Proteins and Identifying Cells - the Antigen
All cells (human, bacterial and everything in between) hold some form of genetic material. This genetic material is expressed into proteins that become part of the surface of the cell, its membrane. The proteins are called antigens in the context of the immune system.
All livings things are made of cells, from one cell to millions of cells – including us and the organisms we refer to as pathogens. In all organisms, each cell holds genetic material in the form of DNA in their nuclei. Combinations of different molecules called nucleic acids make up who we are—they encode for every aspect of our bodies. The formation of our organs, bones, muscles and tissues as a fetus, the color of our hair, eyes, and skin, and even our own immune systems—all expressions of our unique DNA. Even though we each have our own variations of DNA which is most noticeably expressed in physical features, each species has a different set of DNA, except for viruses, which only have RNA (one strand of ribo-nucleic acids instead of two). Likewise, there are millions of different bacteria, viruses, and infectious organisms that exist in the world, and each one has a different genetic makeup.
DNA holds the information, but how does the body use it? Each cell builds proteins from the different combinations of amino acids encoded in the DNA. Proteins carry out many functions in each cell, in the body, and they play a major role in the immune system. At any point in time, each cell in your body is actively producing proteins from its DNA, and these proteins can stay inside the cell, become a part of cell's membrane and even go out of the cell.
Proteins are characterized by having really exquisite 3D shapes that depend on their composition. Since each protein usually has a unique composition, proteins can be distinguished by shape (and by other molecular interactions).
Each cell makes different proteins according to its type (whether it’s a bone or a brain cell, for example) and it also makes different proteins in different circumstances: if it’s healthy, if it’s about to divide, if its dealing with a lack of an essential nutrient, or if it’s unhealthy!. For example. if it is infected by a virus, the virus injects its own genetic material into the cell and so the cell makes proteins from the genetic material of the virus! So, the proteins a cell produces are a pretty good indicator of how the cell is doing.
The proteins produced by a body cell in the course of its natural life is called a self antigen - "self" meaning belongs to the self. Proteins produced by an infected cell (or that belong to a germ cell) are nonself antigens - "nonself" meaning that it does not belong in a healthy body and must be destroyed!
Immune cells take advantage of this and developed a couple of ways to "read" (by binding) the antigen – this is the basis of the specificity of the immune cells.Binding occurs by fitting together a special spot on the immune cells (a binding site) with the antigen - if they fit together kind of like a lock and a key, they bind!
T cells will check the antigens of cells they find in the body to see if they are healthy. If they find a self antigen on a cell, they decide that the cell is healthy and leave it be. If they find a nonself antigen, they know it means that the cell is either unhealthy or it may not belong to the body at all, so they start an immune response to kill it. Each T cell can only bind one kind of infected cell - they are specific.
Learn more about T cells and how they kill unhealthy cells >>
Read on about the molecular basis of T cell specificity >>Macrophages like most swallowing cells don't bind to antigens, they bind to non-specific proteins. This means they are good at recognizing some groups of proteins that are shared by a lot of different bacteria (like some of the proteins in their capsule).
Learn more about macrophages >>B cells can only bind one kind of antigen - they are specific. The specific antigen that it can bind is the match of the unique binding site that each B cell has, the antibody. B cells are usually good at targeting outsider organisms.
Read more about B cells >>We just discussed antigens in the context of body cells - self antigen indicating a healthy body cell and and a nonself antigen indicating an unhealthy cell. Well, how about something that never belonged to the body - like a bacteria?
In any immune response, immune cells can bind to a body cell, whole bacteria, whole infected cells, viruses or just parts of bacteria or infected cells, and it’s easy to become confused about what to call all these different targets that can exist in the body. Always though, this interaction involves the recognition of a protein or group of proteins that an immune cell thinks might mean trouble. We call these antigens. For example, the proteins of the tail of a bacterium, on the membrane of a virus-infected cell, and sometimes even of our own healthy cells can be antigens.
When our immune system targets our own healthy cells, the proteins on their membrane are called self antigens. (“Self” refers to belonging to the body.) Whenever the antigen belongs to a germ or an infected cell it is called a nonself antigen.
Antigen Presenting Cells (APCs) and Professional APCs
Almost all cells in the body present antigens - and they present the antigens in a special protein complex called the Major Histocompatability Complex (MHC). This may sound complicated but MHC is simply a group of proteins that captures proteins within the cell and brings them to the cell membrane. So, (almost) all cells of the body are Antigen Presenting Cells. This makes the immune cells' job easier: they are very good at grabbing onto the MHC and then can take a look at the antigen.
But whenever a germ comes into the body with its own antigens, the immune cells have a harder time grabbing onto them to look at their antigens. So here come in the Professional APC's! Some special white cells, like macrophages and dendritic cells are called professional APC’s. The reason they are “professional” is because their main function is to digest germs and display their antigens. They possess a special kind of MHC (MHC class II) where they display the germ antigen that allows the T cells can bind to.This way T cells can check out the germ's antigens on the macrophage!
The MHC (I and II) is very important in T cell immune response, without it, T cells couldn't get to each cell's antigens!
