The immune system protects the body from infection and disease. It has both innate and adaptive immunity. Innate immunity provides immediate defense against pathogens using mechanisms like phagocytosis. Adaptive immunity develops over time and provides long-lasting, pathogen-specific protection through antibodies and T cells. The immune system is made up of organs like the bone marrow, thymus, and spleen that contain cells like T cells, B cells, macrophages, and dendritic cells which work together to recognize and eliminate pathogens.

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Immune System Overview
The immune system is composed of many interdependent cell types that collectively protect the body
from bacterial, parasitic, fungal, or viral infections, and from the growth of some tumor cells.
Innate immunity refers to antigen-nonspecific defense mechanisms that a host uses immediately or
within several hours after exposure to almost any antigen. This is the immunity one is born with and
is the initial response by the body to eliminate microbes and prevent infection.
Unlike adaptive immunity, innate immunity does not recognize every possible antigen. Instead, it is designed
to recognize a few highly conserved structures present in many different microorganisms. The structures
recognized are called pathogen-associated molecular patterns and include LPS from the gram-negative cell
wall, peptidoglycan, lipotechoic acids from the gram-positive cell wall, the sugar mannose (common in
microbial glycolipids and glycoproteins but rare in those of humans), bacterial DNA, N-formylmethionine
found in bacterial proteins, double-stranded RNA from viruses, and glucans from fungal cell walls. Most
body defense cells have pattern-recognition receptors for these common pathogen-associated molecular
patterns and so there is an immediate response against the invading microorganism. Pathogen-associated
molecular patterns can also be recognized by a series of soluble pattern-recognition receptors in the blood that
function as opsonins and initiate the complement pathways. In all, the innate immune system is thought to
recognize approximately 103 molecular patterns.
The innate immune responses involve:
• phagocytic cells (neutrophils, monocytes, and macrophages);
• cells that release inflammatory mediators (basophils, mast cells, and eosinophils);
• natural killer cells (NK cells); and
• molecules such as complement proteins, acute phase proteins, and cytokines.
Examples of innate immunity include anatomical barriers, mechanical removal, bacterial
antagonism, pattern-recognition receptors, antigen-nonspecific defense chemicals, the complement
pathways, phagocytosis, inflammation, fever, and the acute phase response
Adaptive (acquired) immunity, refers to antigen-specific defense mechanisms that take several
days to become protective and are designed to react with and remove a specific antigen. This is the
immunity one develops throughout life.
An antigen is defined as a substance that reacts with antibody molecules and antigen receptors on lymphocytes. An
immunogen is an antigen that is recognized by the body as nonself and stimulates an adaptive immune response. For
simplicity we will use the term antigen when referring to both antigens and immunogens. The actual portions or
fragments of an antigen that react with antibodies and lymphocyte receptors are called epitopes.
The body recognizes an antigen as foreign when epitopes of that antigen bind to B-lymphocytes and T-
lymphocytes by means of epitope-specific receptor molecules having a shape complementary to that of the
epitope. The epitope receptor on the surface of a B-lymphocyte is called a B-cell receptor and is actually an
antibody molecule called surface immunoglobulin (sIg). The receptor on a T-lymphocyte is called a T-cell
receptor (TCR). It is thought that the human body has the genetic ability to recognize 107 - 109 different
epitopes. In otherwords, the body has 107 - 109 distinct clones of both B-lymphocytes and T-lymphocytes,
each with a unique B-cell receptor or T-cell receptor. In this variety of B-cell receptors and T-cell receptors
there is bound to be at least one that has an epitope-binding site able to fit, at least to some degree, any
antigen the immune system eventually encounters. With the adaptive immune responses, the body is able to
recognize any conceivable antigen it may eventually encounter.

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The downside to the specificity of adaptive immunity is that only a few B-cells and T-cells in the body
recognize any one epitope. These few cells then must rapidly proliferate in order to produce enough cells to
mount an effective immune response against that particular epitope, and that typically takes several days.
During this time the pathogen could be causing considerable harm, and that is why innate immunity is also
essential.
Adaptive immunity usually improves upon repeated exposure to a given infection and involves:
• antigen-presenting cells (APCs) such as macrophages and dendritic cells;
• the activation and proliferation of antigen-specific B-lymphocytes;
• the activation and proliferation of antigen-specific T-lymphocytes; and
• the production of antibody molecules, cytotoxic T-lymphocytes (CTLs), activated macrophages and
NK cells, and cytokines.
There are two major branches of the adaptive immune responses: humoral immunity and cell-mediated
immunity.
1. humoral immunity: humoral immunity involves the production of antibody molecules in response to an
antigen and is mediated by B-lymphocytes.
2. cell-mediated immunity: Cell-mediated immunity involves the production of cytotoxic T-lymphocytes,
activated macrophages, activated NK cells, and cytokines in response to an antigen and is mediated by T-
lymphocytes.

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The Organs of the Immune System
Bone Marrow -- All the cells of the immune system are initially derived from the bone marrow. They
form through a process called hematopoiesis. During hematopoiesis, bone marrow-derived stem
cells differentiate into either mature cells of the immune system or into precursors of cells that
migrate out of the bone marrow to continue their maturation elsewhere. The bone marrow
produces B cells, natural killer cells, granulocytes and immature thymocytes, in addition to red
blood cells and platelets.
Thymus -- The function of the thymus is to produce mature T cells. Immature thymocytes, also
known as prothymocytes, leave the bone marrow and migrate into the thymus. Through a
remarkable maturation process sometimes referred to as thymic education, T cells that are
beneficial to the immune system are spared, while those T cells that might evoke a detrimental
autoimmune response are eliminated. The mature T cells are then released into the bloodstream.
Spleen -- The spleen is an immunologic filter of the
blood. It is made up of B cells, T cells, macrophages,
dendritic cells, natural killer cells and red blood cells.
In addition to capturing foreign materials (antigens)
from the blood that passes through the spleen,
migratory macrophages and dendritic cells bring
antigens to the spleen via the bloodstream. An
immune response is initiated when the macrophage or
dendritic cells present the antigen to the appropriate B
or T cells. This organ can be thought of as an
immunological conference center. In the spleen, B
cells become activated and produce large amounts of
antibody. Also, old red blood cells are destroyed in
the spleen.
Lymph Nodes -- The lymph nodes function as an
immunologic filter for the bodily fluid known as
lymph. Lymph nodes are found throughout the body. Inhabited primarily by T cells, B cells,
dendritic cells and macrophages, the nodes drain fluid from most of our tissues. Antigens are
filtered out of the lymph in the lymph node before returning the lymph to the circulation. In a
similar fashion as the spleen, the macrophages and dendritic cells that capture antigens present
these foreign materials to T and B cells, consequently initiating an immune response.

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Cells of the Immune System – OVERVIEW:
T cells -- T lymphocytes are usually divided into two major subsets or four specific types that are
functionally and phenotypically (identifiably) different. The phenotypic differences relate to surface
expression of CD4 or CD8 proteins.
The T helper cell (CD4+) is a coordinator of immune regulation. The main function of the T
helper cell is to stimulate immune responses by the secretion of specialized factors that activate other
white blood cells to fight off infection.
The CD8+ T cells are the killer cells and suppressor cells. The T killer cells are important in
directly killing certain tumor cells, viral-infected cells and sometimes parasites. The CD8+ T
suppressor cells are important in down-regulation of immune responses. Both types of T cells can be
found throughout the body. They often depend on the secondary lymphoid organs (the lymph nodes
and spleen) as sites where activation occurs, but they are also found in other tissues of the body, most
conspicuously the liver, lung, blood, and intestinal and reproductive tracts.
T-Cells –
• arise from stem cells in the bone marrow
• migrate to the thymus where they differentiate into mature T-cells
- surface proteins expressed (TCR, CD4 or CD8)
• leave thymus:
- circulate in bloodstream
- go to peripheral lymphoid tissues

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Four types of T-cells:
Cellular Immunity:
(1) Cytotoxic T cells (Tc)
• cytolytic for:
– cells with foreign HLA
– virally infected cells
– some tumor cells
• all express CD8
(2) Delayed Hypersensitivity T cells (Tdh)
• all express CD4
Regulatory T-cells:
(3) Helper T-cells (Th)
• promote proliferation and differentiation of Tc and B cells
• all express CD4
(4) Suppressor T cells (Ts)
• suppress cellular and humoral immunity
• all express CD8
NATURAL KILLER (NK) CELLS and KILLER (K) CELLS ‚ (LARGE GRANULAR LYMPHOCYTES)
Natural killer cells, often referred to as NK
cells, are similar to the killer T cell subset
(CD8+ T cells). They function as effector
cells that directly kill certain tumors such as
melanomas, lymphomas and viral-infected
cells, most notably herpes and
cytomegalovirus-infected cells. NK cells,
unlike the CD8+ (killer) T cells, kill their
targets without a prior "conference" in the
lymphoid organs. However, NK cells that
have been activated by secretions from CD4+
T cells will kill their tumor or viral-infected
targets more effectively.
1. (a) NK cells possess cell-surface markers
that are restricted to lymphocytes, but
lack those markers characteristic of B
cells and T cells.
(b) have azurophilic granules containing
cytolytic enzymes (e.g. perforin).
(c) able to lyse a wide variety of tumor
cells and virally infected cells.
(d) non-specific, no prior antigen exposure
needed (no memory), no MHC
restrictions, recognition system
unknown.
(e) NK activity enhanced by lymphokines, specifically -interferon, also IL-2
2. (a) K cells have Fc receptors on their surface by which they recognize and exert cytotoxic activity
toward antibody-coated target cells (called antibody-dependent cell-mediated cytotoxicity or ADCC).
(b) contain azurophilic granules, and are very closely related to NK cells.

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B Cells
- The major function of B lymphocytes is the production of antibodies in response to foreign proteins
of bacteria, viruses, and tumor cells. Antibodies are specialized proteins that specifically recognize
and bind to one particular protein. Antibody production and binding to a foreign substance or antigen,
often is critical as a means of signaling other cells to engulf, kill or remove that substance from the
body.
B lymphocytes:
(1) arise from stem cells in bone marrow
(2) upon reaching functionally mature stage, they emigrate to peripheral lymphoid organs.
(3) upon contact with appropriate antigen, a B-cell differentiates into an antibody-producing
plasma cell.
Cell Surface Markers:
New cytoplasmic and surface markers appear at each step of the B-cell differentiation.
(a) All B-cells possess antigen-specific surface Ig, both monomeric IgM and IgD, which are
capable of recognizing and interacting with only a single predetermined antigenic
determinant.
(b) The antigen-specific surface Ig on any given B-cell represents only one of the several million
possible DNA combinatorial rearrangements of the Ig genes.
Granulocytes or Polymorphonuclear (PMN) Leukocytes -- Another group of white blood cells is
collectively referred to as granulocytes or polymorphonuclear leukocytes (PMNs). Granulocytes are
composed of three cell types identified as neutrophils, eosinophils and basophils, based on their
staining characteristics with certain dyes. These cells are predominantly important in the removal of
bacteria and parasites from the body. They engulf these foreign bodies and degrade them using their
powerful enzymes.
Macrophages -- Macrophages are important in the regulation of immune responses. They are often
referred to as scavengers or antigen-presenting cells (APC) because they pick up and ingest foreign
materials and present these antigens to other cells of the immune system such as T cells and B cells.
This is one of the important first steps in the initiation of an immune response. Stimulated
macrophages exhibit increased levels of phagocytosis and are also secretory.
Dendritic Cells -- Another cell type is the dendritic cell, which also originate in the bone marrow,
and function as antigen presenting cells (APC). In fact, the dendritic cells are more efficient APCs
than macrophages. These cells are usually found in the structural compartment of the lymphoid
organs such as the thymus, lymph nodes and spleen. However, they are also found in the bloodstream
and other tissues of the body.
DENDRITIC and LANGERHANS' CELLS:
- highly branched dendritic cytoplasmic processes.
- high concentration of HLA Class II antigens.
- dendritic cells found in lymphoid tissues.
- called langerhans cells when found in epidermis.
- poorly phagocytic
- highly efficient antigen presenting cells (APC).

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HISTOCOMPATIBILITY ANTIGENS (HLA COMPLEX)
- originally identified as antigens that evoke rejection of transplanted organs; also important in
regulating other immune responses.
- area on the short arm of human chromosome 6 where these genes are found is called major
histocompatibility complex (MHC).
- In humans MHC is called human leukocyte antigen (HLA)
- MHC gene products are classified into 3 categories (based on structure, distribution and
function).
Class 1 antigens
- coded by three regions designated HLA-A, HLA-B, & HLA-C.
- found on all nucleated cells and platelets.
Class II antigens
- coded by region known as HLA-D (which also contains 3 subregions; DP, DQ, & DR).
- found mainly on "immunocompetent cells" (monocytes, macrophages, T cells, B cells, APCs).
Class III proteins
- components of the complement system (C2, C4a, C4b, & Bf)
- do not act as histocompatibility antigens
- Each individual expresses two sets of each HLA-type
• one set from each parent
• co-dominant (therefore heterozygous individual will express 6 different HLA-1 antigens
on each cell)

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Significance of HLA Complex
1. Transplantation, graft rejection
2. Regulation of immune response
Class I - recognition of virally infected cells by CD8+ cytotoxic T cells.
Class II - cell-to-cell interaction (e.g. Th induction activation)
- govern magnitude of immune response (Ir).
ANTIBODIES
Antibodies are one of two important antigen recognition molecules of the immune system. The other
antigen recognition molecule is found on the T Cell, called the T cell receptor (TcR). Antibodies also
act as receptors on B cells but usually we think of antibodies as the soluble factors secreted by plasma
cells. Soluble, or secreted, antibody is structurally slightly different than the antibody on the surface
of B cells but the antigen recognition sites are similar.
There are five different classes of antibodies or immunoglobulins (Ig) known as IgD, IgA, IgM, IgE
and IgG. There are four subclasses of IgG and two subclasses of IgA.

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Antibodies recognize antigen.
An antigen is a substance capable of inducing a specific immune response. The term is derived from the
generation of antibodies to such substances. Specific immune responses require recognition molecules like
the T cell receptor or antibodies which recognize the antigen, or parts of it, and stimulate a response by the
specific arm of the immune response (T or B cells).
Often antigens are foreign proteins (or parts of them) that enter the body via an infection. Sometimes,
however, the body's own proteins, expressed in an inappropriate manner (where or when they are not usually
seen), are treated like antigens by the immune system. It is important to recognize that bacteria or viruses are
not themselves antigens but they contain antigens both on their surface and inside them. Such antigens can
be isolated and used to safely vaccinate against infection with the whole organism.
Antigens are recognized by B cells and their surface antibodies (sIgM) or by the T cell receptor on T cells.
Recognition leads to the growth of specific clones of B and T cells which recognize the antigen.
Although T and B cells may respond to the same antigen, they are usually responding to different parts of
the same molecule. Antibodies on the surface of B cells for example are very good at recognizing the tertiary
structure of a protein (ie - the way it folds). T cells on the other hand, require the same protein to be ingested,
degraded and presented on the surface of a special cell aptly named the antigen presenting cell. Proteins or
glycoproteins make the best antigens because they are the best at stimulating antigen recognition
molecules.Each part of the antigen that is recognized by either an antibody or a T cell receptor is known as an
epitope. Depending on the size of the protein or polysaccharide, there may be hundreds of B cell epitopes
(recognized by different antibodies) or T cell epitopes (presented by antigen presenting cells to different T
cells) in the same molecule. This actually helps the body have a better response to the antigen as many T and
B cells can be activated to respond to a single target.
The ability of antibodies to recognize specific
antigen is an important characteristic . Antigen
recognition and binding allows antibodies to perform
three important functions.
• opsonization
• activating complement
• neutralizing toxins and toxic organisms
Opsonization is a process where bacteria, virus-
infected cells and others are 'tagged' for destruction.
Antibodies are the 'tags' (or opsonins) because one end
(Fab) binds to an antigen on the surface of the organism.
The other end of the antibody (Fc) binds to receptors on
phagocytic cells like macrophages and neutrophils. The
antibody signals the phagocyte to engulf and destroy the
organism or cell. Antibodies may also stimulate
extracellular killing with an oxidative burst and the
release from phagocytes of free radicals and destructive
enzymes. Complement components, like C3b, also act
as opsonins (C3b opsinization).
Antibody also helps to kill foreign organisms by activating complement. IgM and IgG are very good
at this, resulting in the lysing of the target by the C5-9 complex (MAC attack).
In the circulation and in tissues, antibody will bind to toxins to remove them by forming easily recognized
antibody-antigen complexes which are phagocytosed in the liver and elsewhere. Antibodies can also
immobilize and agglutinate infectious agents by binding to surface antigens and prevent them from attaching to
sites of infection like the intestinal mucosa) or from penetrating cells (such as in the case of virus').

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The Immune Response
An immune response to foreign antigen requires the presence of an antigen-presenting cell (APC),
(usually either a macrophage or dendritic cell) in combination with a B cell or T cell. When an APC
presents an antigen on its cell surface to a B cell, the B cell is signaled to proliferate and produce
antibodies that specifically bind to that antigen.
If the antibodies bind to antigens on bacteria or parasites it acts as a signal for
neutrophils or macrophages to engulf (phagocytose) and kill them. Another important
function of antibodies is to initiate the “complement destruction cascade.”
When antibodies bind to cells or bacteria, serum proteins called complement bind to
the immobilized antibodies and destroy the bacteria by creating holes in them. Antibodies can
also signal natural killer cells and macrophages to kill viral or bacterial-infected cells.
If the APC presents the antigen to T cells, the T cells become activated. Activated T cells proliferate
and become secretory in the case of Th (CD4+) cells, or, if they are Tc (CD8+) cells, they become
activated to kill target cells that specifically express the antigen presented by the APC. The
production of antibodies and the activity of CD8+ killer T cells are highly regulated by the CD4+
helper T cell subset. The CD4+ Th cells provide growth factors or signals to these cells that signal
them to proliferate and function more efficiently. This multitude of interleukins or cytokines that are
produced and secreted by CD4+ Th cells are often crucial to ensure the activation of natural killer
cells, macrophages, CD8+ Tc cells, and PMNs.

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MACROPHAGES
Functions in Immune Responses:
(a) process and present antigen to Th (primarily)
(b) produce IL-1
- promotes differentiation of both T & B cells.
(c) antitumor lysing activity (secrete Tumor Necrosis Factor)
(d) delayed hypersensitivity reaction
CYTOKINES
- polypeptide messenger molecules of the immune system.
A. Cytokines induce their effects in three ways:
1. autocrine effect - act on same cell that produces them - e.g. IL-2 produced by activated T
cells promotes T-cell growth.
2. paracrine effect - affect other cells in their vicinity - e.g. IL-1 produced by APCs promotes
proliferation of CD4+ cells and IL-2 release from them.
3. endocrine effect - affect many cells systemically - e.g. IL-1 and TNF-α produce acute-phase
response during inflammation.
B. Receptors -- cytokines mediate their effects by binding to specific high-affinity receptors on their
target cells.

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