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Immunology and inflammation > IMI3: Why is the adaptive immune response so specific? > Flashcards

IMI3: Why is the adaptive immune response so specific? Flashcards

1
Q

What line of defence is the adaptive immune system?

A

Third

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2
Q

What are the 2 key cells involved in adaptive immunity?

A

1) B cells – humoral immunity

2) T cells – cell-mediated immunity

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3
Q

What is the B cell receptor (BCR) made up of?

A

Transmembrane proteins known as immunoglobulins

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4
Q

How do BCRs act?

A

They directly bind to antigens, causing the B-cell to mature into plasma cells (effector B cells)

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5
Q

What do plasma cells (effector B cells) produce?

A

Antibodies (soluble Ig molecules).

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6
Q

Where does the BCR antibody vary?

A

Only by their C-terminus

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7
Q

What are the distinctive features of the adaptive arm of the immune system?

A

1) Specificity in recognising antigens

2) Memory to recognise the same antigen in later infections

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8
Q

What’s the difference between a PAMP and an antigen?

A 
Antigen: part of a molecule recognised by an adaptive immune protein.
PAMP: a broad characteristic of a pathogen class that is recognised by an innate immune protein
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9
Q

What is the BCR made up of?

A

4 polypeptide chains: 2 identical heavy chains and 2 identical light chains. The light chains can be either kappa or lambda.

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10
Q

Completely describe the the structure of BCR

A

Y-shaped molecule. The top contains the antigen binding site (made up of 2 variable regions on each Ig molecule; VL and VH).
There are also 2 constant regions in each Ig molecule: CL and CH.
The constant region on the heavy chain can contain 1-4 CH domains depending on the Ig molecule
The chains are held together by intra and inter chain disulphide covalent bonds

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11
Q

Which region of the BCR has the broadest diversity in amino acid sequence?

A

Antigen binding site (variable regions - VL and VH)

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12
Q

Which type of Ig molecules have CH1-CH3?

A

IgG
IgA
IgD

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13
Q

Which type of Ig molecules have CH1-CH4?

A

IgE

IgM

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14
Q

What mechanism determines whether the Ig molecules will be an antibody or a BCR?

A

Alternative polyadenylation and splicing

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15
Q

What does alternative splicing lead to for antibodies and BCRs?

A

The primary transcript is the same, but:

  • antibodies are coded to be soluble Ig
  • BCRs are translated with a C-terminus containing a transmembrane segment and a short, cytoplasmic tail
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16
Q

What can Papain do?

A

Digest Ig molecules to produce 3 fragments

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17
Q

What are the three fragments Papain digests Ig molecules into?

A
  • 2 fragments (from 2 x Y arms) corresponding to the antigen binding region, called ‘Fab’
  • 1 fragment (from Y stem) called ‘fragment crystallisable (Fc)’
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18
Q

What do the Fab regions do?

A

Its the part of the antibody that binds to the antigen

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19
Q

What do the Fc regions do?

A

Crucial for the effector function by binding to various antibody receptors (Fc receptors)

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20
Q

What are the Fc region effector functions?

A
  • Opsonisation that results in an immune cells’ phagocytosis or degranulation
  • Complement fixation via C1q
  • On the placenta: allows antibodies to transfer from the mother’s blood to the foetal blood.
  • On the baby’s gut epithelium: allows the transfer of antibodies from mother’s milk to the baby’s blood
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21
Q

How do IgG, IgA, IgM, IgD and IgE vary?

A 
Amino acid composition
Size
Charge
Carbohydrate content
Method of assembly
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22
Q

What are the two arms of adaptive immunity and the key players?

A

1) Antibodies - humoral response

2) T cells - cell-mediated immunity

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23
Q

Which cells from the adaptive immune system directly act against pathogens?

A

Cytotoxic T cells (TC, CTLs, CD8+)

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24
Q

Which cells from the adaptive immune system have a modulator role?

A

Helper T cells (CD4+)

Regulator T cells

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25
Q

What’s the difference between B cells and B plasma cells?

A
  • B cells can phagocytose but do so mainly to present antigens, not to kill
  • Plasma cells are the effector cell version of B cells - they act more indirectly by producing many antibodies
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26
Q

What are the two types of immunoglobulin?

A
  • A transmembrane form that studs, or dots, the surface of the B cell. This is called the B cell receptor (BCR) - membrane bound
  • A version missing the transmembrane domain which has a signal peptide instead - soluble
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27
Q

Why does the bonding between the chains in an Ig have to be highly complex?

A

To survive in the circulation for months

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28
Q

What does the constant domain of the heavy chain determines what?

A

The effector function, once an antigen is bound: (eg)

  • activation of a B cell
  • neutralisation of a viral pathogen before it can affect a cell
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29
Q

The V or C regions are encoded by?

A

different exons

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30
Q

What is the secondary structure of Ig chains called?

A

Immunoglobulin fold

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31
Q

What is the immunoglobulin super family?

What molecules does this include?

A

Proteins containing the immunoglobulin fold (structurally similar secondary structure)

  • MHC molecules
  • CD4 / CD8
  • ICAM1
  • IL-1R
  • Some Fc receptors
  • Inhibitory and stimulatory molecules (CTLA-4 and CD28)

B cell receptor and immunoglobulin super-families

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32
Q

Which part of BCR is anchored in the cell’s surface? How?

A

The C-terminus: by a transmembrane domain

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33
Q

What does the C-terminus of antibodies determine?

A

It directs the Ig to the secretory pathway

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34
Q

What happens in alternative splicing to form the BCRs or antibodies?

A

Leaving out either the region encoding the secretion signal (S) or the exons encoding the membrane-bound segment (M1 & M2)

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35
Q

What is the mRNA arrangement for BCR heavy chain?

A

5’ - L, V, D, J, u1, u2, u3, u4, M1, M2 - 3’

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36
Q

What is the mRNA arrangement for soluble Ig heavy chain?

A

5’ - L, V, D, J, u1, u2, u3, u4, S - 3’

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37
Q

Since both transcripts of Ab and BCR come from the same gene, what does this mean about their extracellular domains?

A

The secreted and membrane bound form of Ig must have identical extracellular domains

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38
Q

What is the complement-determining region (CDR)?

A

Three loops that contact the antigen - these loops are called CDR1,2,3

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39
Q

What are the most genetically variable parts of the Variable segment?

A

CDR1 and CDR2

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40
Q

How does CDR3 arise?

A

During VDJ recombination

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41
Q

What are the functions of the constant domains of an Ig heavy chain? Select all that apply.

A
  • Opsonisation

- Transfer of Ig through the Fc receptor across epithelia

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42
Q

What are the different Ig subtypes?

A 
IgM
IgG
IgA
IgE
IgD
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43
Q

What is the first Ig subtype to be expressed on B cells?

A

IgM

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44
Q

Discuss the structure of IgM

A

B cells IgM subunits are connected by a J chain that joins penultimate cysteines to form a pentameric structure.

Each IgM possesses 10 potential antigen binding sites providing the molecules with a high avidity for antigens despite having low affinity in their individual binding sites.

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45
Q

Define avidity

A

Overall binding strength across multiple sites

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46
Q

What is the most abundant Ig subtype?

A

IgG

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47
Q

What are the subclasses of IgG? (They have different heavy chains)

A

IgG1 - gamma (g) 1
IgG2 - g2
IgG3 - g3
IgG4 - g4

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48
Q

What is the main antibody class for dealing with small pathogens inside the body?

A

IgG

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49
Q

What forms can IgA be present in?

A

Present as a monomer or a dimer

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50
Q

What are the two subclasses of IgA?

A

IgA1 - alpha (a) 1

IgA2 - a2

51
Q

What facilitates dimerisation in IgA?

A

J chain

52
Q

What is the major Ig molecule in mucosal secretions?

A

IgA

53
Q

What is one of the least common Ig subtypes found on the surface of basophils and mast cells?

A

IgE

54
Q

How many Ig molecules does IgE have?

A

one

55
Q

What is IgE important for?

A

Responding to parasitic helminth infections, asthma and hay fever

56
Q

What is the Ig subtype that is rare and is membrane bound on naïve, mature B cells? They are thought to play a role in the activation of B cells prior to their differentiation into plasma cells.

A

IgD (role is unknown / regulatory)

57
Q

Where is the human heavy chain locus found?

A

Chromosome 14

58
Q

What regions does the heavy chain locus consist of?

A

V – 40 distinct copies
D – 24 distinct copies
J – 6 distinct copies

59
Q

Where is the human light chain for Ig kappa and Ig lambda found?

A

Chromosome 2 (or 22)

60
Q

What regions does the light chain locus for Ig kappa consist of?

A

V – 46 distinct copies

J – 5 distinct copies

61
Q

What regions does the light chain locus for Ig lambda consist of?

A

V – 36 distinct copies

J – 4-5 distinct copies

62
Q

The heavy chain of every Ig molecule will possess ____ copy(ies) of the V, D and J regions.

A

one

63
Q

What encoded region determines the class of the Ig molecule?

A

Constant region

64
Q

What is VDJ recombination?

A

Creates a unique amino acid sequence in bone-marrow residing stem cells that become immature B cells

65
Q

What are VDJ sequences flanked by?

A

Recombination signal sequences (RSS)

66
Q

What are RSSs recognised by?

A

RAG 1/2 recombinases which bind them specifically

67
Q

What does the gene segments are brought together before the RAG complex do?

A

It cleaves the RSS, leaving a hairpin at the ends of the V and J regions and a DSB at the RSSs.

68
Q

What forms a complex that joins the RSS ends into a DNA-circle and what is this DNA circle known as?
(the complex also cleaves the hairpin complex)

A

DNA-PK, Ku, Artemis, DNA ligase/XRCC4 dimer form a complex.

- signal joint

69
Q

What does the Terminal deoxynucleotidyltransferase (TDT) do?

A

adds additional nucleotides to the cleaved ends allowing them to be re-ligated with their unique combination

70
Q

State the steps of VDJ recombination

A

V, D and J regions are flanked by recombination signal sequences (RSS)

RSS are recognised by RAG 1/2 recombinases which bind them specifically

The gene segments are brought together before the RAG complex cleaves the RSS, leaving a hairpin at the ends of the V and J regions and a DSB at the RSSs.

DNA-PK, Ku, Artemis, DNA ligase/XRCC4 dimer form a complex and join the RSS ends into a DNA-circle known as the signal joint with no more functions. The complex also cleaves the hairpin ends.

Terminal deoxynucleotidyltransferase (TDT) adds additional nucleotides to the cleaved ends allowing them to be re-ligated with their unique combination.

71
Q

When does VDJ begin?

A

when the common lymphoid progenitor cells form pro B cells.

72
Q

In the pro B cell is the heavy of light chain recombined first?

A

Heavy the light

73
Q

In the pro B cell, what is the order of recombination in the heavy chain?

A

D and J recombination followed by V and DJ recombination

74
Q

When do pro B cells transition into pre B cells?

A

Following recombination of the heavy chain

75
Q

What happens in pre B cells?

A

V and J recombination of the light chain occurs, allowing the cells to become immature B cells

76
Q

What immature B cells express and what are they sensitive to?

A

BCR as IgM and are very sensitive to antigen binding

77
Q

During VDJ recombination, if self-antigen is recognised,what happens to the B cell?

A

Undergoes rapid apoptosis due to the high expression of apoptotic genes

78
Q

What do mature B cells up-regulate?

& what do they participate in?

A

IgD alongside IgM and participate in host immune surveillance

79
Q

What is allelic exclusion?

A

The process by which one allele is active whilst the other is silenced in a mature B cell.

80
Q

What does allelic exclusion make the B cell do?

A

Produce only one antibody

81
Q

How many Igs does VDJ allow the recombination of?

A

~2.5million

82
Q

How many Ig molecules can be made in mammals?

A

10^13

83
Q

How does the diversity of Igs increase from 2.5 million to 10^13?

A

The increase in diversity is due to the breaks introduced at the 3’ end of the V region and the 5’ end of the J region

84
Q

The breaks introduced at the 3’ end of the V region and the 5’ end of the J region can be repaired leading to what?

A
  1. Deletion of nucleotides at the junction
  2. Addition of non-germline nucleotides at the 3’-end
  3. Generation of palindromic nucleotides at 5’-end
85
Q

Which part of the heavy or light chain comes into direct contact with antigens? What does this mean for its variability?

A

The complementarity-determining region (CDR)

  • It has greatest variability and determines the specificity of the antibody
86
Q

How is extra variability of Igs generated? What enzyme?

A

Through somatic hypermutation (SHM) which introduces errors into the CDR and is driven by the enzyme Activation-Induced Deaminase (AID).

87
Q

What does Activation-Induced Deaminase (AID) catalyse?

A

The deamination of C to U, which is removed by uracil-DNA-glycosylase.

88
Q

What does the deamination of C to U lead to?

A

Causes faulty repair which results in unique mutations which modify the specificity and affinity of the antibody for the antigen. (The U is changed to an alternative base)

89
Q

Where does SHM only occur? Why?

A

Secondary lymphoid organs as it only occurs after antigen-Ig binding

90
Q

Once a naïve B cell’s antibody recognises an antigen what happens?

A

It proliferates and differentiates into plasma cells and memory B cells

91
Q

What happens in Germinal centres?

A

Active B cells can differentiate into germinal-centre B cells in which AID becomes activated

92
Q

Where are Germinal centres found?

A

Within secondary lymphoid tissues

93
Q

What do active B cells interact with?

A

Follicular Dendritic Cells (FDC) and CD4 T-cells

94
Q

What do Follicular Dendritic Cells (FDC) and CD4 T-cells regulate

A

Regulate SHM and affinity maturation

95
Q

What is Affinity maturation

A

A micro-evolutionary process where antibodies develop greater affinity, as seen in secondary infections and booster vaccines

96
Q

What are FDCs?

A

Follicular Dendritic Cells, which are antigen-presenting cells that are present in a limited number, allowing them to select Igs with high affinity

97
Q

What happens to low affinity Igs that don’t bind to the antigen?

A

They are detected by CD4 T cells that induce apoptosis in these B cells

98
Q

Where does class-switch recombination occur?

A

The germinal centre

99
Q

What is Class-switch recombination (CSR)?

A

A change in the constant region of the heavy chain

100
Q

What does CSR cause at switch regions?

A

DSBs

101
Q

How does CSR cause DSB at switch regions?

A

By a series of enzymes which causes the removal of the intervening DNA and alternative constant regions

102
Q

What is used to re-join the remaining sequence causing a different class of Ig to be coded for during CSR?

A

NHEJ

103
Q

What are the only antibody classes that can be simultaneously expressed by a cell?

A

IgD and IgM

104
Q

What do T-cells express?

A

A T-cell receptor (TCR)

105
Q

Describe the structure of TCR

A

A heterodimeric transmembrane receptor formed by 2 chains – TCR-alpha and TCR-beta. Connected by disulphide bonds

106
Q

What is CD3 made up of in the TCR complex?

A

CD3 gamma, CD3 delta and CD3 epsilon

107
Q

What is the TCR complex made up of?

A

TCR and CD3

108
Q

What chains do the unconventional subset of T cells (that can be activated independently of the MHC) possess?

A

TCR gamma and TCR delta

109
Q

Where are the unconventional subset of T cells (containing TCR gamma and TCR delta) derived?

A

They are derived from haematopoietic stem cells in the bone marrow, seeded into the thymus and then developing into thymocytes before maturing into CD4 or CD8 T cells

110
Q

What are the two classes of MHC proteins?

A

MHC I and MHC II

111
Q

What do MHC proteins get recognised by?

A

The variable region of the TCR

112
Q

Where are MHC Class I found?

What do they do?

A

They are present in every nucleated cell and they recognise and present pathogen antigens following intracellular infection

113
Q

Where are MHC Class II found?

What do they do?

A

present in antigen-presenting cells unless induced in other cell-types by cytokines.

114
Q

To differentiate between MHC classes, What do T cells have?

A

co-receptors called CD4 and CD8 which define the way the cell responds to target cells

115
Q

What are CD4+ T cells also known as?

What do they do?

A

Helper T cells

Recognise antigens on MHC Class II

116
Q

Once bound to the antigen-MHC complex, what do CD4+ T cells do?

A

They activate the APCs to kill off the pathogen. If the antigen is presented on a B cell, it is stimulated to make more antibodies or undergo affinity maturation.

117
Q

What are CD8+ T cells otherwise known as?

A

Cytotoxic T cells and recognise antigens on MHC Class I

118
Q

Upon binding the MHC-antigen complex, what do CD8+ T cells do?

A

CD8+ T cells can directly kill the cells. They are especially important in responding to viral infections.

119
Q

TCR diversity is also formed through?

A

VDJ recombination

120
Q

The alpha-chain locus is on chromosome 14 and includes what V,D,J copies?

A
  • V – 70 distinct copies
  • D – 0 copies
  • J – 61 distinct copies
121
Q

The alpha-chain locus is on chromosome 7 and includes what V,D,J copies?

A
  • V – 52 distinct copies
  • D – 2 distinct copies
  • J – 13 distinct copies
122
Q

True or False, TCR genes can undergo further diversification by SHM

A

False, they cannot

123
Q

Once VDJ recombination has occurred, what happens to TCR genes?

A

They are positively and negatively selected to eliminate T cells that potentially recognise self, or fail to activate

124
Q

NGS estimates TCR diversity lies where abouts?

A

106 different TCRs

Immunology and inflammation (11 decks)

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