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Immunology > Brainscape Spring Semester - Immunology Exam 2 > Flashcards

Brainscape Spring Semester - Immunology Exam 2 Flashcards

1
Q

Where does T-cell activation occur?

A

In the secondary lymph tissues

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2
Q

What does a naive T-cell turn into after encountering an antigen?

A

Naive T-cells activate to become effector T cells (cytotoxic or helper)

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3
Q

What does T-cell activation lead to?

A

1) Interaction with B-cells 2) Cytokine production that causes: altered phagocyte, B cell and T cell activity

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4
Q

What is the function of dendritic cells?

A

They bring antigens from the site of infection to the secondary lymph tissue. They enter the draining lymph node and settle in the T-cell areas.

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5
Q

Do DC’s present antigens on MHC class I , class II or both?

A

Both. DCs use MHC class II to present to CD4 Tcells and MHC class I to present to CD8 Tcells

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6
Q

Are cytoplasmic antigens recognized by MHC class I, class II, or both?

A

MHC Class I present cytoplasmic antigens (viruses) to CD8+ T-cells

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7
Q

In lymph nodes, where can DC’s be found? Where are macrophages found?

A

DC’s are confined to the cortex, macrophages are in both the cortex and the medulla

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8
Q

How do T cells monitor antigens presented by the macrophages and dendritic cells?

A

They crawl over the antigen presenting cells to check for the antigen they are specific to.

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9
Q

What happens if a T cell does not encounter their specific antigen in the lymph node?

A

They will leave the node through the efferent lymph

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10
Q

What happens when a T cell encounters their specific antigen in a lymph node?

A

The T cells that encounter the specific antigen will bind and lock the antigen and begin to proliferate and differentiate into effector cells

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11
Q

How does the path of lymphocytes in a lymph node differ from the path of DC’s?

A

Lymphocytes will exit through the efferent lymph, but DC’s will stay behind.

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12
Q

Describe the structure of a mature TCR.

A

Made of one alpha and one beta chain. The TCR then associates with CD3 and zeta chain.

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13
Q

How does a TCR transmit signals to the nucleus?

A

The cytoplasmic tail of the TCR has no signaling capabilities. The signaling comes from the CD3 and zeta cytoplasmic ITAM regions

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14
Q

Describe the T Cell-HEV interaction.

A

T cells roll along the endothelium of the HEV. Loose contacts are made between the T cell and the HEV endothelium by GlyCAM-1 of HEV and L-selectin of naive T-cell.

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15
Q

How does a chemokine signal change the T Cell-HEV interaction?

A

The chemokine signal leads to a conformational change of integrin LFA-1 causing LFA-1 to bind tightly to ICAM-1. The lymphocyte rolling is stopped, and it is able to enter the lymph node via diapedesis.

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16
Q

Which T cell surface receptors are involved with the interaction with DCs?

A

The same as those involved in leaving the blood stream: Selectins, Ig-type receptors, CCRs

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17
Q

What are the two signals required to generate T-cell expansion?

A

1) TCR/CD4 complex signals stability 2)CD28 co-stimulator binds B7 of the DC, releases second messenger

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18
Q

What happens in the absence of B7?

A

The cell can no longer respond to infection (“Anergic”)

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19
Q

Are costimulatory molecules constantly expressed?

A

No. They are only expressed during infection.

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20
Q

What triggers the expression of MHC class II and B7?

A

Phagocytosis and breakdown of bacteria by macrophages. The co-stimulatory signal is delivered to the T-cells that recognize the bacterial peptide antigen.

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21
Q

What are the three types of professional antigen presenting cells in secondary lymph tissues?

A

DCs (in cortex), Macrophages (cortex and medulla), and B cells (lymphoid follicles)

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22
Q

What is an immunological synapse?

A

The point of contact between T-cell and DC

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23
Q

Describe the molecules involved with the immunological synapse in a resting T-cell.

A

The ITAMs (on CD3 and zeta) are not phosphorylated when the MHC-peptide is not connected to the TCR.

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24
Q

What happens to the ITAMs when a MHC ligand binds the TCR?

A

They are phosphorylated by receptor associated kinases

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25
Q

When does ZAP-70 become activated?

A

When the co-receptor binds to the MHC ligand it is able to bind to the phosphorylated zeta chain ITAMs and is phosphorylated and activated by Lck

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26
Q

What are the 2 major regions of the immunological synapse?

A

The c-SMAC (supramolecular activation complex) is in the center and contains the TCR, coreceptors, costimulatory receptors, and signaling molecules all concentrated. The p-SMAC is the peripheral zone and contains integrin LFA-1, ICAM and talin

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27
Q

Do the high affinity specific interactions occur in the cSMAC or the pSMAC?

A

They occur in the cSMAC

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28
Q

What are the 3 pathways that ZAP-70 activation causes?

A

(1) Second messenger inositol triphosphate leads to transcription factor NFAT activation (2) Activate protein kinase c-Ѳ leading to activation of NFkB (2) Activation of Ras cascade that activates Fos, a component of the AP-1 TF

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29
Q

What do NFAT, NFkB and AP-1 all combine to produce?

A

Cell deivision, proliferation and differentiation to effector T cells

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30
Q

What is the purpose of the cytokine IL-2?

A

IL-2 controls bursts of cell division and acquisition of effector function. This cytokine is synthesized and secreted by the T-cell itself when both signal 1 and signal 2 are received.

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31
Q

What TF activates IL-2?

A

NFAT activates IL-2

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32
Q

How do the IL-2 receptors of naive and activated T-cells differ?

A

The naive T cells have moderate affinity made of beta and gamma subunits. The activated T cells have high affinity IL-2 receptors made of alpha, beta and gamma subunits.

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33
Q

What does the signal of the high affinity IL2 receptor cause?

A

It causes massive T-cell prolifation (x~1000 in a week)

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34
Q

Can T-cell activation occur without both the co-stimulatory signal and the specific signal?

A

No. It needs both. With only specific signal (signal 1), the T-cell will become anergic, preventing IL-2 production. With only co-stimulatory signal, there is no effect.

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35
Q

What are the three types of cells that immature effector T cells can differentiate into?

A

TH1, TH2 and regulatory (Treg) T cells

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36
Q

Compare and contrast TH1 and TH2 cells.

A

TH1 cell development is stimulated by IL-12 (from macrophages and DCs) and IFN-gamma (from NKs). TH1 are associated with cell mediated immunity and are effective against intracellular parasites. TH2 cell development is stimulated by IL4 and IL5 and causes general activation of B cells. TH2 are associated with humoral immunity and effective against extracellular pathogens.

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37
Q

Which cell type requires a stronger co-stimulatory signal for activation: CD4 or CD8?

A

CD8 requires stronger signal than CD4 for activation, which can only be delivered by dendritic cells.

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38
Q

What are the three different means of activating CD8 T-cells?

A

(1) DCs with high B7 expression can activate naive CD8 cells. These cells then produce IL-2 and its receptor driving its own proliferation and differentiation. (2) DC can activate CD4, which can then activate the APC, leading to co-stimulation and activation of the CD8 cell. (3) DC activates CD4, which produces IL-2 that can activate CD8 to express IL-2 receptors.

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39
Q

What are the differences between naive and effector T-cells?

A

Naive T cells require co-stimulation through CD28, but effector cells are CD28-independent. Naive cells have lower [CD2] and [LFA-1]. The effector cells have no L-selectin, but have VLA-4 instead (no HEV extravasation).

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40
Q

What is the purpose of VLA-4?

A

VLA-4 is an integrin expressed in effector T cells. It binds to VCAM-1, which is expressed in the endothelium of inflamed tissues.

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41
Q

Describe cytokines.

A

They are chemicals that alter local behavior. They are short lived and can function via autocrine or paracrine signals. Many cytokines made by T cells are part of the interleukin family (IL).

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42
Q

What is a cytotoxin?

A

A chemical that kills infected cells. They are specialized products of cytotoxic CD8 cells.

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43
Q

What is CD40L?

A

CD40L is a membrane bound cytokine on the T cell surface. Macrophages and B cells have the CD40, which binds to CD40L (ligand). TH1 CD4 cells can induce macrophage activation this way leading to more proficient and deadly macrophages.

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44
Q

How do the intracellular interactions differ if the cell is presenting a viral antigen or not?

A

Cell not presenting the viral antigen throuh the MHC class I are not destroyed. Cells presenting the Ag interact tightly with CD8 T cell through the TCR. The cytoskeloton is rearranged following Ag presentation through TCR. Lytic granules are released at the site of cell contact.

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45
Q

How do cytotoxic T cells initiate apoptosis of target cells?

A

The CTL recognizes the virus-infection cell and programs the target cell to die. It uses granules and FasL to initiate apoptosis in the target cells.

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46
Q

Can TH1 cells activate macrophages on their own?

A

Yes. They can provide both required activation signals (CD40L and IFN-gamma) to the macrophage.

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47
Q

What function do activated macrophages serve?

A

They kill intravesicular bacteria and microorganisms

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48
Q

What are the different cytokines produced by activated TH1 cells in response to infected macrophages and what are their roles?

A

(1) IFN-gamma and CD40L activate macrophages (2) Fas ligand or LT kills chronically infected macrophages to be destroyed by healthy macrophages (3) IL2 induces T-cell proliferation (4) IL3 + GM-CSF induces macrophage differentiation (5) TNF-alpha +LT activates endothelium to induce macrophage adhesion and exit from blood vessel (6) CXCL2 causes macrophage accumulation

49
Q

What happens when a pathogen resists macrophage killing?

A

A ring of macrophages forms around the infected cell. The entire complex is then surrounded by T cells. The pathogen persists within the enclosed structure. It can calcify to produce Ghon complexes visible on X-rays. Cells within the lesion undergo caseous necrosis.

50
Q

Describe the role of TH2 cells in activating B cells.

A

Antigen recognition induces expression of CD40L on TH2 cell, which can then activate the B cell by binding to CD40. Then B cells proliferate and differentiate into antibody secreting plasma cells.

51
Q

How are carbohydrate antigens effectively recognized for vaccinating against pathogens with CH2O Ags?

A

The antigen is coupled to a tetanus toxoid that stimulates a strong MHC class II response. This leads to immune response and production of a polysaccharide antibody.

52
Q

Describe the structure of the HIV RNA and proteins.

A

Has negative strands of RNA, which are converted to positive strands w/ reverse transcriptase for infection. The HIV has a spherical structure with envelope proteins on the outside, matrix proteins inside along with a nucleocapsid containing the RNA genome.

53
Q

What are the three major genes found in the HIV viral RNA?

A

(1) gag: core proteins and matrix proteins (2) pol: reverse transcriptase, protease and integrase enzymes (3) env: transmembrane glycoproteins gp120, gp41

54
Q

Describe how HIV is presented to the immune system following infection.

A

Intraepithelial DCs bind HIV via DC-SIGN. The HIV is internalized into early endosomes. The DCs then migrate to lymph nodes and transfer the HIV to CD4 T cells

55
Q

What does the gp120 of HIV bind to?

A

gp120 tightly binds CD4, which then allows gp41 to mediate fusion of the viral envelope with the host cell plasma membrane

56
Q

Describe the process of HIV fusing with the T cell membrane.

A

After the HIV binds to the CD4 and the co-receptor CCR5/CXCR4 on the T cell, the viral envelope fuses with the cell membrane, allowing the viral genome to enter the cell.

57
Q

What happens once the HIV viral genome enters the cell?

A

The RNA is converted into double-stranded cDNA by reverse transcriptase and then the viral cDNA enters the nucleus and is integrated into the host DNA.

58
Q

What proteins are encoded by HIV and what do they do?

A

Tat and Rev promote replication of the viral genome. Tat prevents transcription from shutting off, thus amplifying the transcription of viral RNA. Rev increases the transport of viral RNA to the cytoplasm. This leads to assembly of new viral particles in the cytoplasm, which can leave the cell and infect more.

59
Q

Describe the immune response to people with HIV over time.

A

Immediately after infection, some express flu-like symptoms. The virus initially becomes abundant in the peripheral blood and the number of circulating CD4 drops dramatically. Seroconversion occurs, leading to detectable amounds of anti-HIV in the blood. An asymptomatic period can last 2-15 years during which the level of CD4 gradually declines. When the CD4 levels are too low to mount effective immune response to other infectious agents, the clinical latency ends leading to onset of AIDS.

60
Q

What is combination therapy?

A

A combination of treatments used to attempt to destroy the entire population of viruses before any one has enough mutations to resist all drug treatments. This was invented in the 90’s and reduced the death rate from AIDS to 30% the original.

61
Q

What are the two categories of dendritic cells?

A

1) Conventional: “steady state” DCs 2) Nonconventional DCs derived from monocytes and inflammation

62
Q

What are antibodies?

A

The secreted form of a B-cell antigen receptor. They are specific meaning they can only bind to one antigen and are made up of immunoglobulins.

63
Q

What are the two types of chains that make up antibodies?

A

2 heavy and 2 light chains with variable region at the amino terminal of each chain. This is where the antibody binds.

64
Q

Describe the folding of immunoglobulins.

A

Each domain is composed of 2 beta sheets that are held together by strong hydrophobic interactions and stabilized by disulfide bonds. There are compact and stable protein domains which vary in number depending on the immunoglobulin isotype.

65
Q

What are the two light chain locii and what chromosomoes are they found on? What about the heavy chain locus?

A

Lambda (c.22) and Kappa (c.2) are the 2 light chain locii. The heavy chain locus is found on c.14

66
Q

Describe the gene segments of the immunoglobulin chains.

A

Leader peptides (L) flank the V regions which are upstream from J and C regions. L and C both contain exons and introns.

67
Q

Describe the rearrangement that occurs in the formation of the heavy chain V region.

A

Germline DNA undergoes somatic recombination to join D with J. This DJ segment is then joined with the V to form a VDJ through another round of somatic recombination. This combination must result in a correct reading frame in order for a viable protein to be produced.

68
Q

Describe the rearrangement that occurs in the formation of the light chain V region.

A

Germline DNA undergoes somatic recombination to join V and J to VJ. No D segment is present in light chains.

69
Q

What is the 12/23 rule?

A

Recombination signal sequences (RSSs) are immediately adjacent to coding regions is a 7 bp heptamer. After the heptamer is either a 12 or 23 bp spacer (which corresponds to 1 or 2 helical turns) which is followed by a 9 bp region. These ensure that the segments are joined in the correct order.

70
Q

How is the accessibility of the DNA regulated?

A

In the absence of transcription, rearrangement does not occur, so the histones can be modified to change the accessibility to the DNA. Methylation increases stability resulting in lower accessibility and acetylation increases accessibility.

71
Q

What is the function of RAG1 and RAG2?

A

genes that activate recombination by binding to RSS and cleave DNA

72
Q

Describe the process of RAG cutting the DNA to form a coding joint.

A

RAGs bind to RSS and align, forming a loop of DNA to be excised. The DNA is cleaved, forming a DNA hairpin at the end of each sequence. The ends are repaired with repair enzymes to bring together the 2 ends. The hairpins are then opened by RAGs by nicking one DNA strand, generating palindromic P-nucleotides (bases that were complimentary are now on the same strand). Then TdT adds N-nucleotides randomly to fill gaps and pair up strands.

73
Q

What gene is mutated in diseases such as SCID and Omenn syndrome?

A

The RAG genes.

74
Q

What is the function of TdT?

A

TdT= terminal deoxyribocele transferase. TdT randomly adds new nucleotides to the 3’ overhang. This is template independent, so the added nucleotides are not found in the germline.

75
Q

What determines whether the developed immunoglobulin will be IgM or IgD?

A

The most proximal C regions to the VDJ are Cμ and Cδ. Alternative splicing determines which will be present.

76
Q

In a resting B cell, which immunoglobulins are expressed?

A

IgM and IgD

77
Q

Describe the structure of a B-cell receptor.

A

They are mebrane bound with the hydrophobic C-terminal sequences of the heavy chains inserted in the membrane. They require Igα and Igβ for transport to the cell surface. These 2 proteins transfer signals from the receptor into the cell.

78
Q

What determines whether the IgM will be transmembrane or secreted?

A

Alternative splicing of the heavy chains. After an encounter with an antigen, isotypes are produced to be secreted by splicing at the c-terminus of the Ig

79
Q

After B-cell activation, is the VJ sequence stable?

A

No. Additional somatic hypermutation occurs after B-cell activation resulting in a much higher affinity antibody being formed by new random mutations

80
Q

In heavy chains and light chains, which CDR has the highest rate of mutation one week after a primary immunization?

A

CDR 3 of the heavy chain shows the greates mutation rate. There is little mutation in the light chain after 1 week.

81
Q

2 weeks after primary immunization which CDRs have the highest rate of mutation?

A

CDR 3 of the heavy chain and CDR 1 of the light chains.

82
Q

What is the function of AID?

A

AID= activation induced cytidine deaminase. An enzyme found only in developing B cells that causes somatic mutation by substituting U’s for C’s during transcription. The cell has mechanisms to repair this, so the U is then removed and replaced by any 1 of the normal DNA bases. This process allows for “testing” of antibody affinities to progressively produce stronger antibodies.

83
Q

What are switch regions?

A

Regions with a very high mutation rate that flank the 5’ side of each C region and mediate recombination. This allows for a changing to a different C region, converting from IgM to a different isotype.

84
Q

Describe the mechanism of switching from IgM to IgG

A

(1) IgM and IgD are produced (2) AID selectively targets the Sμ and Sγ1 switch regions (3)DNA in the Sμ and Sγ1 regions are nicked (after C’s changed to U’s and endonuclease activity) (4) Circular DNA molecule leaves looping out the μ region, leaving the γ IgG gene

85
Q

What is base excision repair?

A

Removing a base from a sugar, which makes the location highly susceptible for mutation and breakage. Conducted by UNG which converts uridine to abasic.

86
Q

What are the fates of an abasic sugar a DNA molecule?

A

APE1 can create single strand nicks that cause gene conversion, or it can cause double stranded breaks that lead to class switch recombination. REV1 can convert the abasic sugar leading to somatic hypermutation.

87
Q

Describe the “competition” between β and γ/δ during T-cell development.

A

They race to produce a successful rearrangement. If the β rearranges before the γ AND δ, then the γ/δ process stops and the β chain is produced and the cell will then undergo selection. If the γ/δ rearranges first, then the T-cell would leave the thymus as a γ/δ T-cell without selection.

88
Q

What is the function of the J-chain?

A

It holds together the pentameric form of the IgM antibody. This complex has 10 antigen binding domains. The J-chain also stabilizes the IgA dimer, which plays a major role in immune response in mucous membranes.

89
Q

Describe the process of hybridoma technology.

A

Allows for the production of monoclonal antibody. B cells from immunized mouse are fused together with myeloma cells. These fusion cells are grown in HAT media that selects for B-myeloma fusion. The antigen specific hybridoma can then be selected and cloned.

90
Q

What are the two pathways for nucleotide synthesis?

A

1) de novo: builiding from scratch 2) Salvage: take up metabolites and Nt’s from environment and incorporate back into DNA/RNA

91
Q

How are m-m fusions prevented from living in HAT media?

A

Myeloma cells are generally deficient in the HGPRT gene required for salvage nucleotide synthesis. The HAT media blocks the de novo pathway, so only feasible immortalized cells will be when myeloma fuses with normal B-cell that have the normal HGPRT sequence.

92
Q

What properties are selected for during T-cell development?

A

(1) Clonal expression of TCR (2) MHC restriction (3) Self-tolerance (4) Lineage-specific effector function

93
Q

What percentage of T-cell precursors actually leave the thymus as mature T-cells?

A

only 4%

94
Q

Describe the location(s) and path that T-cells follow during their development.

A

Begins in bone marrow with hematopoietic stem cells. These develop into common lymphoid progenitors and the NK/TC progenitors, which migrate to the Thymus. Double negative T cells develop in the thymus. These develop into double positive cells which then differentiate into effector T-cells

95
Q

What is the goal of positive selection?

A

To verify that the TCR can recognize self-MHC

96
Q

What is the goal of negative selection?

A

To make sure that the strength of the TCR-MHC is not too strong or too weak.

97
Q

What is the stroma?

A

The network of epithelial cells found in the thymus

98
Q

What is involution of the thymus?

A

Steady degeneration of the thymus begins during 20’s and progresses to produce few T-cells in geriatric population

99
Q

What percentage of cells in the thymus are T-cell progenitors?

A

99%

100
Q

Where does most T-cell development occur within the thymus?

A

Most occurs in the thymic cortex, made of the epithelial stroma

101
Q

What is DiGeorge syndrome?

A

Individuals are born without a thymus, and therefore cannot produce T-cells.

102
Q

What is the phenotype of scid mice?

A

severe combined immunodeficiency. these mice have bone marrow problem but normal thymus

103
Q

What is the phenotype of Nude mice?

A

They are athymic (similar to DiGeorge syndrome)

104
Q

How can scid and Nude mice be used to study the roles of bone marrow and thymus in the immune system?

A

Mice with scid can receive bone marrow transplants from Nude mice to restore immune function. Likewise, Nude mice can receive thymus transplats from scid mice to reconstitute immune system. This shows that: normal lymphocyte precursors in bone marrow develop in the presence of the thymus. In the presence of thymic epithelium, normal lymphocytes can develop into T-cells.

105
Q

What is pTα?

A

A placeholder for the α-chain of the TCR, associates with the β-chain

106
Q

Describe the composition of the earliest T-cell precursors.

A

They are CD3- and do not have either coreceptor (CD4, CD8)

107
Q

Which membrane receptor is expressed first in T-cells: CD3, CD4 or CD8?

A

CD3 is expressed as the race to properly rearrange beta and gamma/delta occurs.

108
Q

During the double positive stage, which receptors are expressed on T-cells?

A

CD4 and CD8 (and CD3)

109
Q

During which stages of T-cell development is Notch expressed?

A

Notch is a transcription factor expressed during all 4 double negative stages and the 2 double positive stages.

110
Q

During which stages of T-cell development is CD44 expressed?

A

During the first three double negative stages

111
Q

During which stages of T-cell development is CD25 expressed?

A

CD25 is expressed in the 2nd and 3rd double negative stages

112
Q

Within the thymus, describe the path that a developing T-cell takes.

A

DN1 cells enter through venules in the medulla. They migrate on medullary DCs to the cortex, where they associate with cortical cells of epithelial origin and mature to DN2, DN3 and DN4. The immature DP cells then return to the medulla and mature to express either CD4 or CD8 thymocytes.

113
Q

Describe the gene rearrangement that occurs during thymocyte development.

A

Dβ-Jβ rearrangement occurs first, which is followed by Vβ-DJβ rearrangement. Then the β-chain protein is produced, and expressed on the surface with the pTα protein. β rearrangement stops, and α rearrangement begins. Vα-Jα rearrangement occurs, and then the α-chain is expressed on the surface along with the β-chain

114
Q

What cell stages does β and α rearrangement occur in?

A

β rearrangement occurs in the DN cells and α rearrangement occurs in the DP cells

115
Q

What determines T-cell commitment?

A

IL-7 and NOTCH

116
Q

Describe the structure of the Notch-1 protein.

A

It is a transmembrane protein that binds epithelial Notch-ligand. Upon binding, the cytoplasmic tail is cleaved and can translocate to the nuclease to regulate gene transcription

117
Q

How many rearrangement attempts are possible during β chain rearrangement?

A
  1. Because there are 2 clusters of D and J, there are 2 tries on each homolog to successfully join the 2 regions to make a useable DJ
118
Q

How many rearrangement attempts are possible during α chain rearrangement?

A

Many attempts are possible because there are numerous repeats of V and J regions within the α gene.

Immunology (7 decks)

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