IPBP IA Exam Study Guide:

Immunology

International Post-Baccalaureate
PharmD (IPBP) Program

Internal Assessment (IA) Exam

STUDY GUIDE

IMMUNOLOGY

2015
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 IPBP IA Exam Study Guide:
Immunology

Study Guide for PHRM 5401- Immunology

International PharmD Program Exam

This document is provided as an abbreviated study guide to the Immunology course

taught at Western University of Health Sciences. As an abbreviated study guide,
this document covers ONLY the most basic concepts and does not replace a
qualified textbook or course notes which should be studied before this review.
Students who do not consult a full set of notes or textbook will not be prepared to
pass the correlating exam.

It is strongly recommended that students access information found here:

http://www.niaid.nih.gov/topics/immuneSystem/Pages/default.aspx

and corresponding material from the free: online version of Immunobiology ;

5th ed. Janeway, Charles A.; Travers, Paul; Walport, Mark; Shlomchik, Mark.
New York and London: Garland Publishing; c2001; found here:
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=imm.TO
C&depth=10
(Notice that you must enter text in the search box to the right, to retrieve
chapter text and figures.)

All material in this document is Copyright Stephen A. OBarr, PhD and David J.
Sanchez, Ph.D. except where noted. Figures are provided by The Immune
System 3rd Edition, Peter Parham; Garland Publishing / Elsevier Science Ltd. NYC,
USA (2009).

Review objectives:

1. History of Immunology
2. Overview of The Immune System
3. Innate Immune Response
a. Innate Recognition of Microorganism
b. Cytokines
c. Complement
4. Adaptive Immune Receptors
a. Diversity of Receptors Leads to Specificity of Function
b. B cells and Antibodies
c. T cell and MHC diversity
5. Allergies (Type 1 Hypersensitivity)
6. Vaccination
a. Immune response to Viruses
b. Types of Vaccines
c. Herd Immunity
d. Controversies Concerning Vaccination
 IPBP IA Exam Study Guide:
Immunology

1. History of Immunology
Immunology, derived from the Latin term immunis which means exempt, is the study of the
bodys defense system, which protects against harmful substances (pathogens) from the
surrounding environment.

Pathogens - Infectious microorganisms (including viruses, bacteria, fungi, protozoa, and

multicellular parasites)

Better stated, infectious pathogens are any infectious organism which can cause disease.

The history of Immunology goes back thousands of years:

Thucydides recorded the plague of Athens, Greece around 430 B.C. which lasted for 3 years
infecting countless individuals, one of which was Thucydides himself. No one is sure just what
caused the plague but some modern medical historians suspect that it was caused by the Ebola
virus.

Thucydides wisely observed that those individuals infected with the plague, but who later
recovered, were able to treat those that had symptoms of the disease without contracting the
disease a second time. Individuals that survived the plague were mostly immune to further
infections.

This active, natural immunity is caused from either a weak strain of a virus, a small amount of a
potent strain, or genetic variations that make the individual better able to resist the infection.

History records, the first attempts to protect individuals from infection were immunizations against
smallpox performed in India and China around the fifteenth century A.D. This method of
vaccination was accomplished by removing smallpox pustules from infected patients which were
shot up the nose of uninfected patients or inserted into an open cut on the skin. Placing the viral
pustule into an open cut is called variolation, and was the method used for vaccination for several
hundred years.

Unfortunately, there were several problems with these first immunizations. Since potency of the
source of smallpox was difficult to measure, the majority of those immunized died due to smallpox
itself. There were also problems with the strength of infection of the strain used. Using a weak
strain of smallpox was the best approach since the strain was less likely to kill the host. However,
even those infected with a weak strain could pass the live virus on to others, uninfected individuals
since they were still infected with a live smallpox strain.

Scientific evidence for immunizations did not come until 1796, when the English physician, Edward
Jenner first started to study cowpox/smallpox infections. Dr. Jenner noted that historically
individuals that milkmaids, women that milked cows for a living, were less likely to get smallpox.
He theorized that these women contracted cowpox during the process of milking the cows.

To prove his theory, Dr. Jenner DID NOT use smallpox to induce immunity (vaccinate) against

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smallpox, rather, he took the fluid of a COWPOX pustule from Sarah Neames, a local milkmaid
and injected it into an eight-year-old boy named James Phipps. As expected, the young boy got ill
and contracted cowpox. Six weeks later, Jenner challenged the boy with liquid from the blisters of
a person who had smallpox. Amazingly, the boy did not develop smallpox symptoms.

In early 1797, Jenner repeated the experiment on several more subjects, and within a year he
published his findings. Jenner named his inoculation process, "vaccination", because the Latin
name for cowpox was "vaccinia" ("cow" is "vacca" in Latin).Within six years of his publication,
Jenner was a worldwide hero and his vaccination method was widely used. By the end of the 19th
century most European countries, would be vaccinated against the smallpox virus.

In 1967 the World Health Organization (WHO) made the eradication of smallpox a priority. At this
time it was estimated that smallpox afflicted up to 15 million people annually, of whom some two
million died with millions more left disfigured and sometimes blind. (Figure 1.1 shows the number
of smallpox cases over time as well as young child with smallpox)

In 1977, Ali Maalim of Merka Town, Somalia was the last

person to have had a naturally occurring smallpox virus
infection. In 1980 the WHO declared victory after more 2
years had passed without a natural occurrence of the
disease.

However, even though there are no naturally occurring

infections of smallpox, the virus has not been eliminated
from the earth. Smallpox was kept in several military
laboratories at least in the U.S.A. and in the former U.S.S.R.
Consequently, though smallpox is not currently spreading
naturally it may one day be reintroduced by people through
accidents or bioterrorism. Thus there is still much worry
about smallpox.

Because the virus exists in laboratories, the military and

others still are vaccinated against it. The smallpox vaccine
used today is actually a weakened, live virus strain called
vaccinia that is different than cowpox but still can induce
immunity against smallpox. The U.S. Government has
ample supplies of the virus, as does the Center for Disease
Control (CDC) and Acambis Laboratories, the only licensed
producer of smallpox vaccine in the United States.

Why does the military use the vaccine?

Although the military stopped routine vaccination for ALL enlisted personnel, the military has
continually vaccinated at risk persons. It is believed that several countries and many radical
groups maintain stockpiles of the small pox virus for use in biological warfare.

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Where does that leave citizens?

In Dec 2001 the U.S House of Representatives and the U.S. Senate approved $2.9 BILLION
toward increasing vaccination supplies including $1 BILLION for enough vaccinations for each
American against smallpox.

In December, 2002, President Bush established the Smallpox Vaccination Program and said:
I'm ordering that the military and other personnel who serve America in high-
risk parts of the world receive the smallpox vaccine, men and women who
could be on the front lines of a biological attack must be protected.

This particular vaccine does involve a small risk of serious health

considerations. As Commander-in-Chief, I do not believe I can ask others to
accept this risk unless I am willing to do the same. Therefore I will receive the
vaccine along with our military.

What cautions do we have to be aware of:

Because the U.S. uses a weakened LIVE virus, those that get vaccinated can contract or carry the
virus to infect others, plus there are other side effects.

Due to even small (50 per 1,000,000) adverse advents (with an estimate of 1:1,000,000 deaths),
the government is working hard to develop non-infectious vaccines. One type of non infectious
vaccine is called the component vaccine. One major vaccine which has been switched to a
component vaccine is Polio. Before 1999, the (OPV) polio virus, caused about 3 cases of polio a
year in the U.S. It has since been switched to a dead (inactive) injected virus (IPV).

So although we have eradicated many diseases by vaccination, we are continuing to improve

vaccines.

There are more than 4,000 current drug trials for vaccine effectiveness in the U.S. as of
September, 2013, about 36 of which study the use of DNA as vectors.
A unique aspect of pharmacy today is the ability to deliver vaccines to the general public.
Vaccination certification is a requirement of your training, and you will most likely be presented
with opportunities to use these skills in your professional career. Moreover, the number and
variety of available vaccines continue to increase over time. For up-to-date information on
influenza vaccines, including information for practitioners, please visit http://www.cdc.gov/flu.

2. Overview of The Immune System

There are many types of pathogens, including bacteria, viruses, fungi and parasites. Most of
these infectious agents never make it into the body due to the complex defenses our body
possesses including hair, skin, nails, mucus and cilia of the respiratory tract (sinus, trachea, lungs)
and digestive tract, and filtering of the urogenital tract. These physical and chemical barriers
represent the first defenses our body has against pathogens.

If pathogens make it past those first defenses, the immune system will respond to it. There are two
major arms of the immune system: the innate and adaptive systems. Below describes the

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categorization of these two immune system arms:

The Two Arms of an Immune response

Innate- first to be activated
fast response
not specific for a particular pathogen
not always as powerful as adaptive response
but can contain the infection.
includes soluble mediators and cells including macrophages

Adaptive- upon first exposure to a pathogen, the response is delayed

often more powerful than the innate response
very specific for a particular pathogen
gives long term memory of a particular pathogen
to immune system (source of immunity from vaccination)
found only in higher species (vertebrates)
includes B cells and T cells

Within these two arms are several soluble and cell mediated processes. The cells of the immune
system include all white blood cells (Leukocytes) which are found within tissues and circulating in
the blood. These cells work together and make up part of both the adaptive and innate systems:

These cells can be broken down into small and large cells due to their size:

Small cells Large Cells

B cells / Ig -->Plasma cells --> Ab NK cells
T cells / TCR Mac/Monocyte
dendritic cells Neutrophil
Basophil
Eosinophil

All immune cells derive from hematopoietic stem cells. Hematopoietic stem cells (HSCs) are cells
in the bone marrow that can differentiate into any of the immune cells but can also regenerate
themselves. The development of these immune and blood cells from HSCs is called
hematopoiesis (See Figure 1.14). Hematopoiesis occurs in the liver and bone marrow of the fetus,
and then in the bone marrow only after fetal development.

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The HSC can differentiate into any of the three major progenitor cell types (lymphoid, myeloid and
erythroid). These progenitors can then differentiate into specific leukocytes including effector cells
and tissue specific cells. A person born missing one of the lineage progenitors will not have any of
the cells that derive from that progenitor. For example, a person born without any myeloid
progenitor cells would lack erythrocytes, platelets, phagocytes and granulocytes.

The B cells develop in the bone marrow and then circulate throughout the lymph and circulatory
systems. B cells develop by interacting with bone marrow stromal cells in the matrix of the bone.
B cells have a B cell receptor on the B cell plasma membrane and use this receptor to bind to
antigens. Antigen is the term used to describe a molecule that can be bound by immune
receptors, especially antibodies. B cells which bind tightly to proteins in the bone matrix are said
to bind to self-antigen are removed via apoptosis (negative selection). Self antigen refers to
proteins in the body that are bound by immune receptors. Self-antigens activating an immune
response is bad and can lead to a process called autoimmunity that can damage tissues and cells
of an individual. Thus, negative selective works to prevent autoimmunity

T cells come from the bone marrow, but mature in the thymus where they are selected to be
functional and useful immune cells. The T cells then circulate throughout the lymph and
circulatory systems. T cells have a T cll receptor that recognizes protein pieces that are presented
on the surface of proteins by the MHC proteins. Positive selection of T cells occurs in the cortex of
the thymus with only those T cells which recognize self MHC surviving. T cells which show high
affinity toward self antigen that are presented on MHC are removed via apoptosis through
negative selection in the Thymus.

Macrophages are cells that go through the tissues and take up things in the microenvironment
through the process of phagocytosis. Macrophages break down these phagocytosed things
(which could include cellular debris and/or pathogens). Macrophages are tissue specific, and
specialized in nature. For example, brain resident monocytes/macrophages called microglia cells
while liver resident macrophages are called Kupfer cells.

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Combining the lymph and circulatory systems are the primary and secondary immune organs (as
in Figure 1.18):

Primary Immune Organs: Thymus, bone marrow

Secondary Immune Organs: Lymph nodes, spleen, mucosal lymph systems (MALT) which
contains M cells and includes the Peyer's patch.

Secondary lymph organs trap pathogens (lymph/blood/mucosal), have B/T cell centers, and have
germinal centers where the activation of lymphocytes (B/T) takes place.

Other cell types of importance are macrophages, which act as antigen presenting cells, and in
response to pathogens, will release soluble mediators such as complement and cytokines.
Macrophages are best categorized as part of the innate immune system though they do interact
and enhance parts of the adaptive immune system.

3. Innate Immune Response

As mentioned above, the innate immune response is an evolutionarily conserved system of
defense that protects the body from many types of microorganism. There are many cells and
soluble mediators that are part of the innate immune response. The innate immune response
works to recognize and respond to a general type of microorganism. This approach is more
general but not as powerful as an adaptive response. Figure 2.2 summarizes different innate
response mechanisms and cell types and what types of microorganisms they target.

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Here, we do not necessarily denote the microorganism as a pathogen because the function of the
innate immune system is to stop environmental microorganisms from causing disease.
Consequently, a majority of the microorganisms that the innate immune response responds to are
not pathogens but still are able to be stopped from becoming pathogenic by the innate immune
system.

Depending on where the microorganism exists, different effectors systems of the innate immune
system can respond. For example, extracellular microorganisms are often stopped by the
complement system, or phagocytes such as macrophages and neutrophils. Phagocytes are cells
that can engulf microorganisms and in the process of phagocytosis, which is similar to
endocytosis, will bring the microorganism into an intracellular vesicle. These vesicles can be a site
of microorganism degradation. This process occurs continuously and not just when a pathogen is
present.

3. a. Innate Recognition of Microorganism

When a microorganism enters a human, the innate immune

system must first quickly recognize what type of microorganism is
present. To do this they recognize particular molecular patterns
that are unique to a general type of microorganism. For example,
peptidoglycan is molecule that is unique for bacteria. These
molecular patterns are called Pathogen Associated Molecular
Patterns (PAMPs) that can be recognized by innate immune
receptors termed Pattern Recognition Receptors (PRRs) because
they recognize the patterns that are representative of the
particular microorganism.

As shown in Figure 2.19, macrophages are important innate

immune cells that can use different PRRs to determine what
general type of microorganism is present in the surrounding area.
Often times they can take up a microorganism by the process of
phagocytosis which can degrade the microorganism exposing the

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molecular patterns that make up the microorganism. The PRRs are then able to bind their
corresponding PAMP ligand and induce cytokine release to activate other parts of the innate and,
later on, adaptive immune response.

3. b. Cytokines

Cytokines are the major messenger proteins in Cell-Mediated reactions:

Small proteins (8-20 kDa)
Autocrine and paracrine in action
Receptor mediated signal transduction
Gene activation (up and down regulation)
They are often released in response to signaling by the cell or stress that is induced by
environment or invading pathogens. Cytokines are important in the development of many
diseases as well as the control of immunity.

Cytokines include:
Interleukines (IL1 to IL-19+)
Interferons (IFNs)
Colony stimulating factors (CSFs)
Tumor necrosis factors (TNFs)
Growth factors (GFs)
Chemokines (RANTES, MCP, MIP, C5a, C3a)

Most are type I receptors with shared subunits which explains cross reactivity and redundant
functions of some cytokines.

Cytokines can be released by a cell like a macrophage after it has encountered a microbial
product as in Figure 2.27.

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Diverse distribution of cytokine receptors allows for diverse functions:

e.g. IL-6:
T cell proliferation and differentiation
B cell plasma cell formation (Antibody production)
Mesangial cell proliferation
Keratinocyte growth
Hepatocyte activation
Osteoclast activation
Platelet secretion from Megakaryocytes

Cytokines stimulate signal transduction pathways leading to changes in gene activity. Many of
these genes code for other cytokines. One set of cytokines are the pro-inflammatory cytokines
which are IL-1, IL-6 and TNF-.

Once released, cytokines induce both paracrine and autocrine activity, influencing and regulating
the immune response.

3. c. Complement

The complement system is composed of several autocatalytic enzymes whos activation results in,
(1) Inflammatory cell recruitment (chemotaxis), (2) Opsonization of pathogens including immune

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complexes (composed of Ig bound to small pathogen) and (3) Cell lysis. Complement proteins
exist in serum as inactive pro-enzymes called zymogens. There are several pathways that exist
to activate the complement pathways and are summarized in Figure 2.5.

Initiation of the Classical Pathway is via antibody (Ab) binding to pathogen which can become
cross linked by C1q. Antibodies are B cell proteins made to bind to pathogens. C1q binds to
the Fc region of Ab. Amplification is at the C3 and C5 steps resulting in both opsonins (C3b)
and anyphylatoxins (C3a, C4a, C5a) being released. Formation of the membrane attack
complex C5b-9 (MAC) results in cell lysis.

The role of anaphylatoxins (C5a, C3a, C4a) includes activation of neutrophils, Induction of
chemotaxis, and the Increased permeability of endothelium.

4. Adaptive Immune Receptors

Whereas innate immunity allows for general defense, adaptive immunity aids in Specific
recognition by formation of millions of specific recognition sites on both the B cell receptors,
antibodies (Ab or Ig) and T-cell receptors (TCR) (Figure 3.1).

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4. a. Diversity of Receptors Leads to Specificity of Function

Diversity is found in the variable

regions (antigen binding domains)
of B cell receptors / Antibody
(BCR-Ig/Ab) and T cells (TCR).
Diversity is generated at the gene
level through gene
rearrangement or gene
recombination and subunit
combinations (heavy-light,
chains).

The antigen binding sites of the Ab

are found in both the heavy and light
chains (Fab fragments) (See
Figures 4.2 and 4.3). This is where
the hyper variable regions are
located. Diversity gene segments
code for the heavy chain antigen
binding site. Macrophages which
have Fc receptors recognize
the heavy chain constant region of the Fc region. Complement components also binds to the Fc
region of the antibody.

Diversity within individual B cell clones is due to hypermutation within the variable binding region
gene sequences which can increase specificity several fold.

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Diversity in the T cell receptor is found in the variable regions of

the TCR. Here though the two chains (an a and a b chain) each
have a diverse sequence/structure that leads to a more unique
antigen-binding site. Note that (as shown in Figure 5.1 to the
left), the Fab and a TCR have a structure similarity.

Within the bone marrow and the thymus, clonal selection

eliminates most B/T cells that react with self antigen. This is
through a process of negative selection.

In the periphery, specific cells that react with a specific antigen

are selected to divide rapidly. This is called clonal selection as
shown in Figure 3.4 (goes from part 1 on left to part 2 on right).
For clonal selection works because the immune system starts
with such a huge set of diverse cells each with unique
receptors. Upon stimulation by binding to a pathogen antigen,
the cell will be selected and clonally expand to a major cell type
that can respond to and eliminate the pathogen.

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Antigen recognized by B-cells include peptide or protein (in its native 3D structure) (carbohydrate
groups, amino acid clusters, glycoproteins, proteoglycans) while antigen recognized by T-cells is
solely processed peptide presented by the Major Histocompatibility complex (MHC). For
intracellular peptides such as virus, and some intracellular bacteria, it is presented on MHC-I
(which is found on all cell types).

For extracellular pathogens such as bacteria, worms, environmental pathogens, peptides are
presented on MHC-II. Only professional antigen presenting cells such as macrophages,
dendritic cells and B cells, expression MHC-II.

There are five isotypes of Ab: IgA, IgD, IgE, IgG, IgM with the most common in blood being IgG,
IgM and IgA. Antibodies aid in opsonization and neutralization of pathogens.

There are two classes of T cells, Cytotoxic T cells (Tc) and Helper T cells (TH1, TH2). Cytotoxic T
cells (Tc or CTL) recognize MHC I (virus/intracellular) while Helper T cells (TH) recognize MHC II
(external pathogens).

While innate immunity does not have memory, adaptive immunity can induce long-term protection
from specific pathogens. This ability to induce long-term protection by vaccination has
revolutionized heath care throughout the world.

Though we can induce long term protection in individuals, diseases form with alterations of the
immune system including:

Compromised:
Most are genetically related

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Acquired/Infectious:
HIV (loss of CD4+ helper T cells and NK/Mac)
Hyperactive:
Allergic response (IgE / cytokines)
Autoimmune disorders (Ig / TCR mediated)
Medically induced:
Transplantation (MHC compatibility)

4. b. B cells and Antibodies

B cells: Cell surface immunoglobin receptors are found on B cells (B cell receptors or BCR).
Once activated, B cells can differentiate into plasma cells which release soluble antibodies (Abs)
(Figure 4.1).

Antibodies have multiple functions including, binding to

pathogens and their toxins, neutralization,
opsonization, and activation of complement (Figure
3.14).

The secreted antibodies come from the clones of

those B cells stimulated by antigen. (i.e. Both the BCR
and the Ab will recognize the same antigen)

Ab is composed of 2 identical heavy and 2 identical

light chains (either or ) with isotypes differing in
heavy chain ( = IgG, = IgM, = IgD, = IgA, =
IgE).

Differences between isotypes include length of Fc

region, number of carbohydrate groups and in
assembly (i.e. dimers (IgA) and pentamers (IgM)).

Antibody tertiary structure includes sheets which

structurally protects antibodies from harsh biological
environments (changes in pH, [salt], enzymes etc).

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The variable region of the Ab (HV=hypervariable or CDR= complement determining regions)

interact with antigenic epitopes. A single antigen (e.g. virus) contains several epitopes (antigen
binding regions). These can be different epitopes or the same epitope which are repeated
throughout the antigen.

Binding between Ab and antigen is non-covalent and includes electrostatic, hydrogen, van der
Waals, and hydrophobic forces.

Binding affinity between various antibodies differs between different epitopes on a given antigen.

Monoclonal antibodies show specificity to a given epitope, since they are all derived from a given
B cell clone.

B cell diversity is due to somatic recombination, and variations in heavy chains. Diversity between
IgM and IgD is due to alternative splicing at the mRNA level.

B cell receptors anchor into the cell membrane but do not interact with intracellular proteins. Ig
and Ig are trans-membrane proteins which interact with intracellular signaling proteins.
Once an Ab encounters an antigen, four major events occur.
Antibody is secreted
Class switching occurs
Hypervariable regions mutate
Plasma cells develop

Upon encounter with antigen, a B cells first secretes IgM and some IgD.

B cells develop into plasma cells which secrete only ONE isotype (subclass) of antibody. Plasma
cells release antibody in primary (bone marrow) and secondary lymph organs (lymph nodes,
spleen) where it enters the blood- stream.

Class switching takes place after antigen recognition with the final class being one of the following:
IgG1, IgG2, gG3, IgG4, IgA1, IgA2, IgM or IgE

IgM
The first antibody (along with IgD) to be produced on surface of B cells. It is secreted as a
monomer from activated B cells and secreted as a pentamer from plasma cells. When IgM is
bound to antigen, it can activate complement, enhance phagocytosis, and lead to IgG production.

IgD
Is found on the surface of nave B cells, can be released from activated B cells, but its effector
function is unknown.

IgG
Is the most abundant antibody in blood and lymph. It is made by plasma cells and cab be one of 4
different isotypes (subclasses) (IgG1-4). It activates complement when bound to antigen, aids in

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killing cells by NK cells, can cross placenta to give passive immunity to fetus and enhances
neutralization and phagocytosis (opsonin) of pathogen.

IgA
Monomeric IgA is found in lymph, spleen, blood, sweat, saliva and tears. It is the most abundant
isotype in the whole body! It can neutralize pathogens as well as IgG and is secreted as a dimer
in lymph surrounding mucus and gut. It is the most important Ab in first contact areas (sinus,
mouth, gut). IgA has two subclasses or isotypes (IgA1 and IgA2). It is the most important
antibody found in breast milk and can transfer passive immunity to an infant.

IgE
Is found at VERY low serum levels and is VERY specialized in its function. It activates mast cells,
causes the release of histamine (allergic response) and aids in the expulsion of worms and
parasites from the body.

The different types of Ab can be found at

specific locations in the body as shown in
Figure 9.23. Of special note are the sites
that have unique antibodies. IgG and
monomeric IgA are spread through most of
the body. IgE, which is associated with
allergies and hypersensitivity, is found at
the external parts of the body. The brain is
termed immune-privileged and is mostly
devoid of B and T cells (thus blank for
antibodies). Dimeric IgA is found in
mucosal lining and is also found in breast
milk which is given to newborns from the
mother. Figure 9.24 shows the time course
of when babies during gestation to after
birth get antibodies. Breastmilk helps
newborns as IgA is produced late after
birth.

4. c. T cell and MHC diversity

T cell Diversity: All diversity in T cells is determined BEFORE the T cell leaves the thymus, unlike
B cells where they continue to diversity after antigen stimulation via affinity maturation and class
switching.

T cell development occurs in the thymus where each T cell undergoes both positive and
negative selection (Refer to Figure 7.1). Positive selection of developing T cells occurs in the
cortex of the thymus with only those T cells recognizing self MHC surviving. Once T cells

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which recognize self MHC are identified, they are then negatively selected if their TCR
binds too tightly to self peptide. This occurs in the medulla of the thymus.

The Thymus is important for the maintenance of an individual with an immune response that can
respond to antigens quickly. If the thymus is removed during surgery or the thymus atrophies as
the person ages, the individual produce less T cells and is thus less able to make a set of T cells
that clonal selection can work with. As shown in Figure 7.4 there is less Thymus that can make T
cells as the Thymus begins to atrophy as we enter adulthood.

There are two classes of T cell receptors, and with the majority being within the blood
stream. T cells make up the majority of T cells within mucosal areas (gut, sinus, urogenital
track etc). For a given T cell, only one pair of chains can be expressed. For example, if is
expressed, it always associates with to and if is expressed, it always associates with .

Gamma delta complex genes are similar to those of the alpha beta TCR, with the delta chain
encoded within the alpha locus. This allows EITHER alpha OR delta to be expressed.

CD4 and CD8 glycoproteins reside on the T cell. CD4 are found on Helper T cells where they
bind to MHCII. These are subcategorized as TH1 interacting with tissue macrophages and TH2
which are specific for B cell interaction. CD8 are expressed on Killer T cells where they bind to
MHCI. These cells kill virus infected cells. Figure 8.3 summarizes the different locations of MHC
and T cell use.

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MHC-I are found on all cells and present processed peptide from within the cell (e.g. virus). MHCII
are found on professional antigen presenting cells. Figure 5.20 shows the different intracellular
pathways that are used to make MHC Class I versus MHC Class II. As you can see the different
locations of MHC synthesis dictate what types of antigens they present and correspond with the
ways the T cells should respond.

Both bind a wide variety of peptides, meaning that for a given MHC, there is a lot of promiscuity

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unlike TCR and BCR which usually recognize just ONE

antigenic epitope.

TCR recognizes both the peptide AND the MHC. Thus the ligand for TCR is
both the peptide and MHC sequence. (See Figure 5.31)

Under certain circumstances, even without antigen within the MHC cleft the super antigen (e.g.
staphylococcal enterotoxin which is associated with food poisoning) can activate the TCR
complex. This is also the case in toxic shock syndrome toxin infection.

Genetically MHC is part of the Human Leukocyte Antigen (HLA) gene complex. The diversity of
the HLA complex is the major reason for transplant rejection.

Some important terms related with the HLA complex include:

POLYGENY - difference within an individual MHC complex (different heavy alpha chains of MHC I
and different alpha and beta chains on MHC II)

GENETIC POLYMOPHISM - differences between people in a population. Each person inherits

one allele (gene cluster) from mother, one from father.

MHCIII genes include some complement proteins and some cytokines.

5. Allergies
Allergens: antigens that elicit hypersensitivity reactions (See Figure 12.1). They are frequently
innocuous proteins that do not threaten the integrity of the body. i.e. if you were able to dampen
the hypersensitivity response, your body would be better off.

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Different types of antigens can induce different forms of hypersensitivity (See Figure 12.2).
Each is mediated by a different type of immune component and leads to different disease
manifestations.

Fc-epsilon receptor (FcR) found on Mast cells, Basophils, and Eosinophils binds almost
irreversibly to IgE, and is called sensitization (See Figure 12.3). By blocking FcRs function,
one could dampen the allergic response.

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When crossed linked there is instant degranulation which results in the release of histamine,
leukotrienes and prostaglandins. There is no activation or division step needed!

Histamine binds to H1 receptors on smooth muscle and endothelial cells surrounding blood
vessels, and
-increases permeability into tissues (vasodilatation)
-constricts airways (smooth muscles)
-increases mucosal secretion
-sneezing, coughing, wheezing, vomiting, diarrhea

Lipid Metabolism:
Leukotriene - similar to histamine (but 100X more potent!)
Prostaglandin (PG) - chemotaxin, increases permeability of BV.

Treatment can include non-steroidal anti-inflammatories (NSAIDs). NSAIDs such as aspirin and
COX inhibitors act by inhibiting Prostaglandins (PG). Aspirin works by binding irreversibly to PG
synthase, and COX II inhibitors by blocking COX II activity.

Activation of eosinophils and basophils is seen ONLY AFTER inflammation has started.
Eosinophil and basophil activation induces chronic damage as seen in chronic asthma.

When antigen enters the blood-stream which leads to IgE mediated hypersensitivity, anaphylactic
shock is possible. This is seen with some drugs (penicillin) and some ingested allergens (peanuts,
bee venoms, etc.)

Epinephrine reverses the effects by decreasing permeability of BV thus increases blood pressure
and relaxes smooth muscle constriction.

It should be noted that allergy inducing IgE is stimulated the same way that normal antibodies are
produced. As shown in Figure 12.14 there is a response to allergens that happens naturally and

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induces an immune response. This leads to the production of IgE which can coat a cell such as a
mast cell.

6. Vaccinations
Vaccinations are a key advancement in medicine and have prevented an uncountable number of
sickness and disease. Importantly, pharmacists are able to provide vaccinations and should
understand the history (see Section 1) as well as the biological basis behind vaccinations.

6. a. The response to viral infection

To understand how a vaccine functions it is useful to review the normal immune response to a
virus infection. As shown in Figure 2.47, an innate response to the virus infection precedes the
adaptive response to the virus. After a virus enters a human, the innate immune response begins

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to produce cytokines and induce effector cells such as natural killer cells (NK) to stop the virus.
The innate immune response initially works to limit the spread of the virus as well as activate the
adaptive immune response. As the virus spreads, antigenic epitopes begin to be presented on
MHC molecules that allows for the clonal selection and expansion of the T cells that expresses a
unique TCR for that pathogen. The T cells work to reduce the levels of the virus.

Vaccines work on the principle of immunologic memory. This is the principle in which adaptive
immune cells that have been properly clonally selected and expanded are now readied for any
second exposure of the body to that pathogen. As shown in Figure 10.18, there are two types of
immunity to prevent an infection. Protective immunity works to block an existing infection. In fact,
when vaccines are administered, they often produce at least a low level of protective immunity
after administration. Initial protective immunity takes several days (about 7) to be active and
effective. However, protective immunity is not a constant process and immunologic memory is
required. Memory is when immune cells can quickly respond to a second exposure to pathogens.
With immunologic memory, there is no delay in protective immunity and thus most exposures to a
pathogen are quickly blocked. Vaccines are equivalent to the first exposure to a pathogen and
work to create a memory response that will quickly induce protective immunity to a person
exposed to a pathogen.

Note: There is no delay upon the second real infection. Also, protective immunity turns all
exposures to aborted infections.

6. b. Types of Vaccinations

The desired outcome of vaccination is to Illicit an immune response in healthy individuals so they
will develop memory B cells (and a good T cell response) against a given pathogen. This
controlled exposure of the healthy individual to a pathogen will allow the individual to produce a
rapid response (secondary immune response) whenever the individual is exposed to the pathogen

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in a natural environment and thus protect the individual from that pathogen.

Strategies which can be used to induce such an immune response include

Whole Live Virus Vaccinations (variolization)
Killed or inactivated virus
Attenuated (Live)
Subunit
Toxoid
Conjugate

Whole Live Virus Vaccinations (variolization)

Variolation, which is introducing the same whole live pathogen in small amounts, or a large
amount of a weak strain. One major problem with this modality is that you have to infect patients
with a live pathogen, leading to some infection and disease. This approach is rarely used
currently but rather a similar type of virus may be used in the vaccine formulation.

By using a similar pathogen, such as Jenners vaccine that used cowpox in place of smallpox, you
can induce a sufficient immune response to a weaker or less infectious agent. The mechanism of
action is called molecular mimicry.

Killed or inactivated virus

One can also inhibit infection by using a killed or inactivated virus, though the downside is the
need of large amounts of vaccine material since it does not replicate. These vaccines are good
since they include the innate inducing PAMPs and the antigenic proteins that the adaptive immune
response will be made against. Examples include the TIV Influenza Vaccine, the Rabies Vaccine
and the Polio (Salk) Vaccine.

Attenuated (Live)
Using a whole attenuated virus vaccine, one can destroy infectious DNA sequences, or
reintroduced the virus after growing with another species cells, minimizing infectiousness. (See
Figure 14.2) These vaccines also include PAMPs and antigenic proteins components that will
induce immunity. They are often better than inactivated vaccines as they allow for low level
replication that produces a more natural immunity and thus a stronger protective and memory
immunity.
Examples of this type of vaccine include the measles, mumps, polio (Sabin) and yellow fever
vaccines. The LAIV for influenza is also an attenuated vaccine.

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Subunit
Subunit vaccines include injections of surface antigen that can illicit immune responses against
specific components of a pathogen. The subunits are proteins that make up microorganism.
Normally, proteins alone cannot make an immune response due to the
need for costimulation and innate immune activation. However, the
subunits are chosen to create a virus like structure that can induce innate
immunity to create a normal immune response. Though an adjuvant is
needed to induce long term memory against the pathogen. Subunit
vaccines can be derived by purification of native or cDNA components.
Examples of this type of vaccine include the HBV (Hepatitis B Virus) and
HPV (Human Papilloma Virus) vaccines.

Toxoid and Conjugate Vaccines

Bacteria vaccine are similar to virus vaccines in that one can introduce
injections of inactive proteins or toxoids (Subunit or Polysaccharide-
conjugates) or whole attenuated bacteria in which there is some mutation
which makes the bacteria non-infectious.

Toxoid vaccines are vaccines that are made to direct immunity against a
toxin that is released by a bacteria. In this case the toxin is inactivated so
that it will not induce a toxic affect in the human. However, the immune
system will still induce an immune response to the toxin protein. When the
bacteria enters an immunized individual, the immune response against the
toxin will block the toxin from hurting the infected individual but will allow a
natural response against the microorganism to stop the infecting
microorganism. Examples of this include the vaccines against Diptheria
and Tetanus.

Similar to a toxoid vaccine is a conjugate vaccine. A conjugate vaccine

does not use a live bacteria but allows for the immune response to be
against a polysaccharide that is on the surface of the bacteria. Normally,
immune response are hard to induce by vaccinating with polysaccharides
alone. To induce an immune response, the polysaccharides are
conjugated to a toxoid, bacterial protein. As shown to the left in Figure
8.38, the polysaccharide and toxoid protein work together to induce

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immunity. The toxoid protein can induce T cell immunity that can then help B cells induce
immunity to the polysaccharides. Examples of this type of vaccine include the Haemophilus
vaccination as well as the pneumococcal vaccination.

Adjuvants
Adjuvants are any substances used to increase the potency (including long term memory) of the
adaptive response to a given antigen. It is always given as a component of the injected
component of the vaccination.

6. c. Herd Immunity

Vaccinations are important from an individual perspective to provide protection from potentially life
threatening infections. However, vaccines also provide protection to the society as a whole
through herd immunity. Herd Immunity is the principle that if enough individuals are protected
from an infecting pathogen, they will stop the spread of the pathogen in a population. It does not
matter if the individuals were vaccinated or got the immunity through natural exposure. As shown
in the diagram below, herd immunity will protected people that are not vaccinated (or even that
have weakened immunity) as the immunized individuals will not allow the infectious pathogen to
grow or spread. However, in populations with low levels of vaccination, the introduction of the
infectious pathogen by an individual could have disastrous consequences as the infectious
pathogen could spread quickly with little preexisting immunological memory in individuals to stop
its spread.
In September, 2013, the CDC reported that there have been several outbreaks of measles
in the United States in unvaccinated individuals, and these numbers are increasing year-to-year as
fewer people choose to go unvaccinated.
(http://www.cdc.gov/mmwr/preview/mmwrhtml/mm6236a2.htm?s_cid=mm6236a2_w).
Pharmacists play a major role in assuring that the general public understands the need for all
children and adults to be vaccinated.

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6. d. Controversies Concerning Vaccinations

It should be noted that vaccination is not as embarked in U.S. society as it once was. There were
several controversies on the potential toxicity that vaccines have as well as if they were associated
with diseases such as autism. In fact, in 1998 a study was published linking the MMR (Measles,
Mumps, Rubella) vaccine to autism. This study was later retracted and was found to have been
falsified. However, damage was done to the public support for the MMR vaccine and even now
people are hesitant to give their children vaccines. It must be emphasized that those studies were
lies and that the health of a child and any person that uses vaccines can be supported and
maintained by proper vaccine use.

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