Exam 2 Flashcards
What do T cell receptors look like?
mirrored alpha and beta chain
What do B cell receptors (immunoglobulin) look like?
2 heavy chains
2 light chains
There are not enough genes to specify all B and T cell receptors, how is there still diversity though?
chromosomal rearrangment (VDJ recombination)
For B and T cell receptors, rearrangment occurs before or after transcription and translation?
before transcription and translation
What is the germline configuration?
gene segments before DNA rearrangment
What genes undergo VDJ recombination?
B and T cell receptor genes
Enzymes that mediate VDJ recombination are __________ which adds to the diversity
imprecise
What are the two domains of T cell receptors?
constant and variable
What holds the alpha and beta chain of TCR together?
disulfide bonds
What are the primary receptors (chains) for TCR in VDJ recombination? and what are the less likely options
alpha
beta
gamma
delta
________ begin as receptors on B cells but after activation they are secreted
antibodies
What segments are rearranged on light chain of BCR?
V
J
What segments are rearranged on heavy chain of BCR?
V
D
J
What does recombination signal sequences (RSSs) do in VDJ recombination?
where RAG binds to DNA ensuring recombination only occurs in gene segments encoding BCR and TCR
What does RAG1/2 do in VDJ recombination?
cleaves DNA
what does artemis do in VDJ recombination?
cleaves hairpins and forms overhangs
What does terminal deoxynucleotidyl transferase (TdT) do in VDJ recombination?
adds N nucleotides to gaps
Where is RSS located relative to the V segment?
downstream
Where is RSS located relative to the D segment?
flanking it
Where is RSS located relative to the J segment?
upstream
What does the RSS 12/23 rule prevent?
prevents joining of inappropriate segments
What are the steps of VJ recombination?
- RAG1/2 binds to RSS and cleaves DNA
- NHEJ repairs cleaved DNA creating a coding joint and signal joint
- DNA hairpin forms
- Artemis cleaves hairpins to create overhangs
- NHEJ fills overhangs with P nucleotides
- P nucleotides are removed and Tdt adds N nucleotides
What is the coding joint?
functional variable region
What is the signal joint?
removed circular piece of DNA
What does Artemis create?
overhangs
What nucleotides are filled into overhangs?
P nucleotides
___ and ___ chain use VDJ recombination not VJ
beta
gamma
_______ chain use VDJ recombination not VJ
heavy chain
In VDJ recombination, ___ and ___ segments link first then they link with ___
D J
V
What are the two additional diversity mechanisms for B cells besides VDJ recombination?
- class switching
- somatic hyper mutation
What is AID as a B cell diversity mechanism?
AID converts Cytosine into Uracil causing a mismatch which must be repaired via somatic hypermutation or class switching (double stranded breaks)
What 2 isotypes of B cells do not require class switching?
IgM
IgD
When a B cell encounters an _________ it induces class switching so the correct Ig is present
antigen
What 3 isotypes of B cells require class switching?
IgG
IgE
IgA
B cells cannot present Ig___ and Ig___ at the same time but Naive B cells can
IgM
IgG
Once you class switch can you go back?
no
B cell class switching requires _______ that generates DNA double stranded break in the switch region
AID
What region does AID act in class switching of B cells?
switch region
Does class switching affect antigen specificity?
no, affects effector function
What enhances the affinity of BCR to an antigen?
somatic hypermutation
somatic hypermutation involves _____ mediated introduction of mutations into the ______________
AID
complementary-determining regions (CDRs)
Where are mutations introduced by AID in somatic hypermutation?
complementary-determining regions (CDRs)
What are the three possible mechanisms of mutation in somatic hypermuation?
- DNA replication
- base excision repair
- mismatch repair
In somatic hypermutation what is the mutations that always cause point mutations?
DNA replication
mismatch repair
In somatic hypermutation what is the mutation that has a 75% chance of a point mutations?
base excision repair
What is the complementary-determining regions (CDRs) in somatic hypermutation?
point of mutation (change of antigen affinity) where antigen binds
There are high-affinity, lower affinity, and same-affinity BCR after somatic hypermutation, which is preferentially selected?
high-affinity
Does class switching or somatic hypermutation change antigen affinity?
somatic hypermutation
What are the 2 mechanisms T and B cell receptors use during VDJ recombination to increase diversity?
- random combination of segments
- junctional flexibility (N nucletides)
B or T cells recognize processed antigens
T cells
B or T cells recognize native (free floating) antigens
B cells
HLA class I is express on what cells?
all cells with a nucleus
HLA class I presents antigens from inside or outside the cell?
inside (endogenous)
HLA class I presents to what cell type?
cytotoxic T cells (CD8)
HLA class I deals with intracellular or extracellular pathogens?
intracellular
HLA class II is present on what cell types?
antigen presenting cells (APC)
HLA class II presents antigens from inside or outside the cell?
outside (exogenous)
HLA class II presents to what cell type?
helper T cells (CD4)
HLA class II deals with intracellular or extracellular pathogens?
extracellular
What is the antigen presenting region of HLA class I?
alpha 1
alpha 2
Does HLA class III deal with antigen presentation?
No
Which class of HLA requires a narrow range of peptides (more specific)?
HLA class II (has more binding motifs)
What are anchor residues in HLA class I?
allow peptides to bind tightly bringing regions together and allowing for more flexibility peptide type
What is the antigen presenting region (peptide binding cleft) on HLA class II?
alpha 1
beta 1
Which HLA class binds with longer/larger peptides?
class II
What is the most diverse gene cluster in human genome?
HLA
HLA genes vary at the ________ level
population
What causes organ transplant rejection?
HLA
Where in the cell does peptide loading occur for MHC class I?
ER
What does Calnexin do in HLA I loading?
facilitates proper folding of the HLA alpha chain and retains it in the ER
What does calreticulin, tapasin and ERp57 do together in HLA I loading?
they form the peptide loading complex
What does TAP do in HLA I loading?
translocate peptides from cytosol to ER lumen
What does proteasome do in HLA I loading?
cleaves intracellular proteins into peptides
What happens to the peptide once it enters the ER in HLA I loading?
peptide is associated with peptide-loading complex
What does tapasin do in HLA I loading?
ensures peptide bound tightly to HLA
What does endoplasmic reticulum aminopeptidase (ERAP) do in HLA I loading?
cleaves peptide if it is too long
When does peptide loading occur in HLA class II?
when HLA II is in a vesicle that fuses with a phagolysosome
Which class of HLA loads first?
class I
Where does HLA class II assemble itself?
ER
What does the invariant chain do for HLA II loading?
blocks peptide binding groove on HLA II preventing accidental binding to intracellular peptides (thats MHC I job)
What is the MHC compartment in HLA II loading?
specialized endosome for transport through the secretory pathway
What does the clip do in HLA II loading?
sits in the peptide groove until fusion with the phagolysosome
What does HLA-DM do in HLA II loading?
removes CLIP to allow peptide binding
What are the two chain lineages of T cells?
- alpha/beta
- delta/gamma
Which chain lineage of T cells do not require antigen processing?
delta/gamma
What does the alpha/beta T cell lineage recognize?
peptides presented on MHC
What does the delta/gamma T cell lineage recognize?
lipids on CD1d
What are the two subsets of the alpha/beta lineage of T cells?
CD8 Cytotoxic T cells
CD4 helper T cells
CD8 T cells use HLA class ____
class I
CD4 T cells use HLA class ______
class II
Where do T cells develop?
thymus
What happens in the outer cortex of the thymus?
VDJ recombination of immature T cells
What happens in the inner medulla of the thymus?
negative selection and become mature T cells
What do thymic epithelial cells (TECs) do?
activates Notch which is required for commitment of T cell lineage
What do thymic macrophages do?
clean up T cells that didn’t make it through recombination
What do thymic denritic cells do?
present antigens to developing T cells to prevent self recognition
What is the order of T cell development?
- double negative
- double positive
- positive selection
- single positive
- negative selection
What happens during double negative stage of T cell development?
Notch I signaling and VDJ recombination of beta, gamma, and delta chain
What is the commitment signal for T cells?
Notch I
What happens during double positive stage of T cell development?
VDJ recombination of alpha, gamma, and delta chain
What is positive selection in T cell development?
ensures TCR can recognize MHC (for activation)
What is negative selection in T cell development?
removal of T cells with self reactive T cells (central tolerance)
When does positive selection of T cells occur?
in between double positive and single positive
When does negative selection of T cells occur?
single positive
Which chain of T cells is rearranged first?
beta
delta and gamma T cells do not express CD4 or CD8 so they remain ___________ T cells
double negative
What is the pre-T alpha chain?
surrogate for alpha chain since beta chain is being rearranged first and needs alpha to test if it’s functional
Once the TCR beta chain is successfully rearranged whats locks it so it cannot change?
allelic exclusion
When the alpha chain of TCR successfully rearranges, the _______ chain is lost in VJ recombination
delta
What are the 3 possible outcomes of TCR once they go through positive selection?
- death by neglect (no interaction to MHC = death)
- weak interaction to MHC = survive
- TIGHT interaction to MHC = death
What are the two models of single positive for TCR?
- instructive model
- kinetic model
What is the instructive model for single positive TCRs?
interactions between TCR and MHC on APC drive selection of CD8 or CD4
if TCR interacts with HLA I = CD8
What is the kinetic model for single positive TCRs?
strong signaling = CD4
weak signaling = CD8
What is AIRE (autoimmune regulator) responsible for in T cell development?
enables promiscuous expression of genes in thymus
(that are usually not present in thymus so T cells won’t become self reactive)
What is an example of central tolerance?
AIRE
Where does T cell activation occur?
secondary lymph tissue
What are the 3 antigen presenting cells?
- B cells
- dendritic cells
- macrophages
What is the most important APC for T cells?
dendritic cells
What APC does not phagocytose but internalizes antigens?
B cells
When do immature dendritic cells become mature?
once they phagocytose pathogen then reach secondary lymph tissue for presentation
Expression of what brings DC to secondary lymph tissue?
CCR7
What are the 2 ways antigens can be expressed to CD8 by dendritic cells?
- direct infection
- cross presentation
What is cross presentation?
When extracellular antigens are presented on MHC I instead of II
(CD4 send signaling that redirect antigens to MHC I)
Unlike dendritic cells, _________ remain in the tissue
macrophages
macrophages are important for the ___________ response
inflammatory
B cells do not phagocytose antigens, what do they do instead?
breaks antigen down in a lysosome and present peptide on HLA II
What is T cell homing?
T cell migration to secondary lymphoid tissue
In T cell homing, CCL21 and CCL19 are secreted by DCs and received by _____ on T cells attracting T cells to HEV
CCR7
In T cell homing, CCR7 on T cells binds to ________ activating the gradient for T cells
high endothelial venules (HEV)
In T cell homing (rolling adhesion), what is the adhesion molecule that binds to CD34 or GlyCAM on high endothelial venules (HEV)?
L-selectin
In T cell homing (tight binding), ______ binds to the ICAM-1 receptor on high endothelial venules (HEV) allowing T cells to exit the and do diapedesis
LFA
What does sphingosine-1-phosphate (S1P) do in T cell homing?
upregulated S1P tells T cells to leave secondary lymp tissue and go to site of infection
What is the immunological synapse?
adhesion molecules bring T cells to DC for T cell activation
What are the adhesion molecules required for thr TCR complex in the immunological synapse?
- TCR
- CD4/CD8
- CD3
- CD28
- CTLA4
What is the job of CD3 for the immunological synapse?
signals in cytoplasm
What is the job of CTLA4 for the immunological synapse?
prevents over activation of T cell activation
What 2 signals are required to activate T cells through the immunological synapse?
- TCR binding with DC’s MHC (antigen present)
- CD28 on T cell binding to DC’s B7
What is B7 expressed on?
APC
What does the B7—CD28 prevent?
binding of self antigens (with the help of CTLA4)
When is B7 present on APC?
only when an antigen is present
What is the signaling cascade for T cells after the immunological synapse?
- CD3 signaling
- ITAMs
- ZAP 70
- Lck
- 3 pathways
What are the 3 genes transcribed as a result of the 3 pathways of the signaling cascade for T cell acitvation?
- NFAT
- NFkB
- AP-1
Increasing activated T cells increases their production in _______
IL-2
depending on the type of infection, different ________ will be released by APC to mediate differentiation of T cells
cytokines
What kinase regulates cytokine mediated T cell differentiation?
JAK
Which T helper cells activate B cells for neutralization?
TH2
TFH
Which T helper cells activate phagocytic cells?
TH1
TH17
Which T helper cells help regulate immune response?
Treg
What is the process of cytokine mediated T cell differentiation (kinases) ?
- JAK is phosphorylated
- STAT is phosphorylated and dimerized
- STAT enters nucleus and turns on genes to determine effector function and cytokine production
_____ T cells require stronger activation between B7 and CD28 than ______ T cells
CD8
CD4
CD4 T cells help induce more signaling of _______ on APC to help CD8 cell activation since they require more signaling
B7
What 2 things do CD8 T cells contain?
perforin
granzymes
T/F? CD8 T cells can jump from cell to cell in the same tissue to scan for infections
True
While CD8 T cells have perforin/granzymes to induce apoptosis, what else do they have to induce apoptosis?
FasL pathway
How does the FasL pathway cause apoptosis?
FasL binds to capase which enters cytosol and induces apoptosis
T/F?? The perforin/granzyme and Fas pathway both cause apoptosis.
true
What do TH1 do? (T helper)
recruit macrophages
CD8 differentiation
B cell class switching
What do TH2 do? (T helper)
activate B cells and degranulation in response to parasites
What does TFH do? (T helper)
activation and differentiation of B cells in germinal centers
What does T17 do? (T helper)
recruits neutrophils
What do Treg do? (T helper)
maintain peripheral tolerance
TH1 cells activate macrophage activity by expressing _______ and _______
INF-gamma
CD40
What happens to a macrophage if it cannot clear an infection?
TH1 induce apoptosis via FasL
TH1 induce B cell class switching with activates the _________ complement pathway
classical
TH1 cells induce the differentiation of naive CD8 into CTL with the secretion of ______ and ______
IL-2
INF-gamma
What are helminths?
parasitic worms
What T helper cell is specific for parasites?
TH2
What two cytokines does TH2 release and what do they do?
IL-4 (IgE production)
IL-5 (degranulation)
What 2 signals does TFH produce to help activate B cells?
CD40
IL-21
What do TH17 specifically target?
extracelluar bacteria and fungi
What cytokine does TH17 produce to recruit neutrophils?
IL-17
What do thymic stromal lymphopietin (TSLP) trigger?
DCs to induce FOXP3 to help development of Treg
What does FoxP3 expression induce?
activation of Treg cells
What T helper cell prevents an overactive immune system?
Treg
How do Treg cells help prevent an overactive immune system?
deactivate CD4 and CD8 cells once they do their job
What do natural killer T cells (NKT) express?
express TCR
express surface receptors of NK cells
On NKT cells, what does their alpha/beta receptors recognize?
glycolipids presented on CD1d
How do NKT cells kill infected cells?
apoptosis via perforin/granzymes
apoptosis via FasL
What is the T cell immunodeficiency, Omenn Syndrome? (inherited)
Rag1/2 are mutated causing VDJ recombination to not occur
What is the T cell immunodeficiency, Mutations in Cytokine Receptor gamma(yc)-chain? (inherited)
prevent JAK3 activation preventing cytokines and important functions for T cells (like development, differentiation, activation and expansion)
What is the T cell immunodeficiency, ADA deficiency? (inherited)
inhibiting DNA synthesis preventing cell proliferation
excess dATP which is toxic to cells causing apoptosis
What is the T cell immunodeficiency,PNP deficiency? (inherited)
inhibiting DNA synthesis preventing cell proliferation
excess dGTP which is toxic to cells causing apoptosis
more common in T cells
What is the T cell immunodeficiency, DiGeroge Syndrome? (inherited
absence of a portion on chromosome 22
impacts thymus development = decreased T cells
What is the T cell immunodeficiency, Bare Lymphocyte Syndrome (BLS)? (inherited)
Class I: TAP (responsible for getting antigens from cytoplasm to ER for class I MHC) is mutated
Class II: MHC II isn’t expressed
What is the T cell immunodeficiency, Mutations in Signaling Proteins? (inherited)
prevents activation of transcription factors (NFAT, NFkB, and AP-1) required for T cell activation
(signaling cascade)
What is the T cell immunodeficiency, immunosuppressant drug cyclosporin? (aquired)
antiviral that prevents activation of NFAT and T cell activation
What is the T cell immunodeficiency, immunosuppressant drug corticosteroid? (aquired)
blocks activation of NFkB, impairing T cell activation
What is the T cell immunodeficiency, HIV and AIDS? (aquired)
reverse transcriptase of HIV infected CD4 cells and induces immunosuppression
What 2 ways are self reactive T cells controlled?
negative selection
peripheral tolerance
What is an example of failure of central tolerance of T cells?
lack of AIRE results in incomplete negative selection causing autoimmunity
What is APECED? (autoimmunity)
absence of AIRE resulting in autoreactive cells that lead to malfunctions of endocrine glands that express tissue specific genes
What are 2 examples of failure of peripheral tolerance of T cells
lack of CD28–B7 = no peripheral tolerance = anergic T cells and autoreactive T cells
lack of CTLA4 = prevents Treg = overactive T cells
What is IPEX? (autoimmunity)
mutation in FOXP3 causing loss of Treg resulting in autoimmune response
The variable region on TCR contains the ________ binding site
antigen
How many antigen binding sites does BCR have?
2
VJ recombination occurs with the ____ and _____ chain?
alpha
light
VDJ recombination occurs with the _____ and ____ chain?
beta
heavy chain
Where on BCR does class switching occur?
heavy chain
In VDJ recombination, what removes the P nucleotides so Tdt can add N nucleotides?
exonucleases
Explain the mutation “DNA replication” in somatic hypermutation?
GC turns into TA causing a point mutation
Explain the mutation “Base excision” in somatic hypermutation?
U is removed and replaced with a random N nucleotide (75% chance of point mutation)
Explain the mutation “mismatch repair” in somatic hypermutation?
removes multiple nucleotides in the sequence and replaces it with a bunch of random N nucleotides causing lots of point mutations
How many proteins make up the MHC I antigen binding groove?
one protein (alpha 1 alpha 2)
What does RAG recognize in VDJ recombination?
RSS
The antigen binding surface of immunoglobulins is ________ chain and _______ chain
1 heavy chain
1 light chain
What are 2 diversity mechanisms in VDJ recombination?
segment joining
junctional flexibility (P nucleotides)
Where does the majority of TCR and BCR come from?
VDJ recombination
What is the structure of HLA I?
alpha chain with beta microglobulin
What is the structure of HLA II?
identical alpha and beta chain
What does HLA class I, -E, -F, and -G do?
(don’t present peptides)
E and G: ligands for NK cells
F: removed HLA when not needed
What does HLA class II -DM and -DO do?
aid in HLA loading on APCs (dont present)
Does HLA genes get rearranged?
no, diversity come from population level (one from mom and one from dad)
What does HLA-DM do in HLA II loading?
removes CLIP when peptide is ready to be loaded
What is the source of peptides degradation in HLA I loading?
proteasome
What is the source of peptides degradation in HLA II loading?
phagolysosome
Where are peptides loaded in HLA II?
endosome
What is the job of CD3 for T cell chain rearrangement?
once beta chain of T cell rearranges it tests to see if it works
How many chances does beta chain get to rearrange in double negative T cells?
4
Does the alpha or beta chain of TCR get more chances to. successfully rearrange?
alpha
What 2 chemokines are required for T cell homing and are secreted by DC cells?
CCL19 and CCL21
IPEX syndrome affect the production of what cell type?
Treg
