I'd assume this is for MST 1

Question 1

Do TCRs undergo somatic recombination like IGs? If so are there any differeces in the gene segments and process

Answer 1

Yes
only 1 constant segment in alpha chain and 2 in beta
process is same

Question 2

compare the structure of mhc I and II

Answer 2

1;
-2 polyeptide chains (down left down right)(a2,a3 and a1 and b microglobulin)
-non covalent binding between a and b
-pbc formed between folded a1 and 2 domains
2;
-2 chains (b1,b2 and a1,a2)
-non covalent bonding
-pbc formed between a1 and b1
-2 things tht corss membrane (stakes)(other i 1)

Question 3

what % of b cell epitopes are conformational/discontinous

Answer 3

90

Question 4

describe what regions generate majority of variability in an immunoglobulin molecule

Answer 4

complementarity determining region/hypervariability region
-3 loops at each end of fab (12 total, CDR1,2,3) that are 10aa long
-cdr3 is most variable as it falls between V and DJ which has junctional diversity due to random N nucleotides (cdr1,2 fall only in V)

Question 5

how do Igs bind to antigens

Answer 5

complementary size and shape, non covalent forces(VDW, es…)

Question 6

compare mhc 1 and 2 peptide binding clefts

Answer 6

1;
-closed, allows short peptide of 8-10aa
-class c and a, peptide ends bound tightly to either end of cleft
2;
-open, allows long peptide
-class b and d, peptide ends not tightly bound to end of cleft
-peptide usually trimmed to 13-17aa

Question 7

what is the mhc pathway in presence of cytosolic, intracellular, and extracellular pathogens

Answer 7

c=mhc 1 and cd8 for cell death
i=mhc 2 and cd 4 for phag
e=mhc2 and cd4 for plasma

Question 8

where on tcr is principal contact made with peptide/mhc

Answer 8

The 3 CDR loops of v alpha and beta

Question 9

how do gamma (y) delta (s) TCRs differ functionally from alpha (a) beta (b) TCRs?

Answer 9

gamma delta TCRs do not require MHC for antigen recognition.
recognise mirobial antigen and or control epithelial barrier function

Question 10

summarise sources of Ig diversity

Answer 10

COMBINATIONAL (~10^7)
1. somatic recombination (selecting from various V(D)J segments in the genome
2. association between different heavy and light chains
JUNCTIONAL (~10^5)
1. junctional diversity - during V(D)J selection random nucleotides are added at the junctions (CDRR3 is found on one of these)

TOTAL 10^13

Question 11

what are n regions

Answer 11

regions between V(d)J segments inserted by TdT that increase diversity but can also cause failiure by frameshift or stop codon

Question 12

describe somatic recombination process

Answer 12

rosettes formed by heptmer/nonamer and 12/23 rule
recombonase enzyme complex removes signal joint
-rag (recombination actiating genes) 1,2 identify recombination signal sequences after splicing and insert dna hairpin
-artemis DNA-PK complex opens DNA-hairpin and generates palindromic p nucleotides
-TdT ads n-nucelotis to p ones so strands can pair up
-unpaired nucleotides removed by exonuclease and dna ligase 4 forms coding joint

Question 13

what causes ig diversity

Answer 13

somatic recombination
rearrangement of ig genes in maturation that generate unique heavy and light chain protein sequences

Question 14

describe details on ig domains

Answer 14

10 aa length, 2 layers of b pleated sheets, 3-5 antiparralel strands
inward pointing hydrophobic residues form stable core
conserved cysteines form disulfide bridges

Question 15

how many ig domains are in heavy and light chains of ig

Answer 15

4-5 and 2

Question 16

what are key differences between surface and secreted igs

Answer 16

surface;
- cytoplasmic tail, transmembrane region, no tail piece, transuce activation signals upon binding to ag with coreceptor present
secreted;
- no ct, no tmr, has a tail piece, canot transduce…

Question 17

describe difference between conformational and linear determinent Ig recognition

Answer 17

Conformational (90%) = recognise shape of protein (could be multiple folds of the same antigen). If protein denatured cannot recognise

Linear (10%) = recognises a specific linear DNA sequence

Question 18

describe key structural differences between cd4 and cd8 cell surface proteins of T cells

Answer 18

CD4 has 4 D regions in chain
CD8 has ladder with cross (bandaid) of 1a and 1b chain

Question 19

what is the hapten carrier complex

Answer 19

complex between hapten (small inorganic molecule antigen with epitope that is not immunogenic) and carrier (protein to allow for immunogenicity) linked covalently

Question 20

what is immunogenicity and what are the factors that affect it

Answer 20

ability to induce specific immune response
foreigness, molecuar weight, chemical complexity, degradability (T cell), immunogen (immunogenic substance), route of administration

Question 21

what are the differences between tcr and ig antigens

Answer 21

TCRs can only recognise processed peptides complexed with MHC molecules

Ig’s can recognise a broader range of antigens as they recognise shape - not requiring processing of antigen (protein, lipid, carb, nucleic acid, metbolite or sugar that is complementary)

Question 22

What are the rules of engagement

Answer 22

speed dating in secondary lymph organs so antigen can efficiently match with lymphocyte.
Rule 1; naive lymphocytes recircuate through nodes and spleen by squeezing through blood vessel walls
Rule 2; antigens and paths funnelled into local nodes from peripheral tissue by lymph in vessels, activated dendritics will travel to node to present these to naive t cells

Question 23

What are anchor residues

Answer 23

specific amino acids on the antigen which bind to the MHC.
- provide stability, do not need to be identical, just related, and fit in same place
- allow a broad range of peptides to bind MHC (given anchors are the same/similar)

Question 24

where are mhc genes located

Answer 24

chromosome 6

note: beta-2 microglobulin of MHC1 is encoded on chromosome 15

Question 25

what is the effect of mhc polymorphism

Answer 25

altered antigen binding and t cell recognition

Question 26

what is a mhc halotype

Answer 26

specific combo of mhc alleles on single chromosome

Question 27

where is allelic variation most common in mhc

Answer 27

pbc some in a and b, diversity increases when diff ones bind

Question 28

what is MHC restriction?

Answer 28

CD4 T cells can only recognise MHC2 CD8 T cells can only recognise MHC1

Question 29

what are the 2 processes that give rise to autoimmune t cells

Answer 29

tcr genes encode self reactive t cells positive selection fails

Question 30

describe 4 methods for alloantigen recogniton

Answer 30

peptide dependant -alloreactive t cell recognise foreign peptide bound on mhc peptide independant -recognise different mhc without peptide direct = t cell recogises foreign peptie indirect=dendritics present it

Question 31

describe process of mhc 1 presentation

Answer 31

pathogen enters cell viral protein synthesized in cytosol proteasome degrades it into antigen antigen peptide created transported into er by tap1 and 2 peptide inserted into binding groove of mhc1 trasported to plasma membrane by secretory pathway

Question 32

what are 2 examples of things that stimulate mhc1 expression

Answer 32

viral infection and altered self/tumour

Question 33

describe process of mhc2 presentation

Answer 33

apc endocytoses pathogen cathepsins degrade pathogen antigen peptides contained in endosomal compartments -broken down by acidification and reduction of disulfide bonds by GILT, allows proteolysis mhc2 molecules synthesized in er mhc2 associates with invariant chain/Ii to prevent antien binding to mhc1 components in er (mhc2 peptides in endosomes) mhc2 peptides in endosome traffic to endosome with antigen and complex formed mhc2/peptide complex travels to surface

Question 34

how does the antigen prevent binding to er components and bind to mhc2 molecules in er

Answer 34

3 mhc2 ab dimers associate in er with 3 Ii to form (ab3li)3 nonamer li zipper region promotes trimer formation 3 ab dimers assemble on (li)3 scaffold CLIP (mhc class 2 associated Ii peptide) Li region occupies pbc of ab dimer li carries molecular code in cytoplasmic domain that tags mhc2-li for transport in endosome protease will cleave zipper regiom of li to make li10, releasing 3ab dimers, each associated with one Ii-p10 fragment Cat-S cleaves Ii-p10 at edge of pbc to make ab CLIP endosomes fuse with others that have degraded peptide chaperone HLA-DM interacts with ab clip to induce open conformation in ab dimer clip is substituted by antigen peptide to form ab peptide

Question 35

what are key differences between mhc1 and mhc2 antigen processing and presentation

Answer 35

1; -ag degraded in cytosol/endogenous mostly -apc infected or tumour, killed by cd8 -expressed by all cells 2; -ag degraded in endosomes/exogenous and endogenous -apc may not be infected -macs, dens, b cells

Question 36

what are the ways macs, b, and dedritic cells endocytose matter

Answer 36

macs = rno/inducible macropinocytosis, receptor mediated endocytosis, phagocytosis b=rme particles that bind to ig only d=all

Question 37

what do professional apcs present when there is no ifnection

Answer 37

self antigens on both MHC1 AND 2

Question 38

what do dendritic cells do when there is infection present

Answer 38

phagocytose pathogen after prr detection cross present/transger mhc 2 material to mhc 1 to activate cd8 present on mhc2 to actvated cd4

Question 39

descirbe process of t cell activation

Answer 39

cd45 dephosphorylases terminal tyrosine of lck cd4/cd8 corecepto bring lck into close proximity of ITAMS of t cell complex to interact with mhc molecule activated lck phosphorylases itams -lck mustautophosphorylate itself once primed to activate itself zap-70 recruited to site of phosphorylated itams, binds to phosphotyrosines where it is activated by lck activated zap-70 phosphorylates LAT and SLP-76 these initiate AKT, PLC-gamma, VaV, and ADAP B7 binding on APC induced CD28 on APC phosphorylation to ativate PIP3 kinase to recruit lck PIP3 recruits PPK1 and AKT PIP3 and lck enhance plc-gamma activation, vav recruitment, ad cdc42 activation

Question 40

Summarise the inflammatory response process

Answer 40

-mast cells, basophils, macrophages, detect invasion and produce cytokines and histamines -this causes vasodilation (increases blood flow causing redness and heat) -vessels also become more permeable (fluid leaks into tissue and interstitial spaces causing oedema and swelling) -cells that line vessels express cell to cell adhesion molecules, allowing leukocyte binding and extravasation -inflammatory cells move to site of infection and release mediators that stimulate nerve endings (pain), which may impair normal function (loss of function) -platelets induce clotting, to block pathgen spread and promote wound healing

Question 41

what changes occur when a dendritic cell is activated

Answer 41

lose capacity to capture other antigens increased mhc 1 and 2 expression expression of co-stimulatory molecules cd80 and cd86 cytokine secretion migration of the dendritic cell from tissue to secondary lymph nodes

Question 42

what are the functions of the complement system

Answer 42

promote lysis by MAC, opzonisation of cells to be phagocytosed, inflammation by recruting leukocytes

Question 43

what are the major effector functions of innate immunity?

Answer 43

- phagocytosis - cytokine secretion - cytotoxicity

Question 44

describe the alternative complement activation pathway

Answer 44

-C3 undergoes spontaneous tickover/hydrolysis to expose thioster domain to bind hydroxyl groups -C3 convertase cleaves C3 into C3A and C3B -C3B binds to hydroxyl groups on microbial surface (becomes discarded and inactivated by hydrolysis if it does not) -Protein B is cleaved by Factor D into Bb and Ba proteins -Bb binds to C3B to form C3 convertase C3BBb

Question 45

Where do all complement activation pathways converge?

Answer 45

Formation of C3 convertase

Question 46

What happens after C3 convertase is formed in classic and lectin complement activation pathways?

Answer 46

-C4BC2A cleaves C3 into C3A and C3B -C3B binds to C3 convertase to form C5 convertase C4BC2AC3B, which cleaves C5 into C5A and C5B

Question 47

What happens after C3 convertase is formed in alternative complement activation pathway

Answer 47

-C3BBb cleaves C3 into C3A and C3B -C3BBb binds to C3b on microbial surface to form C5 convertase C3B2Bb, which cleaves C5 into C5A and C5B

Question 48

what are macrophages?

Answer 48

mature monocytes, that are the first to encounter pathogens using PRRs. They carry out phagocytosis and produce an inflammatory signalling response. Despite being derived from the myeloid progenitor they have long life-spans and have important roles in the adaptive immune response.

Question 49

What is the role of C5a in the immune response?

Answer 49

promotes inflammation (by binding CR on cells which release pro-inflammatory cytokines) EG. basophils, mast cells, endothelial cells NOTE: C3a does the exact same thing lol

Question 50

what is a respiratory burst?

Answer 50

when a phagosome fuses with a lysosome, NADPH -dependent oxidases generate toxic oxygen radicals and hydrogen peroxide. This is accompanied by an increase in transient oxygen consumption. Another pathway would be that of active phagocytes producing nitric oxide which in combination with oxygen radicals peroxynitrite is produced. (peroxynitirte damages DNA) IE. phagocytes which produce oxygen products (NO) when attacking things need to consume more oxygen while attacking those things

Question 51

If respiratory bursts are so damaging, how are our cells not damaged?

Answer 51

this is due to our cells producing enzymes which accompany the synthesis of the respiratory burst in order to inactivate the damaging molecules (such as superoxide or hydrogen peroxide). superoxide dismutase! (biochem coming back)

Question 52

What is the role of C5B

Answer 52

Form the MAC

Question 53

How is the MAC formed

Answer 53

-c5b binds to c6 and c7 -complex inserts into microbial membrane and binds to c8 -complex causes c9 polymerisation -mac is formed easier way to memorise but less sin depth: C5b gets 67 C5b67 gets 8 (S protein) C5b678 gets 9 (CD59) brackets = inhibitors of that step.

Question 54

what does the MAC do

Answer 54

creates pores on cell membrane which leads to apoptosis and lysis

Question 55

what are the 2 roles of complement receptor 1

Answer 55

mediate phagocytosis of microbes by macrophages and neutrophils -c3b binding to c1 receptor and specific IgG-FcYR binding to phagocytes stimulates process -enhanced by C5a receptor binding on phagocytes present on rbcs and lymphocytes to clear immune complexes -antigen/antibody complexes on microbial surface and/or free floating/soluble activate classic pathway which leads to c3b opsonization -cells are then transported to spleen and liver where phagocytes remove complexes

Question 56

what are the pro-inflammatory cytokines secreted by macrophages and what are their main local and systemic effects?

Answer 56

- IL-1B: locally - activates vascular endothelium which increases access of effector cells. systemically - fever and production of IL-6 -TNF-a: locally - activates vascular endothelium, increased permeability and fluid drainage into lymph nodes. systemically - fever, shock and metabolite mobilisation - IL-6: locally - lymphocyte activation and increased antibody production. systemically - fever and induced acute phase protein production - CXCL8 (IL-8): locally - chemotactic factor which recruits: neutrophils, basophils and T- cells to site of infection. - IL-12: locally - activates NK cells, and induced differentiation of CD4T cells into T helper cells

Question 57

what are the roles of complement receptor 2

Answer 57

major function is CR2 acts as coreceptor for B cell - stimulating a stronger response.

Question 58

what are the roles of complement receptor 3 and 4

Answer 58

expressed on macrophages, neutrophils, natural killer cells, binds to iC3b, ICAM-1, and microbes to stimulate phagocytosis

Question 59

what are acute phase proteins?

Answer 59

proteins (C-reactive protein and mannose-binding lectin) which are produced in the liver, and enhance the fixation of the complement on pathogenic surfaces. Aid in the activation of the complement and opsonisation. note: liver also upregulates complement proteins in acute response to IL6

Question 60

what are neutrophils?

Answer 60

they are: the most abundant leukocyte in the blood, short lived (8hrs in humans), terminally differentiated in bone marrow and only once they are in the steady state they migrate out into the blood. they are they move to site of infection through cytokine (IL-8) stimulation, detect PRRs, and are the main immune cell to eliminate BACTERIAL pathogens.

Question 61

outline how cytokines direct neutrophil migration?

Answer 61

Cytokines promote the activation of the vascular endothelium, which leads to an increased expression of adhesion molecules (P-selectin) and stronger interactions (I-CAN-I). These interactions bind the neutrophil to the endothelium which then allows them to squeeze between the cells. once out of the blood vessels they move towards the site of infection through chemokine stimulation.

Question 62

rolling adhesion (first component of neutrophil migration)

Answer 62

Selectin-mediated interactions slow neutrophils in the blood vessels. Selectin is transported and presented on the surface of the endothelium after there is exposure to inflammatory mediators. the Selectins bind to the Siyal-Lewisx (S-LEx) carbohydrate ligand on the neutrophil therefore the neutrophil becomes adhered to the endothelium. Reversible reactions allow neutrophils to roll as well as the current of blood flow pushes them along)

Question 62

tight binding (second component of neutrophil migration)

Answer 62

interaction of the LFA-1 on the neutrophil and adhesion molecules on the endothelium (ICAM-1) causes a strengthening of the adhesion through the up regulation of more receptors. stimulated macrophages release CXCL8 chemokine which further strengthens the ICAM-1 expression on the endothelium which promotes a conformational change leading to a stronger attachments. Now the neutrophil is bound to the endothelium.

Question 63

diapedesis (third component of neutrophil migration)

Answer 63

neutrophil crosses the blood vessels walls via extravasation thanks to proteases (such as elastase) being secreted by neutrophils breaking down the basement membrane.

Question 64

migration (fourth and final component of neutrophil migration)

Answer 64

neutrophil migrates towards centre of infection following a chemokine (CXCL8/IL-8 and TNF-a) concentration gradient.

Question 65

what is the role of C4b?

Answer 65

same as C3b - opsonise microbes (but not as abundant as no positive feedback unlike C3b which has alterative pathway and C3 convertases)

Question 66

How do RBCs remove antibody-antigen complexes from circulation?

Answer 66

1. RBCs use CR1's to bind to C3b-antigen-antibody complexes 2. RBCs then travel to spleen + liver & present to macrophages which steal and phagocytose them 3. no more antigen-antibody complex lol

Question 67

What is the function of membrane-bound factors decay accelerating factor (DAF), membrane cofactor protein (MCP), and CR1?

Answer 67

all break apart C3 convertase DAF/MCP/CR1 bind C4b of C4b2a and dissociate 2a (classical/lectin pathway C3 convertase) DAF/CR1 bind C3b of C3bBb and dissociate Bb (alternative pathway C3 convertase)

Question 68

What is the function of Factor I?

Answer 68

metabolises C3b leaving C3dg 2 possible applications of this function: 1. binds C3b and metabolises it from C3/5 convertase ***given MCP/CR1/Factor H bind C3b beforehand*** - note: only affects C3bBb of alt pathway 2. general clearance of C3b bound to whatever microbe ***requires MCP***

Question 69

How do C3a and C5a stimulate inflammatory responses? What cells do they affect to achieve this?

Answer 69

Mast cells and endothelial cells in particular have C3/5a receptors Endothelial cells will become leaky if bound to C3/5a Mast cells will release TNa and histamine if bound to C3/5a

Question 70

Imagine you are running away from a very large parasite - which immune cells are you calling?

Answer 70

Eosinophils - release granules containing toxic chemicals eg. major basic protein ILC2 - release IL4 to recruit more eosinophils Basophils - release granules as well + release IL4 to recruit more eosinophils

Question 71

oh no, you've fallen into a ditch and cut your leg and bacteria have infected you - which immune cells would protect you?

Answer 71

neutrophils - general toxic secretions, use NETs (neutrophil extracellular traps) to trap and phagocytose bacteria ILC3 - activate more neutrophils

Question 72

you suddenly get up and you have human immunodeficiency virus (HIV) - which immune cells would protect you?

Answer 72

NK cells - very good at detecting altered proteins on surface, will lyse cells directly with granules or via TRAIL pathway (induce apoptosis) ILC1 - release type 1 interferons IFNa/b. These inhibit viral protein synthesis, degrade viral RNA, activate NK cells

Question 72

What does TLR-4 recognise? What does activation of the TLR-4 pathway result in?

Answer 72

TLR4 is in cell membrane and recognises lipopolysaccharides (LPS) of bacteria Pathway: 1. MD2/CD14/TLR4 + LPS complex forms 2. LPS brings another complex in causing dimerisation activating TLR4 3. MyD88 binds intracellularly and activates IRAK4 4. Kinase cascade happens - resulting in IKK activating NFkB by degrading IKB 5. NFkB activates the transcription of inflammatory cytokines

Question 73

What does TLR-3 recognise? What does activation of the TLR-3 pathway result in?

Answer 73

TLR3 is in the endosomal membrane and recognises viral dsRNA Pathway: 1. TLR3 binds viral dsRNA and signals for transcription factor IFN3 to move to nucleus via TRIF 2. IFN3 causes transcription of type 1 interferons IFNa/b (induce anti-viral state) oh and also NFkB pathway is activated - pro-inflammatory cytokines.

Question 74

What does (Rig-I-Like receptor) RLR recognise? What does activation of the RLR pathway result in?

Answer 74

RLR is in the cytosol and recognises viral RNA (both ds and ss) Pathway: 1. virus enters cell and replicates generating viral RNA within cytosol 2. viral RNA alters conformation of RLR causing it to bind to MAVS on mitochondria 3. MAVS recruits TRAFs which activate IRF3 (T1 interferon) and NFkB (inflammatory) pathways **key example of signalling pathway which relies on COFRMATIONAL CHANGE opposed to DIMERISATION**

Question 75

What does cGAS STING recognise? What does activation of the cGAS-STING pathway result in?

Answer 75

cGAS-STING is found in the cytosol and recognises viral dsRNA only Pathway: 1. dsRNA from viruses in cytosol activate cGAS to produce cGAMP 2. cGAMP dimerises STING on the ER causing activation of IRF3 (T1 interferon) pathway

Question 76

What does NLR recognise? What does activation of the NLR pathway result in?

Answer 76

NLR is found in the cytosol and recognises bacterial peptides Pathway: 1. Bacterial peptide binds NOD cause dimerisation then recruitment of RIP2 2. RIP2 activates TAK1 which activates NFkB (pathway IMPORTANTLY: if there are a lot of PAMPs/DAMPs detected by the cell, these will trigger NLRs to come together to form an inflammasome which causes apoptosis via gasdermin D pore formation and caspases.

Question 77

Examples of mechanical barriers are?

Answer 77

anything which produces movement: 1. Cilia (move mucus) 2. Tears (roll down face - move pathogens away from eyes) 3. Saliva 4. longitudinal flow of air/fluid

Question 78

Examples of chemical barriers are?

Answer 78

1. defensins 2. lysozymes in saliva & tears 3. low pH

Question 79

Examples of microbiological barriers are?

Answer 79

gut microbiota

Question 80

Aside from stimulating inflammation - what else can C5a do?

Answer 80

CR1-mediated phagocytosis is enhanced by C5a IE. phagocyte binding both C5a and C3b will produce very strong response

Question 81

The function of dendritic cells, NK cells, and ILC1 cells are particularly against intracellular pathogens, why is this?

Answer 81

NK cells are good at detecting altered proteins on cell surface, lack of MHC1, viruses, and virally infected cells. ILC1 have antiviral activity (viruses are intracellular) dendritic cells - idk actually

Question 81

When and how is mRNA splicing used in the processes of generating diversity in B and T cells via V(D)J recombination?

Answer 81

initially we have somatic recombination IE. choosing which V(D)J segments we want, and joining these together to form the variable segment. We then need to join the variable segment to the constant segment. ***During transcription of DNA to mRNA, we splice out the intron between the variable and constant region to join them.***

Question 82

The 3 APCs (B cell, dendritic, and macrophages) use MHC2 presentation for different purposes - describe them.

Answer 82

Macrophage - present on MHC2 to signal to CD4 T cells, which stimulates macrophage to produce more toxic compounds in the phagosome B cell - also use MHC2 to present to CD4 T cells, which stimulates B cell to produce lots of antibodies Dendritic - use MHC2 to present to CD4 T cells, which activates them causing them to stimulate macrophages and B cells at site of infection

Question 83

Once dendritic cells capture, process, and present pathogen on MHC2, what causes them to travel to LN and allows them to activate CD4 T cells?

Answer 83

Once activated dendritic cells upregulate: chemokine receptor CCR7 (draws them to LN) CD80 and CD86 (allows activation of T cells @LN)

Question 84

How do DCs activate CD8 T cells?

Answer 84

either they themselves are infected OR more realistically - cross presentation forcing engulfed peptides into MHC1 presentation pathway

Question 85

What does TNFa do?

Answer 85

Inflammation (activates vascular endothelium) Upregulates selectin which draws in more neutrophils, monocytes. and eosinophils stimulates migration of dendritic cells to lymph nodes recruits immune cells generally generally recruit immune cells to site via general inflammation of the local area

Question 86

How do Factor I and MCP work together to break down surface bound C3b?

Answer 86

C3b exists as C3b3f3dg on surface FACTOR I cleaves off C3f leaving iC3b3dg FACTOR I with help from MCP cleaves off iC3b leaving **3dg**