IMMUNOLOGY

“What attracted me to immunology was that the whole

thing seemed to revolve around a very simple
experiment: take two different antibody molecules and
compare their primary sequences. The secret of
antibody diversity would emerge from that. Fortunately,
at the time I was sufficiently ignorant of the subject not
to realise how naïve I was being”

- César Milstein

NOTE:
There are videos in every lecture, for better understanding you should watch them
As Albert Einstein said:
“Imagination is more important than knowledge. For knowledge is limited to all we now
know and understand, while imagination embraces the entire world, and all there ever
will be to know and understand.”
 Introduction to immunology

- Immunology: is the immune system and the host reaction when foreign body (Ag)
introduce to the body.
- Immune response: the reaction of an organism's body to foreign materials
(antigens), including the production of antibodies.
- Immunity: the ability of the body to defend itself against specific invading
agents such as bacteria, toxins, viruses and foreign tissues.
- Antibody: are protein that are formed in response to an antigen and that react
specifically with that antigen.
- Antigen: are substance that can stimulate an immune response.
- Intracellular pathogens: inter inside the human cells and multiply .
- Extracellular pathogens: exist outside the host cells they live in tissue and
body fluid.

The functions of the immune system:

a- surveillance: (recognition of non-self) the antigen.
b- defense: initiating an immune response , The immune system can
eliminate threats by isolation , disruption, or ingestion.
c- regulation: control of the immune responses to maintain hemeostasis.
d- immunity: state of resistance (acquire protection) following exposure to
a stimulating agent.
e- tolerance: induction of a state of unresponsiveness toward certain
antigens (mainly self-antigens)

Þ The immune system composed of two defense mechanisms:

• Innate immunity:
Which is non-specific and is the one the human body born with.
• Adaptive immunity:
Which is specific resistance that is defense against specific microorganism.
 Introduction to immunology

INNATE DEFENSE:

The innate defense composed of:

§ First line defense:
o Physical barriers.
Including: skin and mucosa which has both
mechanical function (by block the entry
of the microbes) and chemical function
(by substance inhibit the microbial
growth).
o Antimicrobial substance.
Include: sweat, lysozyme, acids and
lactoferrin they can limit the ability of
invading organism by inhibiting or killing.
o Normal flora.
Are non-pathogenic and they have great
advantages like: they reduce the
availability of oxygen and they compete
for nutrients.
§ Sensor system:
o Complement.
o Phagocytes.
(I’ll explain both of them in more details).
§ Inflammation.
§ Interferons.
IFNs are a group of signaling proteins made and released by host cells in response to the presence of
several pathogens (viruses, bacteria and parasites) and tumor cells. a virus infected cell will release
interferons causing nearby cells to elevate their anti-viral defenses. And they are belong to large class of
proteins known as Cytokines which are used for communication between cells to trigger the protective
defenses of the immune system that help to destroy the pathogens.

§ Fever.
 Introduction to immunology

CELLS OF THE IMMUNE SYSTEM:

- Granulocytes:
Þ Neutrophils: professional phagocytes and its increase during bacterial infection.
Þ Basophils: Involve in the allergic reactions and inflammation.
Þ Eosinophils: Produce toxic proteins against parasite.

- Mononuclear phagocytes:
Þ Monocytes: phagocytic cells circulate in the blood after leaving the BM.
Þ Macrophages (MÆ): when the monocytes migrate to the tissue they called MÆ.
Also considered professional phagocyte in spleen, liver, lungs and lymph nodes.
Þ Dendritic cells: phagocytic cells and more involve in adaptive immunity.

- Lymphocytes:
Þ B cells: produce antibodies.
Þ T cells: destroy infected and abnormal cells.
Þ Natural killer cells (NK): has the ability to kill tumor cells
 Introduction to immunology

ADAPTIVE DEFENSE:
(Acquired immunity / Specific immunity)

- The adaptive immune response is specific to the pathogen presented. The adaptive immune
response is meant to attack non-self pathogens but can sometimes make errors and attack
itself. When this happens, autoimmune diseases can develop (e.g., lupus, rheumatoid
arthritis).
- Materials which induce specific immune reactions are called Antigens and The ways that the
immune system uses to perform this function fall into two categories:

• Cell mediated:
Is an immune response that does not involve antibodies. Rather, cell-mediated immunity is the
activation of phagocytes, T-lymphocytes, and the release of various cytokines in response to antigen.

• Humoral:
Defense is accomplished by means of an antigen, antibody molecules. (Antibodies).
Also called antibody mediated immunity.

NATURAL IMMUNITY:

1- Infection (natural acquired active immunity):

This immunity occurs in recovering from infection by the disease-causing agent.
The pathogen not only stimulate an immune response but also produce the disease.

2- Or with a vaccine (artificially acquired active immunity):

A modified form of the pathogen used to stimulate the immune response often without the disease
symptoms.

PASSIVE IMMUNITY:

1- Artificially acquired passive immunity:

• Is a short term immunization by the injection of Abs that are not produced by the recipients cells.
• Injection of immune serum from an individual previously immunized or recovered from disease.

2- Artificially acquired passive immunity:

• Is from mother to infant during pregnancy IgG Ab transport across the placenta to the fetal blood
stream.
• During breast feeding: IgA Abs transported to the infant.
 Introduction to immunology

CELLS OF THE ADAPTIVE IMMUNITY:

Þ B cells: formed from the stem cells in the BM & mature in the BM.
- Are responsible for the humoral or antibody response.
- When B cells bind to a particular Ag they become activated and then divide and differentiate
into plasma cells, which produce and release Ab that circulate in the blood.
- Some B cells might divide without differentiation into plasma cells, and these
known as long-lived memory cells. On the second exposure to the same Ag these memory
cells responsible for the rapid, and long-lasting response.

Þ T cells: formed from the stem cells in the BM but mature in the thymus.
Ø Classes of T cells:

* T helper (TH): promote B cell and T cell response to Ag, secrete chemical signals (IL-2,
IFN- γ) that activate MÆ to destroy the invading microorganism.
* T suppressor (Ts): can suppress or block the inappropriate lymphocyte response to Ag.
* T cytotoxic (Tc): bring about cytolysis and cell death of target cell.
* Delayed -type hypersensitivity: regulate a variety of nonspecific blood cells and
macrophages in expression of delayed hypersensitivity (type IV) reactions.
* Memory T-cells: which recognise the original invading antigen. When the antigen returns
thousands of memory cells are available to initiate a far swifter reaction than occurred during
the first invasion.
 Introduction to immunology

DIFFRENCES BETWEEN NATURAL AND PASSIVE IMMUNITY:

Natural Active Immunity Passive Immunity

Occurs during infection Occurs by injection

Has memory cells No No memory cells

Immunity is permanent Immunity is temporary

Immunity takes several weeks to become Immediate immunity

active
Antigen is encountered Antigen is not encountered

DIFFRENCES BETWEEN INNATE AND ADAPTIVE IMMUNITY:

Specific Immunity Non-specific Immunity

(Adaptive) (Natural)

Response is antigen independent Response is antigen dependent

There is immediate maximal response There is a lag time between exposure and
maximal response

Not antigen-specific Antigen-specific

Exposure results in no immunologic memory Exposure results in immunologic memory

Principle cells are phagocytes Principle cells are lymphocytes

 Introduction to immunology

Introduction to the immune system:

https://www.youtube.com/watch?v=wHCJUMBKgyo&t=507s

Innate and adaptive immunity:

https://www.youtube.com/watch?v=PzunOgYHeyg&t=31s

Humoral immunity:
https://www.youtube.com/watch?v=y0-BaWcU-SE

Cell mediated immunity:

https://www.youtube.com/watch?v=fBIEwoWz1So (part1)
https://www.youtube.com/watch?v=RzGf7GccEAg (part2)
 Phagocytosis

PHAGOCYTOSIS:

Phagocytosis, process by which certain living cells called phagocytes ingest or engulf other
cells or particles. The phagocyte may be a free-living one-celled organism, such as
an amoeba, or one of the body cells, such as a white blood cells.

Þ Many cells are capable of phagocytosis, but several types of immune cells are
particularly specialised in this role:

• Neutrophils: these are abundant in the blood and important in acute inflammation, as they are
the first immune cells to arrive at the site of infection.
• Macrophages: tissue resident cells that are key as a first defence mechanism and in initiating
the adaptive immune response.
• Dendritic cells: these cycle through the bloodstream, tissues and lymphoid organs, sampling
potential pathogens and acting as a major link between the innate and adaptive immune
systems.

Þ There are 6 general steps in the process pf phagocytosis which include:

1- Chemotaxis.
2- Recognition and attachment.
3- Engulfment.
4- Fusion of phagosome.
5- Destruction and digestion.
6- Exocytosis.

• Chemotaxis:
Present of chemical stimuli from microorganisms, complement components or C-reactive protein attract
the phagocytes to the site of infection and this called opsonization.
• Recognition and attachment:
- Direct binding: occurs with surface receptors.
- Indirect binding: occurs when a particle has been opsonized.
• Engulfment:
Once attachment occurred, the cellular cytoplasm flows around the particle and eventually fuses with
it and forms vacuole called phagosome.
• Fusion with lysosome:
Within the phagocyte the phagosome fuses with a lysosome, and the vesicle filled with digestive
enzymes and this fusion result in the formation of a phagolysosome.
• Destruction and digestion:
Within the phagolysosome the microorganism is broken down with the aid of enzymes.
• Exocytosis:
The vesicle containing the digestive material joins with the plasma membrane and then the vesicle is
expelled to the external environment.
Phagocytosis
 Phagocytosis

Phagocytosis process (Animation):

https://www.youtube.com/watch?v=rsHyQ6A6PcI

Phagocytosis under the microscope:

https://www.youtube.com/watch?v=pl6ijKiHXjU
 Complement

Þ complement is proteins cascade composed of more than 30 soluble and cell-bound

proteins that interact in a very specific way (sequentially) to enhance host defense
mechanisms against foreign cells.
Þ The complement proteins are forms mainly in the liver.
Þ The soluble proteins circulate in an inactive state and each must be activated
sequentially for the reaction to proceed.
Þ The final common pathway must be activated via the classic, lectin or alternative
pathway.
Þ The alternative pathway is relatively primitive and a part of the innate system.
Þ The classic pathway combines with Ab to initiate activation and therefore associated
with adaptive immunity.

TERMINOLOGY OF THE COMPLEMENY SYSTEM:

• Capital C followed by the number for the classic and common pathway (C1, C2, C3, …).
• Capital letter followed by number for the alternative pathway (B1).
• Fragments "which are derived from enzymatic cleavage of the parent molecules": small letter
suffix (C3a, Bb).
• Inactivated components: The letter i prefix (iC3b).
• The active state of isolated complement components: Bar over symbols (C4b 2a).

FUNCTIONS OF COMPLEMENT:

§ Production of opsonins: such as C3b and C4b which are coat the bacteria for opsonization.
§ Anaphylatoxins: C3a, C4a and C5a are known as anaphylatoxins (increase inflammation).
§ Lysis of cells (cytotoxic function): through the formation of membrane attack complex (MAC).
§ Remove of dead and dying cells.
§ Stimulation of leukocytes movement (Chemotaxis) and activation when bound to them.

Ø Three pathways of complement activation are known:

1- Classical pathway.
2- Lectin pathway.
3- Alternative pathway.
 Complement

CLASSICAL PATHWAY:

1- Activation of classical pathway is usually initiated by Ab-Ag complex. Other

activators include aggregates of immunoglobulins (IgM, DNA and CRP).
2- The activation of classical pathway is initiated by activation of C1 through binding by
Ag-Ab complex.
3- Activated C1 causes cleavage of C4 to C4b which continuous the reaction process
and C4a which has other biological activities.
4- C2 is then cleaved by activated C1 into C2b and C2a which combines with C4b to
form the classical pathway C3 convertase (C4b 2a).
5- The cleavage of C3 by C4b 2a forms two fragments:
• C3a which has powerful biological properties.
• C3b which becomes bound to the membrane and to C3b 2a
leading to formation of classical pathway.
6- C5 convertase (C4b 2a 3b), which cleaves C5 which is a component of
the membrane attack complex (MAC).
 Complement

ALTIRNATIVE PATHWAY:

- Pathogen can be destroyed in the absence of Ab by means of the alternative pathway,

which acts as part of innate immunity.
- Activators of the alternative pathway include endotoxin found in gram negative
bacteria cell walls, as well as fungal cell walls and insoluble polysaccharides.
- The main components of the alternative pathway are factor B, factor D and
properdin (factor P) As well as C3b.
1- C3b is formed as result of result of low-grade hydrolysis of C3.
2- C3b bind to hydroxyl groups of proteins and carbohydrates expressed on cell
surface.
3- Factor B combines with C3b forming C3bB.
4- factor D then cleaves factor B, removing Ba fragment and generating Bb which
attached to C3b forming C3bBb complex (extremely unstable unless properdin
bind to the complex) which is the alternative pathway (C3 convertase) which can
cleave C3, when stabilized on bacterial surface.
5- C3bBb (C3 convertase) then cleave more C3 and binds C3b to form C3bBb3b
which initiate the membrane attack complex (MAC).
 Complement

LICTEN PATHWAY:

- Lectin pathway do not need Ab to be activated therefore its innate.

- This pathway provides an additional link between the innate & adaptive immunity.
1- The lectin pathway is initiated by the binding of mannose-binding lectin (MBL) or
ficolin to carbohydrates groups on the surface of bacterial cell.
2- MASP-2 becomes enzymatically active, which cleaves C4 to C4a and C4b.
3- Activated MASP-2 also cleaves C2 to C2a and C2b.
4- C4b bind to the cell surface and C2a bind to C4b forming C4b2a complex
known as C3 convertase which has an enzymatic action to cleave C3.
5- C4b2a binds C3 and cleaves it to C3a and C3b.
6- C3b binds covalently to the microbial surface.
 Complement

MEMBRANE ATTACK COMPLEX:

- This stars by cleavage of C5 by either the classic, alternative or lectin pathway

leading to the formation of the small fragment C5a which is biologically active and
the larger fragment C5b.
- C5b is unstable and is stabilized by C6.
- C5b6 allow C6 and C7 to associate and penetrate a membrane.
- The C5b67 recruits C8 which organizes C9 to form a
membrane attack complex (MAC).
Complement
 Complement

Complement animation:
https://www.youtube.com/watch?v=mfCeCvkQbuI

Complement animation:
https://www.youtube.com/watch?v=DPNnZE4OtCM

Alternative pathway:
https://www.youtube.com/watch?v=qga3Wn76d9w

Lectin pathway:
https://www.youtube.com/watch?v=SJv9gDFgwtw
 MAJOR HISTOCOMPATIBILITY COMPLEX

MAJOR HISTOCOMPATIBILITY COMPLEX (MHC):

- Group of genes on the short arm of chromosome 6 code for proteins found on the
surface of cells that help the immune system to presenting peptide Ag to T cells.
- In human beings the complex is also called human leukocyte antigen (HLA).
- MHC molecules are glycoproteins expressed at the surface of almost all vertebrate
cells.
- Identical twins have same MHC molecules on their cells, so they accept transplant
tissue from each other.
- MHC molecules act as Ag when introduced into a different individual.
- MHC molecules are often called histocompatibility Ags or transplantation Ags.

Þ MHC Haplotype:
• The loci that make up the MHC are highly polymorphic.
• We inherit our alleles in sets, one from each parent.
• Each set of alleles is called a haplotype.
• Codominant expression: are MHC alleles expressed on cells of offspring from both
father and mother, so a person heterozygous for HLA-A, HLA-B, HLA-C express
6 different Class I proteins.

Þ The MHC gene complex:

• The MHC complex contains a number of genes that control several Ags, most of
influence allograft rejection.
• These Ags can be divided into three major classes: class I, class II, class III
• The class I and class II Ags are expressed on cells and tissues while class III Ags
are expressed on proteins in serum and other body fluids.
• Ags of class III gene have no role in graft rejection.

Þ Function of MHC molecules:

• Are Ags molecules proteins on Antigen Presenting Cells (APC) for recognition
by T lymphocyte.
• Each molecule can present only one peptide at a time, because there is only one
cleft. But each MHC is capable of presenting many different peptides.
 MAJOR HISTOCOMPATIBILITY COMPLEX

Þ Processing of protein antigens:

• Peptides derived from the degradation of intracellular pathogen are
formed in the cytosol and delivered to the endoplasmic reticulum (ER),
where they bind
MHC class I molecule.
• Peptides derived from the degradation of extracellular pathogen are taken
up by phagocytosis and are degraded in the lysosome and other vesicle of
endocytic pathways bind MHC class II molecules.

STRACTURE OF CLASS I MHC:

² 1-Large alpha chain (heavy chain) with three external domains

(regions) (α1, α2, α3):
- Contains a transmembrane segment passes through the plasma
membrane of the cell.
- Cytoplasmic anchor segment.
-Peptide binding groove (8-10 a.a).
² Covalently associated with β2-microglobulin:
- Interact with α3 domain.
- β2-microglobulin is non polymorphic.
² The peptide is attached noncovalently in the groove between the
two alpha (α1 & α2) domain.

Þ MHC class I molecule:

Ø Class I Ags encoded by HLA-A, B&C are expressed on all nucleated cells.
Ø Peptide that bind to MHC class I are 8 to 10 amino acids.
Ø Without β2-microglobulin, the class I Ag will not expressed on the cell surface.
Ø Individual with a defective β2-microglobulin gene do not expressed any class I Ag and
hence have a deficiency of cytotoxic T cells.
 MAJOR HISTOCOMPATIBILITY COMPLEX

Þ Processing of Ags for display by class I molecules:

• Antigenic proteins may produced in the cytoplasm from viruses living
inside infected cells.
• Or from phagocyted microbes who escaped into cytoplasm.

STEPS OF PROCESSING THE ANTIGEN BY CLASS I MHC:

1- Production of protein antigens in the cytosol.

2- A protein is marked for destruction by binding to ubiquitin.
3- Antigen degraded to peptides in the proteasome.
4- Transport of of peptides from cytosol to ER by TAP*.
5- Assembly of peptide/class I complex in ER.
6- Transported to the cell surface and recognized by CD8 cells.
- If class I dose not find peptide in the ER, the molecule becomes
unstable and degraded by proteases.

*Antigen fragments generated by proteasomes are delivered to transporter

proteins, TAP1 and TAP2 (Transporters associated with Antigen Processing)
which are gatekeepers that facilitate antigen fragment entry into the
endoplasmic reticulum, where they attach to the antigen binding sites of
class I MHC molecules anchored there by interaction with TAP2, tapasin
and calreticulin.
 MAJOR HISTOCOMPATIBILITY COMPLEX

STRACTURE OF CLASS II MHC:

² Slightly larger alpha chain 2 domains (α1, α2).

² Beta chain 2 domains (β1, β2).
² 2 transmembrane segment (polypeptide).
² Peptide binding groove (12-20 a.a).

Þ MHC class II molecule:

Ø The class II gene complex also contains at least three loci:
DP, DQ and DR.
Ø Each of these loci code for one alpha and one beta chain which associate together to
form the class II antigens.
Ø Class II Ags encoded by genes of the HLA-D region expressed on APCs.
Ø Peptide that binding to MHC II are usually 12-20 amino acid.
 MAJOR HISTOCOMPATIBILITY COMPLEX

Þ Processing of the Ags for display by class II molecules:

• Microbes bind to surface receptors specific for microbial products.
• Or binds to receptors the recognize Abs or product of complement.
• Or by phagocytosis.

STEPS OF PROCESSING THE ANTIGEN BY CLASS II MHC:

1- Microbes is internalized, enters the intracellular vesicles (Phagosome).

2- Which fuse with lysosomes, where proteins are broken down proteolytic enzymes.
3- MHC class II molecule is synthesized in the ER and carries with it protein called (Ii
or CLIP) *.
4- Peptide with phagolysosomes become bound to MHC class II molecules in the vesicle
that contain protein called DM.
5- DM removes CLIP from class II, so the molecule will be able to accept peptides.
6- Class II molecule have been transported to the vesicle via ER and the Golgi apparatus.
7- The peptide/MHC complex are carried to the cell surface in outgoing vesicle and are
recognized by CD 4 T cell.
- Both CD4+ and CD8+ T cells have an antigen receptor called T cell receptor (TCR).
- If MHC molecules dose not find peptide, becomes unstable and is degraded by
proteases in the endosomes.
- Extracellular proteins that enter cells by phagocytosis degraded by lysosome enzymes
in early endosome.
- Late endosome fuse with transport vesicle containing MHC II molecules whose Ag
binding sites are filled with invariant chain.

* invariant chain (Ii) The Ii chain’s purpose is to

keep the peptide-binding cleft of MHC-II free of
the cell’s own peptide] or [class-II associated
invariant chain peptide (CLIP)] that occupies
the cleft.
 MAJOR HISTOCOMPATIBILITY COMPLEX

Þ Clinical significant of class I & II:

Is important in graft rejection of foreign tissues or organs, due to immune response of recipient
to specific MHC Ags present on the surface of grafted cells (from donor) and its absent from
the recipient.

Þ Self MHC restriction:

Refers to the fact that a given T cellwill recognize a peptide Ag only when it is bound to a
particular MHC molecule.
Helper T cells recognize antigen in context of class II self MHC. Cytolytic T cells recognize
antigen in context of class I self MHC. The process whereby T cells become restricted to
recognizing self MHC molecules occurs in the thymus.
 MAJOR HISTOCOMPATIBILITY COMPLEX

DIFFRENCES BETWEEN MHC CLASS I AND CLASS II:

CLASS I CLASS II

Large chain (heavy chain) with three Slightly larger alpha chain (2 domains)

external domains (α1, α2, α3) + Beta chain (2 domains)

Contains a transmembrane segment

Cytoplasmic anchor segment

Peptide binding groove (8-10 a.a) Binding clefts face in opposite directions to form

(Closed) groove (12-20 a.a) (Open)

Polymorphic α and β2-microglobulin Polymorphic chain α and β2-microglobulin

Peptide bound to α chain. Peptide binds to both.

Expressed on all nucleated cells Expressed mainly on APCs

Both on Chromosome 6

Gene encoded on A, B, and C Gene encoded on DR, DQ, and DP

The peptide in the groove 2 α helices is The peptide in the groove between α and β is like a

like a hot dog in a bum pita bread

Able to respond to CD8 Able to respond to CD4

 MAJOR HISTOCOMPATIBILITY COMPLEX

MHC genes and molecules:

https://www.youtube.com/watch?v=DS8myTf4RUk

Antigen processing by MHC (Animation):

https://www.youtube.com/watch?v=fYfetqif2NY

MHC class I processing:

https://www.youtube.com/watch?v=soWtpAO1Nr0

MHC class II processing:

https://www.youtube.com/watch?v=TMnkihN6zVM