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IMM Exam 1 > Antibody Diversity > Flashcards

Antibody Diversity Flashcards

1
Q

chains of antibodies

A
  • 2 heavy chains
  • 2 light chains
  • identical
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2
Q

domains of antibodies held together by

A
  • disulfide linkage
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3
Q

secreted IgG antibody:

  • L chains
  • H chains

How many Ig Domains?

A
  • 2

- 4

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4
Q

variable region

A
  • sequence varies among different antibodies

- antigen binding pocket

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5
Q

constant region

A
  • sequence is the same among different antibodies
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6
Q

light chains (VL and CL)

A

1 VL + 1 CL for each chain

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7
Q

heavy chain (VH and CH)

A
  • 1 VH + 3 or more CH
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8
Q

CL domain functions

A
  • no effector functions
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9
Q

hypervariable regions

A
  • CDR1
  • CDR2
  • CDR3 (most variability)
  • complementarity-determining regions
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10
Q

how do hyper variable regions interact with antigen

A
  • stick away from the protein so they can contact antigen
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11
Q

each antigen binding pocket consists of

A
  • VH and VL chain
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12
Q

each antibody has how many antigen binding pockets?

A
  • 2
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13
Q

IgA in what form?

A
  • dimer

- connect by J chain

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14
Q

H chain isotypes

A
  • IgG
  • IgA
  • IgM
  • IgE
  • IgD
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15
Q

L chain isotypes

A
  • kappa

- lambda

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16
Q

secreted and membrane associated antibodies differ how

A
  • at the C-terminal tail
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17
Q

chain structure of T cell receptor

A
  • has two chains
    • alpha-beta
    • gamma-delta
  • each chain has a V and C region
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18
Q

CDRs in variable region of T cell receptor

A
  • bind antigen
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19
Q

T cell receptor recognizes antigen in what context

A
  • context of MHC
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20
Q

mechanisms of antibody diversity

A
  • Multiple VH and VL genes
  • combinatorial association of different V,D, and J gene segments
  • junctional diversity by nucleotide addition
  • combinatorial association of VH and VL regions
  • somatic hypermutation
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21
Q

heavy chain gene

A
  • V
  • D
  • J
  • C
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22
Q

light chain gene

A
  • V
  • J
  • C
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23
Q

VH CDR1,2 derived from

A
  • VH segment
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24
Q

VH CDR3 derived from

A
  • DH and JH segments
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25
VL CDR1,2 derived from
- VL segment
26
VL CDR3 derived from
- JL segment
27
leader sequence on each V gene segment
- codes for N-terminal signal peptide | - targets the proteins to the ER
28
VDJ recombination
- two gene segments brought together and double strand break made - somatic recombination of V-D-J joining - N and P nucleotides added or removed and ends ligate together - C regions separated from variable regions by introns - DNA splicing of introns bring exons back together
29
what mediates the recombination
- recombination signal sequences - heptameter separated by 12 or 23 nt spacer - followed by AT-rich nonamer
30
prime ends of gene segement
- 3' end of V segment - 5' end of J segment - both sides of D segment - think 3'VDJ5'
31
which segments can pair up
- only 12 bp segment with a 23 bp segment
32
V(D)J recombination by deletion - deleting D in this case
- 12 bp segment synapses with 23 bp segment - ensure D segment not skipped or that two of the same segment don't join together - cut between gene segment and heptamer - ligate gene segments together
33
V(D)J recombination by inversion
- intervening DNA not removed by a circle but remains present - RNA splicing remove intervening sequences
34
rearrangement and transcription
- rearrangement brings enhancers close to promoter allowing transcription to occur - enhancer can be at 3' end or in intervening sequence
35
non-homologous end joining
- uses 1-3 nt single stranded regions of homology to enhance repair
36
non-homologous end joining synapsis
- chromatin opens in developing lymphocyte to allow recombination enzymes access to DNA - chromosome looping brings gene segments together
37
RAG1 and RAG2 in synapsis
- form a complex and recognize RSS sequences | - RAG2 binds to hypermethylated H3K4 sites in chromatin and recruits/activates RAG1
38
non-homologous end joining; cleavage
- RAG1 nicks one strand | - single stranded DNA forms hairpin with other strand
39
non-homologous end joining; hair pin opening end processing an joining
- Ku70/80 binds to break - recruits DNA-PK (protein kinase) - DNA-PK phosphorylates and activates Artemis endo-exonuclease - Artemis endonuclease opens the hairpins - DNA polymerase fills in nucleotides (P nucleotides) - TdT (terminal transferase) adds nucleotides onto broken ends (N nucleotides) - DNA ligase joins ends together
40
P nucleotide addition
- hairpin cleavage and repair | - allows nucleotides to be added to junction by DNA polymerase
41
N nucleotide addition
- terminal transferase adds additional nucleotides at junction
42
why is there greater diversity at CDR3
- junctional diversity | - multiple gene segments
43
importance of CDR3
- most important region for antibody binding specificity
44
allelic exclusion
- if one chromosome undergoes rearrangement successfully, it inhibits rearrangement on the other chromosome - each B cell makes only one antibody
45
allelic exclusion: chromatin on the successful chromosome
- open | - acetylated
46
allelic exclusion: chromatin on excluded locus
- heterochromatized | - methylated
47
light chain isotype exclusion
- if the kappa locus undergoes a productive rearrangement, it inhibits lambda rearrangement
48
how does higher affinity arise
- due to somatic hypermutation in V region by CD40:CD40L signaling - at DNA level - during an immune response, B cells produce antibodies that progressively have a higher affinity for antigen
49
mechanism of class switching
- cytokine stimulation triggers transcription through I exon, switch region, and CH exons - different cytokines dictate which CH gene is switched to - double stranded breaks occur at mu switch region and downstream switch region - intervening DNA lost - RNA splicing yields transcript with new CH
50
activation-induced cytidine deaminase activated by
- activated by CD40
51
activation-induced cytidine deaminase process
- R loop on nontemplate strand - AID converts C's to U's by deamination - Uracil-N-glycosylase removes U residues - Ape1 endonuclease nicks regions without bases - some nicks generated on the template strand - double strand breaks into two switch regions and repair by non-homologous end joining
52
in proliferating B cells, mutation rate for which genes is 1000x higher than for other genes
- V genes | - due to somatic hypermutation
53
As somatic mutation of antibody increases
- Kd decreases | - which means affinity for antigen increases
54
mechanism of somatic mutation very similar process to isotype switching
- AID converts C-> in U in V region MECHANISM - U's changed to T's (C->T mutation) OR - Uracil-N-glycosylase exists bases and repairs with an error prone repair system OR - mismatch repair enzymes remove the U nucleotides and replaces surrounding DNA using an error prone DNA polymerase which generates mutations
55
why do membrane versus secreted forms of antibodies differ in C terminal tails?
- due to RNA splicing
56
antibody membrane form structure
- Cu4 followed by hydrophobic tail and cytoplasmic tail
57
antibody secreted form structure
- Cu4 followed by hydrophilic tail piece - utilizes a poly A cleavage site before the exons encoded the hydrophobic and cytoplasmic tail so those exons aren't included in primary transcript
58
difference of T cell receptor diversity and antibody diversity
- T cell receptors DO NOT UNDERGO SOMATIC MUTATION
59
severe combined immunodeficiency (SCID) caused by
- mutations in recombination enzymes - RAG - Artemis - DNA-PK - DNA ligase 4
60
SCID result
- complete loss of B and T cells
61
Omenn syndrome
- less severe than SCID | - due to mutations with reduced function of RAG and Artemis genes
62
Hyper IgM syndrome caused by
- genetic defects in AID or uracil-N-glycoslyase - defective in class switching and somatic mutation - ALSO CAUSED BY DEFECTS IN CD40
63
Hyper IgM syndrome result
- all antibody is IgM | - susceptibility to infection
64
AID deficiency in somatic mutation
- completely defective
65
AID deficiency in UNG deficiencies
- preserved but reduced
66
lymphoid tumors and translocations
- B and T cell tumors commonly have translocations of oncogenes into antibody loci OR - RAG-RAG and RAG-AID translocations
67
lymphoid tumors and translocations process
- oncogenes suffer double stranded break by AID at sequences related to switch site - join to AID induced class switch recombination break in antibody gene locus
68
lymphoid tumors and translocations result
- over expression of oncogene in B or T cells due to active antibody or TCR promoters

IMM Exam 1 (20 decks)

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