chapter 1

09/14/2013

Medicine and history immunity builds over time

Immunization = exposure to infection without causing infection
First line of defense = innate immunity
Physical and chemical barriers
Next = adaptive immunity = specific target
Refined over course of infection
Provides long lasting immunity
Commensal species = microbial species in the gut
Flora = microbial species from specific region
Pathogens
Bacteria
Virus
Fungi
Parasites
Endemic disease = ubiquidous
Childhood exposure
Skin = first barrier
Forms epithelium (keratinized cells)
Also in lining of respiratory and gastrointestinal and urogenital
tracts usually musosal lining
o Glycoproteins, proteoglycans, enzymes

All epithelia produce antimicrobial peptides called defensin

o These kill pathogens on their turf
Tears and saliva have lysozymes degrade cell wall
Acid from stomach, vagina, skin
Innate immune response
First recognition
Then effectors
Innate immunity inherited
Recognition
o Pathogen is present
o Soluble proteins and cell surface receptors bind to pathogen
and its products or human cells and serum proteins that
become altered in the presence of the pathogens
Effector mechanism
o Kills and eliminates
Effector cells engulf bacteria, kill virus infected cells, or
attack protozoan parasites, and a battery of serum
proteins called complement that help the effector cells
by marking pathogens with molecular flags but also
attack pathogens in their own right.
Overall effect of the innate immune response is to induce a states
of inflammation
Cytokines sent to damaged tissue
Calor heat, dolor pain, rubor redness, tenor swelling
Cytokines induce dilation of capillaries which increase blood flow
gaps in between cells of endothelium edema (swelling) pain
Cytokines cause white blood cells to stick to infected tissue/area
Adaptive immunity
Pathogen specific response

Clonal selection = select a small subset of lymphocytes for

proliferation felt week after infection
Clonal expansion = select a small subset of lymphocytes for
differentiation felt week after infection
Memory cells faster response second time around
First exposure = primary immune response
Subsequent exposures = secondary immune response
Immune cells mainly leukocytes (white blood cells)
Hematopoiesis = continual generation of leukocytes
Leukocytes come from pluripotent hematopoietic stem cells also make
erythrocytes (red blood cells), megakaryocytes (which become platelets)
Place of production changes with age
Embryo blood cells from yolk sac then fetal liver
3-7 months of fetal life spleen
4-5 months of fetal life shifts towards bone marrow
birth onwards bone marrow
adults bone marrow of skull, ribs, sternum, vertebral column,
pelvis, and femurs
mature stem cells commit to one of three lineages:
erythroid
o lead to oxygen carrying erythrocytes and platelet producing
megakaryocytes
platelets are small non-nucleated cell fragments of
plate-like shape that maintain the integrity of blood
vessels important to clotting
megakaryocytes are giant cells that arise from the
fusion of multiple precursor cells and have nuclei
containing multiple sets of chromosomes permanent
residence in bone marrow
myeloid
o granulocytes cytoplasmic granules containing reactive
substances that kill microorganisms and enhance
inflammation

neutrophil (most abundant granulocyte)

capture, engulfment, killing of microorganisms
main ingredient in pus, pimples, boils
neither acidic nor basic stains
eosinophils (second most abundant granulocyte)
defend against parasites
basic subsatances bind to acidic stain eosin
basophils (least abundant granulocytes)
regulate immune response to parasites
little known
acidic substances that bind basic stains
o monocytes, macrophages, and dendritic cells
monocytes = leukocytes that circulate in the blood
bigger than granulocytes, distict indented nucleus
macrophages
travel in blood to tissues
large phagocyte phagocytosis
general scavenger cells of body
live longer
secrete cytokines that recruit neutrophils
and other leukocytes
Dendritic cells in body tissue

act as cellular messengers that are sent to

call an adaptive immune response when
needed
mast cells in connective tissues
involved in activation and degranulation of mast
cells at infection site

lymphoid
o Natural killer cell/T cell precursor
Natural killer cells effector cells of innate immunity
with large granular lymphocytes
Important for viral infections
Prevent spread of infection by killing virus
infected cells
Secrete cytokines that impede viral replication
Small lymphocytes are responsible for adaptive immune
response
Recognize pathogen and drive lymphocyte
selection, growth and differentiation
o B cells and T cells
B-cell cell surface receptors for pathogens =
immunoglobulins
B-cells express single immunoglobulin
T-cell cell surface receptors for pathogens = T-cell
receptors
T-cells express single t-cell receptor
T cells
Cytotoxic T cells
Kill cells infected with either viruses or
bacteria that live and reproduce inside
humans
NK cells of adaptive immunity
Helper T cells

Secrete cytokines that help other cells of

immune system become fully activated
effector cells

B cells
Plasma cells effector cells that secrete soluble
immunoglobulin called antibodies
Most lymphocytes found in lymphoid tissue or lymphoid organs
Lymphoid organs = bone marrow, thymus, spleen, adenoids,
tonsils, appendix, lymph nodes, and Peyers patches
Lymphoid tissue = lining of mucosal surfaces of respiratory,
gastrointestinal, and urogenital tracts
o Two types
Primary/Central lymphoid tissue
Lymphocytes mature and develop to the stage at
which they are able to respond to pathogens
Bone marrow and thymus
B and T lymphocytes originate from bone marrow
B cells mature in bone marrow and enter
circulation
T cells leave bone marrow immature and
migrate in blood to thymus to mature
Secondary/Peripheral lymphoid tissues
Mature lymphocytes become simulated to respond
to invading pathogens
Lymph nodes lie at junctions of lymphatic
vessels
Collect plasma that leaks out of blood
vessels and forms extracellular fluid
o This lymph returned to blood
Lymph flow driven by continuous movement
Adaptive immunity is initiated in secondary lymphoid tissues
Connective tissues usually site of infection (pathogens through
wound)

o Pathogen carried by lymphatic to lymph node receives fluid

collected at infected site ( draining lymph node) blood
cells call upon proper lymphocytes
Spleen provides adaptive immunity to blood infections
Spleen filters blood
Removes damaged or senescent red cells
Defends body against blood-borne pathogens
Splenic macrophages and dendritic cells simulate B and T cells from
blood
Spleen made of two different tissues
o Red pulp (RBC monitored and removed)
o White pulp (WBC gather to provide adaptive immunity)
No spleen = asplenia
o Genetic
o Susceptive to encapsulated bacteria (whose cells surrounded
by thick polysaccharide capsule)
Damaged spleen often removed
o Children with spleenectomy more vulnerable to bacterial
infections than adults
Adults have protective immunity from previous
infections
Most secondary lymphoid tissue associated with gut
GALT (gut associated lymphoid tissues) = tonsils, adenoids,
appendix, and Peyers patches (line small intestine)
BALT (bronchial associated lymphoid tissues) = lining of respiratory
epithelium
MALT (mucosa-associated lymphoid tissues) = mucosal surfaces like
gastrointestinal tract
Adaptive immunity leads to long lived immunological memory cells
Immune system can be compromised by immunodeficiencies and certain
pathogens

Mutations in both copies

Immunodeficiencies once cause death in infants
AIDS and HIV

Adaptive immunity is the bodys third line of defense

1st: physical barriers
2nd: innate immunity
adaptive immunity made up of B cells and T cells (both lymphocytes)
innate immunity and adaptive immunity differ in how they recognize
pathogens
B and T cells recognize pathogens by using cell surface receptors of
just one molecular type (B cell receptors and T cell receptors)
o These proteins can be made in infinite different versions
Adaptive immunity only in vertebrates, innate immunity shared with
many animals and some plants
Advantages:
Strong immune response against particular pathogen effective by
targeting small differences that distinguish that pathogen from
others
Pathogen-specific B and T cells stored as memory cells in case
pathogen returns
Evolving vertebrates have defense against evolving microorganisms
B cell receptors = immunoglobulins
Effector B cells = plasma cells, secrete soluble immunoglobulins =
antibodies
T cell receptors only expressed as cell surface recognition never
secreted
antigen = molecule, macromolecule, virus particle or cell that has
structure recognized and bound by immunoglobulin or T cell receptor
these t cell receptors or immunoglobulins = antigen receptors

immunoglobulins can bind many different structures, TCR can only

bind few
both have specificity for antigens they bind
immunoglobulins and TCR are structurally related
immunoglobulins are Y shaped polypeptides with two identical
heavy and two identical light chains
Both have variable and constant regions
Antibodies are secreted immunoglobulins
TCR has alpha chain and beta chain
Both have variable and constant regions
The constant regions of antibodies contain binding sites for cell surface
receptors on phagocytes and other inflammatory cells
Immunoglobulins have several different types of constant regions (Not
TCR) which confer different effector functions on the secreted antibodies
and can also target then to different sites in the body
Gene rearrangement leads to diversity of immunoglobulins and TCR
Variable regions of immunoglobulins and TCR have separate gene
segments called V, D, J
Immunoglobulin heavy chain and Beta TCR have V D, J segments
Immunoglobulin light chain and Alpha TCR only have V, J
Immunoglobulin and TCR genes are only human genes requiring
rearrangement in order to be functional = rearranging genes
Gene rearrangement: functional exon encoding variable region
consists of one V segment join with one J segment ( cut and paste,
excess DNA removed as circle)
o Germline configuration before
o Somatic recombination occurs
o Rearranged gene: excised DNA circle, and rearranged gene
Proliferation of pathogen stimulated lymphocytes leads to many identical
clones of immunoglobulin or TCR == increases population
Clonal selection = pathogens select lymphocytes for expansion

 Clonal expansion = proliferation of selected clones

Adaptive immune responses are initiated in secondary lymphoid tissues
by antigen-bearing dendritic cells and T cells
Lymph nodes, white pulp of spleen, Peyers patches of gut
First, dendritic cell carries pathogen from infected site to nearest
2ndary lymphatic tissue
o Dendritic cell = phagocytic leukocyte like macrophages, found
in tissues
Link between innate and adaptive immunity
Second, antigen loaded dendritic cell meets and activates TCR with
that antigen receptor
o Native T cells = those that have not met their antigen
o Effector T cells = T cells with receptors specific for bacterial
antigens will bind their antigens on dendritic surface where
they activate to divide and differentiate
Effector T cells needed to activate B cells
TCR recognize degraded fragments of pathogen proteins
TCR antigens recognize short peptides this simplifies the process
Antigen processing = production of antigenic peptides from
pathogen proteins by degradation of dendritic cell
TCR recognize peptide antigens bound to human cell surface molecules
MHC molecules = pathogen derived peptides bound tby
glycoproteins
MHC = major histocompatibility complex = genes that encode MHC
molecules
o 1 MHC molecule binds 1 peptide = MHC
o ligand for TCR
o antigen presenting cells = MHC complexes on cell surface that
stretch out peptide on MHC to make accessible to peptide
binding site
o MHC can bind many different peptides, TCR only binds a few,
thus only small fraction of all peptides produced by pathogen
breakdown are presented by MHC to TCR as antigens
Dendritic cells express many different MHC molecules to increase
efficiency

 MHC polymorphism (allele variability) is the basis for tissue type and
cause of transplanted organ rejection
Two classes of MHC molecule present peptide antigens to two types of T
cell
Two types of microorganisms that infect human tissues
o Extracellular pathogens
Bacteria live and replicate in space between human
cells
o Intracellular pathogens
Viruses live and replicated inside human cells
Two types of MHC to accommodate two types of microorganisms
o MHC class I antigens from intracellular pathogens
Peptides produced by degraded in cytosol of
intracellular pathogens are delivered to ER
Cytotoxic T cells defend against intracellular infections
Cytotoxic T cell recognizes pathogen derived
peptide presented by an MHC class I molecule
Carry CD8 so only recognize MHC class I
o MHC class II antigens from extracellular pathogens
Peptides produced by lysosomal degradation of
extracellular pathogens reside in endosomal vesicles
Helper T cells defend against extracellular infections
Enhance phagocytosis of extracellular pathogens
by macrophages and neutrophils
By direct contact with macrophage
Secretion of cytokines to drive macrophages
to higher state of activation
Helps B cells make antibodies that opsonize
Engulfment NOT interaction

Express CD4
All t cells have CD 4 or CD8 NOT BOTH
MHC I most cells in the body because cytotoxic T cells can attack
the vast majority of infected cells
Helper T cells attack extracellular infections so only interact with
dendritic cells, macrophages, and B cells
class I molecules present antigens of intracellular origin to CD8 T

MHC
cells
Viruses are the only group of pathogens that Must be inside human
cells to replicate and survive
o Cytotoxic T cells important for viral infections
Viral proteins synthesized on ribosomes of dendritic cells and
degraded by cytosolic protease
o Peptides transported to ER so can bind MHC class I
o Bound to MHC I, leaves ER through Golgi to plasma
membrane
MHC class II molecules present antigens of extracellular origin to CD4 T
cells
1/3 T cells are CD8
CD4 T cells activated by antigen, differentiate into helper T cells =
effector CD4 T cells
o Can secrete many different cytokines
More versatile than cytotoxic CD8 T cells
o CD4 T cells respond to pathogens in fluid and spaces that
separate cells
Dendritic cells use cell surface receptors to endocytose pathogens
Helper t cells trave in lymph and blood to infected tissue where they
secrete cytokines that attract neutrophils and monocytes to tissue
Effector CD4 T cells help B cells become antibody producing plasma cells
B cell purpose = make antibodies
Plasma cell = activated B cell by pathogen that has proliferated,
differentiated into dedicated antibody factory

Antibodies target pathogen for destruction by phagocyte or effector

cell
Antibodies recognize all parts of antigen structure (entire)
Native B cells = those that have not yet encountered their antigen
Receptor mediated endocytosis = bacterium binds BCR which
causes engulfing delivered to endocytic vesicles in B cell
cytoplasm
B cells can act as antigen presenting cells to CD4 T cells
Interacting T cell and B cell must both be specific for the same or
different parts of the same antigen
Extracellular pathogens and their toxins are eliminated by antibodies
Immunoglobulins produced by B cells and plasma cells -- 5 classes
o Differ in heavy chain constant region
o IgA
Made in lymphoid tissues mucus surfaces
o IgD
Antigen receptors on circulating B cells that have yet to
encounter antigen
o IgE
Bind tightly to receptors on mast cell surface
Respond when parasites present
Allergic reactions
o IgG
Most important function: facilitate engulfment and
destruction of extracellular microorganism and toxins by
phagocytes
Neutrophils and macrophages have cell surface
receptors that bind IgG heavy chains
o IgM

Antigen receptors on circulating B cells that have yet to

encounter antigen
First antibody to be secrete in immune response
Humoral immunity = immunity due to antibodies and their actions
IgM, IgA, IgG = main antibodies present in blood, lymph and
intercellular fluid
Antibodies secreted into blood from lymph nodes, spleen, and bone
marrow
Antibodies reduce infection by binding tightly to site in pathogen to
inhibit pathogen growth, replication or interaction with human cells
= neutralization
Opsonization = coating of surface of pathogen with molecules that
make it more readily ingested by phagocytosis
Antibody quality improves during the course of an adaptive immune
response
Somatic hypermutation = nucleotide substitution throughout
variable regions of rearranged immunoglobulin heavy and light
chains
o Strengthens the antigen-binding properties of the antibodies,
isotype switching improves recruitment of effector functions
Isotype switching = changes the isotype of the immunoglobulin but
not the antigen binding site
o Germinal center B cells remove gene segments encoding the
mu constant region and bring the rearranged variable region
into juxtaposition with a gene segment encoding a different
constant region
IgM to IgG, IgA or IgE
Lymph nodes and spleen = IgM IgG
Peyers patches of gut and lymphoid tissues in mucosa
= IgM IgE
Enable eosinophils, basophils and mast cells to be
recruited to the adaptive immune response
Somatic hypermutation and isotype switching adaptive immune
response selects for antibodies that bind more tightly to pathogen
and are more efficiently delivered to site of infection and are better
able to involve phagocytes and other inflammatory cells in
pathogen elimination
Immunological memory is a consequence of clonal selection
Once pathogen terminated
o Effector t cells apoptose
o Plasma cells persist

o Pathogen specific antibodies maintained in circulation for

years
Prevent reoccurrence
Memory cells come from clonal expansion
Secondary adaptive immune response leads to earlier detection
Memory B cells make better immunoglobulins than native B cells
because they benefit from somatic hypermutation and isotype
switching that occurred in the primary response
Clonal selection makes T cells and B cells tolerant of self and responsive
to pathogens
Fraction of developing B cells and T cells carry receptors that bind
to normal components of the healty human body
Tolerance to some important self antigens is set up during
lymphocyte development
Immature T cells undergo two rounds of clonal selection
o First positive selection
Identifices and selects T cell bearing antigen receptors
that work effectively with the particular subset of MHC
class I and II molecules the person has
T cells recognize peptide antigens in combination with
own self MHC
Useful T cells recognize receptors for self MHC
and peptide
Those that bind weakly to self MHC apoptose
o Second negative selection
Identifies T cells with receptors that bind too strongly to
self MHC
Apoptose
T cells in circulation are self tolerant
During B cell maturation in bine marrow, negative selection used to
prevent emergence of some cells that could make harmful
antibodies
Regulatory T cells = effector CD4 cells that suppress responses of T
cells reactive against healthy cells and tissues
Unwanted effects of adaptive immunity cause autoimmune disease,
transplant rejection and allergy

 Antibodies clear extracellular pathogens and their toxins

Antibodies = secreted B cell antigen receptors
Recognize all types of biological macromolecules
o Proteins and carbohydrates most common
Antibody + virus/bacterium particle = disabled virus/bacterium
Protective immunity
Secreted form of immunoglobulins
Antigen binds receptor proliferates and differentiates into plasma cell
Secrete large amts of antibodies with same specificity as membrane
bound immunoglobulin
Ex. Of clonal selection
Variable region contains site of antigen binding and specificity of antibody
Constant region interacts with their immune system components
Isotypes distinguished based on structural differences in constant region
and effector functions
Antibodies are composed of polypeptides with variable and constant
regions
Glycoproteins with four polypeptide chains
o Two heavy chains (H chains)
o Two light chains (L chains)
Light chain has only two isotypes kappa and lambda
Each light chain has kappa OR lambda, not both
2/3 human antibodies contain kappa

 immunoglobulin chains are folded into compact and stale protein domains
antibodies function in extracellular environments
VL and VH together form antigen binding site
An antigen binding site is formed from the hypervariable regions of a
heave chain V domain and a light chain V domain
Antigen binding sites vary in shape and physical properties
Epitope = where antibody binds antigen
Antibodies that bind to the end of a polysaccharide/polypeptide
chain use a deep pocket formed between heavy chain and light
chain V domains
Multivalent antigen = antigen that has more than one epitope or
more than one copy of the same epitope
Conformational/discontinuous epitopes = parts of protein separated
in AA sequence that are brought together in a folded protein
The binding of antigens to antibodies is based solely on noncovalent
forces electrostatic forces, hydrogen bonds, van der Waals forces,
and hydrophobic interactions
Affinities = different binding strengths
Catalytic antibodies = antibodies that catalyze chemical reactions
involving bound antigen
Monoclonal antibodies are produced from a clone of antibody-producing
cells
Anticera
o B cells isolated from immunized animal and immortalized by
fusion with a tumor cell to form hybridoma cell lines that
grown and produce antibodies indefinitely
o Hybridomas separated
Monoclonal antibodies are used as treatments for a variety of diseases
Chimeric monoclonal antibodies = combine mouse V regions with
human C regions
o Used to reduce rejection rate
Humanize
Generation of immunoglobulin diversity in B cells before encounter with
antigen

Immunoglobulin genes are in a fragmented form that cannot be

expressed
o All but B cells
Immunoglobulin heavy and light chain loci have families of gene
segments
o Germline inheritance
Before expression, genes must rearrange to become functional
o only occurs in B cell development
o In bone marrow
DNA sequence encoding a V region is assembled from two or three gene
segments
Heavy chain on chromosome 14
Lambda light chain on chromosome 22
Kappa light chain on chromosome 2
Different segments encode the leader peptide (L), V region (V) and
the constant (C) of heavy and light chain
o L and C have exons and introns
o V regions encoded by 2 (VL) or 3 (VH)
Light chain V region = variable (V) and joining (J) gene segments
Heavy chain VJ to diversity (D) gene segment
Difference in V gene segments are in the sequences that encode the
first and second hypervariable region
o Third hypervariable region determined by the junction
between V and J
B cell
o Only one light chain loci (kappa or lambda) functional light
chain genes
o Heavy chain = one V one J one D

First two = differences in sequences of heavy chain V

gene
Third = differences in D gene and junction with V and J
respectively
C of heavy chain = 1 C
Random recombination of gene segments produces diversity in the
antigen binding site of immunoglobulins
Somatic recombination = VDJ segment recombination
Light chain
o All thats needed is single recombination of V and J
(lambda/kappa)
Heavy chain
o Two recombinations
D to J
DJ to V
Somatic recombination done with enzymes that cut and rejoin DNA
o Recombination signal sequences (RSS)
o Flank 3 side of V segment, both sides of D segment, and 5
side of J
o Two types of RSS and recombination can only occur between
different types
Heptamer
Nonamer
o RSS makes sure gene segments joined in correct order
Recombination enzymes produce additional diversity in the antigen
binding site
V(D)J recombinase = enzymes required for VDJ segment combos
2 component proteins made only by lymphocytes
o RAG1 (Recombination activating genes) and RAG2
RAG1 and RAG2 interact with each other and other proteins to form
the RAG complex
One RAG binds one type RSS and other binds another
Two RAGs align two RSSs and cleaves DNA at end of
immunoglobulin gene segments so DNA hairpin at each end
Broken ends joined by DNA repair enzymes
o Brings coding regions together