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Imperial Y2 - Integrative Cell Biology > Selkirk & Dionne - Immunology > Flashcards

Selkirk & Dionne - Immunology Flashcards

1
Q

Definition of an antigen, B-cell receptor and T-cell receptor?

A

Antigen: Any molecule that is recognized by the immune system as foreign, specifically by lymphocyte receptors - can be any type of molecule protein, carbohydrate, lipid, etc.

B cell receptors: antibodies/immunoglobulins that are membrane bound or soluble –> immunoglobulins that are membrane bound are receptors but can also be secreted

T cell receptors (TCR): Receptors that are solely membrane bound

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2
Q

Why study the immune system? Why is it important?

A
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3
Q

What are two major challenges facing people’s health related to the immune system?

A
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4
Q

What are some examples of different types of vaccines?

A

Different types of vaccines developed to counter infection

  1. Whole organism - killed/inactivated (eg heat/formaldehyde)
  2. Whole organism - live attenuated (passage/genetic alteration)
  3. Subunit (purified product)
  4. DNA/RNA (encodes selected protein antigen)

Both Whole organism vaccines were initially used and quite effective

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5
Q

Have vaccines been succesful at treating/reducing disease incidence?

A
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6
Q

What are the different physical barriers to infection? What are some examples of mechanical, chemical and microbiological methods employed by these barriers against infection?

A
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7
Q

What is the innate immune system?

A

Innate immunity – Cells and components of the immune system which act without prior exposure to the pathogen

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8
Q

What is the complement system and what is it’s cascade?

A

Complement – a cascade of proteolytic enzymes which promote inflammation and cytotoxicity/

Apart from recruting effector cells, complement can form a membrane attack complex which inserts in the membrane of microorganisms to eliminate them - important for the initiation of immunity

Inflammation is another effect of activating complement

Cascade

  1. Presence of bacterial cell surfaces will induce cleavages and activation of complement fragments.
  2. One complement fragment binds to bacterium whereas the other acts as a chemo-attractor for effector cells
  3. Complement receptor binds to bacterium with bound complement fragment
  4. Effector cells perform phagocytosis - killing the bacteria cell + Chemo-attract fragment attracts further effectors
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9
Q

What is inflammation? Outline the inflammatory response created when there is a cut in the skin

A
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10
Q

What are cytokines and chemokines?

A

Cytokine: secreted protein which changes the behavior/response of neighboring cells  think of them as short range hormones

Cytokines otherwise known as Interleukins (messages between leukocytes) – classified by numbers, e.g. IL-4, IL-5

Chemokine (specific cytokine) : Chemoattractant cytokine – attracts specific classes of cells

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11
Q

Differences between the innate and adaptive immune system?

A

Innate and adaptive immunity work in concert to control or eliminate pathogens

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12
Q

What does this graph show? What can we takeaway?

A

Red –> no immune response (infection grow exponentially)

Green –> Only innate immune system (intial response but lacks adaptive immunity to help clear pathogen)

Yellow –> innate and adaptive working properly

Primary (first) infection cleared by combination of innate and adaptive immunity

Innate immunity initiates first and is required to prime the adaptive immune response, whereas adaptive immunity required (generally) for pathogen clearance

Both are necessary and work together

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13
Q

What are the receptors expressed by macrophages called and what type of molecules do they recognize?

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14
Q

What are Toll-like receptors?

A
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15
Q

What is the adaptive immunity?

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16
Q

Outline the general life cycle of B lymphocytes?

A
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17
Q

What is Haematopoiesis and what organs are responsible for carry out this role?

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18
Q

What is the composition of immune cells in the blood?

A
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19
Q

What are NK cells?

A

NK cells - specific type of lymphocyte known as a natural killer cell – even though it is a lymphocyte it is part of the innate immune system

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20
Q

Outline the different lineages that a Haematopoietic stem cells gives rise to?

A

Haematopoietic give rise to different lineages

a) Lymphoid Lineage
b) myeloid lineage

Lymphoid - Differentiation to B-cells (plasma or memory cells) or NK or T cells

Myeloid - includes White blood cells and red blood cells

a) Erythroid Progenitor gives rise to
- Erythrocyte – Red blood cells

Platelets - fragments of cells involved in blood clotting

b) Granulocyte-macrophage progenitor give rise to
- Mast cells
- Neutrophil, Eosinophil and basophil
- Macrophage and dendritic cell

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21
Q

From a Haematopoietic stem cell, what determines the cell’s fate?

A

Lineage differentiation and development is controlled by transcription factors

Expression of these transcription factors is influenced by the environment - e.g. cytokines mediates the way in which the precursor cells differentiate

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22
Q

What are small lymphocytes, plasma cells, dendritic cells and mast cells?

A
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23
Q

What are dendritic cells?

A
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24
Q

What are the roles of NK cells, Neutrophils, Monocytes and Macrophages?

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25
Q

Macrophages Visualization?

A
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26
Q

What does opsonisation mean?

A

Opsonization is coating a pathogen with a molecule that facilitates its uptake, e.g. antibodies and complement

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27
Q

How do macrophages normally respond to the presence of pathogens (2 things)?

A
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28
Q

Outline the role of Neutrophils in response to infection

A
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29
Q

What are eosinphils, basophils, Megakaryocyte and Erythrocytes?

A
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30
Q

What is the primary/central lymphoid tissue?

A

Primary (or central) lymphoid tissues - where lymphocytes develop (produced, mature and selected), this happens in…

Bone marrow - Naïve B-cells released by Bone marrow + T-cells start in bone marrow but move to the Thymus

Thymus – bi-lobed organ at the top of the chest - development of T-cells

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31
Q

What are the secondary/peripheral lymphoid tissues?

A

Secondary (or peripheral) lymphoid tissues - where adaptive immune responses initiated and lymphocytes maintained - lymphocytes are activated + maintained in the secondary tissues

Where are these secondary lymphoid tissues found?

  1. Lymph nodes - Located all-over but specifically at sites of potential infection – drain mucosal sites
  2. Spleen
  3. Mucosa-associated lymphoid tissue (MALT)
    - Peyer’s patches (Gut)
    - Tonsils
    - Appendix
    - BALT – Bronchus (lungs)
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32
Q

How are immune cells circulated through the body?

A
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33
Q

Role of the primary lymphnoid organs?

A
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34
Q

Outline the development of T-cells from the bone marrow to their presence in secondary lymphoid tissues

A
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35
Q

Outline the cellular organisation of the thymus

A

Cellular organization of the thymus

Bi-lobed organ, lying over heart and major blood vessels

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36
Q

What is the trend in T-cell production as we age?

A
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37
Q

What does Cluster of Differentiation (CD) refer to? What is it used for?

A
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38
Q

Outline the first stage of development/maturation of T-cells in the thymus, whereby T-cells form ‘double-negative’ thymocytes.

A
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39
Q

After creating double negative t-cells in the thymus, how do we end up with mature t-cells?

A

Research how we go from double negative to double positive

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40
Q

Where in the thymus do we get positive and negative selection of thymocytes? Why are these processes important?

A
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41
Q

How is +ive selection in the thymus thought to happen?

A

CD8 or CD4 selection?

Instructive model, signals received through CD4 shut off the CD8 gene and cause the cell to differentiate into a Th, while signals received through CD8 shut off CD4 expression and induce Tc differentiation. According to the instructive model, the cell could go equally easily down either pathway and the first strong enough signal decides its fate.

Stochastic model, the cell is somehow randomly committed to becoming either a Tc or a Th before positive selection. If it gets the correct signal during positive selection, it proceeds down its predetermined pathway; if it doesn’t get signaled through the correct co-receptor, it dies.

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42
Q

How is -ive selection thought to happen in the thymus?

A
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43
Q

Provide a general summary of T-cell maturation and differentiation in the thymus

A
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44
Q

Once B-cells and T-cells have matured and entered circulation, where do they go?

A
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45
Q

What is the general structure of a lymph node?

A
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46
Q

If a dendritic cell picks up an antigen in a peripherical tissue (site of infection), what does it do next?

A
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47
Q

How do Naive T and B lymphocytes enter into the lymph node?

A
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48
Q

How does activation of naive lymphocytes in the lymph node occur?

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49
Q

Outline the proces of B cell activation via specialised Follicular Dendritic Cells

A
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50
Q

How do lymphocytes cirulate through the body?

A
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51
Q

What is the structure and role of the spleen?

A
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52
Q

Where are secondary lymphoid tissues normally found?

A
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53
Q

What are Peyer’s patches (GALT)?

A
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54
Q

How could you divide up a immune response in accordance to time since the begining of infection?

A
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55
Q

What does the immediate immune response entail (0-4 hours)?

A
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56
Q

What does the early induced response entail (4-96 hours)?

A
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57
Q

What does the adaptive immune response (late) entail (>96 hours)?

A
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58
Q

What key event has to take place to intiate the innate immune response?

A
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59
Q

What are the four different mechanisms by which innate immune system detects foreign organisms?

A
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60
Q

What makes a good PAMP (pathogen associated molecular patterns)?

A
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61
Q

What are some bacterial PAMP examples? What PAMPs are common in gram +ive, -ive and mycobacteria?

A
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62
Q

What fungal PAMPs are detected by the innate immune system?

A
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63
Q

What are the two different broad categories of PPRs (pattern recognition receptors) and what role does each type play?

A
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64
Q

What are Phagocytic receptors (PRRs) and what do they do?

A
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65
Q

What are signalling receptors (PRRs) and what do they do?

A
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66
Q

Provide three examples of Signalling PRR’s in animals + what type of cells usually express them?

A
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67
Q

What is the structure of Toll-like receptors?

A
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68
Q

What two feature characterize TLRs?

A
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69
Q

Of TLRs 1-9, what is their localization in the cell? What are the consequences of receptor activation?

A
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70
Q

What proteins do cell surface TLRs normally signal via?

A
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71
Q

Role of NFκB in TLR’s downstream signalling?

A
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72
Q

How do the innate and adaptive immune system recognize the presence of viruses?

A
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73
Q

Role of endosomal TLRs in viral detection & response (innate immune system)?

A
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74
Q

Outline how endosomal detection of viruses via TLRs takes place?

A
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75
Q

Why do antiviral TLR’s depend on recognising endosomal nucleic acid?

A

Viruses are detected as nucleic acids in the wrong place because they’re otherwise indistinguishable from host –> create from host proteins

Futhermore, extracellular animal viruses are basically never in the form of exposed nucleic acids

So one needs to ‘catch’ the virsu when it uncoats in the endosome

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76
Q

Outline the activation of IRF3, in response to endosomal TLR activation

A

Endosomal pathways activate a second transcription factor, IRF3

IRF3 is key transcription factor in engaging the antiviral response in mammals

Endosomal (primarily) TLR activation triggers a signalling pathway that results in phosphorylation of IRF3 using TBK-1 (activated by TRIF), facilitating dimerization and nuclear localisation of IRF-3, where it drives transcription of its target genes (but not completely exclusive to endosomal pathways)

Key target is type 1 interferons (specific class of antiviral cytokines)

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77
Q

What proinflammatory cytokines and chemokines are produced in response to TLR-NFκB activation?

A
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78
Q

What is the mechanism behind controlling IL-1 expression?

A
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79
Q

Why is the presence of cytosolic/intracellular bacteria a problem?

A
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80
Q

How are cytosolic bacteria recognized by the host cell?

A
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81
Q

Explain how NLRs help create the inflammasome complex and how that drives production of IL-1β and how it fits into the bigger picture of TLR/IL-1R activation?

A
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82
Q

What are the two inputs required for IL-1 amplification?

A
  1. Extracellular signal (microbes) –> TLR, IL-1R and TNFR –> priming step producing pro-IL-1 & inactive NLRP3
  2. Intracellular signal (microbes, ROS production, K+ efflux) –> inflammasome activation
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83
Q

How does viral detection in the cytosol take place? What are the three classes of sensors?

A
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84
Q

Outline the different segments of a RIG-I like receptor? What downstream targets does it act on?

A
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85
Q

What are the specific viral RNA structures that are recognized?

A
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86
Q

What effect does TNF (cytokine) have? (secreted by macrophages and DCs)

A
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87
Q

What is the main target for Type-1 Interferon?

A
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88
Q

What cells are responsible for the production of Ifnα, Ifnβ and Ifnλ?

A
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89
Q

What are the consequences of Type-1 interferons?

A
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90
Q

Why do T cells that have not recognise any antigens leave the lymph node? Are there still other sites of antigen presentation?

A

Lymphocytes are constantly being circulated why?

Because many of them will not get activated in their lifetime so to keep the system “unclogged” and moving there is constant circulation via the circulation and lymphatic system

Lymph node is suited for antigen presentation but if they are not activated they are simply re-circulated

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91
Q

How do type-1 interferons enhance expression of tumour-associated surface antigens?

A

Ordinary Transcriptional mechanism - drives Stat TF heterodimer into the nucleus to drive expression of tumour associated antigens

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92
Q

Do B cells enter the lymph nodes using the same mechanism as T cells?

A

Yes, same mechanism but they tend migrate to a different site in the lymph node

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93
Q

If a target is too big to phagocytose, what can Eosinophil and Basophils do?

A

Eosinophil and Basophil don’t typically perform phagocytosis - Macrophages are the professionals

But….

If the target is too big there are several mechanisms different effector mechanisms

  • Eosinophil binds to foreign invader and releases the contents of their secretory granules
  • Neutrophils can release extra-cellular traps
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94
Q

Difference between Phagocytosis and endocytosis?

A

Size of molecule taken up – phagocytosis is in relation to larger entities (cells) whereas endocytosis is normally associated to smaller molecules

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95
Q

How is heat produced as a side effect of inflammation?

A

Heat production due to circulatory (warmer) loss into tissues - heating up the tissue

Alternatively…

Fever - Systemic inflammatory heat production - cytokines signalling to the hypothalamus to set the body temperature higher –> heat production via brown fat cells

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96
Q

What happens to complement C3 after it gets activated by random hydrolysis but there is no pathogen nearby to bind to?

A

C3 has a short half-life if cleaved via random hydrolysis

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97
Q

Can neutrophils recognise 3Cb via a 3Cr receptor and clear opsonized bacteria or is it just the role of Macrophages?

A

Primarily Macrophage role

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98
Q

Do cells express all 10 TLRs at once? Does it depend on the cell type to some extent?

A

TLR is cell type dependant

But macrophages are critical for surveillance will express many/ if not all 10 TLRs at once

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99
Q

Is IL-1B mainly produced by immune cells?

A

Yes IL-1B receptors are widely expressed but the production is mainly confined to immune cells

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100
Q

What is the complement system?

A
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101
Q

Does the complement system require antibodies to function?

A
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102
Q

What are the names of the complement proteins in the complement system?

A

Complement components have a defined nomenclature, from the days when they were named as proteins from serum

C1-C9 are classical complement components

B, D, H, I are regulatory factors that also play key roles

When complement factors are cleaved, the products get a letter appended: so C3 is cleaved to C3a and C3b

Complexes are often described by putting these names together: so C3bBb is a complex of a fragment of C3 and a fragment of B

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103
Q

Which complement pathway is the most common in the complement system?

A

The “alternative” complement pathway

The most general/common complement pathway is called the alternative complement pathway - central protein in this pathway is C3

C3 is ordinarily present at high concentrations in serum

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104
Q

What reaction does C3 undergo at a small frequency? Outline the mechanism

A
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105
Q

What role does C3 cleavage play in the alternate complement pathway?

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106
Q

Where in the C3 protein does the thioester bond hydrolysis take place (which two residues)?

A
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107
Q

After activation of 3C in presence of a generic bacterium, what happens?

A
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108
Q

When we get amplification of 3CBb on the surface of a bacterium, what does this refer to (process)?

A
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109
Q

What higher order complexes form in the alternate complement pathway?

A
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110
Q

What are the respective functions of C5a and C5b?

A
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111
Q

Outline the mechanism by which membrane attack complex (MAC) is formed?

A
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112
Q

Summarize the alternative complement pathway (all the different mini-pathways)

A
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113
Q

What is the classical complement pathway?

A

The “classical” complement pathway: a role for antibody

The “alternative” pathway (initiated by spontaneous C3 hydrolysis) drives 80-90% of successful complement activation

The “classical” pathway affords a mechanism for complement to be activated by specific antibodies  it helps to recruit complement to the bacteria

  • Explains why previous exposure to bacteria increases the efficiency of the mechanism
  • An example of adaptive immunity using innate immune mechanisms to promote microbial killing – Recurring theme the adaptive immune system uses innate mechanism as an effector to kill foreign invaders
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114
Q

What antibody gets involved in the classical complement pathway?

A
115
Q

Classical complement pathway - What Complement protein binds to the antibody + consequence of binding?

A
116
Q

Classical complement pathway - After C1 binding, what is the next player(s) to get involved?

A
117
Q

Classical complement pathway - Upon C4bC2a binding, what happens next?

Hint - What other pathway is recruited?

A
118
Q

How does the complement pathway facilitate phagocytosis by macrophages/recruiting innate-immune system?

A
119
Q

Does the classical complement pathway only rely on antibodies?

A

The mechanisms of the “classical” pathway generalises to other circulating receptors (not only antibodies)

  • The best studied example of this is the MBL (mannose-binding lectin) pathway

MBL binds mannose (on the surface of some bacteria, fungi, protozoa, but not animal cells), recruits MASP1 and MASP2 (MBL-associated serine proteases; analogous to C1r and C1s)

MASP1/2 cleave and activate C4, then C2, as in the classical pathway – feeding back into the C3 alternative pathway

These mechanism are important but are less frequently used for activating complement

120
Q

What is the key central protein in the complement pathway?

A
121
Q

Why is it important to control the complement pathway?

A
122
Q

Outline the role of regulatory factors: H, I, P, CD46 in controlling the complement pathway

A
123
Q

How do we know complement is important?

A
  • We can examine people that lack complete functioning complement system
  • Several bacteria have developed mechanisms to avoid it
124
Q

What are the consequences of complement deficiencies?

A

1. People who lack C1q or C2 (specific to classical pathway) have autoimmune disease – potentially due to failure to clear complexes of cell debris with antibodies?

2. People who lack C3 are susceptible to infections with many pyogenic bacteria, mostly gram-negative but also some gram-positive

  1. People who lack MAC components (C5-C9) are similar, slightly weaker phenotype, particularly susceptible to Neisseria meningitidis

Shows us that phagocytosis and MAC can compensate for each other when one is lacking but this is less likely for Neisseria meningitidis infection

125
Q

How do bacteria evade complement-mediated killing?

A

Large number of mechanisms to evade complement

  1. Polysaccharide capsules
  2. Inhibition of antibody binding – prevent classical pathway
  3. Mimickry of host cell surfaces
  4. Hiding inside host cells
126
Q

How do bacterial capsule impair complement?

A

Polysaccharide Capsule is common is bacteria that can cause blood infections

  1. Capsule (dense) excludes efficient diffusion of C3 to bacterial surface—so that activated C3 is mostly exposed to capsule - Consequently, C5 convertase is bound at capsule surface, efficiency of membrane attack is severely diminished
  2. Diffusion within the capsule is inefficient—so that the effective distance between activated C3 convertase complexes is high, reducing the effectiveness of amplification - Diffusion barrier
  3. Capsule also inhibits phagocytosis, both by increasing the effective size of the bacterium and by making it hard to effectively bind its surface (main) - mucus like capsule – hydrated Polysaccharide
127
Q

Are capsules still a targetted by complement and antibodies?

A

For many bacteria (e.g. Streptococcus pneumoniae, Haemophilus influenzae) serovars are defined by antibody specificity for specific capsule compositions

  • Capsular polysaccharides are recognized as non-host (because there are antibodies)
  • Capsular polysaccharides are diverse, even within very tight bacterial groupings indicating a selective pressure….

meaning that antibody binding to capsule is still unfavourable – mostly likely indicating that complement activation at the capsule still hurts the bacteria but not as effective

128
Q

How does Streptococcus pyogenes mimics the host - avoiding the immune system?

A
129
Q

How does Neisseria meningitidis uses mimickry and interference to avoid the immune system?

A
130
Q

How does Staphylococcus adopt mutliple mechanisms to avoid the immune system?

A
131
Q

What are the two principal ways that Antibodies combat infection/effector mechanisms?

A
132
Q

Whart is the structure/components of a generic immunoglobulin/antibody molecule?

A

Basic structure of antibodies is a 4 chain unit – 2 identical H chains (5 types) and 2 identical L chains (2 types) –> a single lymphocyte (plasma cell) produces one type of antibody

Each chain unit has a variables domain and constant domain(s) - Generally, 3 C domains in H chain, some have 4

Note - Heavy chain type defines Antibody Class/sub-class – Why? The heavy chain interacts with cells in different ways

Each immunoglobulin (Ig) domain is about 110 amino acids – stabilized by S-S bond + 4 chain units held together by S-S bonds

133
Q

Are anitbody molecule bifunctional?

A

Antibodies are bifunctional molecules, mediating

a) antigen binding – Variable domains
b) Various biological activities such as complement fixation, cell binding, crossing tissues e.g. placenta, mucosal epithelium - Constant domains

134
Q

What did papain and pepsin digestion of antibodies reveal about their function?

A
135
Q

What specific region in VL and VH provides specificity in binding?

A
136
Q

When the variable domains are folded, what happens to the CDR regions?

A
137
Q

What type of interactions are formed between CDRs and the antigen?

A
138
Q

Do protein antigens contain multiple epitopes? How are these epitopes categorized?

A
139
Q

What is meant by polyclonal antibodies and monoclonal antibodies?

A

Polyclonal - antibodies which recognize different epitopes

Serum antiboides are polyclonal - The normal response to infection/antigen exposure is polyclonal since antibodies from multiple cells/clones of cells have been produced each with own binding specificity and binding affinity

Monoclonal - antibodies made by a single plasma cell are IDENTICAL in sequence – bind one epitope with specific affinity

The precise specificity of Monoclonal Abs gives multiple diagnostic/therapeutic uses - targeting drugs to particular sites in the body

140
Q

Originally, how were monoclonal antibodies produced?

A

Originally monoclonal antibodies were created by

  1. Injecting antigen into mice
  2. Removing spleen plasma cells
  3. Hybridize with myeloma cells to form hybridomas (immortalize)
  4. Dilute the solution so that when plated into a well you have a single cell per well - isolate monoclonal antibodies

Nowadays, it easier to engineer them genetically

141
Q

When using antibodies for treatment of diseases, what should we keep in mind?

A
142
Q

What are the different immunoglobulin classes?

A
143
Q

Does each antibody isotype has specialized functions?

A
144
Q

What happens during B cell activation once it has been presented a new foreign antigen?

A
145
Q

Outline the changes that take place on the antibody level during a primary and secondary infection

A
146
Q

What is the general structure of IgG subclasses (1-4)?

A
147
Q

Examine the table of that highlights similarities and differences between the IgG subclasses

A
148
Q

What is the structure of the secreted pentameric form of IgM?

A
149
Q

Where is IgA normally found and what form is it in?

A
150
Q

Outline the process by which dimeric IgA gets produced and secreted into the mucosal sites?

A
151
Q

Outline how cross-linking of IgE antibodies on basophils or mast cells causes degranulation

A
152
Q

Do Fc receptors have different structures and cellular distributions?

A
153
Q

What are the different responses when a Fc receptor binds to a antibody bound to pathogens/antigens?

A
154
Q

What was the theory presented by Dreyer and Bennetts model (1965)?

A
  • V-region and C-region encoded by separate genes which create one protein
  • Went against one gene = one polypeptide dogma
  • Hundreds or thousands of V genes and single copy C genes
  • No direct evidence, without precedent in biology
155
Q

Why did Tonegawa and Hozumi (1976) win a Nobel Prize (generation of immunoglobulin diversity)?

A

Tonegawa and Hozumi (1976) - 1987 Nobel Prize

Used restriction endonucleases to prove gene rearrangement to provide wide degree of diversity observed

156
Q

What chromosome are the genes for antibody heavy and light chains found on?

A
157
Q

How many gene segments are present for heavy and light chain variable regions?

A

DNA sequence encoding a V region is assembled from 2 or 3 gene segments

Light chain V region encoded by V (variable) and J (junctional) gene segments

λ chain has roughly 30 variable gene segments and 4 junctional gene segments which are arranged in tandem with constant regions –> L is the leader peptide to acts as a signal peptide

κ chain has roughly 35 variable gene segments, 5 junctional gene segments and one constant gene segment

Heavy chain V region encoded by V, D (diversity) and J gene segments

Locus contains 40 variable gene segments, 6 junctional gene segments, 9 constant gene segments and 23 diversity gene segments

  • VJ (light chain) or VDJ (heavy chain) gene segments must first be selected and assembled to produce an exon that can be transcribed
  • Gene segments for Constant regions (C) and Leader peptide (L) are ready to be transcribed
158
Q

Explain how recombination of variables regions in both heavy and light chains takes place and which gene segements are responsible for CDR1-3?

A
159
Q

How does recombination of gene segements create combinatorial diversity?

A
160
Q

What allows the recombination of the V, D and J segements to take place?

A
161
Q

What enzymes are responsible for the recombination that gives rise to combinatorial diversity? Outline a general mechanism of action?

A
162
Q

How does the 12/23 rule prevent ‘D’ gene segment from being claved out?

A

‘D’ gene segment is flanked by nucleotide spacers that are 12 bases long –> needs to be matched with a 23 nucleotide spacer from VH and JH to uphold 12/23 rule

163
Q

What is junctional diversity?

A

Junctional diversity created by addition and subtraction of nucleotides at the joints between gene segments

164
Q

Outline how junctional diversity arises via the creation of new palindromic nucleotides and the addition of nucleotides?

A
165
Q

What is somatic hypermutation and how does it lead to even more diversity?

A
166
Q

Explain how somatic hypermutation allows for the selection of B cells with the highest affinity antibodies?

A

Process is called - AFFINITY MATURATION

If mutation is in antigen binding site (CDR) and increases affinity of binding, B cells with high affinity receptors preferentially selected to mature to plasma cells

Illustrated experiment shows mutations in CDRs following immunisation - increase in mutations across all CDR regions the after 2 week following 1o immunization

Somatic mutation increases number of antigen specificities to over 109 variants – once increased variation is created the antibodies with highest affinity are selected - extremely rapid evolution to keep pace with pathogen antigenic variation

How? Highest affinity antibody on B-cell – more likely to bind/be selected against antigen during maturation

167
Q

Once we have produced our Variable regions, how do we get our constant domain in our exon coding for our chain unit?

A
168
Q

Using IgM and IgD as an example, explain how the cell adds/joins the constant domains to the variable domains?

A
169
Q

Explain how a B cell produces immunoglobulin of a single specificity given that we have two allelic copies of the H and L chains (paternal and maternal)?

A
170
Q

What ‘general’ process governs whether the antibody is membrane bound or secreted? When do B cells normally express MB and secreted antibodies?

A
171
Q

What is the difference between membrane bound and secreted IgM?

A
172
Q

What does antibody classs switching refer to?

A
173
Q

In simple terms, what happens duroing class switching on the genomic level and what governs which class is produced?

A
174
Q

Explain how the process of class switching takes place on the genomic level?

Hint - switch sequences

A
175
Q

Summary of changes in immunoglobulin genes during B cell development and maturation

A
176
Q

In the context of B cell development when does combinatorial & junctional diversity + somatic hypermutations take place?

A

Note - high rate of proliferation of B-cells is coupled with somatic hypermutation – allows for affinity maturation – Check

177
Q

What gets presented on the self-surface as an antigen?

A

Anything in abundance within the cell can be screened and be presented on the surface as an antigen - antigen presenting cells

Intracellularly, there is no way to distinguish any foreign or self-antigen –> everything is presented

178
Q

In the cleavage of C3, what happens if c3b reacts with water instead of hydroxyl or amine group?

A

Binding to hydroxyl from water results in conformational change allowing for factor B binding to form active complex C3(H2O)Bb in solution but this is less stable in comparison to being bound to a microbial surface

Most spontaneous C3 activation is non-productive most of the time - requires binding to microbial surface hydroxyl or amine to lead to productive amplification

179
Q

How does factor D activate Bb?

A

Factor D is a serine protease - cleaves B and active serine protease Bb remains bound to C3

180
Q

What is an example of indirect detection of microbes?

A

Any detection of infection that does not rely on direct detection of molecules (PAMPS) produced by microbes themselves, examples include…

DAMP detection – danger signals from endogenous cells

Damage detection

181
Q

Why do we need multiple B-cell receptors to cross-link to their antigen to produce a response?

A

Basically, multiple B cell receptors required to bind to their target in order to induce a response - pass threshold to induce signal transduction pathway

182
Q

What is the function of the secretory component that is left bound on IgA when it is secreted?

A

No concrete answer - potentially provides protection against enzymatic degradation and stabilization of the dimeric molecule

183
Q

What determines whether Fc region of IgG binds to complement C1 complex or to Fc receptors on e.g. myeloid cells? Is it a stochastic event?

A

Yes, it is a stochastic event but the proportion of receptors at a particular target will influence the likelihood of binding

184
Q

Why is the expression of Fc receptors lower in lymphoid cells than myeloids?

A

Purpose of Fc receptor - convert antibody-antigen binding into an effector mechanism

Since myeloid cells carry out most of the effector mechanism this accounts for high expression of antibody receptor (Fc receptor)

But Lymphoid cells do perform some effector functions – NK cells

185
Q

Does AID convert C to U on ssDNA or RNA?

A

ssDNA during strand separation during transcription

186
Q

What is the role of booster vaccine dose?

A

Antibody level - After the exposure to antigen we get antibody production which remains in circulation but eventually due to their half-life they will naturally decline

But…

Memory Cells – Booster shot amplifies the number of memory cells by several orders of magnitude - allows for the quick response and production of plasma cells upon re-exposure

Likely also produces a further round of hypermutation and affinity maturation increasing the antibodies affinity

187
Q

How are the high affinity antibodies selected for during Affinity maturation?

A

Through Equilibrium – antigen in limited supply, hence the cell with the highest affinity antibody is more likely to bind

188
Q

Is the J chain part of the immunoglobulin or is it a distinct peptide that associate with it?

A

J chain is a distinct chain (different gene) but it is required for multimeric assembly in ER

189
Q

General structure of TCR? What is their role?

A
190
Q

What structure does the T cell receptor resemble?

A
191
Q

How is TCR diversity created?

A
192
Q

Similarities and differences between the process of diversity generation between TCR and antibodies?

A
193
Q

What are the different components of the T-cell receptor?

A
194
Q

Apart from the TCR complex, what other co-receptors are found on T-cells? What role do they play?

A
195
Q

What MHC class do CD4 and CD8 recognize respectively?

A
196
Q

What are the different roles that CD4 and CD8 T-cells perform?

A
197
Q

Apart from the antigen specific signal, what other co-stimulatory signals are required for T-cell activation?

A
198
Q

Are both main and co-stimulatory signals required to activate T-cells? Related to this, why do self-reactive T-cells that escape negative selection not become activated?

A
199
Q

When a T-cell and a DC interact with eachother, what ‘structure’ is formed and how is it organised?

A
200
Q

Explain the mechanism T-Cell signalling upon binding to MHC

A
201
Q

Do both naive and activated effector T-cells require a co-stimulatory signal?

A
202
Q

What role(s) do Effector Helper T cells (Th Cells) normally perform?

A
203
Q

What are the different functional classes of CD4+ T cells? What factor determines their differentiation and what role do the following T-cells perform…

a) Th1
b) Th17
c) Th2
d) Tfh
e) Treg

A
204
Q

What role do Cytotoxic T cells normally perform? What factors helps to regulate the strength of its response?

A
205
Q

What role do γδ T cells perform? Do they need any co-receptors?

A
206
Q

Compare αβ and γδ T cells

  1. Site of development
  2. Gene diversity/receptor diversity
  3. Co-receptors
  4. Target antigens
  5. Region within the body with highest conc.
  6. Activation
A
207
Q

Is γδ receptor expression (V gene segments) is tissue-specific?

A
208
Q

Example - What do Vγ9:Vδ2 T cells (γδ) recognize?

A

Phosphoantigens - Phosphorylated intermediates of isoprenoid biosynthetic pathway – e.g. HMBPP made by bacteria & parasites i.e. foreign antigen

  1. HMBPP binds to CD277 (butyrophylin-3A1 (BTN3A1)) on tissues cells (structurally similar to B7 protein)
  2. This is then presented and recognized by Vγ9:Vδ2 T cell receptor
  3. γδ cell activation
    - Receptors of innate immunity
209
Q

What is CD1?

Hint - Type of Antigen presenting molecule

A
210
Q

Example of CD1 and γδ recognition in action

A
211
Q

Outline the structure of MHC class I and class II molecules?

A
212
Q

What accessory molecules allow direct binding of T cells to class II and class I MHC molecules?

A
213
Q

How are peptides being presented bound to MHC 1 and MHC 2?

A
214
Q

Compare the peptide binding of class I and class II MHC molecules

A
215
Q

How do peptides from antigens become processed and displayed in the MHC molecule at the surface of the cell?

A

Peptides destined for presentation by class II and class I mols come respectively from external (extracellular) or internal sources (intracellular)

216
Q

In the MHC class I presentation pathway, what happens to the proteasome complex upon infection?

A
217
Q

In the MHC Class I Pathway, how are Cytosolic proteins degraded in proteasome and transported into ER?

A
218
Q

Outline the process by which peptides are loaded onto the MHC Class I - Dig deep goggins style lmao

A
219
Q

How does peptide trimming of peptides on MHC Class 1 molecules found in the ER?

A
220
Q

In simple terms, how are peptides loaded onto MHC class II molecules?

A
221
Q

Give a detailed explanation of peptide loading onto MHC class II molecules?

A
222
Q

Can MHC class I present external antigens? If so, how does this happen?

A
223
Q

Once MHC displays antigen on the cell surface, can they now be recognized by T-cells?

A
224
Q

Outline the peptide-MHC:T cell receptor complex upon T cell receptor binding?

A
225
Q

How are MHC class I and II distributed across the cells in our body?

A
226
Q

Are there different types of MHC Class I or Class II molecules?

A
227
Q

Explain how MHC class I, II and III genes are organised

A
228
Q

Are MHC genes highly polymorphic? What decides the MHC happlotype of an individual?

A
229
Q

Where does the variation between MHC allotypes occur?

A
230
Q

Do MHC class I and II peptides have a peptide binding motif’s?

A
231
Q

What is MHC restriction?

A
232
Q

Do infectious diseases have a selective pressure on MHC diversity?

A

YEAHHH buddy

233
Q

How are new MHC alleles created?

A
234
Q

What are cytokines? What function do they play and how can they act on target cells?

A
235
Q

Do most cytokines exhibit autocrine, paracrine and endocrine activity?

A
236
Q

Do cytokines exhibit pleiotropic effects?

A
237
Q

In the context of cytokines, what does redundant, synergistic or antagonistic refer to?

A
238
Q

What are the 5 structurally distinct cytokine families?

A
239
Q

What function do Haematopoietic cytokines play?

A
240
Q

Explain the role of IL-2 in T-cell expansion/proliferation

A
241
Q

Explain the mechanism of IL-2 in Proliferation and differentiation of activated T cells

A
242
Q

How do TFH cells aid in the expansion of antigen-activated B cells in lymph nodes using cytokines?

A
243
Q

Do cytokines from TH cells regulate B cell Ig class switching?

A
244
Q

Do cytokine receptor families common features

  1. Class I
  2. Class II
  3. IL-1 family
  4. TNF receptor
  5. Chemokine receptors
A
245
Q

What commonalities do Class I cytokine receptor subfamilies have?

  1. GM-CSF subfamily
  2. IL-6 subfamily
  3. IL-2 subfamily
A
246
Q

How does sharing signalling subunit helps to explain redundancy of action and antagonism (competition) between cytokines in subfamily?

A
247
Q

Outline the general model of signal transduction mediated by most class I (haematopoietin) and class II (interferon) cytokine receptors? How is this pathway controlled?

A
248
Q

Do all Class I and Class II cytokine receptors have the same JAK/STAT signal transducers?

A

NAHHHHH m8

249
Q

What role does the cytokine environment play in the activation and development CD4+ T cells?

A
250
Q

How does the initial cytokine environment come about to manipulate T-cells activation and development?

A

Potential factors

  1. Produced locally by lymphoid follicles
  2. Innate response to microbes
    e. g. Bacteria have specific PAMPs that induce IL-12 and IFN-g
    e. g. Parasitic worm have specific PAMPs that induce IL-4 production or damage to epithelial cells leading to IL-4 release
251
Q

Using two examples (Viruses/Bacteira + Worms), explain how the presence of specific pathogens manipulates the cytokine environment?

A
252
Q

What are the two main factors to consider when it comes to the cytokine environment present?

A

Two main factors to consider

  1. Innate immunity (response to specific pathogens) primes and guides adaptive immunity  e.g. Influencing the T-cell response
  2. Epithelial cells also act as initial source of polarizing cytokine
253
Q

Outline how TCR and cytokine receptor activation influence production of Th1 and Th2-promoting transcription factors resulting in T-cell differentiation?

A
254
Q

What cytokines are produced by Th1 cells and what effect do they have?

A
255
Q

What cytokines are produced by Th2 cells and what effect do they have?

A
256
Q

Summary - What are TH1 and Th2 cells used for in the body? Under what circumstance are they normally expressed?

A
257
Q

Do CD4+ T cells and CD8+ T cells have secrete different cytokine profiles?

A

YEAHHHHHH BUDDYYYYY

258
Q

What are the two types of Cytotoxic Lymphoid cells?

A
259
Q

How do virally infected cells induce NK cell cytotoxic activity?

A
260
Q

Apart from being cytotoxic, how do NK cells activate macrophages cytotoxic activity?

A
261
Q

How does antigen recognition in NK cells work? How does it know which cell to attack?

A
262
Q

Do NK cells express a diverse range of activating & inhibitory receptors? Provide example

A
263
Q

Provide an example for NK cells being activated by the innate immune system and the adaptive immune system

A
264
Q

Outline the general mechanism by which CD8 T-cells and Nk cells induce apoptosis of a target cell

A
265
Q

Can a single Tc and NK cells kill multiple targets?

A

Yes but….

Reset time - Killing of multiple cells requires re-synthesis of granules with lytic contents

266
Q

Explain the importance of perforin for NK/Tc cell induced apoptosis and how the mechanism works

A
267
Q

Outline the structure of perforin monomer and how the different regions aid in the formation of the perforin pore

A
268
Q

What does the attached image show us (Note - CD8 T-cell in action)

A
269
Q

What are granzymes?

A
270
Q

What is one key target of Granzyme A?

A
271
Q

How does granzyme B mimics caspases in order to induce apoptosis?

A
272
Q

What is the main difference between cytotoxicity induced by myeloid cells and lymphoid cells?

A
273
Q

What different modes of cytotoxicity are exhibited by Macrophages and neutrophils?

A
274
Q

Explain the mechanism by which oxidative burst is used by neutrophils and macrophages to induce apoptosis and why this may result in death of the myeloid cell during the process?

A
275
Q

How are defensins (oxygen-independant killing) are used by myeloid cells to inducing apoptosis?

A
276
Q

How to nuetrophils induced cytotoxicity of a pathogen if it’s too big too Phagocytose?

Hint- NETs

A
277
Q

How does Nitric oxide (oxygen dependant) induce toxicity and how is it produced?

A
278
Q

How are the cytotoxic granules in Eosinophils different?

A
279
Q

Takeaway message about Myeloid and lymphoid cell cytotoxicity?

A
  1. There is significant redundancy in methods of cytotoxicity in myeloid and lymphoid cells - covers as many bases/situations as possible
  2. Lymphoid cells and myeloid cells have different methods of inducing cytotoxicity
  3. Lymphoid cells can be recycled whereas myeloid cells can not
280
Q

During affinity maturation of antibodies, where do the mutations in the heavy chain go to?

A

Mechanism by which AID targets the CDR (hypervariable region)

281
Q

Can anergic T cells become active again?

A

Yes, they can be active once entered into an anergic state

282
Q

For a particular cytokine that has more than 1 effects on e.g. B cell, is it due to the binding to different isotypes of receptor?

A

Possible binding to different isotypes but it is likely that there are other signalling components at play

283
Q

What is the missing-self hypothesis and where does it comes form? (Nk cells)

A

MHC I used by TCR to recognize self-cells - different class I MHC isotype is the cause of organ transplant rejection

MHC I represent your personal immunological signal

Missing self-hypothesis - refers to virally infected cells decreasing MHC I expression to prevent recognition by cytotoxic T-cells - This is where NK cells come in

284
Q

In myeloid cells are there any mechanisms to detoxify HOCl when produced?

A

Nope not really according to Shelkirk - will only reduce in levels by acting on targets

During an inflammatory response we get a build-up of macrophages and neutrophils which can create HOCl, resulting in tissue damage

Myeloid cells limit this tissue damage by phagocytosing the pathogens creating a barrier to other cells/tissues but tissue damage is inevitable - Results in health complications even after infection - Long-term covid

Imperial Y2 - Integrative Cell Biology (4 decks)

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