequence; all of the IgEs have the same constant sequence. But then there's a second region called the variable region. They vary between each B cell. Then within the variable regions, there's even further variation called hypervariable regions. These are the 5 to 10 amino acids where the antigen is actually going to bind. Here we have an antibody. This is an IgG antibody. Now, you can see this notation here: CH and BH, CL, VL. This is going to be the constant region in the heavy chain and the constant region in the light chain. This is the variable region in the heavy and the same variable in the light. You see here that you have these variable heavy, variable light, constant heavy, constant light. The constants are going to be the same sequences. Anything with the C is going to be the same sequence for antibody classes. All IgGs are going to have the same sequence. For the variable regions, they are going to be different based on every single antibody because this is where the antigen binds. Of course, you need it to be different because those binding sites are going to be different based on the different antigens. The variable region is around the same size and it's going to be different. Then there are these specific hypervariable regions that are even more unique, and that's really where the antigen makes its most connections. So, with that, let's turn the page.

Antibody Variation

Okay. So in this video, we're going to be talking about the variation in antibodies. We know that antibodies have to be there; there has to be a ton of them. So, how do we actually create that diversity? Now you may say, "Oh, it's just encoded in the genome. Right? Like, of course, we have all these different proteins. Why wouldn't antibodies just be encoded in the genome?" Well, they are encoded in the genome; of course, they're a protein, but it's not that every single antibody that could ever be produced is encoded in the genome. It's just not feasible. We don't have enough room. It would be so much DNA that it would just, like we would be huge creatures. It just wouldn't work. So instead, we use this process called VDJ recombination. And this is responsible for creating these variable regions in the antibody that can recognize these, you know, millions, if not billions of antigens. So, to do this, cells use special gene recombination to produce the antibodies against as many antigens as they possibly can. So how we do this is there are 3 antibody segment genes located in different genomic locations in the cell. So there's a V gene segment, a J gene segment, and a D gene segment. And so, the V and J focus on the light chain variable regions, whereas the D gene segment encodes for the heavy chain variable regions. And so, there are multiple V, J, and D regions in a genome, and they're recombined in different combinations to form antigen-binding sites. So for instance, for humans, we have 50V5J35D, which when all of those recombinations are made, will actually form 1.9×106 antigen binding sites. So it's a huge, huge, huge diversity that allows us to create this without actually having to encode every single antibody itself. So what this looks like is if you are to look at the genome, what you see is you just see a string of V regions, a string of D regions, and a string of J regions, and then eventually a constant region. Now, if we had to encode each one of these individually, we'd have to do this one paired to all of these paired to all of these, and it would take up so much room in the genome. So instead, we just order them all the V's, all the D's, all the J's. Then, through a variety of steps, which I'm not gonna go through, we start cutting them out. We start saying, "Okay, we don't want these D regions, we don't want these J regions, we don't want these V regions." So, what we end up with is a VDJ region that can be connected to a constant that is unique, because it has, you know, this D compared with this D and this J, and this will go on to create an antibody that's specific for one antigen. So super important in creating this diversity without filling our gene up with all these different recombinations.

Now that's obviously not enough. Right? That was 1.9×106, which is a lot, but isn't actually the number of bacteria on Earth, you know, that's a much higher number. So we have to create a variation in other ways. So one of the ways we do this is through somatic hypermutation. This is a characteristic which B cells have at the variable gene segments, either on the light chain or on the heavy chain. And essentially, somatic hypermutation means that there's a mutation in the variable region about once every division. So it's super high. I mean, none of our other cells do that. If we did, we'd have all sorts of cancers and mutations, and we wouldn't live very long. But the antibody regions, these variable region segments, actually mutate once per division. So you can imagine, B cells divide so quickly, so fast, so all of these variable regions are constantly being mutated after every division, and that's called somatic hypermutation. Now, most of these aren't going to do anything. Right? They're not gonna change the affinity, but some of them will increase the affinity for antigens. Some of them will actually recognize different pathogens or different antigens, and that will result in further diversity and further strength of the reaction. And then finally, all B cells undergo what's known as class switching during development. So remember that there are all these different classes of antibodies. IgM and IgD are called the primary antibodies because these are the ones that B cells first produce. These are found in the plasma membrane, they're not secreted, and B cells produce either or both. Then, somatic hypermutation occurs after B cell activation, and so the class switches. So the type of antibody produces switches to E, A, or G, depending on what kind of response it needs, and this is called the secondary antibody repertoire. So what we see here, again, we've seen this image before, but don't worry about any of the text. Should have taken it out, but just I'll leave it there in case you feel like reading it. But, essentially, what you see here, we'll say this is IgM. And this is a B cell that's recognizing an antigen. Eventually, it goes through all this maturation process, which we'll talk about. But, then what you get is you get a class switching to a different antibody. We'll say this is IgE. So class switching occurs and the antibody that was originally produced on the surface, this gray thing here, is not the antibody that is released, so that it is going to be a different antibody that can actually be secreted, but is specific for the same antigen. So, with that, let's now turn the page.

Which of the following processes allows for the creation of so many diverse antibodies?

• A. V(D)J recombination
• B. V(J) recombination
• C. Class switching
• D. Constant regions

Answer: (A)

Which of the following antibodies is secreted into the blood for an allergic reaction?

• A. IgM
• B. IgD
• C. IgA
• D. IgE
• E. IgG

Answer: (D)

Which of the following variable gene segments encodes for the variable sequence on the heavy chain?

• A. V
• B. D
• C. J
• D. M

Answer: (B)

Here’s what students ask on this topic:

What is the structure of an antibody and how does it function?

An antibody, also known as an immunoglobulin, has a Y-shaped structure composed of four polypeptide chains: two heavy chains and two light chains. The heavy chains are larger, while the light chains are smaller. Each chain has a constant region and a variable region. The variable regions of both the heavy and light chains form the antigen-binding site, which is highly specific to particular antigens. Antibodies function by binding to antigens at these sites, marking the pathogen for destruction by other immune cells. The binding strength relies on non-covalent interactions between the antibody and antigen.

What are the different classes of antibodies and their functions?

There are five classes of antibodies, each with distinct functions: IgM, IgD, IgA, IgE, and IgG. IgM and IgD are primarily found on the plasma membrane of B cells and act as initial responders. IgA is found in mucosal areas and body secretions like tears and saliva. IgE is involved in allergic reactions and defense against parasitic infections. IgG is the most abundant antibody in blood and extracellular fluid, providing long-term immunity and can cross the placenta to protect the fetus. Each class is defined by the type of heavy chain it possesses.

How does VDJ recombination contribute to antibody diversity?

VDJ recombination is a process that generates antibody diversity by rearranging variable (V), diversity (D), and joining (J) gene segments. In B cells, multiple V, D, and J segments are randomly combined to form the variable region of the antibody's heavy and light chains. This recombination allows for the creation of a vast array of unique antigen-binding sites, enabling the immune system to recognize millions of different antigens. For example, humans have approximately 50 V, 5 J, and 35 D segments, which can combine in numerous ways to produce around 1.9 million unique antigen-binding sites.

What is somatic hypermutation and how does it enhance antibody diversity?

Somatic hypermutation is a process that occurs in activated B cells, introducing mutations at a high rate in the variable regions of antibody genes. This results in the generation of antibodies with slightly altered antigen-binding sites. Most mutations do not affect binding affinity, but some can increase it, allowing the immune system to produce antibodies with higher specificity and stronger binding to antigens. This process, combined with VDJ recombination, significantly enhances the diversity and adaptability of the antibody repertoire, enabling effective responses to a wide range of pathogens.

What is class switching in antibodies and why is it important?

Class switching is a process where a B cell changes the class of antibody it produces without altering the antigen specificity. Initially, B cells produce IgM and IgD antibodies. Upon activation and exposure to specific signals, they can switch to producing IgA, IgE, or IgG. This switch allows the immune system to tailor the antibody response to different types of pathogens and immune challenges. For example, IgG is effective in blood and extracellular fluid, while IgA is crucial for mucosal immunity. Class switching enhances the versatility and effectiveness of the immune response.