How Our Immune System and Vaccines Protect Us From Diseases

Our immune system is made up of different cells and organs that work to defend us against pathogens. Pathogens are microorganisms that make us sick. They include harmful bacteria (like Salmonella or E. coli, which cause food poisoning), microscopic fungi, viruses (ranging from measles to the flu), and more.

Once a pathogen enters our body, our immune system goes through a series of processes called the immune response. Any "foreign substance" that causes an immune response is called an antigen. Antigens can be entire pathogens, specific parts of a pathogen, allergens, toxins, or specific molecules. They function as markers that tell our immune system that something in our body is harmful.

Once our immune system encounters an antigen, an immune response is triggered. The immune response consists of two parts: the innate immune response and the adaptive immune response. The innate immune response is the first line of defense against pathogens and includes physical, chemical, and cellular defense mechanisms. The physical and chemical barriers consist of our skin and mucous membranes, which prevent pathogens from entering our bodies. Once pathogens breach these barriers, the innate immune cells are activated. These immune cells are special white blood cells that can detect invaders and destroy them. They include phagocytes, such as macrophages, neutrophils, and dendritic cells, as well as other cells called natural killer cells. The most important task of these innate immune cells is to detect a pathogen.

Innate immune cells have pattern recognition receptors—special proteins in and on their cell membranes that can detect molecules frequently found in pathogens. Once a pathogen is identified, the immune cell's receptor binds to the pathogen. Then the pathogen is destroyed. Using these pattern recognition receptors, innate immune cells can identify and quickly respond to a broad range of pathogens. The innate immune response is quick but non-specific. While it can recognize and destroy different types of pathogens, it cannot distinguish between them.

Once a pathogen slips through the innate immune response, the second line of defense is the adaptive immune response. The key players in the adaptive immune response are T cells and B cells. Like innate immune cells, T cells and B cells carry specialized receptors on their surfaces. The difference is that these receptors only bind to one specific antigen; they are antigen-specific.

The adaptive immune response is usually triggered by innate immune cells, specifically dendritic cells. When dendritic cells encounter a pathogen and destroy it, they display parts of the pathogen—its antigens—on their cell surface. Subsequently, any T cell with a matching antigen receptor gets activated and divides rapidly to produce many more T cells with the same T cell receptors.

Once activated, T cells can become either helper T cells or cytotoxic T cells. Cytotoxic T cells directly destroy cells infected with a pathogen in a process called cell-mediated immune response. Helper T cells, on the other hand, activate B cells with matching B cell receptors. Once activated, these B cells become plasma cells that produce antibodies—y-shaped proteins—which they release into the body.

Antibodies are our immune system's ultimate weapon against a specific pathogen. Each antibody consists of a conserved or constant region and a variable region, as shown in Figure 1. The tips of both y-arms contain variable antigen-binding sites. They are tailored to the specific antigen the immune system is currently fighting. Once an antibody encounters a matching antigen, it binds to it and flags it for destruction, as shown in Figure 2. This process of antibodies fighting a specific pathogen is called the humoral immune response. B cells continue to produce antibodies until the body is cleared of pathogens and the infection is over.

On the left, 12 rectangular shapes arranged into a y-shape show the basic structure of an antibody. The rectangles at the tips of the y have indentations representing antigen-binding sites. On the right, squiggly lines arranged into a y-shape respresent a more realistic visualization of the y-shaped protein structure of antibodies.

Figure 1. Schematic drawing (left) and protein structure (right) of an antibody. Image credit: OpenStax College, CC BY 3.0, via Wikimedia Commons.

Figure 2. During the immune response, antibodies (shown in blue) bind to a pathogen (a bacterium here, shown in red). Once bound to the pathogen, the antibodies often get help from white blood cells to destroy the pathogen. Note: These are simplified drawings that are not to scale.

Although the adaptive immune response is relatively slow—it can take up to several weeks to successfully fight an infection—it has one more powerful function: memory. While most B cells and T cells die after infection, some of them develop into memory cells. This usually happens during a primary immune response, which is the first time the immune system encounters a specific pathogen. Memory cells are able to remember a specific antigen and can quickly be reactivated when the immune system encounters the same pathogen again. As a result, the secondary immune response is usually much more rapid and powerful. Figure 3 provides an overview of the processes involved in the innate and adaptive immune responses.

Figure 3. Schematic overview of the processes involved in the primary immune response, including innate and adaptive immune cells. Image credit: Sciencia58 and the makers of the single images Domdomegg, [1], Fæ, Petr94, Manu5, CC BY-SA 4.0, via Wikimedia Commons.

Scientists have figured out how to harness our immune system to protect us from certain diseases. One major tool that has been developed in preventative medicine is the vaccine. Vaccines are a good way to build up immunity against certain diseases. They prime an individual's acquired immune system so it has antibodies to recognize and fight off a potential pathogen without ever having to experience the harmful or even deadly symptoms of the disease. Some vaccines contain inactivated viruses or bacteria. Others contain specific antigens of viruses or bacteria (or, in the case of mRNA vaccines, instructions to make the antigens). The vaccines trigger a primary immune response against that pathogen without causing an actual infection or disease. As a result, our body makes antibodies that are ready to help recognize and destroy the pathogen should we become infected for real.

Some vaccines offer long-term protection, but others have shorter effects. To protect us from the flu, for example, we need a new shot every year. Other vaccines, such as the COVID vaccine, need to be updated as well. This is in part because pathogens evolve to survive. Viruses, because of their short generation time, can be especially quick to evolve. Evolving means accumulating mutations in their genes. These genetic mutations can change the structure of their antigens. This process is called antigenic drift, and it can result in many different pathogen variants, each with a slightly different genetic makeup.

When a genetic mutation affects the antigen, the new pathogen variant becomes capable of escaping an existing immunity. The new antigens will no longer bind to the antibodies or immune cell receptors. As a result, the new virus variant is able to infect people who were immune to the original strain due to prior infection or vaccination. To counteract the antigenic drift of the influenza virus, a new flu shot is developed every year to cover new virus variants. Our immune system also evolves in an effort to outsmart new pathogens. This results in a constant arms race between our immune system and pathogens.