Immunology Flashcards
1
Q
A collective and coordinated protective response to the introduction of a pathogenic organism is known as ____________.
A
The immune system.
2
Q
Physical barriers, preformed effectors, induced innate responses such as pattern recognition receptors, inflammation, are part of the _________________.
A
Innate immunity.
3
Q
Sites of pathogenic replication include ________ and _______.
A
Extracellular spaces such as bodily fluids and epithelial surfaces
AND
Intracellular spaces such as cytoplasm and vesicles
4
Q
Pathogens cause direct and indirect damage via ______________.
A
Production of exo and endotoxins
Direct cytopathic effect
5
Q
Three types of innate barriers which prevent pathogens from crossing epithelial surfaces or colonizing tissues are ________, _________, and ____________.
A
Mechanical
(Tight junctions, air or fluid flow,
mucus)
Chemical
(Low pH, enzymes, antimicrobial
peptides/defensins (Paneth
cells)), and fatty acids.
Microbial
Microbiota/Commensal bacteria
6
Q
Pathogens must overcome the innate immunity to establish a focus of infection. This happens in what stages?
A
Penetration of epithelium
Local infection of tissues underneath: inflammatory response
Recruitment of more effector
cells and molecules
Blood clotting.
7
Q
Epithelial Cells and Phagocytes produce antimicrobial proteins:
A
Lysozyme: glycosidase
Lectins: Carbohydrate-binding
proteins
RegIII: Pore-formation in bacterial
membrane.
Kills G+ bacteria preferentially.
Defensins: Cationic, amphipathic,
and disrupt bacterial and fungal
membranes via insertion and
pore formation.
8
Q
Phagocytes do what to pathogens?
A
Recognize, ingest, and kill pathogens.
9
Q
Types of phagocytes?
A
Macrophages and Monocytes, or “Large eaters”
Neutrophils: Loaded first responder
10
Q
Where are monocytes found?
A
In the blood
11
Q
Where are macrophages found and what are their functions?
A
Found in tissues.
Main functions are to destroy pathogens and activate the immune responses via inflammation activation and antigen presentation.
12
Q
Name the different forms of macrophages through the bodily tissues.
A
Liver: Kupffer cells
Lung: Alveolar Macrophages
Spleen: Splenic macrophages
Brain: Microglia
13
Q
Where are neutrophils found and what are their primary functions?
A
Neutrophils, or PMN’s (polymorphonuclear leukocytes) are phagocytes that mainly target bacteria and fungi via releasing antimicrobial peptides and by the release of NETS (extracellular traps)
The neutrophils contain granulocytes which contain various granules containing antimicrobial peptides, chemicals, and enzymes.
14
Q
Phagocytosis can be triggered via the direct recognition of the pathogen and by the recognition of opsonin. How does this function>
A
Soluble proteins binding to the surface of pathogens are called opsonin and mark them for destruction (opsonization)
15
Q
Define the basic processes of phagocytosis:
A
Innate immune system recognizes pathogenic microbes. Pathogenic microbes may be marked for destruction or opsonization. Phagocytes bind to the receptors/antigens and the pathogen is pulled inward (endocytosed), where the pathogen + vesicle complex is called a phagosome.
The phagosome containing the pathogen with lysosome form the phagolysosome.
Lysosomes contain antimicrobial peptides, chemicals, and enzymes.
16
Q
Question: In patients with lymphomas, the cancer cells invade the bone marrow and destroy the environment required for normal hematopoesis. The leads to bone marrow failure, which disrupts the production of hematopoietic cell lineages. All of the follow cell types would be affected by this EXCEPT:
A. Red blood cells
B. Endothelial cells
C. Lymphocytes
D. Dendritic cells
E. Granulocytes,
A
B. Endothelial cells
17
Q
Name the preformed molecules which aid in the innate immune system:
A
Lysozyme, lectins
Antimicrobial peptides (such as
defensins)
Complement system
Recognition
Effector
18
Q
The complement system is composed of (how many?) ____ proteins.
A
More than 30.
19
Q
The complement system is composed of soluble _____ and ____ molecules.
A
Soluble PRR (pattern recognition receptors) AND effector molecules.
20
Q
With the complement system, the soluble proteins are circulating where?
A
In the blood and bodily fluids.
21
Q
True or false: some of the complement system exists as protease zymogens (inactive enzymes) that are activated via proteolytic cascades.
A
True.
22
Q
Is the complement system slow or fast in its response time?
A
Rapid response time.
23
Q
What is a protease?
A
A protein enzyme that cuts another protein.
24
Q
The complement system consists of three pathways. Name them and briefly describe them.
A
Classical pathway: pathogen or
pathogen-antibody complex
Lectin pathway: carbohydrates on
pathogen surface
Alternative pathway: Amplification
and spontaneous iteration of
response
25
What is the general flow of the complement system?
Stages of complement action:
1. Pattern-recognition trigger
2. Protease cascade
amplification/C3 convertase
3. Inflammation
3.1 Phagocytosis
3.2 Membrane attack
26
All complement pathways lead to what formation?
C3 convertase
27
c3b and c4b are
opsonins
28
NK cells recognize and kill what kind of cells?
Human cells, both damaged and infected.
They do NOT kill pathogens by seeking them out.
These cells search out for HUMAN cells.
Granule dependent and death-receptor dependent.
Antigen is not important due to placement of polymorphic spot on receptor.
29
What is a zymogen?
Inactivated protease.
30
What is an inactivated protease called?
A zymogen
31
What is proteolytic cleavage?
Proteolytic cleavage is when proteases cleave other proteins.
32
What is a proteolytic cascade?
A cascade of proteases cleaving each other via via proteolysis.
33
Classical Pathway involves what protein complex?
C1q binding to pathogen surface.
34
Lectin Pathway involves what complex?
MBL and ficolin (Mannose binding lectin) binds to the carbohydrates on pathogen surfaces.
35
Alternative pathway involves what?
Amplification and spontaneous activation. Involves C3 spontaneously and without cue undergoing hydrolysis.
36
All pathways generate a C3 convertase. But... what IS the function of C3 convertase?
The C3 convertase, or Complement-3-convertase, is a protease which cleaves C3, or Complement-3 proteins.
The cleavage generates a short strand (C3a) and long strand (C3b). C3b binds to the pathogen surface.
37
What happens to pathogens tagged with a C3b?
Phagocytes have multitudes of receptors, some of which bind to C3b. This is the CR1 receptor, or Complement-Receptor-1.
Pathogens with a large amount of C3b on their surface are consequently bound to the phagocyte at the CR1 receptor.
When C5a binds to a C5a receptor, the bound pathogen is then endocytosed and consequently phagocytosed.
38
What purpose do C3a and C5a have as they freely float about?
C3a and C5a recruit phagocytic cells to the site of infection and promote inflammation.
Specifically, cleaved C3a and C5a activate epithelial cells and mast cells.
Mast cells consequently release cytoplasmic granules containing vasoactive histamines and increase the permeability of blood vessels.
39
What is the composition of a C3 convertase?
C4b2a, or C4b + C2a.
40
What is the composition of C5 convertase?
C4b2a3b OR C4b + C2a + C3b
41
Describe the processes of the formation of the membrane attack complex (MAC).
1. After C5 is cleaved by C5 convertase, soluble C5b binds to C6 and C7.
2. C5b67 complexes bind to the membrane via the C7 component.
3. C8 then binds and inserts into the membrane.
4. C9 consequently binds and polymerizes 10-16 units of other C9.
5. Leads to pore formation in the pathogen. Think of a fucking green pipe from Super Mario.
Hole in pathogen. Pathogen leaks, shit rushes in, pick your flavor of its inevitable death.
42
What is a cytokine?
‘Cytokine’ is a term for any protein secreted by immune cells that affects the
behavior of nearby cells bearing appropriate receptors.
43
Pattern Recognition Receptors (PRR's) recognize what?
Pathogen-associated molecular patterns (PAMPS)
44
Four canons of inflammation:
Pain
Redness
Heat
Swelling
45
What are the ligands for signaling PRR's?
PAMPs
46
TLR's (Toll-like Receptors) recognize what?
PAMPs
47
Ligand binding induces TLR _____ or ________.
Dimerization OR conformational change in preformed TLR dimers.
48
Describe TLR4 signaling, step by step:
(A complex of TLR4, MD2, CD14 and LPS is assembled at the macrophage surface)
----------------
1. An LPS molecule is extracted by an LBP (LPS binding molecule) from gram negative bacteria.
2. LPS is transported to TLR4-MD2 complex via cofactor CD14 on surface.
3. LPS binding induces TLR4 dimerization
------------------
(Dimerized TLRs recruit IRAK1 and IRAK4, activating the E3 ubiquitin ligase TRAF-6)
---------------------
4. Dimerized TLR4 recruits MyD88 and/or MAL through TIR : TIR interactions.
5. Oligomerized MyD88 recruits Ser/Thr kinases IRAK1 and IRAK4 through DD interactions.
6. Active IRAK's recruit an E3 ligasee,e TRAF6, together with heterodimeric E2 Ubc13/Uev1A.
---------------------
(TRAF-6 is polyubiquinated, creating a scaffold for activation of TAK1)
----------------------
7. K63-polyubiquinated TRAF6 serves as a platform to recruit and activate TAK1 kinase.
8. TAK1 phosphorylates and activates MAPK kinase, leading to activation of AP-1 transcription factor.
----------------------
(TAK1 associates with IKK and phosphorylates IKK-Beta, which phosphorylates I-Kappa-Beta)
------------------------
9. IKK/NEMO is recruited to the platform by binding to K63-polyubiquitin chains
10. TAK1 phosphorylates and activates IKK-Beta
11. Activate IKK-Beta phosphorylates I-Kappa-Beta (inhibitor of NF-kappa-beta)
---------------------------
(I-Kappa-Beta is degraded, releasing NF-kappa-beta into the nucleus to induce expression of cytokine genes)
----------------------------
12. Phosphorylates I-K-B is degraded through K48 ubiquitination.
13. NF-kappa-beta is free to translocate to the nucleus, inducing expression of pro-inflammatory cytokines, chemokines, and antimicrobial peptides depending on cell types.
49
A more consolidated version of TLR4 Signaling:
Ligand LPS induced dimerization of 2 TLR4 ectodomains brings cytoplasmic
TIR domains close
TLR-TIR domains interact with TIR domain of cytoplasmic adaptors molecules
(MyD88/MAL)
Death domain of adaptor molecules recruit serine-threonine kinases
IRAK4/IRAK1
Recruitment of ubiquitin ligase TRAF6 which generate a polyubiquitin scaffold
on the ligase itself but also on another protein NEMO (also known as IKKγ)
These newly poly-Ub proteins recruits and activate new Ser/Thr kinase TAK1
This last kinase will activate other cascade involving kinases such as
MAPK leading to activation of AP-1 transcription factor
IKK complex leading to activation of NF-κB transcription factors
Transcription factors translocate into nucleus and induce production of pro-
inflammatory cytokines, chemokines, and antimicrobial peptides depending
of the cell type
50
TLR3 Activation of IRFs (a much simpler process)
1. TLR3 recruits adaptor protein TRIF (instead of MyD88)
2. TRIF recruits ubiquitin ligase TRAF3 to produce K63 polyubiquitin chain, eventually activating kinase TBK1
3. TBK1 phosphorylates and activates transcription factor IRF3, which then translocates to the nucleus to initiate type 1 interferon genes.
51
What are RLR's (RIG-I like receptors (RIG = Retinoic acid Inducer Genes)?
RLR's are intracellular sensors of *cytoplasmic* viral RNA, that result in production of pro-inflammatory cytokines and interferons.
Two members of RLR's expressed across cells and tissues:
RIG-I binds to 5' triphosphate viral RNA
MDA5 binds to long viral dsRNA.
52
What is cGAS-STING and where is it located?
An intracellular sensor of infection and mitochondrial damage.
It is located in the cytoplasm.
Ligand is dsDNA and its transcription factor is IRF3.
53
What is IRF3?
Interferon regulatory factor 3 (IRF3) is a transcription factor that controls multiple interferon (IFN)-inducing pathways. IRF3 is activated by phosphorylation in the cytoplasm of a virus-infected cell
54
What are NLR's, where are they located and what are their ligands?
NLR's are NOD-like Receptors are intracellular sensors of bacterial infections located in the cytoplasm that bind peptidoglycan.
Their transcription factor is NF-kappa-beta.
55
What is the response of intracellular NLR's to cell stress/cell damage?
In the presence of extracellular ATP, crstalline uric acid, RNA, toxin, or flagellin, NLR's respond to PAMP's or cell damage and oligomerize into an inflammasome.
The assembled inflammasome recruits and activates caspase 1 which in turn cleaves pro-IL-1Beta and pro-IL-18 and gasdermin D.
Formation of gasdermin D pore allows releases of IL-1Beta and IL-18 and induces pyroptotic cell death.
56
What does cleaved gasdermin D do?
Pore formation from the interior of a damaged or infected cell, caused by NLR inflammasomes.
Pore-forming Gasdermins
Gasdermins (GSDMA-E) exist in cells in an autoinhibitory form.
Inflammatory caspases (activated by inflammasomes) cleave gasdermins
to relieve them from the autoinhibitory state.
Cleaved gasdermins insert the newly generated portions into the plasma
membrane and oligomerize, forming pores to allow the efflux of certain
cytokines and other cellular contents.
57
What is an ALR?
An ALR is an AIM2-like receptor that acts as an intracellular sensor of bacterial/viral infection as well as a sensor of mitochondrial damage.
It is located in the cytoplasm and its ligands are strands of dsDNA.
It functions to activate inflammasomes.
58
What are cytokines?
Cytokines are small proteins, approximately 25kDa, that function in autocrine, paracrine, and endocrine manners.
They are grouped into four families.
59
What are the four cytokine families?
Interleukin-1 (IL-1) family including IL-alpha, IL-beta, and IL-18.
Hematopoietin superfamily including IL-6 and GM-CSF
Interferons (IFNs) including IFN-alpha, IFN beta and IFN gamma.
TNF family including TNF-alpha.
60
How do interferon and hematopoietic receptors signal?
Through the JAK-STAT Signaling Pathway
61
What is the JAK-STAT signaling pathway?
It is the pathway by which interferon and hematopoietin receptors signal. Janus kinases (JAKs) bind to the cytoplasmic tails of cytokine receptors, which induces receptor dimerization, JAK trans-activation, and receptor phosphorylation at tyrosines.
Inactive STATs bind to phosphorylated receptors using the SH2 domain and are then themselves phosphorylated.
62
Chemokines are ...
Chemokines are chemoattractants for leukocytes that work over a distance. They recruit monocytes, neutrophils and other effector cells to the site of infection.
They induce cell adhesiveness and changes in the cytoskeleton.
63
Cyokines activate the _____ phase response.
Acute.
64
Activated macrophages secret a range of cytokines. Name some.
IL-1B
TNF-a
IL-6
CXCL8
IL-12
65
Cytokines have a wide range of autocrine, paracrine, and endocrine effects. What 3 are mainly responsible for inducing fever systemically?
IL-1B, TNF-a, IL-6
66
What is IL-1B?
What does it do locally?
What does it do systemically?
A cytokine that locally activates vascular endothelium, activates lymphocytes and increases access of other effector cells.
Systemically it induces fever and persuades the production of IL-6
67
What is TNF-a?
What does it do locally?
What does it do systemically?
TNF-a is a cytokine that locally activates vascular endothelium and increases vascular permeability which leads to the entry of IgG, complement, and cells to tissues, and increased fluid drainage to lymph nodes.
Systemically it induces fever, mobilization of metabolites, and induces shock.
68
What is IL-6?
What does it do locally?
What does it do systemically?
IL-6 is a cytokine that locally activates lymphocytes and increases antibody production.
Systemically it induces fever and acute phase protein production.
69
What is CXCL8?
What does it do locally?
Chemotactic factor that recruits neutrophils, basophils and T-cells to site of infection.
70
What is IL-12?
What does it do locally?
IL-12 is a cytokine that activates NK cells and induces the differentiation of CD4 T cells into TH1 cells.
71
The selectin-mediated adhesion to leukocyte sialyl-Lewis-x is weak, but allows the leukocytes to ______ the vascular endothelial surfaces.
This allows for other _______ to ________ ligands between the leukocyte and endothelial wall.
Roll along.
receptors on the leukocyte to bind to
72
What is extravasation and what does it involve?
The leakage of vesicant fluids or medications from the vein into the surrounding tissue.
It involves:
Rolling: s-Le-x and selectins, where after weak adhesion via s-Le-x, tight adhesion occurs.
The tight adhesion of a leukocyte to the endothelial wall involves a chemokine induced conformational change in LFA-1 on the leukocyte surface and then tight binding between LFA-1 (leukocyte/neutrophil for example) and ICAM-1 (on endothelial wall)
Subsequent migration and diffusion of leukocyte through the endothelial wall into surrounding tissue occurs.
73
Tumor Necrosis Factor (TNF) alpha (TNF-a) contains infection ______ but induces shock _______.
Locally but induces shock systemically.
74
Describe the stages of both a local infection and a systemic infection (sepsis) involving the release of TNF-a by macrophages. What are the end results?
Locally:
Infection with gram-negative bacteria causes activated macrophages to secrete TNF-a into the tissue.
This causes the increased release of plasma proteins into tissue, phagocyte and lymphocyte migration into tissue and increased platelet adhesion to blood vessel walls.
Phagocytosis of bacteria occurs and the local vessel occludes. Plasma and cells left over after infection drain to local lymph node.
Conclusion: Removal of infection + New adaptive Immunity
Systemically:
Systemic infection with Gram-negative bacteria leads to sepsis.
Macrophages activated in the liver and spleen secrete TNF-a into the bloodstream (not the tissue like before)
Systemic edema causing decreased blood volume, hypoproteinemia, and neutropenia followed by neutrophilla. Decreased blood volume causes collapse of blood vessels.
Disseminated intravascular coagulation leading to wasting and multiple organ failure.
Conclusion: Death
75
TNF-alpha, IL-1Beta, and IL-6 are cytokines but are also known as _________ ________.
Endogenous pyrogens
76
Which three cytokines are responsible for activating the acute phase response?
TNF-a
IL-1b
IL-6
77
Where do the endogenous pyrogens send signals to?
Liver (c-reactive proteins + MBL)
Bone marrow endothelium (neutrophil mobilization)
Hypothalamus (fever)
Fat, Muscle (protein and energy mobilization to accommodate fever)
78
What is secreted by the liver as a result of IL-1B/IL-6?
Pentraxin (C-reactive protein) that is an opsonin and activates the classical pathway of complement.
Collectin (Mannose-binding lectins)
79
What is an interferon?
A cytokine that interferes with viral replication
80
Describe the three types of interferons.
Type 1: IFN-alpha and IFN-beta. These bind to an IFN-a/b receptor and signal through the JAK-STAT pathway. They have antiviral properties that decrease viral replication, activate NK cells and dendritic cells. Synthesized by dendritic cells.
Type II IFN: IFN-y (gamma) binds to IFN-y receptor, has anti-viral and immunoregulatory and anti-tumor properties.
Produced in large quantities by NK cells and some T-cells.
Type III IFN: IFN-delt
81
What are the purpose of Natural Killer (NK) Cells?
They are lymphocytes that are activated by type 1 interferons and macrophage-derived cytokines (IL-12) with germline encoded receptors. These cells have lytic proteins within their granules, produce IFN-gamma and induce death by apoptosis and pore-forming agents.
82
How does the NK function?
How does it distinguish between good and bad cells?
All healthy cells contain a major histocompatibility complex class 1 (MHC 1) on their surface. They also have NK-cell activating ligands.
NK cells bind to the MHC 1 and NK-ligands on cell surfaces. MHC 1 acts as a signal inverter or inhibitory signal, inhibiting binding of the NK-complexes to trigger apoptosis.
However, in the absence of MHC 1 or a healthy MHC-1, the negative signal normally provided by MHC-1 is absent, and as a result nothing stops the NK-cell activating ligand complex and activating receptor on the NK cell from triggering.
Consequently, the activated NK cell releases granule contents, inducing apoptosis and pore formation in the target cell.
83
How do NK Cells kill infected cells?
Death receptor-dependent kill: TRAIL or FasL (NK cells) --> DR4/DR5 or Fas on target cells.
Granule-dependent kill:
Perforin -> Pore forming
Granzymes (proteases) -> apoptosis
84
What are ILCs?
Innate lymphoid cells, or cells with lymphoid lineage, but no specific antigen receptor.
NK cells
ILC1
ILC2
ILC3
85
What do dendritic cells do?
Primarily present pathogen antigen to adaptive immunity
86
Dendritic cells bridge _____ and _____ immunity.
innate and adaptive
87
Name the properties of dendrites.
Tissue resident
Express pattern recognition receptors
Phagocytic
Migrate to lymph nodes to present antigens (APCs), activate naive T-cells and initiate adaptive immunity.
88
Immature dendritic cells reside in peripheral tissue where they encounter _____.
pathogens
89
Immature dendritic cells migrate via lymphatic vessel to regional lymph nodes after encountering a pathogen, where they activate T-cells by presenting ________.
Antigens on their surface
They then become mature dendrites.
90
What are the lymphocytes?
B and T cells
91
What do naive B cells produce after maturation and exposure?
Antibodies
92
What do naive t-cells produce after maturation?
Effector T-cells.
93
These consist of B and T cells, express antigen specific receptors BCR and TCR and are humoral or cell-mediated.
Lymphocytes
94
The part of the antigen that is recognized by an antibody or an antigen-receptor.
Epitope
95
Epitopes can involve key amino acids that are __________ in the sequence, or located ________ in the sequence.
continuous (linear) - - - o o o - - -
OR
discontinous (conformational/discountinuous)
- - o - - - o - -
A disproportional number of linear epitopes are found on loops rather than the N or C terminus of the antigen.
96
Papain cuts _________.
Pepsin cuts _________.
Papain cuts before the hinge region. (disulfide bond remains on heavy regions after cleavage)
Pepsin cuts AFTER the disulfide bond.
97
Name the five isotypes of immunoglobulins.
IgM
IgD
IgG
IgE
IgA
98
The ____ part of the heavy and light chains determine the specificity of the antibody.
amino terminal part
99
The __________ part of the heavy chains determine its effects,
polymerization state and if it is secreted or cell-bound
carboxy terminal part
100
What is a TCR?
A T-Cell antigen Receptor
They recognize antigens presented on host cell surface
Recognize peptide fragments (may be burried)
Always membrane bound, heterodimeric
101
Epitopes recognized by T-cell receptors are often buried and must first be broken down into peptide fragments.
The epitope peptide then binds to a self-molecule, or an _____________ molecule.
The T-cell receptor then binds to a complex of MHC molecule and epitope peptide.
MHC molecule.
102
MHC1 are found
On all surfaces of nucleated cells
103
MHC II are found on
Antigen-presenting cell surfaces such as macrophages, B-cells and dendritic cells.
104
TCR's (T-Cell antigen Receptors) recognize both ____ and ______.
Peptide and MHC.
105
On TCR's, the __ region primarily contacts the ___ half of the peptide, while the ____ region contacts with the _____ half of the peptide.
Va region makes contact with the N-terminal half
Vb region makes contact with the C-terminal half.
106
MHC binding induces conformational changes in _______.
TCR (T-Cell antigen Receptors)
107
TCR co-receptors do what?
Their binding contributes to T-cell response effectiveness.
108
What are the types ot TCR co-receptors?
CD8 and CD4
109
What is CD4?
CD4 is a TCR co-receptor on CD4 cells that is a single-chain receptor that recognizes MHC II molecules. Single chain of four Ig-like domains. Helper T(T subH) cells
CD4 Cells are helper T cells
110
What is CD8?
CD8 is a TCR co-receptor on CD8 cells that recognizes MHC 1 molecules.
Involved with Cytotoxic T cells (Tc Cells)
Heterodimer of disulfide bond linked a/b chains
CD8 cells are cytotoxic T cells.
111
