Lesson Explainer: Structure and Function of Antibodies Biology • Third Year of Secondary School

In this explainer, we will learn how to distinguish between an antigen and an antibody and describe the structure and function of antibodies in the immune response.

Did you know that every tissue in your body has immune cells circulating through it, vigilantly watching out for signs of infection? The human immune system is capable of mounting incredibly fast and effective responses to infection. These responses can be nonspecific, for example, physical barriers such as the skin, which helps to keep dangerous microorganisms called pathogens out of the body. These responses are always present or are activated very quickly. Sometimes, these pathogens manage to get through these defenses nonetheless, and at this point, the specific immune response will be activated.

The specific immune response is much slower than a nonspecific response, and it can take up to 14 days to respond effectively. However, due to the presence of memory cells, which remain in the immune system after an initial infection and recognize the pathogen that caused it, a second response can be very fast!

One part of the specific immune response is called humoral immunity and involves antibodies. Antibodies target specific molecules called antigens found in blood plasma and other body fluids. In this explainer, we will be focusing on how the structure and function of these antibodies assist in protecting us against infection and disease.

First, let’s look at what antigens and antibodies actually are.

All cells have antigen molecules on their cell surface membranes. Antigens are also found on the outer coat of viruses and can also simply be any molecule or substance that can trigger an immune response.

The human body can distinguish between its own antigens, which are called self-antigens, and non-self-antigens on the cell surface membrane of a foreign cell. The human body recognizes the non-self-antigens and initiates an immune response to potentially harmful pathogens. Some toxins act also as antigens, as they also trigger a specific immune response.

You can see antigens on the surface of a bacterial cell and a virus in Figure 1 below.

Antibodies, sometimes called immunoglobulins, are soluble proteins produced and released by white blood cells called B lymphocytes. Antibodies can also remain bound to the surfaces of B lymphocytes.

Antibodies are produced when the immune response is triggered by non-self-antigens on the surface of a pathogen or a toxin. These B lymphocytes also have immunoglobulin receptors on their cell surface membranes, which allows antibodies to remain bound to the B cell. You can see an image of antibodies bound to the surface of, and being released by, a B lymphocyte in Figure 2 below.

Antibodies only bind to specific antigens on a pathogen or toxin through complementary binding.

The shape of a particular antibody’s binding site is specific to the shape of a particular antigen, so complementary binding can only occur between these molecules. This is much like how only certain specifically shaped keys can fit into a complementary-shaped lock. There are specific antibodies for every different antigen, much like how there are keys for each different lock.

You can see the lock-and-key model of complementary binding involved in the immune response in Figure 3 below.

When an antibody binds to its complementary antigen as in Figure 3, it forms an antigen–antibody complex. Upon making contact with an antigen on the surface of a pathogen, the B lymphocyte attached to the antibody divides by mitosis. This produces groups of cells that can each produce and secrete specific and identical antibodies that are complementary to this specific antigen. These cells will then circulate the body via the blood and lymph to target any other invading pathogens with the same antigens on their surfaces.

Let’s look at the structure of an antibody protein before we delve into details about its functions.

Antibodies are Y-shaped glycoproteins, which is a protein attached to a carbohydrate chain. Antibodies are sometimes called immunoglobulins, an example of which you can see in Figure 4 below.

Antibodies are globular proteins, which means that they are spherical or “globe shaped.” Globular proteins tend to be soluble in water, such as antibodies that are not bound to the surfaces of B lymphocytes. This is important as they are transported via bodily fluids to efficiently access all body tissues to help combat infection wherever it may occur. They can also be found bound to the membrane of a B lymphocyte.

Each antibody protein consists of two identical long polypeptide chains called the heavy chains and two different smaller chains called the light chains, which are also identical to each other. These four polypeptide subunits are joined together by disulfide bridges, giving the overall antibody molecule its quaternary structure. The quaternary structure of a protein is formed when two or more protein subunits associate with each other.

The heavy and light chains in an antibody overlap. Parts of both the heavy and light chains form a variable region at the top of the molecule, and other parts of the heavy and light chains form the constant region at the base of the antibody molecule.

At the top of both the heavy and light chains of the antibody is the variable region that is shown in the diagram in Figure 4 in blue. It is called the variable region as it varies between different antibodies.

The variable region consists of 110 amino acids in total, 55 on each of the two tips of the “Y” that forms the antibody’s structure. The variable region on each antibody contains two antigen-binding sites, specific to a complementary antigen. This specificity is provided by the specific sequence and spatial arrangement of amino acids in the variable region. Each of the two antigen-binding sites on a single antibody are identical to each other. This means that two antigens can bind to one antibody, though only one is about to bind to the antibody in Figure 4 above.

As the rest of the molecule is the same for each different antibody, this region of heavy and light chains is called the constant region and is shown in Figure 4 in green. At the base of a soluble antibody is a receptor binding site that allows it to bind to receptors on the cell surface membranes of different cells such as phagocytes that can engulf and digest the pathogen.

Example 2: Describing the Structure of an Antibody

Which is the best description of an antibody?

1. The antigen-binding site is in the light chain and the constant region is in the heavy chain.
2. The amino acid sequence and 3D shape of all antibodies are the same.
3. It is composed of two subunits, one heavy chain and one light chain.
4. The molecule is a globular protein composed of four different polypeptide chains.
5. It is a globular protein with a quaternary structure that includes two types of polypeptides.

Answer

Antibodies are globular proteins, which means they are spherical or “globe shaped.” Globular proteins tend to be soluble in water, and antibodies that are not bound to the surface of B lymphocytes are soluble. This is important as they are transported via bodily fluids to efficiently access all body tissues to help combat infection wherever it may occur.

Antibodies assist in the immune response by binding to complementary-shaped antigens that are either toxins or are on the cell surface membrane of a nonself cell such as a pathogen that can cause disease.

Let’s have a look at the structure of an antibody so we can discuss which of the options is correct.

Each antibody protein consists of two identical long polypeptide chains called the heavy chains and two identical smaller chains called the light chains. These four polypeptide subunits are joined together by disulfide bridges, giving the overall antibody molecule its quaternary structure as you can see in the diagram below.

The variable region is a different shape on each antibody, depending on the sequence, arrangement, and shape of the amino acids it consists of. As the rest of the molecule is the same for each different antibody, this region is called the constant region. At the base of each antibody is a receptor binding site. The binding site allows the antibody to bind to receptors on the cell surface membranes of different cells.

Let’s use the information in the diagram to eliminate the options that are incorrect.

We can see that the statement saying that the antigen-binding site is in the light chain and the constant region is in the heavy chain is incorrect, as the heavy and light chains overlap. Parts of both the heavy and light chains form the antigen-binding sites at the top of the molecule, and other parts of the heavy and light chains form the constant region at the base of the antibody molecule.

The option stating that the amino acid sequence and 3D shape of all antibodies are the same is also incorrect, as the variable region of different antibodies varies, as the name suggests. This is because different amino acids form the variable region, so different antibodies are specific to different antigens.

The option stating that it is composed of two subunits, one heavy chain and one light chain, is also incorrect. This is because, as we can see in the diagram, an antibody consists of four polypeptide chains: two identical heavy chains and two identical light chains.

This also makes the option stating that the molecule is a globular protein composed of four different polypeptide chains incorrect, because though antibodies are globular proteins, the two heavy chains are identical to each other, as are the two light chains. This means that the four polypeptides are not all different from each other.

Therefore, the best description of an antibody is that it is a globular protein with a quaternary structure that includes two types of polypeptides.

Example 3: Identifying the Location of Antigen Binding

The figure represents the structure of an antibody. Where does an antigen bind?

Answer

To identify where an antigen binds to this antibody, let’s first look at the different parts of the antibody.

An antibody, or immunoglobulin, protein is made up of four chains of polypeptides. There are two identical long heavy chains forming the central part of the molecule and two shorter light chains that form the exterior of the antibody and are also identical to each other. These chains are joined together by disulfide bridges, two of which are indicated on the diagram in the question with an “A.” Let’s label the information we have so far on the diagram.

At the base of the heavy chains in an antibody is a binding site, labeled on the diagram with a “D.” This binding site allows antigens to attach to receptors on the cell surface membranes of self (host) cells, particularly those involved in the immune system.

There are other two binding sites at the top of each point forming the “Y” shape of the antibody. These two binding sites, labeled here as “B” and “C,” are identical to each other and have a complementary shape to a particular antigen depending on the antibody. This allows one antibody to attach to two antigens through complementary binding.

Therefore, the locations where antigens can bind to this antigen are at B and C.

There are five different types of soluble antibodies that circulate in the blood and lymph: IgA, IgD, IgE, IgG, and IgM. Table 1 shows the main differences between each of these antibody types, including their structures and functions.

You can see that the variable region in each type of soluble antibody differs, and this is indicated by their different colors and how some of them group together in solution. Table 1 describes the differences in their functions and structures and which can be found bound to antibody receptors on the cell surface membrane of B lymphocytes.

Now that we know more about antibody structure, let’s see how they function to limit the effects of pathogens and toxins.

Antibodies do not directly destroy pathogens themselves but facilitate other immune processes that break down and remove pathogens and toxins from the body. There are six main mechanisms we will look at: opsonization, neutralization, agglutination, precipitation, lysis, and antitoxin action.

Let’s start with opsonization, which is summarized in the diagram in Figure 5 below.

Stage 1 of Figure 5 shows that the antigens and antibodies are separate.

An opsonin is a molecule, such as an antibody, that binds to the antigens on the cell surface membranes of pathogenic cells, tagging them. This tagging process is called opsonization, and you can see it occurring in stage 2 of Figure 5. This antigen–antibody complex tag allows white blood cells called phagocytes to recognize them more easily. Receptors on the cell surface membrane of the phagocyte can bind to receptor binding sites on the antibodies once they have formed antigen–antibody complexes with the pathogen.

The phagocyte then engulfs the pathogen, as you can see in stage 3 in Figure 5. Once the pathogen is engulfed, the phagocyte breaks it down by digesting the pathogen with enzymes. This process is called phagocytosis, and its efficiency is greatly increased in the presence of antibodies.

In addition, most pathogens cannot invade host cells once they are part of an antigen–antibody complex, which greatly reduces their infectiousness and harmful effects on host cells. This is the basis for neutralization, which is the next mechanism we will discuss.

Neutralizing antibodies can block the harmful effects of viruses in particular. The word neutral in neutralization refers to the fact that antibodies are rendering a virus as harmless.

Neutralization is a reaction between an antigen on the outer coat of a virus and the antibody that is complementary to it. When the antibody binds to a virus, it renders the virus inactive or otherwise ineffective.

Neutralization can also stop viruses from changing their structures and shapes, known as conformational changes. An antibody binding to the viral antigen prevents these conformational changes occurring. Therefore, the virus cannot enter host cells so easily and so cannot replicate within them. This means that the spread of the pathogen around the host’s body is reduced.

If the virus does manage to enter the host cell, neutralizing antibodies keep the protein coat of the virus sealed. This prevents the nucleic acids (DNA or RNA) within the virus from exiting its coat and replicating. Once a virus has been neutralized by an antibody, the pathogen is degraded by white blood cells, and the remains will be filtered and excreted.

Let’s have a look at agglutination next, which is outlined in Figure 6 below.

IgM antibodies provide a good example of how antibodies can act as agglutinins. As IgM antibodies consist of five antibody molecules linked together, it has up to ten binding sites for antigens, so they can attach to many individual pathogenic cells at once.

Agglutination describes how pathogens carrying antigen–antibody complexes clump together. Forming clumps prevents the pathogens from spreading through the body so easily. This also makes it easier for phagocytes to engulf several pathogens at once. It is important to note that as at least two antigen-binding sites are present on all antibody molecules, any antibody, not just IgM, is capable of cross-linking and agglutinating several pathogens.

Example 4: Describing Antibody Processes Facilitating Phagocytosis

Which process best describes what is happening in the given figure?

Answer

The question is asking us to identify what process is occurring in the diagram, so let’s first identify what the different structures are, so we can work out what they are doing.

The Y-shaped molecules are antibodies, or immunoglobulin proteins. Antibodies have binding sites that have a complementary shape to specific antigens that are present on the cell surface membranes of cells. This is helpful for the immune system, as it allows antibodies to distinguish between cells belonging to the host that contains self-antigens and cells that might be pathogenic and will have non-self-antigens on their surfaces.

The large pink circles in the diagram represent the nonself cells of a pathogen that might cause disease, and the shapes on their surfaces are non-self-antigens. As the triangular antigens have antibodies bound to them, they have formed antigen–antibody complexes. Let’s label these structures on the diagram before we look in more detail at what is occurring in the image.

You might have noticed in the diagram that multiple pathogenic cells have been linked together by the antibodies. This is because each antibody has two binding sites that can join to complementary triangular antigens on the surfaces of pathogens. This means that the antibodies are able to group, or clump, together many pathogens at once.

This process is called agglutination, and it makes the antigen–pathogen complex easier for phagocytes to identify. This means that phagocytosis, where pathogens are engulfed and digested by phagocytes, is much more efficient as many pathogens can be broken down simultaneously.

Therefore, the process happening in this figure, which facilitates phagocytosis, is agglutination.

Let’s see how precipitation can be helpful in the immune response.

Antigens and antibodies are both soluble molecules, which means that they are not visible in a solution. When enough antigens and their specific antibody molecules react at an optimum temperature and pH, they precipitate out of solution. This is because the antigen–antibody complex is insoluble, as a lattice forms between the antigens and antibodies when multiple complexes are joined together. The formation of a lattice of many antigen–antibody complexes means they become visible as a band of precipitation.

For the precipitate to form, the antigen and antibody must be complementary, and they must be in an appropriate concentration relative to each other, forming an equivalence. An excess of either antibodies or antigens prevents efficient lattice formation. You can see this demonstrated in Figure 7 below.

Much like agglutination, the formation of a precipitate makes it much easier for phagocytes to efficiently engulf and digest pathogens.

Precipitation reactions can be helpful in immunology studies and medical applications. They can be used to detect an unknown antibody to diagnose infections. For example, the Venereal Disease Research Laboratory (VDRL) test contains antibodies to test for the presence of antigens found on bacteria that cause syphilis. The antibodies in the VDRL test will bind only to antigens on these specific bacteria, and so, only the presence of these bacteria will cause a precipitate to form and the condition to be diagnosed.

Let’s look at lysis next.

Lysis is a term that refers to the breaking down of a membrane of any sort of cell.

You might recall the word lysis from several different biological terms. One such term refers to a cellular component called a lysosome found within most cells but is especially vital in white blood cells, such as phagocytes. Lysosomes within the phagocytes are responsible for breaking down engulfed pathogens with digestive enzymes called lysozymes.

Lysis is often triggered by a viral infection. Viruses can disrupt cellular membranes, causing them to be broken down leading to the death of the host cell. The virus particles that have replicated many times are then released, along with the cytoplasmic contents, and exposed to other uninfected cells within the host. Lysis can even occur as a result of a high osmotic pressure on animal cells that contain too much water! Lysis is displayed in Figure 8 below.

Lysis is assisted by a group of proteins called complements that circulate in the blood. Complements are different proteins, specifically enzymes, that are activated by antibodies. Complement proteins form pores in a nonself cell, which allows water into a cell causing it to lyse and burst. This can break down the cell walls or cell surface membranes of pathogens once they have formed antigen–antibody complexes. A broken down pathogen is much easier for a phagocyte to engulf!

Finally, let’s take a look at antitoxin action to see how this helps antibodies defend us against the dangerous effects of pathogens.

Some pathogens produce toxins. As you can see in Figure 9 below, toxins can cause significant damage to host cells and destroy them. Antibodies can act as antitoxins to prevent this damage occurring.

The top part of the diagram in Figure 9 shows what would happen without antibodies acting as antitoxins. The bottom diagram shows this process being prevented by antibodies detoxifying the toxic particles. You can see that the antibodies are acting as antitoxins by binding to toxins to form complexes between the two substances. This prevents the toxins from entering a host cell and means the host cell remains healthy. It also allows the toxins to be readily engulfed and digested by phagocytes.

Antibodies are just one part of the specific immune response, targeting extracellular antigens in plasma and body fluids. There are several other components of the immune system that monitor and control the spread of disease to keep us as healthy as possible.

Let’s recap some of the key points we have covered in this explainer.