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ODDR- immunology (host Defenses) > imm 3 > Flashcards

imm 3 Flashcards

1
Q

What are antibodies composed of?

A

They are Y shaped molecules copses of 2 light chains and 2 heavy chains

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2
Q

How heavy are the heavy chains that make up antibodies?

A

50 kDa

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3
Q

How heavy are the light chains that make up antibodies?

A

25 kDa

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4
Q

What hold the 4 polypeptide chains together in antibodies?

A

Disulphide bonds

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5
Q

What specifically do the disulphide bonds link in antibodies?

A

2 disulphide bonds link the heavy chains1 disulphide bond links each light chain to its heavy chain partnerSo 4 disulphide bonds in total

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6
Q

What are the 2 main groups of functions antibodies have?

A
  1. To recognise and bind antigens| 2. To elicit effector functions
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7
Q

Name the 2 different regions of the antibody

A
  1. The variable region| 2. The constant region
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8
Q

What function does the variable region complete?

A

It provides the antigen binding function of the antibody
2 binding sites

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9
Q

What function does the constant region complete?

A

It elicits the effector function (eg recruits additional immune cells OR cells to destroy pathogens following antigen binding)

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10
Q

Where are the variable region found?

A

At the amino (end) terminals of the polypeptides

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11
Q

Where are the constant region found?

A

At the C terminus

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12
Q

Define affinity

A

The strength of binding of one molecule to another at a single site

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13
Q

Give an example of an event that shows affinity

A

The binding of a monovalent Fab fragment of antibody to a monovalent antigen

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14
Q

Define avidity

A

The sum of the strength of bonding of 2 molecules or cells to one another at multiple sites

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15
Q

Antibodies are bifunctional. What does this mean?

A

It means they have 2 functions:1. To recognise and bind antigens2. To elicit effector functions

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16
Q

How are antibodies digested?

A

By different proteases

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17
Q

What has the digestion of antibodies allowed us to do?

A

Dissect antibodies an be able to view them at a molecular level to see what bit does what function

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18
Q

Name the 2 enzymes that perform important digestive functions

A
  1. Papain| 2. Pepsin
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19
Q

What does papain do?

A

It cleaves the antibody to produce 2 Fab fragments and 1 Fc fragment

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20
Q

What does a Fab fragment do?

A

It recognises the antigen

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21
Q

Why is the Fc fragment given this name?

A

It is the easiest fragment to crystallises| fragment crytaliseable

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22
Q

Why is the Fab fragment given this name?

A

Means fragment antibody binding

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23
Q

What does an Fc fragment do?

A

It binds to cell receptors to recruit other ells of the immune system

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24
Q

What does pepsin do?

A

It cuts the antibody to give a F(ab’)2 fragment

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25
Q

Describe the F(ab’)2 fragment

A

It has 2 antigen binding sites as the 2 Fab arms are still linked together

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26
Q

Do the Fab and F(ab’)2 have the same AFFINITY for antibodies?

A

Yes it is the same

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27
Q

Do the Fab and F(ab’)2 have the same AVIDITY for antibodies?

A

No it is different

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28
Q

What are the 2 types of light chains found in humans?

A
  1. Kappa (k)| 2. Lambda (λ)
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29
Q

Which type of light chains do each antibodies have?

A

Any particular antibody has either 2 K chains or 2 λ chains| never one of each

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30
Q

What is the average ratio of B cells prosecuting kappa light chained antibodies to lambda?

A

02:01

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31
Q

Name a situation where the ratio of B cells prosecuting kappa light chained antibodies to lambda?may be skewed?

A

If someone were to have cancer

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32
Q

What are the 5 different classes of antibodies called?

A
  1. IgG2. IgA3. IgM4. IgD5. IgE
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33
Q

Which heavy chains make up IgG?

A

Gamma chain

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34
Q

Which heavy chains make up IgA?

A

Alpha chain

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35
Q

Which heavy chains make up IgD?

A

Delta chain

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36
Q

What 2 forms can IgA take?

A

The monomeric| The polymeric form (a diamer)

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37
Q

What 2 forms can IgM take?

A

The monomeric| The polymeric form (a pentamer)

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38
Q

What do both heavy and light chains contain?

A

A repeated similar domain called the immunoglobulin fold

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39
Q

How may immunoglobulin folds are there in IgG light chains?

A

2

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40
Q

How may immunoglobulin folds are there in IgG heavy chains?

A

4

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41
Q

Where is all variability in the antibody found?

A

At the amino (N) terminal domains of the light and heavy chains

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42
Q

Give some other examples of cells that have immunoglobulin folds but are not immunoglobulins?

A
  1. T cell receptors 2. MHC3. CD5
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43
Q

Where is the antigen binding site found?

A

At the amino (N) terminal domains of the light and heavy chains (the variable regions)

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44
Q

What is each immunoglobulin fold composed of?

A

2 antiparallel beta pleated sheet held together by disulphide bonds?

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45
Q

What are beta strands linked by?

A

Flexible loops

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46
Q

What do the flexible loops linking beta strands allow?

A

Allow strands to alternate direction

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47
Q

What is amino acid sequence variability concentrated in?

A

In the hypervariable regions or Complementarity Determining Regions (CDRs)

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48
Q

What is located at the tip of each Fab arm?

A

3 CDRs in the heavy chain and 3 CDRS in the light chain

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49
Q

What dies CDR stand for?

A

Complementarity Determining Regions

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50
Q

What do the 6 CRDs at the tip of each Fab arm combine to generate?

A

Combine to generate antigen binding sites

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51
Q

How do changes in amino acid sequences lead to changes in antigen binding specificity?

A

Changes in amino acid sequence at hypervariable regions alter the Complementarity Determining Regions which in turn leads to changes in antigen binding specificity

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52
Q

What is Combinatorial diversity ?

A

Different specificities created by different combinations of heavy and light chains.

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53
Q

Antigen and antibody bind via non-covalent interactions which can be disrupted by what?

A
  1. High salt concentrations 2. Extreme pH3. Detergents 4. High concentrations of purified epitope
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54
Q

Name some of the non-covalent interactions which can bind Antigen and antibody?

A 
1. Electrostaticforces2. Hydrogen bonds3. Hydrophobic forces4. Van der Waals forces
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55
Q

Where are Electrostatic| forces found?

A

Between oppositely charged amino acid side chains on antibody and antigen

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56
Q

What can disturb electrostatic forces and H2 bonds?

A

High salt

57
Q

Where are Hydrogen bonds found?

A

When Hydrogen is shared between negatively charged atoms.

58
Q

Where are hydrophobic| forces found?

A

Found when Hydrophobic groups pack together, excluding water| Has a short range

59
Q

Where are Van Der Waals| forces found?

A

Where fluctuations in electron clouds occur leading to opposite polarisations in neighbouring atoms.

60
Q

What are antibodies used in?

A

Diagnostics Research In drugs

61
Q

What are the functions of different Ig classes determined by?

A

The Fc regions

62
Q

Gives some ways antibodies complete their function

A
  1. Neutralisation 2. Opsonisation 3. Activation of the complement pathway to act as opsonin or lysis.
63
Q

What is neutralisation

A

Antibodies bind to pathogen and toxins, and prevent binding to the cellular receptors pathogens used to gain entry to cells.

64
Q

What is Opsonisation?

A

The coating of pathogen with antibody| This results in phagocytes recognising the Fc region of that pathogen causing the phagocyte to engulf the pathogen

65
Q

Where are antibodies present

A 
In a lot of different places in our body:Much Lining airway SerumFluid that bathes our tissues
66
Q

Describe the process of neutralisation

A
  1. Antibody blocks the binding of microbes to cells2. Antibody clocks the infection of adjacent cells3. Antibody clocks the blinding of toxin to cellular receptor
67
Q

What is the newest potential role of antibodies?

A

If an antibody bound to a virus is taken up by a cells an intracellular receptor called TRIM21 detects the antibody inside the cell and recruits the proteasome machinery

68
Q

What do proteasome do inside the cell?

A

The proteasome degrades the antibody virus complex.

69
Q

Where is TRIM21 found and what is it?

A

It is an enzyme found inside cells

70
Q

Name where our central (primary) lymphoid organs are found?

A
  1. Thymus (T cells)| 2. Bone marrow (B cells)
71
Q

Name where our Peripheral (secondary) lymphoidal organs are found?

A
  1. The adenoids2. Tonsils 3. Lymph nodes4. Spleen 5. Peyer’s patches6. Appendix
72
Q

Define Antibody repertoire

A

The total range of antibody specificity

73
Q

What is the estimated Antibody repertoire ?

A

1 x 10^11

74
Q

Why is a diverse Antibody repertoire required?

A

required to recognise vast array of more rapidly evolving pathogens.

75
Q

what do dendritic cells do

A

Cells that have taken up antigens from the site of infection to the lymph nodes in order to display the antigens to keep the immune repose going

76
Q

What is the estimated total number of lymphocytes in the body? An why

A

4x10^11 and 2x10^12
Why = some members of same clone

77
Q

Where does variation in Ig derive from?

A

Ig variation is derived from changes in the amino acid sequences which occur within the CDRs, altering the antigen binding sites.

78
Q

What is the problems with great Ig diversity?

A

Theres not enough genomic space

79
Q

What is the solution our body has to the lack of genomic space to code all the different Ig variations

A

Somatic Recombination.

80
Q

What have Ig genes in B cells been rearrange by?

A

Somatic Recombination.

81
Q

What are gene segments?

A

Variable regions of Ig genes are encoded in multiple pieces

82
Q

What is germline diversity?

A

Multiple choices for each gene segment

83
Q

What provides combinational diversity?

A

The process where by Segments are randomly selected and brought together in different combinations

84
Q

The variable region in light chains are encoded by what segments?

A

2 types of segment:| Variable (V) and Joining (J)

85
Q

The variable region in heavy chains are encoded by what segments?

A

3 types of segment:| Variable (V), Diversity(D) and Joining (J)

86
Q

Name the 3 sets of immunoglobulin chains

A
  1. Kappa light chain2. Lambda light chain3. Heavy light chain
87
Q

What MUST genes encoding the variable region be present in?

A

Must be present as multiple gene segment

88
Q

Name the 3 immunoglobulin loci

A
  1. Kappa chain locus2. Lambda chain locus3. Heavy chain locus
89
Q

At the 5 prime end of each locus what is present?

A

A cluster of V (variable) gene segments

90
Q

What is each V segment associated with?

A

A leader (L) sequence

91
Q

What does the L sequence encode?

A

It encodes a signal or leader peptide that facilitates the transport of Ig protein through the endoplasmic reticulum

92
Q

Is the leader sequence present in mature Ig?

A

No it is cleaved before hand

93
Q

At the 3 prime end of each locus what is present?

A

A cluster of J (Joining) gene segments

94
Q

What do J gene segments code for?

A

The portions of variable region of Ig chains

95
Q

How are the 2 segments in light chains ( the variable and the joining) brought together?

A

They are Brought together by one somatic recombination event

96
Q

Describe the process of Light chain gene rearrangement.

A

1 .Gene rearrangement of V and J occurs via one somatic recombination event to give an exon 2. The Gene is transcribed3. The remaining introns are removed during RNA splicing 4. The leader sequence is translated targeting protein for secretion or expression on the cell surface.5. Leader sequence is cleaved off post translation

97
Q

What is V (D) J recombination?

A

A process by which B cells randomly assemble immunoglobulin gene segments (ie v, d, j gene segments) to form the function variable region exon

98
Q

When does V (D) J recombination occur?

A

During early development of lymphocytes

99
Q

What does somatic DNA recombination do during Light chain gene rearrangement?

A

The gene segments are rearranged to form a complete variable region coding sequence

100
Q

Give one word or phrase to describe each step in the process of Light chain gene rearrangement.

A
  1. somatic DNA recombination2. Transcription3. Splicing4. Translation5. Cleaving
101
Q

Describe the process of Heavy chain gene rearrangement.

A
  1. Gene rearrangement of D J via a somatic recombination event 2. ANOTHER gene rearrangement occurs of V-DJ via a somatic recombination event to give a complete exon 3. The Gene is transcribed4. The remaining introns are removed during RNA splicing 5. The leader sequence is translated targeting protein for secretion or expression on the cell surface.6 . Leader sequence is cleaved off post translation
102
Q

What is a key difference between light and heavy chain rearrangement?

A

In light chain rearrangement there is only 1 gene rearrangement event (V-J joining)In HEAVY chain rearrangement there are TWO gene rearrangement events (V-J joining AND V-DJ joining)

103
Q

What controls the V(D)J recombination?

A

Controlled by non-encoding, conserved DNA sequences| Recombination Signal Sequences (RSS)

104
Q

What does a Complete functional rearrangement require?

A

One of each type of segment is joined in the correct order and in the correct transcriptional orientation

105
Q

Where can recombination only occur?

A

Recombination can only occur between one gene segment flanked by a 12 spaced RSS and another with a 23 spaced RSS.

106
Q

How Many types of RSS are there?

A

2:One with 23 base pair spacer One with a 12 base pair spacer

107
Q

Why do the number of segments in each Ig vary in the population?

A

Because humans are very polymorphic

108
Q

Approx how many heavy chain combinations are there?

A

V x D x J45 x 23 x 6=6000

109
Q

Approx how many kappa light chain combinations are there?

A

V x J35 x 5= 175

110
Q

Approx how many lambda light chain combinations are there?

A

V x J30 x 4= 120

111
Q

Approx how many light chain combinations are there IN TOTAL?

A

potential kappa + potential lambda| 175+120= 295

112
Q

Why are the number of potential light and heavy chains number very varied?

A

Because segment numbers are varied| Some combinations produce non-functional pseudogenes

113
Q

What is the third level of diversity called (after gremlin and combinatorial)?

A

Junctional diversity

114
Q

When does junctional diversity occur?

A

When selected gene segments have to be joined together

115
Q

Describe how junctional diversity is achieved

A
  1. RAG proteins cleave the DNA. 2. Nucleotides are added or subtracted to make a viable joint by TdT (terminal deoxynucelotidyl transferase).3. The position of the cut adds P nucleotides to the sequence, whilst the TDT adds N nucleotides.
116
Q

What does RAG stand for in RAG proteins?

A

Recombinase-activating genes 1 and 2

117
Q

What are RAG protein responsible for?

A

For cutting and cleaning DNA

118
Q

Is the process of achieving junctional diversity efficient?

A

No there’s a lot of wastage because in the process of deleting and adding nucleotides we can get frame shifts

119
Q

Name the 3 layers of diversity in T cells and antibodies?

A
  1. Germline2. Combinatorial3. Junctional
120
Q

What can genetic immunological disorders affect?

A
  1. Severe combined Immunodeficencies (T and B cell function)2. Deficiencies in antibody production3. Phagocytic disorders4. Complement deficiencies.
121
Q

Which fragments of antibodies have the same AFFINITY?

A

the Fab and F(ab’)2

122
Q

What hold together the 2 antiparallel beta pleated sheets in each immunoglobulin fold?

A

Disulphide bonds

123
Q

Which fragments of antibodies have different AVIDITY?

A

the Fab and F(ab’)2

124
Q

Gamma heavy chains make up which class of antibodies?

A

IgG

125
Q

Alpha heavy chains make up which class of antibodies?

A

IgA

126
Q

Mui heavy chains make up which class of antibodies?

A

IgM

127
Q

What does the Fc region determine?

A

The different classes of antibodies

128
Q

Delta heavy chains make up which class of antibodies?

A

IgD

129
Q

Exelon heavy chains make up which class of antibodies?

A

IgE

130
Q

What is the immunoglobulin fold?

A

A repeated similar domain found on both light and heavy chains

131
Q

What is considered the super family?

A

All molecules that contain the immunoglobulin folds

132
Q

When purifying preparations of antibodies, why is the ability to disrupt the interactions important?

A

The ability to disrupt the interactions is important when purifying preparations of antibody that have been generated in the lab which have research or therapeutic uses.
Antibody can be separated by other proteins and chemicals in a mixture by binding to antigen coated matrix, then eluted later by changing some on the conditions listed here.

133
Q

What happens in the primary or central lymphoid organs (bone marrow and thymus)

A

Where the b and T cells develop from progenitors and differentiate into naïve lymphocytes

134
Q

What happens after the naive lymphocytes differentiate in the primary/ central lymphoid organs

A

exit the primary lymphoid organs and recirculate between the secondary also called peripheral lymphoid organs (highlighted in green) via the blood where the mature but naive cells are looking to encounter their specific antigen.

135
Q

How many amino acids does the V segment of the light chain encode?

A

95-100

136
Q

How many residues does the G segment of the light chain encode?

A

Up to 30

137
Q

What are pseudogenes

A

Non functional segments, some have accumulated mutations which render them unable to encode functional molecules

138
Q

Why do pseudogenes occur at a relatively large frequency compared to many other gene type

A

Due to reduced evolutionary selection pressure

ODDR- immunology (host Defenses) (6 decks)

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