Immunochemistry, or

Biochemistry of the immune

system
• Definition:
• The immune system is a
network of cells and molecules
which protect our bodies
against invading
microorganisms and their
toxins
• Invading microorganisms;
viruses, bacteria, fungi,
parasites (protozoan, metazoan)
• They have different routes and
different habitats in the body,
thus, flexible wide-spread
defense system is needed
• Immune system:
• 1- innate, natural; body make-
up, phagocytic cells
• 2- acquired, adaptive; it is the
function of lymphocytes, T and
B cells.
• It is only in vertebrates
• Properties of the adaptive
system:
• 1- specificity
• 2- memory (vaccination)
• 3- differentiation between self
and non self (transplant)
• 4- high versatility
An antigen provides multiple
epitopes (antigenic determinants)

Fig. 43.14

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

 Fig. 43.15

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

• Definition:
• Antigen (immunogen) foreign
substance gaining access to
vertebrate body and induces an
immune response (T or B or both).
• Haptens are small molecules
which fail to provide epitopes
for B or T cell by themselves.
• They need a carrier.
• The immune response:
• In the first exposure to the
antigen we get a primary
immune response after a latent
period of about 1 week.
• On subsequent exposure to the
same antigen we get secondary
immune response which is
immediate and brisk.
 Cellular elements of the
immune system
• All cells of the immune system
originate from pluripotent
hematopoietic stem cell in the
bone marrow which
differentiates to give different
cell lines
 The B cells (humoral immunity)

• The B cell develops from the

stem cell in the bone marrow
(primary lymphoid tissue) as
pre-pro B pro B mature B
cell or virgin B cell which has
membrane bound receptor IgM
or IgD (antibody).
• Then it migrates to the
secondary lymphoid tissues
(spleen and lymph nodes).
• When it encounters the specific
antigen it proliferates and
differentiates into plasma cell or
antibody forming cell.
• The plasma cell synthesizes
antibodies and secretes them.
 The Clonal selection theory
• B cells and T cells are produced as
millions of clones each with
specific receptor.
• Few thousands of cells are
produced from each clone and
migrate from the bone marrow to
the secondary lymphoid tissues
• When activated by the specific
antigen the clone of cells
proliferate and differentiate to
effector cells.
• Problems??.... Millions of
different receptors. How?
• Limited number of genes
• How does B and T cell diversify
their antigen receptors?
 Fig. 43.6

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

 Immunogloblins (antibodies)
• They are antigen receptors of B
cells.
• They are membrane bound on
virgin B cell, and secreted in body
fluids by plasma cells.
• The basic structure is made of two
identical heavy chains and two
identical light chains
• The light chain can be either
kappa or lambda
• The heavy chain can be either
gamma, alpha, delta, mua,
epsilon(б, α, µ, δ, ε).
• According to the heavy chain
we have 5 classes IgG, IgA, IgM,
IgD, IgE.
 Antigen antibody interactions
• Variable region….
• 3 Hypervariable regions or
complementarity determining
regions (CDR) in each binding site
of an antibody.
 Fig. 43.15

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

An antigen provides multiple
epitopes

Fig. 43.14

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

• An epitope (antigenic
determinant) is the part of
antigen recognized by the
binding site of the antibody.
• An antigen (e.g a protein of 200
amino acids) provides
thousands of epitopes which
can be recognized by multiple
clones of B cells.
• Each B cell clone produces
antibody with specificity for one
epitope.
• The antibody-epitope interaction is
by non covalent bonds;
electrostatic, hydrogen,
hydrophobic, …
 Fig. 43.6

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

 Fig. 43.16
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Hybridoma technology
 Monoclonal and polyclonal
antibodies
• Monoclonal antibodies are
produced by a single clone of B
cells. They are identical,
homogeneous, monospecific (one
epitope).
• Polyclonal antibodies are produced
by multiple clones of B cells with
specificity for multiple epitopes.
Monoclonal antibodies

Monoclonal antibodies are very useful

As diagnostic, imaging and therapeutic
Reagents in clinical medicine
 Diversity of immunoglobulins
• DNA rearrangement
• Point mutation
• Alternative splicing
• Class switching
• Isotypic variation
 Somatic gene recombination in B cells
Heavy chain gene rearrangement and generation of heavy-chain proteins
Germ-line
Heavy chain DNA
D-J joining

V-DJ joining
Rearranged
H-chain DNA
Transcription

Primar RNA
transcript
Polyadenylation,
RNA splicing

mRNA
Translatio
n
Nascent polypeptide

 or  heavy chain
 heavy chain  heavy chain
 Somatic gene recombination in B cells
Kappa light chain gene rearrangement and generation of k light-chain protein

Germ-line
 chain DNA
V-J joining

Rearranged
-chain DNA
Transcription

Primar RNA
transcript
Polyadenylation,
RNA splicing

mRNA
Translatio
n
Nascent polypeptide

 light chain  light chain

 T-cells
• Thymus  secondary lymphoid
• Cytotoxic T cell
• Helper cell
–Helper 1
–Helper 2
–T cell receptors……..
 Primary lymphoid organs

The thymus

• Is located under the

sternum
• Consists of two lobes
• Is an encapsulated
organ
• Specific organ for T
cell maturation
• Place for induction of
Thymus central T cell tolerance
T Cytotoxic Lymphocyte

CD28 (binds to CD 80/86 on B cells for activation)

LFA-1 (binds to ICAM-1) (adhesion molecule)

CD2 (binds to LFA-3) (adhesion molecule)

CD3 (a signal complex associated with TCR)

T cell receptor (TCR,  or  dimer)

CD8 (binds to MHC class I molecule and strengthen

the antigen recognition
T helper Lymphocyte

CD28 (binds to CD 80/86 on B cells for activation)

LFA-1 (binds to ICAM-1) (adhesion molecule)

CD2 (binds to LFA-3) (adhesion molecule)

CD3 (a signal complex associated with TCR)

T cell receptor (TCR,  or  dimer)

CD4 (binds to MHC class II molecule and strengthen

the antigen recognition
Functions of T helper lymphocytes

• Participate in adaptive
immune responses
• Produce different
cytokines
• Help B cell to produce
antibodies
• Help cytotoxic T cell to
kill the infected cells
 Th1 and Th2 cytokines and their functions

Cytokine/function Th1 Th2

Secretion
Interleukin 2 (IL-2) ++ -
Interferon  (IFN-) ++ -
TNF- ++ -
IL-4 - ++
IL-5 - ++
IL-10 - ++
IL-13 - ++

Functions
Help for antibody production + ++
Mast cell activation - ++
Cytotoxic T cell activation ++ -
 Structure of T Cell Receptor
Alpha Beta
chain chain

CHO CHO Variable region “V”

CHO CHO
Constant region “C”

Hinge “H”
Disulfide bridge

+ + Transmembrane region
+
Cytoplasmic tail
 CD3 Complex With TCR
TCR

Recognition
α β

CD3 CD3

ε δ γ ε

+
- - +
+ - -

ζζ Signaling
 Antigen recognition by B and T lymphocytes
B and T cells antigen receptors differentially recognize the antigens
B cell receptor

Peptide
T cell receptor

MHC

Epitope Digested Ag

Antigen Antigen (Ag)

Largely recognize the surface

(conformation) of an antigen— APC
but can also bind to linear
determinants. Do not recognize Ag until it has been
digested into ~10 amino acid peptides
Bind intact antigen directly then by “Ag presenting cells”APC, captured
Interact with helper T cells to by Major Histocompatibility Complex
Switch to one of 5 types of Molecules (MHC) and cycled to the
antibodies (IgM IgG, IgA, IgE..) cell surface where T cells can see them.
 MHC molecules
MHC molecules are encoded by a family of genes that are called
the H-2 complex in the mouse and the HLA complex in humans
Two main classes of MHC molecules are present on the surface
of body cells; Class I and Class II MHC molecules

MHC Class I MHC Class II

 Fig. 43.9

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

 MHC molecules and antigen presentation
MHC class I molecules are found on almost all nucleated cells

MHC class II molecules are restricted to a few specialized cells

including B cells and machrophages

MHC class I molecules present MHC class II molecules present

antigens to cytotoxic T cells antigens to cytotoxic T helper cells
Antigen presentation by MHC class I
Antigen presentation by MHC class II
 Fig. 43.11

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

 Immunoglobulin superfamily
• Igs
• TCR
• MHCI/II
 Complements
• A group of plasma proteins produced
by the liver (~30)
• They are produced as proenzymes
which are activated as part of an
immune response
• Two major pathways for activation
• Classical pathway
• Alternative pathway
• Activation takes place by
proteolytic cleavage.
• Each complement molecule is
cleaved into two fragment a and b
• .usually b is the large fragment
which is involved in the pathway.
• All complement pathways
converge in the activation of C3
which activates the subsequent
steps toward the MAC.
 The classical complement
pathway
• Complexed antibody is needed for
activation of complement 1 C1 qrs,
then C4 and C2 to give C3
convertase.
 Fig. 43.17

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

 Cytokines
• A group of low MW glycoproteins
produced by immune competent cells
and many other cells and have many
functions; activation, proliferation,
differentiation factors for immune
competent cells and have many other
effects as well.
• They are signaling molecules with
receptors on target tissues.
• They include;
• 1- interleukins
• 2- interferons
• 3- chemokines
• 4- growth factors
• 5- tumor necrosis factors
Cooperation of cells and
molecules in the IR
 Immunochemical techniques
• 1- ELISA
• 2- RIA and SPRIA
• 3- Blotting techniques
• 4- Immunofluorescence
• 5- affinity chromatography
• 6- precipitation techniques
• 7- FACS
Enzyme-Linked Immunosorbent Assay (ELISA)

(Serrially diluted serum)

Western blotting
Immunofluorrescence