Immunology is the study of the organs, cells, and chemical components of the immune system. The immune system creates both innate and adaptive immune responses. The innate response exists in many lower species, all the way up the evolutionary ladder to humans, and it acts through relatively crude means against large classes of pathogens. The adaptive response is unique to vertebrates, reacting to foreign invaders with specificity and selectivity.
The immune system must maintain a delicate balance, with potent defensive responses capable of destroying large numbers of foreign cells and viruses while refraining from undue destruction of the host's body. When the immune system cannot mount a sufficient defense of the host, there is an immune deficiency; this is seen in HIV infection and SCID . If, on the other hand, the immune system acts too vigorously and begins to attack the host, we have autoimmunity. This is a defiance of the integral immune system property of self/nonself recognition. That is, the immune system begins attacking or forming antibodies against the host's own body tissues. Examples of autoimmune diseases include Graves' disease, Hashimoto's thyroiditis, myaesthenia gravis and type I diabetes mellitus.
The History of Immunology 
The human immune system recognizes non-self entities and mounts an effector response to neutralize the organism. A faster and stronger memory response may occur upon later exposure. The memory response has been used throughout history to confer immunity upon several populations, even previous to our understanding of the physiological basis for such a response. Thucydides wrote in his History of the Peloponnesian War that persons who had been exposed to plague previously
could care for the sick without danger. In the 19th century,
variolation was commonplace; this was the removal of smallpox (variola virus) skin pustules which were subsequently put into small cuts in the skin of healthy people. This was itself a crude form of vaccination, with the crusty dry pustules acting as an incubator of attenuated virus.
Edward Jenner would later use the cowpox virus to vaccinate (from
vacca, Latin for "cow") patients against smallpox, and Louis Pasteur
attenuated rabies and injected it into a small boy, naming this
substance a vaccine in honor of Jenner's earlier studies in the science of immunology.
As immunology progressed, many people began to question how these vaccines worked. Why should exposure to plague in Thucycides' time confer protection only against plague and not all disease? Why should cowpox, a similar disease to smallpox but clearly a less severe virus, give milk maids sufficient immunity to resist full smallpox infection? In short, what has caused this memory response to be relatively (yet not
absolutely) specific as well as selective?
The Basics 
First, some vocabulary:
- Serum--liquid, noncellular component of blood after coagulation has occurred (and thus devoid of clotting factors).
- Immunoglobulin--a serum fraction (aka gamma globulin) that has antitoxin, precipitin, and agglutin factors (abbreviation: Ig)
- Antigen--"Antibody Generator"; a foreign organism or molecule that generates a humoral immune response, causing the release of antibodies (abbreviation: Ag)
- Epitope--the molecular sidechain of an antigen that each antibody attaches to; there can be many epitopes on a single antigen
- Antibody--refined, Y-shaped proteins that make up the immunoglobulin fraction of serum; antibodies are specific to certain foreign bodies; antibodies can be membrane-bound or free in the serum (abbreviation: Ab)
Note: Often, antibody and immunoglobulin are used interchangably.
There have been several competing theories of the immune response mechanism. The instructional theory of antigen interaction postulated that the antigen itself caused antibodies to fold around the antigen in a certain way; this theory was later disproven. The selection theory states that the body creates many different sidechains on antibodies, and the antigen "selects" the correct antibody; in other words, the body creates every possible permutation of chemical sidechain-specific antibodies, and when an antigen enters the body, it is matched up with antibodies that correspond to its epitopes. The current theory of immune response is known as the clonal selection theory, which states that an individual lymphocyte (specifically, a B cell) expresses receptors specific to the distinct antigen, determined before the antibody ever encounters the antigen. Binding of Ag to a cell activates the cell, causing a proliferation of clone daughter cells.
Innate Immunity 
Innate immunity is basic and nonspecific. It includes:
- Phagocytic cells (macrophages, neutrophils; more generally,
antigen-presenting cells (APCs))
- Barriers (e.g. skin)
- Antimicrobial compounds
Phagocytic Cells 
Certain cells "eat up" foreign invaders; this is termed phagocytosis. Many of these cells are known as Antigen-Presenting Cells (APCs) because
they break apart the ingested pathogen and display certain epitopes of
the antigen on their surface. In this way, they localize the presentation of antigen, forming a vital link between the innate response and the adaptive response. Lymphocytes (such as B cells and T-helper cells) will have antigen presented to them, initiating the adaptive response. Monocyte-derived cells are common APCs, and they include tissue macrophages and monocytes within the blood; neutrophils are also APCs. APCs are discussed further below, in the section on cells of the immune system.
The skin contains epidermis and dermis. The epidermis contains tightly packed epithelial (cytokeratin positive) cells with keratin waterproofing. The dermis contains connective tissue blood vessels hair
follicles, sweat glands, and sebaceous glands. Sebaceous glands
secrete sebum; this contains fatty acids and lactic acid, lowering
skin pH to 3-5.
Mucous membranes contain normal flora, mucus, and cilia. Mucous membranes are found in the nose, eyes, mouth, urogenital, and anal regions of the body. Flora refers to bacteria that inhabit the human body in a relative steady-state; the gastro-intestinal tract contains a large number of these bacteria, and different areas of the world contain
different flora. It is for this reason that people contract Traveler's Diarrhea; in short, flora from one region of the world are more
dangerous because the body has not acclimated to their presence. Mucus contains certain mucin proteins, inorganic salts, and water; it is secreted from goblet cells. Cilia acts to sway back and forth during two phases, known as the power stroke and the recovery stroke; this allows mucus to be swept out of the body, either proximodistally from the lungs up the respiratory tract, or down the GI tract through the intestines, culminating in defecation. The enteric nervous system causes contractions of the gut, moving foodstuffs, waste, and bacteria/toxins down the digestive tract. This is just one example of disparate systems of the body working together with the immune system proper. Other examples are skeletal muscles, which squeeze blood along the veins and lymph along the lymph vessels, or the nervous system, which supports a rise in body temperature in response to infection.
Some bacteria can attach to mucous membranes via fimbriae or pili, which attach to special glyoproteins/glycolipids on the epithelial cells of mucous membranes.
Antimicrobial Compounds 
Several antimicrobial compounds mediate the innate response.
- Lysozyme--hydrolytic enzyme in tears and mucous; cleaves
peptidoglycan in bacterial cell walls
- Interferon--produced by virus-infected cells; binds to nearby
cells (it is a paracrine factor), inducing a generalized antiviral state
- Complement--inactive circulating serum proteins that act on
pathogen cell membranes
- Collectins--surfactant materials; kills bacteria by disrupting
their lipid membranes or agglutinating them
- Toll-Like Receptors---(TLRs) membrane-bound receptors that react
via pattern recognition to certain classes of molecules; TLR4, for example, recognizes lipopolysaccharide (LPS) on gram-negative bacteria
Classical biology put several characteristics together as an inflammatory response. These included redness (erythema, rubor), heat (calor), swelling (edema, tumor), pain (dolor), and loss of function (functio laesa). The physiological processes that bring about these symptoms are central to the innate immune response.
Erythema results from constriction of post-capillary venules in tissue beds and vasodilation in pre-capillary arterioles/metarterioles. This results in an increase of hydrostatic pressure in the capillary bed, overcoming the osmotic pressure of the interstitial fluid and causing exudate (high-protein fluid with acute-phase proteins like C-reactive protein and macrophages) to flow into the interstitial tissue. This flowing of exudate also allows the factors of the clotting
cascade to enter areas of tissue damage, forming clots and, eventually, scars. Certain inflammatory factors also cause phagocytic cells to
enter the damaged tissue. The now-permeable capillaries are traversed by these phagocytes in response to chemotaxis, the release of factors that lure the cells to the site of injury. The cells first approach the side of a capillary (margination), move through the spaces between capillary endothelial cells (diapedesis), and then enter the tissue itself. Histamine helps to mediate this response, and certain factors (such as bradykinin and possibly prostaglandins) stimulate skin pain receptors. Thus, blood flows into the tissue, causing redness, warmer steady-state temperature, swelling, and pain; loss of function is a secondary effect of these four states.
Adaptive Immunity 
Adaptive immunity occurs in response to antigen exposure. It is specific, and it shows memory. As long as an antigen is made of the normal chemical elements we experience in biological systems (e.g. Carbon, Nitrogen, Sulfur, Hydrogen, Oxygen), we can form an adaptive response to it. This is how we fight off new diseases, and it has even been shown that we can create antigens in the laboratory that have never
before existed on Earth, only to have animals mount competent immune
reactions to them. As stated earlier, the adaptive immune system's specificity is tempered with an ability to differentiate between self and non-self antigen; simply put, the body doesn't attack its own cells,
unless they have been invaded by virus and ask to be sacrificed for the sake of the host. When the immune system does attack the body, this is a disease state: autoimmunity.
The primary response takes 5-6 days, but the memory (secondary) response
will be swifter and deadlier. It includes:
Blood cells are made in the bone marrow of adults. Leukocytes are white
blood cells (WBCs). This includes monocytes (which become myriad cell
types in the body, most importantly macrophages), granulocytes (neutrophils, basophils, eosinophils), and lymphocytes. Of all the leukocytes, the lymphocyte class are the most preeminent in the adaptive
immune response. On a peripheral blood smear, lymphocytes are
approximately the size of erythrocytes (red blood cells, RBCs), although
they can be larger if activated and have a characteristic "clock-face"
nucleus if they are B cells. Lymphocytes are so named because fewer than 1% are present in the circulating blood; the rest lie in the lymph nodes, spleen and other lymphoid organs. T lymphocytes leave the bone marrow, travelling to the thymus gland, where they mature and gain their specificity for the diverse antigens the body might come into contact with; additionally, any T cells that react against the body's own epitopes are selected against (killed) in the thymus, in an effort to stop any possible autoimmunity. A similar process occurs in the bone
marrow in the case of B lymphocytes. B cells are conveniently
named ("B for bone marrow"), but this is just a coincidence; it turns out that they are named B cells after the Bursa of Fabricius, a small pouch in the cloaca (lower large intestine, cloaca Latin for "sewer") of birds.
B cells leave the bone marrow with their specific membrane bound Ig (antibody) already specified. The Ig itself is made up of two medial heavy chains (both identical) with two lateral light chains (also identical) attached to the "top" of the heavy chains, which form a Y shape. Before they encounter antigen, B cells are known as "naive." Once they encounter antigen, the naive B cells will undergo clonal expansion; an activated B cell will form some daughter memory B cells and some plasma cells. The memory cells will lie in wait
for a second encounter with the antigen, while the plasma cells will
begin a massive secretion of antibody (Ig). B cells can bind to antigen when it is free and unprocessed in the body, much like APCs can.
Before moving on to T lymphocytes, it should be noted that certain cell surface molecules distinguish each person's unique immune system profile. The Major Histocompatibility Complex (MHC, or HLA) is a type of protein expressed on the surface of host cells that interacts with T-cell receptors (TCRs) of T cells. Virtually all the body's cells, including APCs, express class I MHC (MHC-I) on their surface. Only APCs express class II MHC (MHC-II). Thus, most body cells express MHC-I, while APCs express both MHC-I and MHC-II. When antigen enters a body cell and is broken down, the products of this breakdown are sent to the surface of the cell coupled with MHC-I. This forms the MHC-I/Ag complex, and usually occurs when a virus or bacterium enter a cell and are broken down by intracellular defenses. This can also occur
in APCs, but APCs additionally process the antigen that they
phagocytose, presenting it as an MHC-II/Ag complex on the surface of their cells.
T cells can be subdivided into two broad types: T helper cells and T cytotoxic cells. T helper cells express a T-Cell Receptor (TCR) that will interact with APC surfaces. Specifically, they interact with the MHC-II/Ag complex on the surface of APCs, and the TCR is stabilized in its binding by a CD4 receptor. CD stands for "cluster of differentiation," and is simply a class of cell receptor which occurs predominantly on T cells. T helper cells contain CD4 receptors and T cytoxic cells contain CD8 receptors. Upon binding, T helper cells release cytokines, which act as chemotactic agents to call for more T helper cells, T cytotoxic cells, APCs, and B cells.
T cytotoxic cells encounter body cells that have been invaded and are presenting MHC-I/Ag on their surface. Tc cells extend their TCR to the MHC-I/Ag complex and stabilize this interaction with their CD8 receptor arms. Upon binding, the CD8+ cells differentiate, much like naive B cells, into memory T cells and cytotoxic T lymphocytes (CTLs), effector cells that cause the MHC-I/Ag-presenting cell (the "altered self cell") to die (apoptose). CTLs trigger apoptosis by secreting a perforin that allows the entry of a serine protease (Granzyme B) which activates intracellular executioner caspases. It should be noted that cancer cells can also become altered self cells, and CTLs are very important in
the destruction of cancerous cells.
T cells can interact with antigen only after it has been processed, either by a normal body cell (MHC-I) or by an APC (MHC-II).
Difference between the two types of T cells:
- T helper cells react to exogenous antigen, phagocytosed by APCs,
presented on MHC-II, via binding with TCR and CD4.
- T cytotoxic cells react to endogenous antigen (such as viral or cancer
proteins), broken down by lysosomes in many types of body cells, presented on MHC-I, via binding with TCR and CD8.
Note that it is both the antigen and the MHC that is presented to T cells; each person has a unique MHC. This is why we must type for bone marrow transplants--we don't want people producing tons of new immune cells in bone marrow that think every MHC in the body is actually just antigen; when this does occur, it is called graft-vs.-host disease. Not only would the new bone marrow make cells that attacked
every body cell's MHC, but when the body did present Ag on MHC, the
lymphocytes from the transplant would not be able to recognize this MHC-I/Ag complex (although the MHC-II complex cells would be made in the
new bone marrow, and thus APCs could, in some cases, still present).
Unfortunately, these APCs would be very busy presenting the host's own body cells; clearly MHC typing (also known as HLA typing) for bone marrow transplants is a necessary result of the elegant self-nonself recognition of the human immune system. It is also worth noting that we
are only as good as our presenting molecules. Some people have MHC
genes that are not as good at presenting antigen, and thus some people have more vigorous immune respones than others.
The cellular and humoral responses of the adaptive immune system are linked via the T helper cell-B cell interaction. The T helper cell secretes cytokine factors to encourage chemotaxis of B cells to the site
of infection as well as B cell differentiation and growth. B cells
themselves, in their effector plasma B cell form, release antibodies into the blood. Antigens, or foreign substances that enter the body,are very harmful to the Immune System. But when specific antibodies are produced to bind with an antigen, the foreign substance becomes harmless and is delivered
to the lymph. Antibodies are also very important in the complement
system; this is an example of the vertebral adaptive immune response making good use of the relatively primitive innate immune response. Antibodies to the body's own cells are a very real danger. Type I diabetes may be caused by an autoimmune response, where the body makes antibodies to its own Beta cells in the pancreatic Islets of Langerhans.
Graves' disease is a condition where the body produces antibodies to
receptors in the follicular cells of the thyroid; these Ab keep the cells constantly activated, giving the patient hyperthyroidism and increasing their metabolism, to adverse effect. The interesting counterpoint to this is Hashimoto's thyroiditis; here the body makes antibodies to thyroid follicular cells' receptors, but in this case the cells are shut down by the Ab, and the patient endures hypothyroidism.
Autoimmunity due to antibody overreaction (hypersensitivity) is a huge problem, and it is a much greater problem in women than in men. Women tend to have a higher titer of immunoglobulin (antibody), and thus they exert a stronger (and sometimes overwhelming) immune response. For example, for every one man who gets Graves' disease, 8 women will contract it.
Antibodies are often given to produce a short-lived humoral immunity in emergency situations. Many antivenoms are actually horse immunoglobulin, produced in order to bind the venom until it can be cleared from the body.
Theory Meets Function 
It should be noted that all of the above-mentioned immune responses result in the destruction or agglutination of foreign pathogen. The goal of the immune response is three-fold:
- Destroy foreign antigen via innate or humoral responses such as complement fixation or endocytosis by macrophages.
- Attract immune cells to the site of infection so they can engulf, process and present the antigen to T cells
- Move the antigen to the site of differentiation (e.g. lymph nodes, thymus) via the lymphatic system, so that it can interact with naive B cell. This process creates new effector and memory cells which can return to the site of infection and destroy the foreign cells in a highly effective fashion via the adaptive response.
The immune responses listed above show the intimate interaction between the innate and adaptive immune systems, as well as the subclasses of adaptive responses. The clonal selection theory of immune response, introduced above, is clear in the action of lymphocytes. Clonal selection simply means that antigen is presented to many circulating naive B and (via MHC) T cells, and the lymphocytes that match the antigen are "selected" to form clones of themselves, both memory and effector. This mass production of daughter cells is termed clonal expansion, and it is essential in the understanding of the theoretical basis of immunology. Not only this; clonal selection is used negatively in the lymphoid organs. Here, the body's own epitopes are presented to the infant lymphocytes; those that react are recognized as traitors and destroyed before they (and their future cloned daughters) can leave and wreak havoc in the body.