Adaptive Antigen Recognition in the Immune System

Question 1

Where are plasma cells (activated B cells that secrete Abs or memory cell) primarily found?

Answer 1

Lymphoid Organs

Question 2

The highly variable chains in BCRs are NH-terminus of H and L chains (Vh and Vl), what are they in TCRs?

Answer 2

NH-terminus of Valpha and Vbeta

Question 3

What are the antigens, diversity, signaling and effector functions of BCRs (Ig)?

Answer 3

Macromolecules like lipids/proteins
Unique specificity
IgA and IgB (signaling)
Fc region of Ab is effector

Question 4

What are the antigens used for TCR, how do they signal, and what are their effector functions?

Answer 4

Antigens are peptides presented by APC (linear short AA)
Signaling by CD3 and (Zeta) subunit?
No effector function

Question 5

Antibodies are used interchangeably with immunoglobins, most Abs are found in the third slowest migrating group of globulins, known as?

Answer 5

Gamma gobulins (followins B and Alpha)

Question 6

Antibodies have four polypeptide chains- two light (L) chains and two heavy (H) chains bound together by what?

Answer 6

Disulfide bridges

Question 7

Both H and L chains are divided into V and C regions, V regions contain the Antigen binding site and the C region determines?

Answer 7

The fate of the Ag

Question 8

If an antibody is cleaved, it will yeild two Fab fragments (fragment Ag-binding) and a what?

Answer 8

Fc fragment (fragment crystallized) responsible for effector functions

Question 9

Papain is a enzyme that cleaves IgG before the heavy chain constant area into what?

Answer 9

2 Fab fragments and an Fc fragment

Question 10

Which enzyme will generate a single bivalent antigen-binding fragment (F(ab’)2) from IgG?

Answer 10

Pepsin by proteolysis of IgG

Question 11

There are 5 different types of H chains known as IgM,D,E,A,and IgG. There are two different light chains, how many different light chains can each Ab have?

Answer 11

Abs can only have one of the two different light chains

Question 12

how are polypeptide loops of 110 amino acids created on Abs?

Answer 12

By H and L intrachain disulfide bridges every 90 amino acid residues

Question 13

What are some cells that recognize, bind and adhese to cells, that are part of the immunoglobin superfamily?

Answer 13

TCRs, MHC 1/2, CD4, CD28, and ICAM-1

Question 14

For IgG, the Ag-binding sites are formed by Vl and Vh domains, the heavy chain C regions end in tail piecesand Fc/compliment receptor binding sites are in the heavy chain constant regions. IgM on B cells (membrane bound) has a C terminal transmembrane and cytoplasmic portion that anchor the molecule in plasma membrane, what does it have one more of than IgG?

Answer 14

IgM has one more Ch4 domain

Question 15

Where are hinge regions on antibodies located and what do they do?

Answer 15

They are located between Ch1 and Ch2 domains, allowing flexibility to bind 2 surface antigens close or far away

Question 16

What are the five classes or isotypes of immunoglobulins (Ig)?

Answer 16

IgG, IgA, IgM, IgE, IgD

Question 17

Abs formed in the primary response soon after Ag has lower affinity to stick to Ags. Abs produced from memory response have…?

Answer 17

A higher affinity (1000x higher) than primary response

Question 18

Valence of an Ab is the maximum number of antigenic determinants it can react with… since IgG has two Fac regions, it can bind two molecules of Ag. It will have a valence of?

Answer 18

Valence of 2

Question 19

Avidity gives a measure of overall strength of Ab-Ag complex and is dependent on what two things?

Answer 19

1. affinity of Ab for Ag

2. Valence of both Ab and Ag

Question 20

What are the steps in making monoclonal Antibodies?

Answer 20

1. Splenocytes from immunize mouse with known Ag are isolated
2. Isolated cells fused with meyloma via polyethylene glycol to form hybrids (myeloma cells do not secret own Ig)
3. Hybrid cells placed in selection medium (HAT) that permits survival of only immortilized hybrids
4. HAT consists of hypoxanthine, aminopterin, thymidine

Question 21

Myeloma cells lack hypoxanthine-guanine phosphoribosyl transferase (HGPRT) used for purine salvage pathway in most cells, and aminopterin blocks de novo purine synthesis and have to rely on a salvage pathway resulting in what?

Answer 21

Only hybrid cells survive in HAT medium

Question 22

TCRs are composed of alpha and beta chains, each chain containing one variable and one constant region (just like Ig’s) what is in the Variable region of each TCR chain?

Answer 22

3 hypervariable complementarity-determining regions (CDR), each corresponding to a loop in the V domain

Question 23

Since the cytoplasmic regions are too small to transduce signal from the TCR, CD3 and zeta(?) proteins are on either side and serve as?

Answer 23

Signal transducing subunits of the TCR complex

Question 24

CD4 has four EC Ig-like domains (single chain) with a hydrophobic trasnmembrane region and a highly basic cytoplasmic tail (38AA long). What chains compose CD8?

Answer 24

CD8 alpha and beta chains

Question 25

Like CD4 coreceptors, CD8 have a hydrophobic transmebrane region and a basic cytoplasmic tail that is (25AA long different than 38 in CD4). How many extracellular Ig domains does it have?

Answer 25

Only 1 as compared to 4 in Cd4

Question 26

What are the different stages of B cell development?

Answer 26

``` Stem cell Pre-B cell (surrogate light chain) Immature/Naive B cell (IgM only) Mature B cell (both IgD and IgM) Activated B cell Plasma cell/Antibody secreting cell ```

Question 27

What are the chromosomes related to the BCR genes, including Ig H chain locus, Ig k chain locus, and Ig(lambada) chain locus?

Answer 27

H at chromosome 14 k at chromosome 2 lambda at chromosome 22

Question 28

What are the chromosomes associated with TCR genes including TCR B chain locus and TCR A chain locus?

Answer 28

B at chromosome 7 | A at chromosome 14

Question 29

There are mutltiple different exons that encode different domains of the C regions for Ig and TCR.. this allows?

Answer 29

The generation of diverse BCRs and TCRs

Question 30

What are the three unlinked gene groups at different chromosomes which encode immunoglobulins?

Answer 30

one for u H-chain one for k Lchain one for lambda L chain

Question 31

Allelic exclusion occurs in B and T cells, which means only one light chain and one heavy chain is expressed in a single B cell.. this means?

Answer 31

Either parental or maternal alleles are expressed! However, they will be expressed equally since there are many different types of B cell and T cell receptors

Question 32

What is the major mechanism of epitope-specific diversity of BCR and TCR?

Answer 32

DNA chromosomal rearrangement which will switch up the location of variable chains.

Question 33

What 3 mechanisms of rearrangement can alter the expressivity of genes?

Answer 33

Somatic Recombination mRNA splicing Junctional diversity

Question 34

RAG 1 and RAG2 proteins initiate V(D)J recombination by making double strand breaks, which are repaired by homologous recombination and nonhomologous end-joining (NHEJ). What are Rag-mediated breaks exclusively resolved by?

Answer 34

NHEJ

Question 35

There are many different types of variable, diversity and joining segments in each gene which allows for?

Answer 35

multiple different types of receptors and genes being made...heavy chains are most diverse(?)

Question 36

BCR diversity acheived by heavy chain.. has 4 separate gene segments; V, D, J, C with multiply copies of each. In a b cells all copies are randomly deleted besides for one in each segement... this leads to?

Answer 36

Leading to each B cell generating its own VDJ sequence, making them all very different

Question 37

During developmental stages of B and T cells only, Recombination-activating genes (RAG)s are expressed which do what?

Answer 37

Encode enzyme performing recombination of BCR and TCR during the proces VDJ recombination

Question 38

What is the difference between and immature B cell DNA and a mature B cell DNA?

Answer 38

In mature cell, each DNA segment (VDJ) is present as a single copy, in immature there are many copies

Question 39

In BCR recombination, D and J are chose and DNA between them is deleted first. Second, a V segment is chose and DNA between V and DJ is deleted. What happens third?

Answer 39

A C is chosen and DNA between VDJ and C is delete.

Question 40

The chance to produce a 'productive rearrangement is about 10%, there is a test that can be done to check. When confirmed by the test, what happens?

Answer 40

the competition between paternal and maternal H genes is over and recombination of other segments is stopped

Question 41

Once Vh recombination in heavy chain is productive thenB cell proliferates and then will start light chain. which light chains do not have the D segment (diversity)?

Answer 41

K and lambda

Question 42

The recombination rules for the light chain is the same for heavy chain, with the final result being one kind of Vh and one kind of Vl...... meaning that the B cell can?

Answer 42

recognize any Ag possible

Question 43

What are the difference in copies of VDJ between the alpha and beta chains of TCRs?

Answer 43

Alpha chains have more V and J copies while Beta chains have less V and J copies, but have two D copies

Question 44

For TCR gene rearrangement, what chain goes first?

Answer 44

B chain then A chain

Question 45

What does terminal deoxynucleotidyl transferase (TdT) do in junctional diversity?

Answer 45

It adds or removes nucleotides to the exposed ends of the V, D, or J genes before they are reunited

Question 46

VDJ recombination alone woulf not be enough to recognize all antigens possible, so junctional diversity mediated by terminal deoxynucleotidyl transferase (TdT) with do what?

Answer 46

Increases the diversity of TCRs from 3x10^6 to 10^16 and diversity of BCRs from 10^6 to 10^11

Question 47

Junctional diversity is generated at points between joining genes and results from the loss of nucleotides through the actions of exonucleases and from the addition of N and P necleotides. What generates P nucleotides?

Answer 47

Asymmetric opening of hairpin loops by RAG ( which have a palindromic appearance)

Question 48

What does the opening of the hairpin loop produce ?

Answer 48

short, self-complimentary single stranded extensions that can be incorporated into junctions or can be removed

Question 49

TdT adds N nucleotides after P nucleotides are added, resulting in?

Answer 49

finished product of junctional diversity

Question 50

What are the different Ig DNA and RNA throughout each step in maturation of B cells?

Answer 50

Stem cell: germline DNA Pro-B: germline DNA Pre-B: recombined H chain Immature B: Recombined H and light chain (IgM) Mature B: Alternative splicing is done (IgM/IgD)

Question 51

There are many checkpoints in lymphocyte development that can only be passed if they complete the proceeding step. The first checkpoint is after the production of?

Answer 51

the first polypeptide chain of two-chain Ag receptor is completed

Question 52

What is the second checkpoint in lymphocyte development?

Answer 52

Follows the production of the second polypeptide chain of the Ag receptor is completed

Question 53

The selection process eliminates potentially harmful...?

Answer 53

self-reactive lymphocytes due to lack of both chain rearrangment processes being completed

Question 54

Pre-ag receptors deliver signals to continue on, also known as pre-BCRs and pre-TCRs. The pre-Ag receptors contain only one polypeptide chain present in a mature Ag receptor and a ?

Answer 54

surrogate receptor chain

Question 55

Pre-BCRs contain Ig u heavy chain and pre-TCRs contain?

Answer 55

TCR B chain

Question 56

Ig heavy chain is first receptor gene to be rearranged, once this is done the gene express the u heavy chain protein and assemple the what?

Answer 56

pre-BCR

Question 57

T cell that make a productive TCR B chain gene arrangement synthesize TCR B chain protein and assemple the what?

Answer 57

Pre-TCR

Question 58

30% of B/T cells make productive inframe rearrangements of the Ag receptor gene. If out of frame rearrangements are made then...?

Answer 58

pre-ag receptors are not expressed and cells do not receive survival signal and undergo apoptosis

Question 59

The second checkpoint has positive and negative selection for some cells, how is a cell preserved through positive selection?

Answer 59

If they are function pre-ag receptors they express genes encoding the second chain and if they are successful and express useful Ag receptors they go through positive selection

Question 60

Positivie selectrion of T cells ensures the maturation of CD8 or CD4 t cells whose receptors dont recognize self-ags but can do what?

Answer 60

recognize MHC molecules class I or II

Question 61

What is the main role of negative selection at the second checkpoint of lymphocyte maturation?

Answer 61

They eliminate harmful t cells and alter harmful b cells who Ag receptors bind strongly to self Ags present in the thymus/bone marrow

Question 62

Harmful T cells w high affinity for self ags are eliminated by apoptosis (clonal deletion) while B cells are given a second attempt in Ig gene rearrangement, by a process called?

Answer 62

Receptor editing, if this fails, B cell dies (called clonal deletion)

Question 63

B cells that develop from fetal liver-derived stem cells differentiate int B-1 lineage, B lymphocytes that arise from Bone marrow precursors after birth give rise to?

Answer 63

B2-lineage

Question 64

B1 cells express limited BCR diversity because TdT is not expressed in fetal liver (NO JUNCTIONAL DIVERSITY). The large number of B1 cells are found as?

Answer 64

a self-renewing population in peritoneum and mucosal sites

Question 65

B1 cells, called natural antibodies, contribute to most serum IgM during early phases of infection. What do IgM most often react with?

Answer 65

microbial polysaccharides and lipids and oxidized lipids

Question 66

B2 cells develop in bone marrow and relocated to spleen once they are immature b2 b cells. What two things can immature B 2 B cells differentiate into?

Answer 66

either marginal zone (Mz) Bcells or mature follicular (FO) B cells

Question 67

FOB2 cells are recirculating lymphocytes while MzB2 cells are abundant in the spleen but can also be found in?

Answer 67

Lymph Nodes (localized in splenic marginal zone and respond to blood borne Ags)

Question 68

FOB2 cells respond to protein Ags in a T-cell dependent manner and undergo Ig isotype switching and affinity maturation. Only FOb2 cells upon t cell dependent activation can develop into....

Answer 68

long lived- plasma cells or memory cells

Question 69

MZ B cells are in the marginal sinus in the spleen and lymph node, like B1 cells they have BCRs w limited diversity. Mz B cells respond rapidly to,,?

Answer 69

blood borne microbes and turn into short lived IgM secreting plasma cells

Question 70

Thymus epithelium has cortical thymic epithelial cells (cTECs) and medullary thymic epithelial cells (mTECs=stroma). Thymocytes evolve to mature T cells featuring cell differentiation antigens (CDs) which characterize phenotypically distinct stages known as...?(3)

Answer 70

Double-negative (DN) Double-Positive (DP) Single-positive(SP)-based on expression of the coreceptors CD4 and CD8

Question 71

Stroma or mTECs express genes coding for organ specific proteins, also known as promiscuous gene expression (PGE), what role doe PGE play?

Answer 71

Plays a role in central tolerance to self-antigens which prevents autoimmunity

Question 72

DP cells are programmed to undergo apoptosis unless a rescue signal is delivered via TCR. 95% of DP cells dont signal and undergo...?

Answer 72

death by neglect or apoptosis

Question 73

Some DP cells are able to bind MHC with mild avidity, allowing them to be saved from apoptosis. TCR signals DP maturation to SP thymocytes... also known as?

Answer 73

CD4+CD8- or Cd4-Cd8+ single-positive cells (POSITIVE SELECTION)

Question 74

Negative selection (clonal deletion) is the process by which high-avidity TCR selfpeptideMHC ligation induces cell death... Negative selection occurs in the?

Answer 74

Thymic medulla

Question 75

If TCR and CD28 are engaged in binding, DP/SP thymocytes undergo apoptosis. Stroma cells express self-peptide-MHC and costimulatory molecules....?

Answer 75

CD80/CD86

Question 76

When CD80/86 is High in medulla than cortex, this suggests?

Answer 76

medulla as the more favorable environment for negative selection

Question 77

Elimination of self-ractive thmocytes through clonal deletion requires a complete representation of tissue specific Ags (TSAs) in the thymus. Control of TSA expression is controlled by genes such as?

Answer 77

the Autoimmune regulator (AIRE)