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Immunology > Week 2 > Flashcards

Week 2 Flashcards

1
Q

AA length of Ig domains and number per antibody chain (in IgG)

A

Approximately 110 amino acids long: two per light chain; four per heavy chain

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2
Q

Papain cleavage of antibodies

A

Produces two identical Fab fragments and one Fc region.

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3
Q

Pepsin cleavage of antibodies

A

Produces two fragments: an F(ab)’ fragment conwisting of the two linked Fab fragments and the pFc’ which consists of partially degraded Fc region

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4
Q

Most variable of the hypervariable regions in antibody variable chains

A

HV3

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5
Q

Regions of the variable chain of antibodies that show markedly reduced variability compared to and are inbetween the HV regions

A

Framework regions (FR1 - FR4)

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6
Q

Five types of noncovalent interactions that contribute to antibody-antigen binding

A

Electrostatic forces, Hydrogen bonds, Van der Waals forces, Hydrophobic forces, and Cation-pi interaction.

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7
Q

Structure of MHC class I molecules

A

Four domains, three encoded by the MHC-encoded alpha chain, one of which spans the plasma membrane. The fourth domain is the B2-microglobulin, which is not polymorphic, does not contribute to protein specificity, and does not span the membrane.

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8
Q

MHC class I peptide binding length

A

8-10 amino acids long

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9
Q

MHC class II peptide binding length

A

unlimited, as peptides extend from each end of groove, are at least 13 amino acids long

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10
Q

Structure of CD4 molecule

A

Four Ig-like domains (D1 - D4), with a flexible region between D2 and D3. D1 binds a hydrophobic region of the MHC class II molecule comprised of both the a2 and B2 domains.

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11
Q

Structure of CD8 molecule

A

Comprised of an alpha chain and a B chain, each containing one Ig-like domain and attached to the membrane by a highly glycosylated polypeptide. Forms mostly CD8a:B heterodimers, except for rare instances in highly activated or memory T cells in which the CD8a:a homodimer predominates.

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12
Q

Lineage (Lin) markers

A

TCRβ, CD3, CD19, B220, NK1.1, and Ter119 for mice

CD20, CD14, and CD16 for humans

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13
Q

Mouse cDC markers

A

Lin-CD45+CD135+CD11c+ and MHC-II+

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14
Q

CD135

A

FLT3

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15
Q

FLT3

A

Receptor for FLT3L, expressed primarily in hematopoietic stem cells, as well as being required for the development of cDC1s.

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16
Q

C-type lectin receptors (CTLs) active in the gut

A

dectin 1, dectin 2, dectin 3, mincle, mannose receptor,

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17
Q

C. albicans hyphal secretions recognized by the immune system

A

canadidalysin, aspartic proteases such as SAP3 and SAP6

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18
Q

Fungal HTS methods

A

amplicon sequencing of the Internal Transcribed Spacer region 1 or 2 (ITS1/2)

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19
Q

CD8+ DCs transcription factors

A

IRF8, Batf3, and Id2

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20
Q

Gut homing receptors imprinted on lymphocytes in the MLN

A

CCR9 and integrin α4β7, from signals from the DCs and stromal cells of the MLN

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21
Q

Transcription factor that all three cDC subpopulations in the LP depend on for differentiation

A

Zbtb46

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22
Q

Function and locations of LP XCR1+ cDC1

A

required for the generation and maintenance of intestinal intraepithelial T cells. They also cross-present iEC-derived antigens to CD8+ T cells and promote the differentiation of Th1 cells and Tregs in the GALT

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23
Q

Function and locations of LP CD103+cDC2

A

induce Th17 cells and IgA+ B cells under steady-state conditions (26, 28) and protective Th2 immunity to the parasitic worms, Nippostrongylus brasiliensis and Schistosoma mansoni

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24
Q

CX3CL1

A

Expressed on the basal surface of intestinal epithelial cells; interacts with CX3CR1 on LP Mqs (also known as fractalkine)

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25
Q

CD74

A

MHC class II-associated invariant chain (Ii), which prevents newly synthesized MHCII molecules from prematurely binding to peptides in the ER.

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26
Q

Two types of chains composing an antibody and their approximate molecular weights

A

Heavy chain (50 kDa/each) and Light chain (25 kDa/each). Light chains can be kappa or lambda

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27
Q

What are the typical ‘arrangements’ of Beta strands in Ig domains, with letters A-G corresponding to amino acid sequence?

A

Light chain C domain - D, E, B, A, G, F, C, with a disulfide bond between B and F

The light chain variable domain is the same, except that it has an additional C’ and C” on the right-most side that continue the antiparallelism before beginning the D strand on the leftmost side.

28
Q

What is the difference between a conformational epitope and a continuous epitope?

A

In antigen binding, a conformational epitope is recognized by the CDR of the antigen regardless of it’s amino acid sequence; it is the tertiary structure of the protein that provides complementarity.

A continuous epitope is a when an antigen is recognized by a sequential order of amino acids that are present in the primary structure of the peptide/protein and thus binding is often undeterred by denaturation.

29
Q

Four ways to disrupt antibody binding

A

High salt concentrations, pH extremes, detergents, and competition with high concentrations of pure epitope.

30
Q

Ligands for 􏰇:gamma:delta: T cell Receptors

A

MHC class Ib molecules, heat-shock proteins, nonpeptide ligands such as phosphorylated ligands or mycobacterial lipid antigens, unorthodox nucleotides or phospholipids.

31
Q

True or False: An antibody proteolytically cleaved by papain yields a fragment with higher avidity to the cognate antigen than an antibody cleaved by pepsin.

A

False. Papain cleaves the antibody into two identical Fab fragments and an Fc fragment. Pepsin cleaves the constant region from both Fab fragments, which are still attached to one another. Since the fragments from the pepsin cleavage have two binding sites compared to the one remaining on the papain fragment, the statement is false.

32
Q

How is CD4 and CD8 co-receptor binding to MHC important for T-cell receptor signaling?

A

CD4 and CD8 co-receptor binding to MHC is important
for TCR signaling because CD4 and CD8 bind Lck on
their cytoplasmic tails and brings the kinase into proximity
with the T-cell receptor complex and helps to activate
the signaling cascade induced by the T-cell receptor after
antigen recognition.

33
Q

Why and how is it advantageous to have heterozygosity in the MHC locus?

A

It is advantageous to have heterozygosity of the MHC
locus because having different alleles increases the
diversity of the set of peptides that can be presented byeach allele for a specific pathogen, thus increasing the chance of efficiently targeting a pathogen-derived epitope.

34
Q

describe the structure of an immunoglobulin fold?

A

One 􏰁 sandwich of two sheets folded together and linked by a disulfide bond

35
Q

For heavy chain genes, how are germline regions arranged (before recombination)?

A

J (joining) region and C (constant) region are close. The D (diversity) and V (variable) regions are from far away and are spliced in during recombination.

36
Q

What are pseudogenes?

A

Genes that do not code for a functional protein. One common pseudogene example are various V, D, or J gene segments within the gDNA that do not lead to a productive antibody when used in recombination. B cells choosing these segments will be unable to produce a working BCR without further recombination.

37
Q

How is the germline lambda light chain gene locus arranged in humans and on which chromosome?

A

At the 􏰊 light-chain locus, located on human chromosome 22, a cluster of (29-33) V􏰊 gene segments is followed by four (or in some individuals five) sets of J􏰊 gene segments each linked to a single C􏰊 gene.

38
Q

How is the germline kappa light chain gene locus arranged in humans and on which chromosome?

A

In the 􏰆 light-chain locus, on chromosome 2, the cluster of (34-38) V􏰆 gene segments is followed by a cluster of (5) J􏰆 gene segments, and then by a single C􏰆 gene.

39
Q

How is the germline heavy chain gene locus arranged in humans and on which chromosome?

A

The organization of the heavy-chain locus, on chromosome 14, contains separate clusters of (38-46) VH, 23 DH, and 6 JH gene segments and of CH genes. The heavy-chain locus differs in one important way: instead of a single C region, it contains a series of C regions arrayed one after the other, each of which corresponds to a different immunoglobulin isotype

40
Q

What are recombination signal sequences?

A

These are conserved noncoding DNA sequences that are found adjacent to points in the genome wherein somatic recombination takes place.

41
Q

What does a recombination signal sequence consist of?

A

A Recombination signal sequence consists of a conserved heptamer (5’􏰈CACAGTG3􏰈’), followed by a nonconserved spacer that is 12 or 23 bp long, followed by another conserved bp sequence block called the nonamer (5’􏰈ACAAAAACC3􏰈’)

42
Q

What is the 12/23 rule in DNA somatic recombination?

A

Recombination signal sequences have two conserved sequences separated by a nonconserved sequence called a spacer. This spacer can only be 12 or 23 base pairs long, and these motifs are always found directly adjacent to V, D, or J gene segments in the germline. A motif with a 12 bp spacer can only be joined to a gene adjacent to a motif with a 23 bp spacer and vice veresa.

43
Q

Why does CDR3 have the highest diversity in both heavy and light chains of antibodies?

A

Whereas CDR1 and CDR2 are both entirely coded for by the chosen V gene segment, CDR3 is encoded by the combination of the V gene segment, and the J segment (as well as the D segment in heavy chains). The combination of the two segments, as well as the high likelihood of the addition or deletion of random nucleotides where the segments are joined leads to a much higher diversity in CDR3.

44
Q

What is a signal joint?

A

In V(D)J recombination, when two RSSs are brought together by endonuclease complexes, the ends of the conserved heptamers are joined in a head-to-head fashion, this is the signal joint.

45
Q

What is a coding joint?

A

In V(D)J recombination, when two RSSs are brought together by endonuclease complexes, the ends of the chosen V and J segments are joined together; this is the coding joint.

46
Q

double-strand break repair (DSBR)

A

In all cells, this process is responsible for rejoining the two ends at the site of a double-strand break in DNA. The DSBR joining process is imprecise, meaning that nucleotides are frequently gained or lost at the site of joining.

47
Q

Ku

A

An ubiquitous protein contributing to double-stranded break repair - heterodimer (Ku70:Ku80); this forms a ring around the DNA and associates tightly with a protein kinase catalytic subunit, DNA-PKcs, to form the DNA-dependent protein kinase (DNA-PK)

48
Q

DNA-PK

A

DNA-dependent protein kinase - formed from Ku70:Ku80, catalytic DNA-PKcs, and Artemis,

49
Q

Artemis

A

Protein in the DNA-dependent protein kinase complex that has nuclease activity and leads to a somewhat random single stranded break in the hairpin formed by the coding joint in somatic recombination

50
Q

DNA ligase IV

A

Along with XRCC4, joins the two blunt ends of the heptamers in the recombination signal sequences and forms a signal joint between them.

51
Q

terminal deoxynucleotidyl transferase (TdT)

A

lymphoid-specific enzyme that is part of the recombinase complex and randomly adds nucleotides to the single strand ends of the broken hairpin loop that makes up the coding joint.

52
Q

What are the four main processes of diversity in the Immunoglobulin repertoire?

A

gene segment combinatorial diversity,
junctional diversity,
heavy-chain / light-chain combinatorial diversity
somatic hypermutation

53
Q

P-nucleotides

A

so called because they make up palindromic sequences added to the ends of the gene segments. This comes from the opening and straightening out of the hairpins, and the subsequent filling in of the complementary nucleotides by DNA repair enzymes

54
Q

N-nucleotides

A

Non-template coded nucleotides added to the exposed single strand ends of broken hairpins during somatic recombination. Added by TdT.

55
Q

Gene segments of the TCR-alpha chain

A

like the loci of the immunoglobulin light chains, contains V and J gene segments (Va􏰀 and Ja􏰀)

56
Q

Gene segments of the TCR-Beta chain

A

like the locus of the immunoglobulin heavy chain, contains Db gene segments in addition to Vb􏰁 and Jb􏰁 gene segments

57
Q

To what components of the MHC:peptide complex do the different CDR regions of the TCR contact?

A

CDR1 and CDR2 mostly contact the less-variable MHC molecules. CDR3, which is the most variable of the TCR CDRs, mostly contacts the peptide held within the MHC molecule.

58
Q

Where is the highest variability in the TCR and why?

A

Because the TCR􏰀 locus has so many J gene segments, the variability generated in this region is even greater for T-cell receptors than for immunoglobulins. Thus, most of the diversity resides in the CDR3 loops that contain the junctional region and form the center of the antigen-binding site.

59
Q

ZFP318

A

a protein structurally related to the U1 small nuclear ribonucleoprotein of the spliceosome that is required for alternative splicing of the long pre-mRNA from the VDJ exon to the C-delta􏰌 exons. Is required for splicing mRNA for IgM to mRNA for IgD.

60
Q

TAP proteins

A

ATP-dependent transporters associated with antigen processing-1 and -2, normally associated with the endoplasmic reticulum membrane that specifically transport peptides between 8 and 16 amino acids long into the ER lumen

61
Q

What are the ‘preferrences’ of TAP proteins for transporting peptides into the ER?

A

The transporters prefer hydrophobic or basic residues at their carboxy end, and bias against proline in the first three amino acids

62
Q

TCP-1 ring complex (TRiC)

A

Cellular chaperone in the Endoplasmic reticulum that prevents further degradation of imported peptides so that they can be loaded into MHC class I molecules.

63
Q

endoplasmic reticulum aminopeptidase associated with anti- gen processing (ERAAP)

A

Enzyme that trims the amino terminus of ER-resident peptides so that it can fit in the limited groove of. the MHC class I molecule. Expression is increased by IFNg signaling.

64
Q

calnexin

A

General-purpose chaperone protein that binds to newly formed MHC class I alpha chains upon their entry into the ER, keeping them in a partly folded state. Disassociates when the alpha chain binds with B2 microglobulin.

65
Q

peptide-loading complex (PLC)

A

The PLC maintains the MHC class I molecule in a state that is receptive to peptide binding and mediates the exchange of low-affinity peptides bound to the MHC molecule for peptides of higher affinity, a process called peptide editing.

66
Q

Sec61

A

ATP-dependent transport complex that appears to transport peptides back out from the endoplasmic reticulum lumen if they cannot bind to an MHC class I molecule.

67
Q

membrane associated ring finger (C3HC4) 1, or MARCH-1

A

An E3 ligase that targets the lysine residue in the cytoplasmic tail of MHC class II molecules and tags them for degradation. expressed constitutively in B cells and induced by the cytokine IL-10 in other cells. This pathway is. shut down in infection to increase the levels of MHC II molecules.

Immunology (17 decks)

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