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immunology > Part 5 > Flashcards

Part 5 Flashcards

1
Q

how many BCRs are in the B cell repetoire

A

10^11-13

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2
Q

how many genes make up the human genome

A

20-25,000

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3
Q

how many TCRs are in the T cell repetoire

A

10^18

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4
Q

what percentage of DNA is coding DNA

A

2%

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5
Q

what is germ line theory

A

each antibody-producing cell has genes coding for all possible antibody specificities, but expresses only the one stimulated by antigen;
there is a separate gene for each different immunoglobulin chain and that the antibody repertoire is largely inherited.

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6
Q

what is somatic diversity theory

A

antibody-producing cells contain only a few genes, which produce antibody diversity by mutation; There is a limited amount of genes that we inherit that have function.

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7
Q

how are antibodies generated genetically

A

Antibodies are generated by gene segments (light or heavy) that generate the hypervariable regions (which are residues).
These regions make up the 3 types of CDRs.

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8
Q

what are the three gene segments of antibodies

A

Variable (V)
Diversity (D)
Joining (J)
All three encode for the hypervariable residues.

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9
Q

what is the bottom part of the antibody encoded by

A

the Constant (C) segment

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10
Q

what segments are the light chains made of

A

V and D

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11
Q

what segments are the heavy chains made of

A

V, D, J

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12
Q

what is somatic recombination

A

a process for generating antibody and TCR diversity during mammalian B and T cell development. It involves the excision and recombination of multiple germline V, J, and D gene segments, which are combined randomly in the immunoglobulin and TCR loci.

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13
Q

why is somatic recombination important

A

Antibodies must have enough antigen-binding diversity to recognize every possible pathogen (many V regions) while maintaining the biological effectiveness of their C regions

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14
Q

what is the recombination signal sequence

A

allows the right segments to combine correctly
3 parts

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15
Q

what is a heptamer

A

7 nucleotide sequence; GTGTCAC (consensus: most commonly found there)

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16
Q

what is a spacer region

A

either 12 or 23 nucleotides.
How many rotations the DNA takes.

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17
Q

what is a nonamer

A

9 nucleotide sequence; TGTTTTTGG.

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18
Q

what is the 12/23 rule

A

requires that V(D)J recombination only occurs between recombination signals with 12 and 23 base pair spacers

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19
Q

what is the rule for light chain somatic recombination

A

23 and 12 must come together in order for V segment and J segment to come together (12/23 rule) for orientation purposes

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20
Q

what is the rule for heavy chains somatic recombination

A

the D segment must have the opposite of the V and J to come together, still 12/23 rule

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21
Q

what cdr has high variability and why

A

CDR 3 is prone to high variability because it is partially made with the V, D, and J.

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22
Q

what can v and j do

A

J can combine to any V region at random

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23
Q

what will happen if V and J encode the same direction (5’ to 3’)

A

they will line up together. This will create a loop with the V2L2 and VnLn.
After recombination, this loop is excised from the chromosome.

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24
Q

what will happen if V and J encode in opposite orientations

A

the RSS regions are coiled
After recombination, the coiled region is retained but in an inverted orientation

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25
Q

what do both orientation processes form

A

coding joints

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26
Q

what are coding joints

A

the rearranged variable regions of antigen receptor genes

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27
Q

what are recombination activating genes (RAG)

A

types 1 and 2
Endonucleases (cleave DNA)
Only expressed in developing lymphocytes.
Without RAG gene, there would be no third line of immunity (T or B cells).
Genes for RAG are unique
SCID mice have mutated RAG genes, they are severely immunocompromised.

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28
Q

what is the function of RAG

A

initiate recombination of the variable (V), diversity (D), and joining (J) genes by cleaving, allowing for the generation of T and B cells with a broad antigen recognition specificity

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29
Q

what are Ku70 and 80

A

These are repair proteins.
Bind broken DNA, which form rings
They come in the form of heterodimers

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30
Q

what is DNA-protein kinase (DNA-Pk)

A

plays a critical role in DNA double-strand break (DSB) repair and in V(D)J recombination. DNA-PK also plays a very important role in triggering apoptosis in response to severe DNA damage or critically shortened telomeres.

31
Q

what is Artemis

A

Has nuclease activity
Can be a endo or exonuclease
Cut within or at the ends of DNA strands
bound with DNA-PK

32
Q

what is TdT

A

An enzyme that adds nucleotides without using a template.
Similar to telomerase.

33
Q

what is DNA ligase

A

binds end of split DNA, forming a coding joint of VDJ

34
Q

what is the order of proteins in somatic recombination

A

RAG1:2
Ku70:80 heterodimers
DNA-PK:Artemis
TdT
Ligase

35
Q

what is the excised DNA is somatic recombo called

A

signal joint

36
Q

what is the full somatic recombo process

A

RAG 1:2 binds to the RSS and cleaves the RSSs (arrows)
For coding joints:
Ku70:80 binds DNA ends
Brings in DNA-Pk and Artemis which open a hairpin.
TdT process DNA ends by adding nucleotides.
DNA ligase which creates variability and ligates at DNA ends.
Imprecise coding joint

37
Q

what are P nucleotides

A

nucleotides that are generated from artemis

38
Q

what are N nucleotides

A

nucleotides generated from TdT

39
Q

what chains in T cells go through similar recombo

A

alpha and beta

40
Q

what is the total diversity of immunoglobulin

A

5x10^13

41
Q

what is the total diversity if alpha and beta TCRs

A

10^18

42
Q

what is the main function of having constant regions of antibodies and T cells

A

for effector functions

43
Q

what is the difference between light and heavy chain segments

A

Light and heavy chains have constant regions, but heavy chains have a longer segment.

44
Q

how many subclasses does IgG have

A

4

45
Q

how many IgA subclasses

A

2

46
Q

what immunoglobulins do not bind to the complement

A

A
D
E
G4

47
Q

what binds an antibody to the a macrophage

A

FcReceptor

48
Q

What receptors are found on Mast cells

A

Fc(IgE)Receptors

49
Q

what Ig do Mast cells have

A

Mast cell then has antibodies (IgE) on surface, which cause secretion of IL1, 3, 4, 5, and 6, chemokine, PAF, leukotriene, histamine
All are triggers for inflammation and allergic reactions.

50
Q

describe the relationship of FcRs and placenta

A

There are FcRs on the outside of the placenta. This will allow antibodies (IgG) to be bound and transferred across the placental barrier.

51
Q

what percentage of IgG make up of bloodstream

A

IgG make up between 75-85% of all soluble antibodies in bloodstream

52
Q

what make Igs unique

A

Number of sugars and their locations.
Numbers of disulfide bonds and their locations.
The length of the hinge (allows flexibility and binding at different angles).
Number of constant regions

53
Q

properties of IgA

A

secreted in saliva, mucus, gastric juices, tears
Only secreted in dimers

54
Q

what do IgM and D have in common

A

first expressed when infection is present

55
Q

what happens after VDJ is encoded for

A

all genes for IgRs are expressed.
All antibodies are made at the same time.
After it goes into mRNA, the RNA is spliced for the specific antibody

56
Q

where is VDJ expressed

A

variable region

57
Q

what does MC code for

A

the membrane coding for the tails that allow the antibody to be attached to a membrane

58
Q

what does SC code for

A

SC is secretion coding, therefore it is a soluble antibody

59
Q

what is special about IgM

A

forms a pentamer
if one part of pentamer is bound, the full unit is bound

60
Q

what is primary generation

A

V region generation (light and heavy chains)

61
Q

what is class switching

A

can start off with one antibody but switch to another
IgM to IgG
IgD to IgG2
This is variability

62
Q

what is somatic hypermutations

A

a programmed process of mutation affecting the variable regions of immunoglobulin genes. Unlike germline mutation, SHM affects only an organism’s individual immune cells, and the mutations are not transmitted to the organism’s offspring

63
Q

when do somatic hypermutations occur

A

occurs in the presence of an antigen

64
Q

where do somatic hypermutation occur in the body

A

The germinal centers of peripheral lymphoid tissues are the sites where somatic hypermutation, positive selection and differentiation of B cells with high-affinity receptors occur. Germinal centers are the only places in the body where antigen is retained for months or years in an extracellular location.

65
Q

what is AID

A

an enzyme that is activated when the B cell is actively proliferating

66
Q

what is the role of AID

A

introduces mutation by modifying cytidine into uridine
AID binds to single stranded DNA and attached to cytidine

67
Q

what does MSH2/6 do

A

switches A:T, which ends in somatic hypermutations

68
Q

what is UNG

A

base-excision repair, switches uridine to abasic, and leaves behind ribose sugar and phosphate residues.

69
Q

what does REV1 do after UNG

A

mutations at C:G; SHM

70
Q

what does APE1 do

A

a repair mechanism protein that removes sugar and phosphate, and leaves to a missing nucleotide open nick DNA.

71
Q

what happens when APE1 has a single strand nick

A

gene conversion

72
Q

what happens when APE1 has a double strand break

A

class switch recombo

73
Q

what do mutations allow for the CDRs/antibody

A

allow better binding of the antibody to the epitope
Each time an epitope is exposed, the B cell/antibody is better at binding to the epitope each time due to better mutations.

74
Q

where do mutations specifically occur

A

CDR1-3

immunology (11 decks)

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