This document summarizes cell-mediated immunity. It discusses how T lymphocytes are responsible for cell-mediated immunity, with cytotoxic T cells destroying infected cells and helper T cells activating other immune cells through cytokine release. Antigens from intracellular pathogens are presented on MHC class I to cytotoxic T cells, while extracellular pathogens are presented on MHC class II to helper T cells. The document also describes T cell receptor structure and diversity, antigen recognition, and the mechanisms of cytotoxic T cell and helper T cell activation.

1. Cell-mediated Immunity
R. C. Gupta
M.D. (Biochemistry)
Jaipur, India

2. Our defenses against infections include
innate immunity and acquired immunity
Innate immunity acts non-specifically
against all pathogens
Acquired immunity is specific; one cell or
molecule acts against one pathogen

3. Acquired immunity comprises humoral
immunity and cell-mediated immunity
Humoral immunity acts against pathogens
that haven’t entered any self-cell
Cell-mediated immunity acts against
pathogens that have entered some self-cell

4. Lymphocytes play a key role in humoral
as well as cell-mediated immunity
Lymphocytes are formed from stem cells
in bone marrow

5. T lymphocytes (T cells) are processed in
thymus
B lymphocytes (B cells) are processed in
bone marrow itself
Lymphocytes differentiate into two types -
B lymphocytes and T lymphocytes

6. The cells responsible for cell-mediated
immunity are T lymphocytes
B lymphocytes are responsible for
humoral immunity

7. T lymphocytes
are of four types:
Cytotoxic (Killer) T cells
Helper T cells
Suppressor T cells
Memory T cells

8. Each T cells possesses a number of
receptors for a particular antigen
The T cell receptor (TCR) is in many ways
similar to an antibody
It can recognize a specific antigen

9. Each chain (a and b) of TCR has:
Two extra-cellular domains
A trans-membrane region
A short cytoplasmic tail
TCR is a protein made up of an a chain
and a b chain joined by a disulphide bond

10. chain
b chain
T cell
T cell receptor (TCR)
a
EMB-RCG

11. The a-chain has got two extra-cellular
domains – a1 and a2
The b-chain has got two extra-cellular
domains – b1 and b2
The a1 and b1 domains are on the
periphery

12. The a1 and b1 domains are similar to the
variable regions of antibodies
These are also known as Va and Vb
domains
The a2 and b2 domains are similar to the
constant regions of antibodies

13. Like antibodies, TCRs can recognize and
bind antigens
Antigen-recognition is the function of
variable regions
The antigen-binding site (or cleft) is
formed by the a1 and b1 domains

14. T cell receptor

15. T cell receptors have a diversity similar to
antibody diversity
TCR diversity also arises from gene re-
arrangement
TCR diversity

16. One of the 70 V segments
Thousands of different combinations are
possible
The gene for the variable region of a
chain (Va) is constructed from:
One of the 61 J segments

17. One of the 52 V segments
One of the 2 D segments
One of the 13 J segments
Thousands of different combinations
are possible
The gene for the variable region of b
chain (Vb) is constructed from:

18. When an a chain combines with a b chain,
millions of combinations are possible
A given T cell has one combination, and is
specific for one particular antigen

19. The T cell receptor cannot bind a free
antigen
The antigen must be attached to a cell, and
it should be a self-cell
If a T cell is transferred from one person to
another, it will not recognize the antigen
MHC proteins and MHC genes

20. The T cell receptor recognizes a foreign
antigen combined with a self-molecule
The self-molecules are Major Histo-
compatibility Complex (MHC) proteins
MHC proteins are present on all cells and
are unique to each individual

21. MHC Proteins

22. MHC genes
MHC proteins are encoded by MHC
genes
MHC genes can be divided into:
MHC class
I genes
MHC class
II genes
MHC class
III genes

23. MHC class I genes encode MHC I proteins
MHC I proteins are present on the surface of
all the cells
Foreign antigens combined with MHC I
proteins are recognized by cytotoxic T cells

24. MHC class II genes encode MHC II
proteins
MHC II proteins are present on
macrophages, B cells and follicular
dendritic cells
Foreign antigens combined with MHC II
proteins are recognized by helper T cells

25. MHC class III genes
encode:
Complement
proteins
Some other
plasma proteins

26. MHC proteins are trans-membrane proteins
They are synthesized on the endoplasmic
reticulum
They get inserted in the cell membrane
They have a peptide (antigen) binding cleft
on their extracellular surface
MHC proteins

27. While on their way to the cell membrane,
MHC proteins pick up peptide fragments
formed by degradation of:
The fragments are bound firmly and
displayed on the surface of the cell
Endogenous
proteins
Exogenous
proteins

28. Endogenous peptides bound to MHC
proteins are ignored by the immune
system
If a T cell finds a foreign peptide bound
to an MHC protein, cell-mediated immunity
comes into operation

29. MHC class I proteins are made up of a
large a subunit and a smaller b subunit
(b2-microglobulin)
The a subunit has three extra-cellular
domains (a1, a2 and a3), a trans-
membrane region and a cytoplasmic tail

30. The a1 and a2 domains form the
peptide binding cleft

31. MHC I protein – View from above
‒‒‒ Peptide

32. MHC I proteins bind fragments of proteins
degraded by cytosolic pathway
In cytosolic pathway, the proteins are
degraded by 26S proteasome

33. MHC class II proteins are made up of
almost equal sized a subunit and
b subunit
Each subunit has two extracellular
domains, a trans-membrane region and
a cytoplasmic tail
The a1 and b1 domains form the peptide
binding cleft

35. ‒ Peptide
MHC II protein – View from above

36. MHC class II proteins bind fragments of
proteins degraded by lysosomal pathway
These proteins first enter intracellular
vesicles called endosomes
The endosomes fuse with lysosomes to
form endolysosomes

37. The proteins present in endolysosomes
are degraded by lysosomal enzymes
The lysosomal proteolytic enzymes are
cathepsins

38. The proteins present in
endosomes include:
Proteins of extracellular pathogens
Proteins of pathogens that reside
in endosomes
Proteins taken up by the cells by
endocytosis

39. MHC Class II
Protein
Antigen
fragment
a2 b2
b1
Cell membrane
Newly synthesized MHC II proteins bind
peptide fragments, and go to the cell
membrane
MHC II proteins get inserted in the cell
membrane, displaying the bound peptide
on the surface of the cell

40. Cytotoxic T cells destroy infected self-cells
along with the pathogen present inside
them
This prevents the spread of infection to
healthy cells
Function of cytotoxic T cells

41. Most viruses and many bacteria reside and
replicate in cytosol of the infected cells
Their proteins are degraded by 26S
proteasome
Peptide fragment are displayed on the
surface of the cell by MHC class I proteins

42. The foreign peptide bound to a self
MHC I protein is recognized by a
particular cytotoxic T cell
The T cell receptor binds to the
peptide:MHC I complex

44. A trans-membrane protein CD8, present in
cytotoxic T cells, acts as a co-receptor
CD8 is made up of an a and a b chain
linked to each other by a disulphide bond
The extracellular portion of CD8 binds to
the a3 domain of MHC class I protein

45. The cytoplasmic tail of CD8 is associated
with Lck, a cytosolic tyrosine kinase
The cytoplasmic tail of T cell receptor is
associated with a trans-membrane protein,
CD3 complex

46. CD3 complex consists of a g chain, a d
chain, two e chains and two x chains
Cytoplasmic portions of these chains have
immunoreceptor tyrosine-based activation
motifs (ITAMs)

47. Phosphorylated ITAMs act as a docking site
for ZAP-70 (zeta associated protein of 70 kD)
On binding of T cell receptor and CD8 to
MHC I protein and antigen fragment, Lck
becomes active
Active Lck phosphorylates the ITAMs of CD3
complex

48. ZAP-70 phosphorylates the tyrosine
residues of some target proteins in the
cytotoxic T cell
This results in release of stored granules
from the cytotoxic T cell targeted at the
infected cell
The granules contain perforin, granzyme
and granulysin

49. Action of cytotoxic T cell

50. Several perforin molecules get inserted in
the cell membrane of the infected cell
These are polymerized to form trans-
membrane pores
Granzyme and granulysin can enter the cell
through the pores

51. Cell contents can leak out of the pores
Granzyme is a serine protease
It hydrolyse the proteins of the infected cell
and the pathogen
Granulysin activates apoptosis of the
infected cell

52. Thus, combined action of perforin,
granzyme and granulysin results in:
Destruction of the infected cell
Destruction of the pathogen
present in the infected cell

53. Function of helper T cells
Helper T cells share some common
features with cytotoxic T cells
But they also differ in some respects

54. Helper T cells and cytotoxic T cells
share the following common features:
• Their TCRs are made up of a and b
chains
• Cytoplasmic tail of TCRs is associated
with CD3 complex having ITAMs
• They have co-receptors associated
with Lck

55. Helper T cells and cytotoxic T cells
differ in the following respects:
• The co-receptor in helper T cells is
CD4 instead of CD8
• Their TCR recognizes a foreign
peptide bound to MHC class II
protein

56. CD4:
Is made up of a single
polypeptide chain
Has four domains – D1,
D2, D3 and D4

57. D3
D4
D1
D2
Four domains in
CD4 protein

58. Antigen-presenting cells
MCH II proteins are present on
macrophages, follicular dendritic cells
and B lymphocytes
These cells are known as antigen-
presenting cells (APCs)

59. Antigen-presenting cells
Dendritic cell
Macrophage
B lymphocyte

60. TCR of a helper T cell binds to an antigen
fragment displayed by MHC II protein of APC
The D1 domain of CD4 binds to b1 domain of
MHC II protein
After this binding, intracellular Fyn is activated
by CD45

61. Fyn phosphorylates ITAMs of CD3 complex
Phosphorylated ITAMs are the docking site
for ZAP-70
ZAP-70 binds to phosphorylated ITAMs and
is phosphorylated by Lck

62. ZAP-70 phosphorylates the tyrosine
residues of some target proteins
This results in the release of cytokines
(lymphokines) from the helper T cell

63. Action of helper T cell

64. Lymphokines include:
• Interleukins (ILs) e.g. IL-2, IL-3, Il-4,
IL-5, IL-6 etc
• Granulocyte colony stimulating
factor (G-CSF)
• Granulocyte-macrophage colony
stimulating factor (GM-CSF)
• Tumour necrosis factor (TNF)
• Interferon-g (IFNg)

65. Actions of lymphokines
IL-2 stimulates multiplication of helper T
cells themselves
IL-3 stimulates the proliferation of bone
marrow stem cells
IL-4 stimulates the proliferation of B cells,
T cells and mast cells
Continued

66. IL-5 stimulates the growth of eosinophils
IL-10 stimulates growth of mast cells and
synthesis of MHC II proteins in B cells
GM-CSF stimulates growth of granulo-
cytes and macrophages
Continued

67. IFN-g activates macrophages and natural
killer (NK) cells
TNF activates macrophages
Some lymphokines attract the phagocytic
cells to the site of infection
Continued

68. Thus, release of lymphokines leads to:
• Increase in the number of helper T cells
• Increase in the number of cytotoxic T
cells
• Increase in the number of B cells and
plasma cells
• Increase in the number of antigen-
presenting cells
• Increase in the number of phagocytic
cells
• Activation of phagocytic cells

69. Thus, both innate and adaptive immunity
are geared up to fight against the pathogen
A co-ordinated and effective immune
response is mounted against the pathogen

70. Helper T cells respond to calls for help
The call is given by antigen-presenting
cells
The call is in the form of an antigen
fragment displayed on MHC II protein

71. Helper T cells have no direct role in
destroying the antigen
They activate different arms of the defense
system and co-ordinate their actions

72. Helper T cells are described as the
Commanding Officer of the defense force
If helper T cells are depleted or debilitated,
the entire immune system is crippled

73. Also known as regulatory T cells
Shut down the immune response after the
invading organisms are destroyed
Play a regulatory role in immune response
Possess TCR and CD8
Function of suppressor T cells

74. Suppressor T cells release some
lymphokines after an immune response
has achieved its goal
Suppressor T cells also prevent immune
response against self-molecules
This signals all other immune system
participants to cease their attack

75. Functions of memory T cells
Retain memory of antigen after first exposure
Spread throughout the lymphoid tissue
Are released quickly into circulation if the
same antigen enters again
Help in mounting a quick immune response

76. Different arms of defense system do not act
in isolation
Innate immunity acts in co-ordination with
adaptive immunity
Humoral immunity and cell-mediated
immunity also act in co-ordination
Integrated immune response

77. Many molecules having antigenic
properties are present in our body also
Our immune system doesn’t act against
these self-antigens
Tolerance to self-antigens is known as
self-tolerance
Self-tolerance

78. Suppressor T cells have some role in self-
tolerance
They suppress immune reaction against
self-antigens
But there is a second and more important
mechanism

79. Newly-formed lymphocytes are processed
during foetal life
The purpose of this processing is two-fold:
To allow only the immunologically
competent lymphocytes to mature
To eliminate those lymphocytes
that can react with self-antigens

80. Developing T cells express the genes
for TCR, CD4 and CD8
Some of the TCRs are incapable of
recognizing any self-MHC protein
Such T cells would be functionally
useless, if allowed to mature
Processing of T cells

81. Developing T cells are first subjected to
positive selection
If the TCR and CD8 bind to some
MHC I protein, the cell is allowed to
mature into a cytotoxic T cell
Expression of CD4 gene is suppressed
Positive selection

82. If the TCR and CD4 bind to some
MHC II protein, the cell is allowed to
mature into a helper T cell
Expression of CD8 gene is suppressed

83. The positively selected cells are subjected
to negative selection
If the TCR binds some self-antigen:self-MHC
complex, the T cell is pushed into apoptosis
Thus T cells capable of acting against self-
antigens are eliminated
Negative selection

84. Receptor editing
Clonal deletion
Anergy
Immunological ignorance
Developing B cells recognizing self-
antigens can have the following fates:
Processing of B cells

85. Receptor editing
Developing B cells that can react with
multivalent self-antigens undergo further
light chain gene re-arrangement
Re-arrangement continues until the
antigen receptor is so modified that it
cannot bind the self-antigen

86. Multivalent antigen
Antigen

87. Clonal deletion
If self-reactivity is not lost by
receptor editing, the developing
B cell is pushed into apoptosis
Thus, the entire clone of self-reacting
B cells is deleted

88. Anergy
Developing B cells that encounter
self-antigens of low valency
become anergic
Their antigen receptors remain
within the cell and signal
transduction is impaired

89. Antigen of low valency
Antigen
Epitope Epitope

90. Immunological ignorance
Some sites in our body are
immunologically privileged
Immune cells and molecules
cannot reach these sites

91. Immunologically privileged sites
Brain Eye
Testes Foetus

92. Self-antigens present in these areas do
not come in contact with immune system
The immune system remains ignorant of
such self-antigens

93. This results in self-tolerance
Thus, potentially self-reacting
T cells and B cells are:
Deleted or
Modified or
Incapacitated

94. Self-tolerance is sometimes lost,
resulting in self-reactivity
When the immune system reacts
against a self-antigen, it results in an
autoimmune disease
Autoimmune diseases

95. • Some self-molecules
have a structural
resemblance with
foreign antigens
• These may be
treated as foreign
antigens by the
immune system
Autoimmune diseases can occur because:
• Some self-molecules
combine with
microbial proteins to
form new molecules
• These molecules are
treated as foreign
antigens by the
immune system

96. Some diseases resulting from auto-
immunity are:
• Hashimoto’s thyroiditis
• Myasthenia gravis
• Systemic lupus erythematosus
• Rheumatoid arthritis
• Some cases of type 1 diabetes
mellitus, male infertility and pernicious
anaemia

97. Occurs due to impairment of immune
system
May be inherited (primary) or acquired
(secondary)
Immunodeficiency

98. Both
Cell-mediated immunity or
Humoral immunity or
Inherited immunodeficiency
may affect:

99. Examples of immunodeficiency diseases
Type of immunity Example
Humoral Agammaglobulinaemia
Cell-mediated DiGeorge syndrome
Both humoral
and cell-
mediated
Severe combined
immuno-deficiency
disease

100. Congenital agammaglobulinaemia is a
disease in which only humoral immunity
is impaired
It is an x-linked disease in which gamma-
globulins are totally absent

101. In DiGeorge syndrome, only cell-mediated
immunity is impaired
DiGeorge syndrome occurs due to lack of
development of thymus

102. Both humoral and cell-mediated immunity
are impaired in severe combined immuno-
deficiency disease (SCID)
SCID is most commonly caused by a
deficiency of adenosine deaminase

103. Acquired immunodeficiency
may result from:
Severe malnutrition
Irradiation
Immunosuppressive drugs
Viral infections
Acquired immunodeficiency

104. A very sinister form of acquired immuno-
deficiency is caused by human immuno-
deficiency virus (HIV)
The disease caused by HIV is known as
acquired immuno deficiency syndrome
(AIDS)
HIV and AIDS

105. HIV is a retrovirus
Retroviruses have an RNA genome
They also possess reverse transcriptase

106. After infection by a retrovirus:
Its genomic RNA enters the
infected cell
Reverse transcriptase also
enters the infected cell

107. Reverse transcriptase prepares a DNA
copy of the viral genome
This copy is incorporated in the DNA of
the infected cell
Viral genome becomes a part of the host
cell genome

108. The structure is similar to that of other
retroviruses
Its core is made up of two copies of its
RNA genome and some enzymes
The genomic RNA and the enzymes are
surrounded by a conical capsid
Structure of HIV

109. The capsid is made up of core proteins
(p 24, p 7 and p 6)
The capsid is surrounded by a spherical
envelope
The envelope is made up of lipid bilayer
and some proteins

110. The envelope is formed when the virus
buds out of an infected cell
The virus takes a part of the host-cell
membrane with it

111. The envelope contains two viral glyco-
proteins, gp 120 and gp 41
The glycoprotein gp 41 is embedded in
the lipid bilayer
The other glycoprotein, gp 120 is attached
to gp 41 by non-covalent interactions

112. gp120 gp41
p6
Integrase
Protease
Reverse
transcriptase
p24
p17
p7
Genomic
RNA
Lipid bilayer

113. The HIV genome is made up of 9,749
nucleotides
Three genes, env, gag and pol, are
common to all retroviruses
There are six accessory genes unique
to HIV
Genome of HIV

114. The accessory genes in HIV are: (i) tat, (ii)
rev, (iii) nef, (iv) vif, (v) vpu and (vi) vpr
Fifteen proteins are synthesized from
these nine genes

115. HIV genes

116. The name of env gene is derived from
envelope
It encodes a poly-protein, gp160
After translation, gp160 is cleaved by
protease
The products of cleavage are gp120 and
gp 41

117. gag gene is named after group-specific
antigen
It encodes the core proteins of the virus
It is translated into a poly-protein

118. The poly-protein encoded by gag gene is
cleaved into – p 24, p 17, p 7 and p 6
p17 forms the inner lining of lipid bilayer
The other proteins are present in the
capsid

119. The name of pol gene is derived from
polymerase
It encodes the viral enzymes
It is translated into a poly-protein

120. The polyprotein encoded by pol
gene is cleaved into:
Reverse transcriptase
Integrase
Protease
Reverse transcriptase possesses
ribonuclease H activity also

121. HIV infection and immunodeficiency
HIV is present in infected persons in:
Some blood cells
Genital secretions
An infected person can transmit the virus
to other persons

122. HIV can be transmitted from an infected
person to an uninfected person through:
Sexual contact (vaginal or anal)
Transfusion of infected blood
Sharing of contaminated needles
Mother to foetus transmission in
pregnancy

123. The molecule exposed on the surface of
HIV is gp 120
This happens to have a structure comple-
mentary to that of CD4
Due to this complementarity, gp 120 binds
avidly to CD4
CD4 molecules are present on the surface
of helper T cells

124. HIV and helper T cell
gp 120 of HIV binds avidly to CD4 of helper T cells

125. Lipid bilayer surrounding HIV fuses with
the cell membrane of helper T cell
The virus sheds its envelope and its core
enters the helper T cell
Viral reverse transcriptase synthesizes a
complementary DNA strand
A cDNA-RNA hybrid is formed

126. The ribonuclease H activity of the enzyme
hydrolyses the genomic RNA
The single DNA strand then acts as a
template
A second complementary DNA strand is
synthesized

127. Thus, a double-stranded DNA is formed
This is a DNA copy of the viral genome
This is incorporated in the host cell DNA
by the viral integrase
Thus, the viral genome becomes a
permanent part of the host DNA

128. The viral genome incorporated in host cell
genome is called proviral DNA
The proviral DNA is transcribed to mRNA
by the host cell
The mRNA is translated to form viral poly-
proteins
These are cleaved by protease

129. The mRNA and the viral enzymes are
surrounded by the core proteins
The core is surrounded by p 17 and
envelope proteins to form a new virus
The virus buds out of the cell
Thus, a new virus is released by the
infected cell

131. The new virus infects another uninfected
helper T cell
This cycle is repeated
New virus particles are formed and
released
More and more helper T cells are infected

132. Multiplication of HIV inside helper T cells
leads to rupture of cells

133. Viral proteins are cleaved inside the
infected helper T cells
Viral peptides are picked up by MHC I
proteins of the infected cells
They are displayed on the surface of the
cell
Helper T cells displaying viral peptides are
destroyed by killer T cells

134. Rupture and destruction of helper T cells
results in their depletion
Massive depletion of helper T cells cripples
the immune system
The affected person becomes extremely
prone to infections due to immunodeficiency