1. Introduction to immunology
Antigen
An antigen is any molecule that can be recognized by special receptors on the T and B-cells or antibodies, and they induce either an immune response or immune tolerance. The last part is important, because an antigen isn’t just something foreign that triggers an immune attack. We mostly think of antigens as something that’s only found on pathogens like bacteria or viruses. However, every protein in your body is an antigen, but none of the proteins in your body will induce an immune response, luckily! This is a part of the immune system tolerance. When tolerance is impaired the body will attack itself and there will be an autoimmune disease.
Immune cells bind antigens from your own cells all the time, to check if they’re infected with a virus or are cancerous. If they are, they are killed, but if not, they are tolerated, so no response is given. Structurally, they can be anything, any protein in either your own cells or in a bacteria cell. Anything you can find in and on the outside of a cell can be an antigen. The name comes from antibody generator, as antigens are recognised by so-called antibodies.
Epitope
Strictly speaking, an antibody doesn’t bind to an antigen, it binds to a specific site on the antigen called the epitope. While an antigen is a molecule, the epitope is the specific part of the molecule that the antibody can bind to. One antigen can have many epitopes, so many antibodies can bind to the same antigen.
The immune system
The immune system is a complex structural and functional network of cellular and molecular elements that work together to maintain the integrity of the individual. It doesn’t just protect against outside threats, but inner threats like mutations and cancers as well. It’s also essential that the immune system knows to not attack the body itself. This is called tolerance. The immune system controls the balance between attacking and tolerating responses. It’s important to keep in mind that tolerating the body is just as important a reaction as attacking foreign pathogens.
The immune system is artificially divided into three main parts. Artificially, because they’re not separated this way in the body: they work together with no clear border.
Innate immune system
The innate immune system is the first line of defence. It alone removes 90% of the external pathogens that enter the body. It’s innate (born with it) because it does not change during the life of an organism. Certain immune cells have receptors that recognize and bind certain molecules that are found only on pathogens. These molecules are called pathogen associated molecular patterns (PAMPs), and the receptors are called pattern recognition receptors (PRRs). Some examples of PAMPs are mannose residues, lipopolysaccharides, flagellin, double stranded RNA and many more that we will see in more detail later. When one of these receptors binds something foreign, they will activate the immune response which will kill the pathogen.
Other important components of the innate immune system are antibacterial peptides, complement factors, heat shock proteins, Fc receptors, inflammatory cytokines, growth factors and histamine, all of which will be covered later. The innate immune system cells are macrophages, monocytes, NK cells, granulocytes and mast cells.
Adaptive immune system
The adaptive immune system is based on the famous antigen-antibody binding. It works by creating infinitely many antibodies, where each can only bind to one part of an antigen, with the hope that at least one of these antibodies will recognize and bind to the pathogen. When an antibody does find something to bind to, the B-cell that created the antibody is cloned so the antibody can be mass-produced. The molecular components of this immune system are antibodies, MHC molecules, T and B cell receptors and lymphatic cytokines. The cells belonging to it are T and B cells and antigen-presenting cells.
Natural immune system
The natural immune system is somewhere in between the adaptive and innate immune systems. It consists of lymphocytes that do not act as the lymphocytes of the adaptive system. Unlike the adaptive lymphocytes, the lymphocytes of the natural immune system have very limited antigen-binding diversity. They can only bind to polysaccharides and lipids on the bacteria. They are among the first to respond to an infection, just like the innate immune cells. Unlike the adaptive immune cells, they have no memory.