Selkirk & Dionne - Immunology Flashcards

Question

Macrophages Visualization?

Answer 1

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

Answer 2

**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

Answer 3

**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)

Answer 4

Cellular organization of the thymus Bi-lobed organ, lying over heart and major blood vessels

Answer 5

Research how we go from double negative to double positive

Answer 6

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.

Answer 7

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

Answer 8

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)

Answer 9

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

Answer 10

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

Answer 11

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

Answer 12

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

Answer 13

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

Answer 14

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

Answer 15

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

Answer 16

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

Answer 17

Primarily Macrophage role

Answer 18

TLR is cell type dependant But macrophages are critical for surveillance will express many/ if not all 10 TLRs at once

Answer 19

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

Answer 20

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

Answer 21

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

Answer 22

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

Answer 23

**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

Answer 24

- We can examine people that lack complete functioning complement system - Several bacteria have developed mechanisms to avoid it

Answer 25

**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 3. **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

Answer 26

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

Answer 27

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

Answer 28

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

Answer 29

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

Answer 30

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**

Answer 31

**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

Answer 32

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

Answer 33

- 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

Answer 34

**Tonegawa and Hozumi** (1976) - 1987 Nobel Prize Used restriction endonucleases to prove **gene rearrangement to provide wide degree of diversity observed**

Answer 35

**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**

Answer 36

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

Answer 37

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

Answer 38

**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 1^o 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

Answer 39

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

Answer 40

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

Answer 41

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

Answer 42

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

Answer 43

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

Answer 44

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

Answer 45

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

Answer 46

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

Answer 47

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

Answer 48

ssDNA during strand separation during transcription

Answer 49

**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

Answer 50

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

Answer 51

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

Answer 52

**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

Answer 53

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

Answer 54

YEAHHH buddy

Answer 55

NAHHHHH m8

Answer 56

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

Answer 57

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

Answer 58

YEAHHHHHH BUDDYYYYY

Answer 59

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

Answer 60

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

Answer 61

Mechanism by which AID targets the CDR (hypervariable region)

Answer 62

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

Answer 63

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

Answer 64

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

Answer 65

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