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MCDB 436: Immunology > Unit 1 Flashcards > Flashcards

Unit 1 Flashcards

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1
Q

What are commensal microorganisms?

A

a microorganism that consistently lives on or in the human body
- does not normally cause disease or harm
- can be beneficial

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2
Q

what is the microbiota?

A
  • live in or on humans
  • doesn’t normally cause disease or harm
  • often provides positive benefits for human health
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3
Q

What are opportunistic pathogens?

A

a microorganism that causes disease only in ppl whose immune systems are compromised

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4
Q

What are parasites/how do they differ from other pathogens?

A
  • unicellular protozoa and multicellular worms that infect animals and humans
  • live within the host, causing disease
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5
Q

What does the innate immune system depend on?

A
  • complement
  • neutrophils
  • macrophages
  • NK cells
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6
Q

What are effector mechanisms?

A

the processes used by the immune system to destroy and remove pathogens from the body

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7
Q

What are effector cells?

A

any terminally differentiated cells in an innate or adaptive immune response
- responsible for killing and removing pathogens

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8
Q

what are memory cells?

A
  • generally lymphocytes
  • responsible for immunological memory
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9
Q

What are leukocytes?

A
  • white blood cells
  • lymphocytes
  • granulocytes
  • monocytes
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10
Q

What are hematopoietic cells?

A

any blood cell or blood-cell precursor

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11
Q

What types of differentiated cells are in the myeloid lineage?

A
  • granulocytes
  • monocytes
  • macrophages
  • mast cells
  • dendritic cells
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12
Q

What are granulocytes?

A
  • a type of WBCs
  • irregularly shaped
  • multi lobed nuclei
  • cytoplasmic granules
  • AKA: polymorphonuclear leukocytes
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13
Q

What are the types of granulocytes?

A
  • eosinophils
  • neutrophils
  • basophils
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14
Q

What types of cells are phagocytes?

A
  • macrophages
  • dendritic cells
  • neutrophils
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15
Q

What is pus?

A
  • dead and dying WBCs (mainly neutrophils)
  • tissue debris
  • dead microorganisms
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16
Q

What are monocytes?

A
  • phagocytic WBCs
  • have a bean-shaped nucleus
  • precursor of the hematopoietic macrophage
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17
Q

What are mast cells?

A
  • cells from the bone marrow
  • resides in connective tissues
  • have large granules that store chemical mediators (histamine)
  • interacting with an antigen produces an immediate systemic hypersensitive reaction
  • play a big role in allergic reactions and anti-parasite immunity
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18
Q

What are large granular lymphocytes?

A
  • AKA a natural killer (NK) cell
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19
Q

What are natural killer (NK) cells?

A
  • large, granular, cytotoxic lymphocyte
  • circulates in the blood
  • central to the innate immune response to intracellular pathogens
  • have receptors to recognize and kill virus-infected cells and tumor cells
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20
Q

What are small lymphocytes?

A
  • recirculating/resting B or T-cell
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21
Q

What are B cells?

A
    • one of the lymphocytes in adaptive immunity
  • makes immunoglobulins in the form of cell-surface antigen receptors and antibodies
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22
Q

What are T cells?

A
  • another type of lymphocytes in adaptive immunity
  • originate in the bone marrow
  • develop in the thymus
  • has cell-surface antigen receptor
  • there are various subtypes: like cytotoxic T cell, regulatory T cell, and many helper T cells
  • aid in macrophage activation and antibody productionW
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23
Q

What are plasma cells?

A
  • terminally differentiated B lymphocytes
  • dedicated to the synthesis and secretion of antibodies
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24
Q

what is humoral immunity?

A

immunity mediated by antibodies and can be transferred to a non immune recipient

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25
What are primary lymphoid tissues?
-site of lymphocyte development ex: bone marrow, thymus
26
What are secondary lymphoid tissues?
- tissues where the immune response is initiated ex: lymph nodes, spleen, and mucosa-associated tissues
27
What are lymphatic vessels?
- thin-walled vessels that carries lymph (interstitial fluid) - transports lymph from tissues to secondary tissues minus the spleen - transports lymph from secondary tissues to the thoracic duct
28
What are ILCs?
- innate lymphoid cells - NKs, ILC1-ILC3 - don't express variable antigen receptors - express Pathogen-Recognition Receptors (PRR), characteristic of the induced innate immunity
29
What are interferons?
- cytokines with pro-inflammatory functions - activates macrophages in innate an adaptive immunity
30
What are dendritic cells?
- antigen-presenting cells - from the bone marrow - present in secondary lymphoid tissues and can stimulate T cells, forming a bridge between the innate and adaptive immune system - interactions between dendritic cells and NK cells determine whether the adaptive immune response needs to be made
31
what is the main Role of the immune system?
to protect the host from environmental microbes and toxins
32
What problem are their with trying to protect a host from their microbial environment?
1) live in a sea of organisms 2) doesn't take many microbes to start infection 3) microbes are adaptable to independently evolving threats 4) can be hard for the immune system to discriminate self vs non-self.
33
What are the sites of extracellular infection?
- interstitial spaces: blood/lymph - epithelial surfaces
34
What are the types of protective immunity for infection in the extracellular interstitial spaces?
- complement system - phagocytosis - antibodies
35
What are types of protective immunity from extracellular epithelial surfaces?
- antimicrobial peptides - antibodies
36
What are the intracellular sites of infection?
- cytoplasm - vesicles
37
what types of organisms infect through the extracellular interstitial spaces?
- viruses - bacteria - fungi - protozoa - worms/parasites
38
What types of organisms infect through the extracellular epithelial surfaces?
- bacteria - worms
39
What types of organisms infect the cytoplasmic region?
- viruses - protozoa - some bacteria
40
What types of organisms infect the vesicles of the cell?
- mainly bacteria
41
What types of protective immunity is found in the cytoplasm of the cell?
- NK cells - cytotoxic T cells
42
what types of protective immunity is found in cell vesicles?
- T cell and NK cell- dependent macrophage activation
43
About how many deaths are infectious diseases responsible for each year?
~14%
44
How do microbes evolve to hide from immunity?
- evolve into structures similar to self so that it's hard to discriminate the infection
45
What are the three types of immunity?
- physical barriers i.e. skin - innate immunity - adaptive immunity
46
What are characteristics of innate immunity?
- rapid - little specificity - always present - modest efficacy
47
What are characteristics of adaptive immunity?
- slow - high specific, recognized precise 3D structures of microbes - highly effective - memory - tolerance to self
48
What are the main types/areas of physical barriers?
- Skin: stratified epithelium - Gut: single cell layer of columnar epithelium - Lung: pseudo stratified columnar epithelium in upper airway and single cell layer of columnar epithelium in lower airway - eyes. nose, and oral cavity: pseudo stratified columnar epithelium
49
What is a mechanical immunity present in all 4 types of physical barriers?
- epithelial cells are joined by tight junctions - not permeable to many microbes
50
what is a mechanical immunity characteristic of the skin?
- longitudinal flow of air or fluid
51
what is a mechanical immunity characteristic of the gut?
- longitudinal flow of air or fluid
52
what is a mechanical immunity characteristic of the lungs?
- movement of mucus by cilia
53
what is a mechanical immunity characteristic of the eyes/nose/oral cavity?
- tears - nasal cilia
54
what are chemical immunity characteristics of the skin?
- fatty acids - beta defensins, lamellar bodies, and cathelicidin
55
what are chemical immunity characteristics of the gut?
- low pH - enzymes (pepsin) - alpha defensins, cathelicidin, lecticidins, cryptdins
56
what are chemical immunity characteristics of the lungs?
- pulmonary surfactant - alpha defensins + cathelicidin
57
what are chemical immunity characteristics of the eyes/nose/oral cavity?
- enzymes in tears and saliva (lysozyme) - histatins + beta defensins
58
What are the microbiological immunity characteristics of all 4 physical barriers?
- good microbes crowd out the bad microbes (normal microbiota)
59
True or false: the innate immunity is present under all mucosal surfaces?
true
60
What cell types are present in innate immunity?
- dendritic cells - macrophages - granulocytes (neutrophils) - NK cells - ILCs - infected cells
61
What are the types of phagocytes in innate immunity?
- macrophages - dendritic cells - Granulocytes
62
What do infected cells do during innate immunity?
- secrete interferons that signal the need to increase defenses of cells nearby
63
What do ILCs do for innate immunity?
- send signals causing cells to die
64
What do NK cells do for innate immunity?
- recognize and kill virally infected cells
65
What are the types of effector mechanisms present in innate immunity?
- neutralization - membrane attack "opsonization" - targeting NK cells (ADCC) - sensitizing mast cells - complement activation
66
What soluble factors are present in innate immunity?
- interleukins (cytokines) - complement
67
What are cytokines?
- secreted polypeptide signaling molecule used for intercellular communication - soluble mediator of innate immunity - can turn off/on immune responses - mediate inflammation
68
How are cytokines delivered to other cells?
- autocrine - paracrine - endocrine
69
What are chemokines?
- subset of cytokines that specialize in regulating cell motility (chemotaxis) - recruits cells to sites of inflammation
70
What do phagocytes do?
use degradative enzymes against extracellular bacteria and fuses with vesicles and digest bacteria
71
What is the complement system?
- assembles pores/holes in bacterial membranes to cause lysis
72
what are the effector mechanisms of B lymphocytes?
- complement - ADCC/opsonization - neutralization
73
What is the effector mechanism of T lymphocytes?
- cytotoxic cells
74
What are the soluble factors of B cells?
secretes antibodies
75
What are the soluble factors of T cells?
- interleukins
76
What are the immunity responses in B cells?
secrete surface antigen receptors (antibodies) - antigen comes in contact - antibodies leave cell surface and coat the microbes - tags the microbes to get rid of them
77
What are the immune responses of T cells?
- T- cell receptor recognizes antigen and tags the microbes with antibodies - cytokine secretion when antigen is recognized - T-cells will also kill infected cells when antigen is present
78
What are the types of lymphocytes?
- ILCs - B cell - T cell
79
What are the immunity characteristics of ILCs?
- innate lymphoid cell - Recognition: cytokines - effector function: cytokines - does not have memory
80
What are the immunity characteristics of B cells?
- recognition: Ig - effector function: antibodies; antigen presentation - has memory
81
What are the immunity characteristics of T cells?
- recognition: TCR - effector function: cytokines; preforin - Has memory
82
What are the immunity characteristics of Phagocytes (macrophage + granulocytes)?
- recognition: PRRs, Fc Receptor, and Complement Receptor - Effector mechanism: cytokines, phagocytosis, antigen presentation - has no memory
83
What are the immunity characteristics of NK cells?
- recognition: MHC, Stress, Fc Receptor - effector mechanism: apoptosis, cytokines - sort of has memory
84
What are the immunity characteristics of Dendritic cells?
- activated T-cells + secretes cytokines and interferons - Recognition: Bacterial products + inflammation mediators - Effector Mechanisms: antigen presentation - does not have memory
85
What cell type do all immune cells come from?
the multi-often hematopoietic stem cell
86
What intermediate cell does B, T, NK, and ILC cells come from?
Common lymphoid progenitor cell
87
What intermediate cell do dendritic cells come from?
- common myeloid progenitor
88
what intermediate cell do granulocytes, mast cells, and monocytes come from?
- granulocyte/macrophage progenitor
89
What intermediate cell do platelets come from?
- Megakaryocyte
90
What does the bone marrow do?
- hematopoietic cell development
91
What does the thymus do?
- t-cell development after leaving the bone marrow
92
What does the spleen do?
- blood filter
93
What do lymph nodes do?
- lymph filter
94
What is lymph?
- interstitial/tissue fluid - dead cells
95
What are the roles/characteristics of the lymphatic system?
- deals with body fluids and migrating cells outside of the bloodstream - moves interstitial fluid around - microbes travel lymph nodes via lymphatic vessels - where B and T cells and phagocytes congregate
96
What is happening in inflammation/infection site?
- microbes release vasoactive and chemotactic factors - factors are sensed and cytokines are secreted to make capillaries leaky - effectors leak in (complement) + microbicidal proteins
97
What are diseases associated with immune system disfunction?
- autoimmunity - immunodeficiency (inherited, acquired) - allergy - cancer (leukemia, lymphoma)
98
What is Grave's Disease?
- a hyper-thyroid disease
99
What occurs in a normal pituitary/thyroid communication?
- pituitary gland secretes Thyroid-stimulating hormone (TSH), inducing the release of thyroid hormones - Thyroid hormones go through a negative feedback loop and act on the pituitary gland to shut down TSH production
100
What pituitary/thyroid communication occurs in Grave's disease?
- Autoimmune B cell makes antibodies to TSH receptor, stimulating thyroid hormone production - causing constitutive thyroid hormone production because TSH shutdown in the pituitary gland has no effect.
101
What is myasthenia gravis?
A neuromuscular disease
102
What normal events occur at the neuromuscular junction?
- on neuronal impulse, Na+ is released into the junction - acetylcholine receptors in the muscles receive the Na+ influx = muscle contraction
103
What event occur at the neuromuscular junction in myasthenia gravis patients?
- Antibodies attach to acetylcholine receptors, which are internalized and degraded - when neuronal impulse causes an Na+ influx, there is no muscle contraction because no receptors are present in the junction
104
What is SCID?
- severe combined immunodeficiency - caused by little to no B and T cells - treated with Bone marrow transplant to get B and T cell production
105
What are some causes of immunodeficiency?
- AIDS - Cancer chemo
106
What does immunodeficiency do?
- no adequate immune response - susceptible to many more easily fought off diseases/infections
107
What are the types of therapeutics for immune system disfunction?
- vaccinations - immunotherapy - transplantations
108
what is the most major success in therapies for immune system dysfunction?
- vaccines
109
What was the only disease ever eradicated?
- small pox
110
How is cancer treated with a tumor-specific antibody?
- antibodies bind to the tumor cell - NK cells with Fc Receptors (CD16) are activated to kill the tumor cells
111
How is cancer treated with tumor-specific antibody/antibody fragment conjugated to a toxin?
- antibody-toxin conjugates bind to the tumor cell - conjugates are internalized, killing the cell
112
How is cancer treated with tumor-specific antibody conjugated to a radionuclide?
- radioactive antibody binds to the tumor cell - Radiation kills the tumor cell and neighboring tumor cells
113
What do checkpoint inhibitors do?
- activate the immune system against cancer - antibody drug directs T cells to kill cancer cells
114
What are examples of biochemical barriers?
- things in secretions - lysozyme in most secretions
115
What are examples of biological barriers?
- commensal organisms in gut and vagina
116
What are examples of physical barriers?
- mucus - cilia lining trachea - skin
117
What are some features of epithelial surfaces that give protective immunity?
- Tight junctions - Mucous - Cilia - Anti-microbial Peptides (AMPs)
118
What are some disease that occur from issues in epithelial surface defense?
- Cystic fibrosis (no cilia in the lungs) - Kartageners Syndrome (cilia don't beat, infertile Sperm/can't swim; often develops pneumonia)
119
What are defensins?
- small polypeptides secreted at mucosal surfaces/ epithelial + other cells - direct bactericidal properties - insertion into biological membranes leading to target cell lysis - inhibited by cholesterol - amphipathic structure promotes membrane insertion
120
What are some biochemical defenses?
- sequestration of essential nutrients ( Lactoferrin/iron and Psoriasin/zinc) - Enzymatic attack against bacterial cell wall and membrane (via lysozyme and Phospholipase A2)
121
What do epithelial cells secrete?
Psoriacin
122
What does psoriacin do?
- a peptide that kills E. coli but not staph
123
True or False: certain cell types/regions of the body protect against different types of microbes with different features.
True
124
What are the general 4 steps of immune system response?
- be ready (innate immunity) - recognize a microbe or toxin as foreign - contain/localize it - Eliminate it
125
How does the innate immune system recognize what's foreign?
Pathogen-Associated Molecular Patterns (PAMPs) by Pattern Recognition Receptors (PRRs)
126
How does the acquired/adaptive immune system recognize what is foreign?
- 3D chemical structure specific to different microbial components recognized by antibodies and T cell receptors
127
What are the major components of innate immunity?
- Barriers - Phagocytes - PRRs
128
What is the response to repeat infection of the innate immune system?
- Same each time, but can be trained
129
What are the major components of adaptive immunity?
- T and B lymphocytes - Antigen-specific receptors - antibodies
130
What is the response to repeat infection for the adaptive immune system?
- more rapid and effective with each subsequent exposure (memory)
131
What are the advantages of the innate immune system?
- PRe-existing receptors recognize common features of classes of microbes - allows for immediate response to protect host
132
What are the disadvantages of the innate immune system?
- Pathogens evolve ways to interfere with recognition - No specific memory for past exposures
133
What are the 4 hallmarks of inflammation?
- redness - pain -swelling - heat
134
What causes the 4 hallmarks of inflammation?
- increased vascular diameter and blood flow (warmth, redness) - activation of vascular endothelium = adhesion molecule expression, increasing leukocyte binding - Increased vascular permeability (swelling, pain) - PMNs are the first cell type recruited to site, followed by monocytes
135
What is causes pus in an infection?
- many dead granulocytes that died trying to kill the infections/microbes
136
What is the definition or inflammation?
- local injury or infection causing release of mediator like histamines, promoting vasodilation and chemotaxis
137
What are the functions of neutrophils?
- phagocytosis - ROS + RNS - Antimicrobial peptides
138
What are the functions of Macrophages?
- Phagocytosis? - Inflammatory mediators - antigen presentation - ROS + RNS - Cytokines - Complement proteins
139
What are the functions of Dendritic cells?
- antigen presentation - costimulatory signals - ROS - interferon - cytokines - link innate and adaptive immunity
140
What are the functions of NK cells?
- lysis of viral infected cells - interferon - macrophage activation
141
How do inflammatory cells exit circulation?
1) rolling along the vessel walls due to low affinity/binding, HBonding their way along: Signaled by selectins + chemokines 2) Receive signals from infection/damaged tissue: signaled by Integrins, Ig members, and chemokines 3) arrest/adhesion of granulocytes to undergo diapedesis: signaled by Integrins, Ig members, and chemokines 4) slips through junctions: signaled by Integrins, Ig members, and chemokines
142
What are E-selectins?
- Carbs that bind mucins - responsible for initial binding and rolling of neutrophils/granulocytes
143
What do epithelial cells do in response to damages tissue?
increase ICAM (intercell adhesion molecule) production
144
What do ICAMs do?
- after granulocytes increase ingrain production, they bind to them to signal for diapedesis
145
What are the functions of inflammation?
- recruit additional immune effector cells - Provide a physical barrier to spread of infection (coagulation in local vessels) - promote repair of damaged tissue
146
What are the 3 main functions of PRRs and Other innate immunity receptors?
- phagocytic receptors to stimulate pathogen uptake - Chemotactic receptors guide phagocytes to site of infection - Activate cell to secrete cytokines/chemokines that induce innate responses; influence downstream adaptive immune responses
147
What are some examples of PAMPs?
- sugars - lipids - protein modifications - Lipoproteins - DNA oligomers - Super-antigens - exotoxins - peptidoglycan - endotoxins/lipopolysaccharides
148
What couldn't you have adaptive immunity as your first line of global defense?
- would be overwhelming for the immune system to have very precise initial immunity
149
What would innate immune receptors recognize on microbes?
- flagellum - familiar, but misplaced macromolecular structures (DNA in the cytoplasm)
150
What are the 5 classes of PRRs?
- Toll-like Receptors (TLRs) - C-type Lectin Receptors (CLRs) - Nucleotide-binding oligomerization domain (NOD) receptors - Retinoic acid-inducible gene 1 (RIG-1) helices reporters - cGas/Sting receptor
151
What is the Toll-dorsal pathway responsible for in flies?
- important for immunity: mutants are more susceptible to fungal infections - allows for the development of the front on flies (front back distinction)
152
What is NF-KappaB?
- a transcription factor which binds to many inducible immune system genes - transcriptional control element inside of the kappa light-chain gene - Binds ot IgKappa locus enhancer
153
Where was the NF-KappaB TF found?
- in mouse B cell lines
154
What happens when you remove the NF-KappaB or its binding site?
- the immune genes still work in B cells - means its not essential for activity of light-chain gene in mice
155
True or False: the situation in which a factor is discovered is not necessarily its most important role.
True
156
What is NF-KappaB homologous in?
- Dorsal pathway as a TF - homologous as a TF for many immune genes
157
What are the contents of the NF-KappaB complex?
- p50 - p65 - IkappaB
158
What are characteristics of the inactive form of NF-KappaB?
- IKappaB is an inhibitory molecule - in the cytoplasm - cactus
159
How is NF-KappaB activated?
- activated by the IKappaB molecule getting phosphorylated, released and degraded - goes into the nucleus as a TF
160
What are characteristics of the active form of NF-KappaB?
- no longer has the IKappaB molecules - goes into the nucleus and activates genes (kappa light-chain locus)
161
What is a TLR?
- Toll-like receptor - cell-surface signaling molecule - links microbial products to TF activation for immune gene upregulation - binds to a ligand (specifically a PAMP)
162
What is the process of immune gene activation with TLRs?
1) ligand/PAMP binds with TLR 2) changes conformation which activates a kinase 3) IkB kinase phosphorylates the IkB molecule on NF-kB 4) IkB molecule falls off/gets degraded 5) active NF-kB goes into the nucleus and binds to NF-kB binding sites 6) activates genes important for inflammation and activation for acquired immunity.
163
What are the shape characteristics/features of TLRs?
- exterior/cell-surface domain is Leucine-rich repeats that typically form a hook - transmembrane protein - the interior domain is called the Toll/IL-1R domain (TIR domain) - IL-1 is a type of cytokine - TIR domain is a signaling scaffold and multimerization - TIR domain has homology to cytokine signaling - all TLRs form either homo or heterodimers on cells
164
Why are there so much variety in TLRs?
- each is specific for different classes of microbial products - amount varies between species, but generally about 10 - there are extracellular TLRs and ones specialized to be in endosomes
165
What is special about endosomal TLRs?
- recognizes viruses and intracellular bacteria - the leucine-rich repeat region is congruent with being on the exterior face of the cell membrane cytoplasm - TIR domain is in the - intracellular transmembrane protein
166
What do variations of MyD88 molecules do?
- binds to the cytoplasmic domains of all TLRs except 1 kind of TLR - transmit signals from TLRs
167
True or false: TLR signaling pathway is not conserved in mammals and drosophila.
False - MyD88 vs dMyD88 - IRAK vs Pelle
168
What other molecules can TLRs activate?
- MAP kinases - other TFs like IRF3
169
What would happen if all MyD88 molecules were gone?
all but 1 kind of TLR would no longer function
170
What kind of genes do NF-kB regulate?
- Dendritic cell maturation - Differentiation/Activation of T cells - pro-inflammatory gene induction (Macrophage) - neutrophil recruitment - Adhesion molecules (ICAMs) - Chemokines - Cytokines - Cell cycle regulators - Anti-apoptotic factors
171
In general, what are C-type lectin receptors?
- requires calcium for binding - extracellular domain binds to sugars
172
What are the characteristics of the Macrophage Mannose Receptor?
- C-type lectin receptor - binds to mannose-containing molecules on many bacteria and fungi - recognition very similar to mannose binding lectin (MBL) - functions as a phagocytic receptor
173
What are Dectin-1 Receptors?
- Recognizes fungal B-(1,3) gluten polysaccharides - switches the gluten linkage from beta to alpha - increased alpha-(1,3) correlates to increased virulence - virulent strains have learned to hide B-glucan so it can't bind with Dectin-1 receptors underneath alpha-(1,3) blocks
174
What are some characteristics of cytoplasmic sensors of infection?
- many recognize/share the same domains - each is homologous to others, but not the exact same - chemical patterns that are recognized
175
What are NOD/NOD-like receptors?
- intracellular cytoplasmic receptors - detects bacteria - structurally similar to TLRs (has LRRs) - ligand binding results in dimerization = signaling to TFs - activation = chemokine and antimicrobial peptide production - activation secretes chemoattractants that bring in more phagocytes
176
177
What are the ligands of many NOD/NOD-like receptors?
- bacterial degradation produces from a phagolysome.
178
What is a special type of cell death that NLR can trigger?
- pyroptosis via inflammasome activation
179
What is the process of causing pyroptosis via NLR activation?
1) TLR stimulation increases expression of IL-1B and IL-18 pro-forms (inactive forms) 2) NLRs respond to PAMPs/pathogen activity and form an inflammasome (8 NLRs) 3) Inflammasome recruits and activates caspase 1 4) CC1 cleaves prol-IL-1B, pro-IL-18, and gasdermin D to activate them 5) activated gasdermin D oligomerizes and forms a pore in the cell membrane 6) releases active IL-1B and IL-18 as cytokines/signalling molecules for other immune cells 7) holes also cause cell lysis/pyroptosis
180
What are RIG-1 like receptors?
- retinoic acid-inducible gene - detects cytoplasmic viral RNA - binds to unmodified 5' triphosphorylated (uncapped) RNA
181
What is the process of RIG-1 detection and reaction?
1) cytoplasmic replication of virus produces uncapped RNA with a 5'-triphosphate (doesn't belong there, indicates presence of a virus) 2) Viral RNA binding CARD domain opens up RIG-1 so it can now multimerize 3) RIG-1 multiuser becomes poly-ubiquinated 4) poly-ubiquinated RIG-1 interacts and binds to MAVS 5) MAVS/RIG-1 complex recruits TRAFs and induces the activation of IRF3 and NF-kB pathways
182
What are the parts of the RIG-1 receptor?
- helices domain - C-terminal domain (CTD) - CARD domain (associated with the helices domain) - exists in its inactive form, floating in the cytoplasm
183
What is MAVS?
- membrane-associated virus sensor - has a CARD domain that binds to the RIG-1 CARD domain - bound to the mitochondrial membrane
184
What is the cGas and Sting receptor complex/system?
- recognizes cytoplasmic dsDNA - activates interferons - Sting activation via cyclic GGMP and AAMP by cGAMP - cyclic di-nucleotides are either a direct bacterial product or synthesized by cGas DNA sensor - some viruses can evade this system by degrading cGAMP
185
What is the process of cGas/Sting detection and reaction?
1) dsDNA from viruses binds to cGas, creating a cyclic dinucleotide (cGAMP) 2) cGAMP, cGGMP and cAAMP (from bacteria) bind to Sting, an ER protein 3) binding to Sting causes it to dimerize, turning into a scaffold protein 4) Sting's dimerized cytoplasmic face can recruit proteins and kinases (TBK1) to activate TFs like IRF3 ( induces expression of type 1 interferons)
186
What types of Pattern Recognition Receptors are extracellular?
- TLRs - CLRs
187
What types of PRRs are intracellular?
-NLRs -RIG-1 - cGas/Sting
188
What is DNA microarray?
- compares all gene expression under 2 different conditions
189
What has DNA microarrays been replaced with?
- mRNA sequencing
190
What is the process of a DNA microarray?
1) Isolate RNA samples from two different conditions (normal sample + sample treated/infected with bacteria) 2) Generate cDNA 3) Labeling of probe: each sample gets tagged with a different color 4) tagged sample gets put into a hybridization array
191
What does it mean if a well on a DNA microarray is black?
- no RNA bound/produced/found at that gene
192
What does it mean if a well on a DNA microarray is red?
- more RNA is present at that gene from sample 1
193
What does it mean if a well on a DNA microarray is green?
- more RNA is present at that gene from sample 2
194
What does it mean if a well on a DNA microarray is yellow/intermediate color?
- there is a relatively similar amount/ a mixture of RNA from that gene in both samples
195
What can DNA microarrays tell us about different microbial infections?
- different sets of genes are differentially regulated based on which microbe is causing the infection - pathogen-specific patterns of gene expression
196
what are the 2 types of phagocytic cells that recognize pathogens in the innate immune system?
- Macrophages - neutrophils
197
What are the characteristics of macrophages?
- generated in the bone marrow - migrates and lives in the tissues for its life - lives especially in the submucosal layer of the GI tract, lungs, and liver - from blood-borne monocytes - involved at the very beginning of infection because they already reside in the tissues
198
What are he characteristics of neutrophils?
- aka polymorphonuclear leukocytes (PMNs) - short-lived (<2 days), abundant in blood - recruited into inflamed tissue - Can move very fast - uses glycolysis for energy because there is little blood flow to the tissue it enters, uses an anaerobic process like glycolysis - use rolling and diapedesis mechanisms to leave circulation
199
True or False: Recognition, ingestion, destruction of pathogen by phagocytes doesn't require an adaptive immune response.
- true - however, T cells and antibodies make phagocytes more efficient
200
What are distinctive features of granulocytes like neutrophils?
- its granules are vesicles packed with antimicrobial proteins, peptides, and machinery to create oxygen radicals and kill phagocytose microbes - many nuclei -nuclei make it rigid and hard to squeeze through the endothelial cell junctions in blood vessels
201
What are the 6 classes of antimicrobial mechanisms of phagocytes?
- acidification - toxic oxygen-derived products - toxic nitrogen oxides - antimicrobial peptides - enzymes - competitors
202
When do macrophages begin using/producing their antimicrobial mechanisms?
- once it receives a pathogen signal, begins production
203
When do neutrophils begin using/producing their antimicrobial mechanisms?
- mechanisms are always present/premade in their granules
204
What common enzyme is used as an antimicrobial in phagocytes?
- lysozymes
205
What is the pH present in phagocytes?
- 3.5-4 - bacteriostatic or bactericidal
206
What is the type of phagocytes that link the immune and the adaptive immune systems?
dendritic cells
207
What are the steps of phagocytosis/
1) bacterium attaches to membrane 2) bacterium is ingested. forming, phagosome 3) phagosome fuses with the lysosome 4) lysosomal enzymes digest the bacteria 5) digested material is released from the cell
208
What does the NADPH oxidase complex do?
- generates ROS/ Oxygen radicals
209
What is Chronic Granulomatous Disease?
- can't generate oxygen radicals because there is a defect in NADPH oxidase complex - increased bacterial and fungal infections because phagocytosis doesn't kill microbes effectively (phagosome doesn't have radicals with defect NADPH oxidase) - defective killing allows for abscesses and granulomas to form via chronic inflammatory reactions - reduces NETs
209
what is the process of the NADPH oxidase complex?
1) NADPH oxidase converts O2 molecule to superoxide O2- 2) O2- to hydrogen peroxide (H2O2) via superoxide dismutase 3) hydrogen peroxides to hypochlorite and hydroxyl radical ions via other peroxidase enzymes
210
How do radical ions affect microbes?
- ions will covalently attach microbes and kill them
211
What are NETs?
- Neutrophil extracellular traps - activate neutrophils release nuclear chromatin into extracellular space (NETosis) - forms a fibril matrix called NETs - formation requires ROS generation - takes nucleus apart/decondenses chromatin - localizes microbes
212
What are the two types of NETosis?
- slow cell death NETosis - Non-lytic NETosis (rapid release from live cells)
213
What happens to the PMNs that undergo non-lytic NETosis?
- nuclear chromatin explodes out - leaves a phagocytic cytoplast behind (doesn't kill cell)
214
What do activated macrophages secrete?
- cytokines - chemokines - all are polypeptide signaling molecules
215
What are the types of cytokines that activated macrophages secrete?
- IL-1B - TNF-a - IL-6 - CXCL8 - IL-12
216
What does IL-1B do?
- Local effects: 1) activates vascular endothelium 2) activates lymphocytes 3) increases access of effector cells - systemic effects: 1) causes fever 2) IL-6 production
217
What does TNF-a do?
- Local effects: 1) activates vascular endothelium 2) increases vascular permeability 3) increased entry of IgG 4) increased entry of complement 5) increased movement of cells to tissues 6) increased fluid drainage to lymph nodes - systemic effects: 1) causes fever 2) mobilization of metabolites 3) shock
218
what do IL-6 do?
- local effects: 1) lymphocyte activation 2) increased antibody production - systemic effects: 1) causes fever - induces acute-phase protein production
219
What are the effects of CXCL8?
- local effects: 1) recruits neutrophils, basophils, and T cells to site of infection as a chemotactic factor
220
What are the effects of IL-12?
Local effects: 1) activates NK cells 2) induces differentiation of CD4 T cells into Th1 cells
221
What do IL-1B, IL-6, and TNF-a inflammatory cytokines do to the liver?
- acute phase proteins CRP and MBL are produced - activate complement opsonization
222
What do IL-1B, IL-6, and TNF-a inflammatory cytokines do to the Bone marrow?
- mobilize neutrophils - phagocytosis
223
What do IL-1B, IL-6, and TNF-a inflammatory cytokines do to the hypothalamus?
- increase body temperature - decreased viral and bacterial replication
224
What do IL-1B, IL-6, and TNF-a inflammatory cytokines do to the Fat and the muscle?
- metabolism increases body temperature - decreased viral and bacterial replication
225
What is a plasmacytoid dendritic cell?
- myeloid cell lineage - in blood and lymphoid tissue - senses viral infection via TLRs - produces a lot of interferons - systemic spread of interferons and these cells to combat viral infection
226
What are interferons?
a type of cytokine
227
What are types of cell autonomous defenses for viruses?
- a, b, and gamma interferons secreted by infected cells, activated MP, PDCs - tells nearby cells to activate defense mechanisms including PKR system - infected cells can also undergo apoptosis as a self sacrifice (also for bacteria)
228
What are the protective roles of IFN-a/B during viral infection?
- induces resistance to viral replication - increase MHC class 1 expression and antigen presentation in all cells - activate NK cells to kill virus-infected cells -inhibit translation - mRNA degradation - inhibits transcription
229
What are the general characteristics of apoptosis?
- nuclear fragmentation - blebbing - proteolysis - Death remnants undergo phagocytosis
230
How have viruses evolved to evade innate immunity mechanisms?
- avoiding PRR recognition - inhibiting transcription of genes encoding Type 1 IFN proteins - preventing receipt of IFN signaling by infected cells
231
What isotopes of immunoglobulins are present as a cell-surface protein?
all of them
232
What isotypes of immunoglobulins are soluble?
all except IgD
233
T/F: Different Ig isotypes have different specialized effector mechanisms.
True
234
What is IgM best effector mechanism?
complement activation
235
Where are all the types of IgG found in the body?
- blood - serum - tissue fluid - between cells
236
Where are IgA molecules found?
- in secretions across mucosal and epithelial barriers
237
What is IgE main role?
- activate mast cells - engages in allergy responses
238
What does the heavy chain do for the antibody?
- when the antibody reacts with the antigen, it relays/enacts a response to the cell/body
239
What is special about the concentration of IgE in the body?
- very low serum concentration means that it's receptors have to have a high binding affinity
240
What is a j chain?
- joining chain - joins constant regions of multiple of the same antibody together (also held together by disulfide bonds) - same J chain present in all isotypes
241
What does an antibody having a valence of 10 mean?
- it's a pentamer antibody - has 10 antigen binding sites, 2 per antibody
242
What is the benefit to having a high valence antibody?
- more binding sites = more binding avidity - good for microbes that are consolidated - good for microbes that produce a lot of the same surface protein - antibody is less likely to fall off
243
What does having a higher avidity mean?
- synonymous with multivalency - physically bound more tight because there are more binding sites/events to keep it attached
244
What types of isotypes typically form pentamers?
- IgM - IgA
245
What type of Isotype doesn't form a pentamer complex?
- IgG
246
how do antibodies bind to the surface of cells?
- constant region (Fc) receptors - gives the cell antigen specificity
247
T/F: Fc Receptors differentiation in distribution, signaling, and binding affinity levels
true
248
What are the 3 main types of FcRs?
- y, epsilon, and alpha
249
T/F: FcRs are only present on the surface of the cell.
False, some dip into the cytoplasm
250
What type of FcR has a high affinity for IgE molecules?
- epsilon
251
What process is enhanced by FcR and PAMPs signaling?
phagocytosis
252
What is the relationship between multiple Igs that are bound to an antigen and cellular FcRs?
- the aggregation of Igs increases the avidity to FcRs - Free Igs by themselves tend to bind to FcRs poorly
253
What is the process of forming a secretory IgA molecule?
-a plasma/secretory B cell on the basal side of the epithelial barrier will secrete dimeric IgA - IgA is held together by the J chain - The poly Ig receptor connected to the basal face of the epithelial cells binds to the dimeric IgA - Once bound, receptor pulls in IgA into the epithelial cell (transcytosis) - as the IgA molecule is being released into the lumen, an enzyme in the epithelial cells will cleave the receptor - a fragment of the poly Ig receptor is left stuck to the constant region of the IgA dimer (secretory piece)
254
What portion of the receptor gets stuck to the IgA molecule during secretion?
- the ectodomain
255
What is the role of the secretory piece?
- protects the Fc region of the antibody from being recognized and degraded by other secreted enzymes
256
What is secretory piece protection an example of in terms of antibody effector mechanisms?
- neutralization
257
What effector mechanism does IgA normally work through?
- neutralization
258
T/F: IgA doesn't usually use FcRs
true
259
What are the characteristics of IgE molecules?
- present in low amounts in the serum - binds to FcRs on mast cells and basophils from the bone marrow - gives specificity to mast cell activation - levels increase in setting of parasitic infection - can transfer allergy between individuals
260
What is a characteristic of a mast cell at a steady state?
- FcRs on the surface fo the cell are already filled with empty antibodies
261
What causes degranulation of a mast cell?
- when the IgE molecules bound to FcRs bind to its antigen target
262
What do mast cells release when they come in contact with their allergy antigen targets?
- histamines - heparin - proteases all cause an increase of local inflammation
263
What is the process of making an antiserum/antibody?
- combine a purified antigen + adjuvent and do multiple injections over the course of weeks into an animal - purify total immunoglobulin populations from serum - can purify antibody that binds to a specific antigen via affinity chromatography - yields a mixture of many different antibodies that bind to different surfaces of your antigen
264
What are polyclonal antibodies?
- population of many different antibodies and FAB types from many different B cells
265
What does having low immunogenicity correlate to?
- low immune response
266
What are the characteristics of/ what contributes to immunogenicity?
- foreignness - size - molecular complexity - susceptibility to phagocytosis - genotype of host - route of administration - dose
267
How does foreignness from host relate to immunogenicity?
- greater distance from host = more immune response - antigens don't look like self molecules
268
How does size relate to immunogenicity?
- the bigger the molecule, the more immune response - smaller molecules can be used if they are covalently attached to bigger carrier proteins that cells can recognize as foreign
269
Why is more immunogenicity important for vaccinations/ antiserums?
- you want a higher immunogenicity to elicit a greater immune response - this can leave a better memory for future infections
270
How does molecular complexity relate to immunogenicity?
- a more lengthy/complex protein would elicit a greater immune response
271
How does susceptibility to phagocytosis relate to immunogenicity?
- a normal, stable protein would create a good immune response - wouldn't be easily phagocytosed - more likely to be phagocytosed = increased immune response
272
How does route of administration related to immunogenicity?
- needs to cause a little tissue damage or inflammation or immune system won't recognize it
273
How does dose relate to immunogenicity?
- too few or too many molecules won't generate an immune response
274
How does the genotype of the host relate to immunogenicity?
- different genotypes respond to antigens differently - better or worse
275
How do adjuvants enhance immunogenicity of an antigen?
1- causes inflammation/tissue damage - can also cause an immune response by containing dead microbes
276
What is the main mechanism on how adjuvants work?
- PRR activation
277
What is a commonly used adjuvant?
- Freund's complete adjuvant
278
What is the process of measuring affinity of an antigen target using equilibrium dialysis?
- In the initial state, antibodies and antigens are separated in 2 wells by a semi-permeable membrane - membrane allows antigen to pass through, not antibodies - the wells reach a state of equilibrium when the amount of FREE antigen, not those bound to the antibodies, are the same concentration in each well
279
Is the avidity of a multivalent antigen higher or lower than a monovalent antigen
higher
280
What is cross-reactivity
- antibodies elicited by one antigen also bind to another structurally similar one - cause of rheumatic fever - streptolysin - useful for vaccine effectiveness - problems for self-tolerance
281
What is an example of cross-reactivity
- ABO blood group antigens
282
What is a characteristics of cross-reactive antigens?
- multiple epitopes can bind to the same antibody
283
What causes MISC-C post-COVID?
cross-reactivity
284
How does cross-reactivity to streptococcus cause self-reaction in disease?
- produces an antiserum with antibodies against streptococcus - antibodies target streptolysin molecule on surface - there is a structurally similar protein found in heart valve that your antibody antiserum can bind to, causes heart to fail
285
What is MIS-C?
- Multisystem Inflammatory Syndrome in Children - develops 2-6 weeks after COVID infection - causes many inflammatory disease/symptoms around the body - stomach, skin, liver, kidney, heart
286
How does PHIP-seq work to identify antigen targets in antibody population?
- make snippets of all overlapping peptides in the viruses DNA - clone DNA that codes for these peptide/RNA chains - inject DNA in bacteriophage so that each individual bacteriophage expressed 1 type of protein - combine population with antibody so that it binds to different antigens on the surface of the virus. - wash to isolate the bacteria/antigen combo to see what it binds to - can do this multiple times to get rid of random antigens
287
How does cross-reactive antibody work in MIS-C?
- MIS-C make an antibody against an unusual region of SARS-CoV-2 - children who recovered from COVID-19 and did not have MIS-C didn't make this antibody -the region that the different antibody recognizes on the virus is identical to the SNX-2 human protein found in many tissues - could be a genetic bias their immune response hastowards that antigen
288
What is cow pox an example of?
- cross-reactive
289
What is in gamma serum/globulins?
- many antibodies are produced by many different B cells = polyclonal antiserum
290
What is a polyclonal antibody?
- a mixture of many different Igs specific for the same complex antigen (found in antiserum)
291
What is a monoclonal antibody?
- a single species of Ig whose idiotype binds to a specific epitope on a particular antigen (secreted by a single clone of B cells)
292
What is a special about polyclonal antiserum that monoclonal antibodies don't have?
- forms aggregates because antibodies can bind to many epitopes on the same antigen - aggregates get so big that they form precipitates. - can gum up your tissues
293
What is the agglutination reaction in pregnancy tests?
- there are HCG molecules with multiple of identical surface proteins - there is an anti-HCG antibody - when someone is not pregnant, HCG + carrier bind to antibodies and cause clumping, won't see second band - when someon is pregnant, they produce a lot of free HCG without its carrier in urine - if there is a high enough concentration of HCG in the urine, the antibodies will bind to that instead causing no clumping and an extra band
294
How does an agglutination assay work to test for Rh incompatibility with mother and fetus?
- can test directly from fetal RBCs to see if they are coated with maternal antibody, add rabbit, anti-human antibody and see if it agglutinates - if it does= Rh incompatibility - can test indirectly with maternal serum to see if they will bind to knownw Rh+ RBCS to see if it agglutinates - if it does, Rh incompatibility - causes erythroblastosis fetalis: can kill fetus in future if it has Rh proteins
295
What is a preventative treatment for Rh incompatibility?
- at the time of birth, inject mother with a large dose of anti-Rh antibody - gets rid of Rh antigen before it has a change to bind to mom's antibodies - a form of passive immunization
296
What does a clump of RBCs mean in an agglutination assay?
- there was an antigen/antibody reaction that caused the clumping
297
What is the process of creating a monoclonal antibody?
- inject animal with antigen/adjuvant combo - isolate spleen cells because the spleen contains individual B cells secreeting different antibodies that might bind to the different epitopes on the antigen - hybridize plasma/B cells with myeloma celsl to make them immortalized, myeloma cells no longer produces its own antibody - clone hybridized cells and put 1 cell per well to isolate them = isolated antibodies
298
What happens when a plasma cell is isolated by itself?
- dies in culture - is HPRT wildtype
299
What happens when myeloma cells are isolated?
- immortal - HPRT null, would die in HAT media
300
What is HAT selection in plasma-myeloma cell hybridization?
- H = hypoxanthine: substrate for HPRT - A = Aminopterin: blocks de novo nucleotide synthesis - T = Thymidine: substrate for thymidine kinase - H and T are nucleotide precursors - select hybridized cells with HRT to kill any non-hybridized cells = don't make nucleotides - can't make nucleotides from hypoxanthine or thymidine without HPRT - later see if new clones have an antibody to initial antigen from monoclonal isolation
301
What are the advantages of Monoclonal antibodies?
- consistent between samples and times used -limitless supply of specific reagent/antibody- serum would normally run out at some point - more easily tested for cross-reactivity because it only has 1 specificity.
302
What is the purpose of Radioimmunoassays?
to measure/quantify how much of a specified hormone or antigen in a mixture of other hormones and antigens
303
What is the purpose of an ELISA experiment?
- Enzyme-linked immune sorbant assay - tells you how much of your target protein is present in your sample
304
How does a radioimmunoassay work?
- a monoclonal antibody is used to select for a certain antigen - use a known amount of your your antigen of interest that is radioactively labels - add increasing concentrations of unknown mixture in different wells. - unlabeled antigen of interest from your random mixture will compete with your labeled known sample. - can tell how much of your antigen of interest is present in your sample based on how much labeled sample is left stuck to the antibodies
305
How does an ELISA work?
- have a primary, monoclonal antibody stuck to a membrane - use it to capture antigen of interest from an unknown concentration - add a secondary antibody that is conjugated with a fluorescent enzyme (also monoclonal) - use a colorometric assay to generate light and calculate the concentration of light= concentration of your antigen of interest
306
What are some characteristics of ELISAs that are different from RAs?
- not as sensitive - not toxic - less expensive - since there are 2 antibodies used, each will bind to a different epitope on the antigen
307
How does a lateral flow essay work like the ones in covid tests?
- the sample will first encounter a primary antibody against an antigen that is attached to colloidal gold - if there is the antigen present, it will bind to the antibody, get stuck, and precipitate - antibody will roll along and get stuck on the anti-covid antibody (secondary) = a line will form - if there is no covid antigen, the primary will get stuck further down the flow capillary on an anti-Ig antibody (secondary) = makes a control line
308
What is the purpose of an immunoprecipitation assay?
- to tell if your protein/antigen of interest is present in a mixture of proteins from a cell lysate - can also tel; you what your protein of interest binds to.
309
how does an immunoprecipitation assay work?
- mix a monoclonal antibody that will work for your protein of interest and an unknown sample - antibody will bind to protein of interest and will equilibrate - add in either a protein A or a protein G to bind to your primary antibody as a carrier protein - wash to get of extras - you have your target protein
310
What antibodies does protein A and G in immunoprecipitation assay normally work?
- are bacterial proteins that bind to most Ig Fcgamma region = many IgG classes
311
what do you use to radiojlabel cell surface proteins in an IP assay?
- iodine, then wash excess away
312
what are some types of detergents that are used in an IP assay to lyse the cells?
- NP40 - Digitonin: less destructive to the macromolecular structure and interactions of proteins.
313
What is used to analyze an IP assay?
- running the protein on a denaturing PAGE gel
314
What do you use for a control on a Gel analyzing for an IP assay?
- a non-specific Ig
315
What is the purpose of immunoaffinity chromatography?
- to purify and create a concentration of an antigen of interest
316
How does immunoaffinity chromatography work?
- use a primary antibody for your antigen of interest - add in unknown sample - antibody will bind to your antigen of interest - wash away extra unbound molecules - elute your antigen of interest
317
What happens to wavelengths in Immunofluorescence assays?
- light excites photons at 1 wavelength and emits photons at a higher wavelength
318
What is the purpose of flow cytometry?
to tell what kind of proteins are present on the surface of cells
319
How does Flow cytometry work?
- mix a sample of cells with antibodies that are fluorescently labeled (can be multiple different ones with different colors) - create a high pressured stream so that at most 1 cell will fall in a droplet at a time - cell will fall through a light laser to analyze what color(s) are present on the surface of the cell. - can tell you how much of each color or antibody is present
320
what are the types of plots that can be used to analyze flow cytometry results?
- histograms - dot plots - contour plots
321
How do you tell if a peak on a histogram for flow cytometry is a population of cells or just background?
- by comparing it with a control: use a random antibody that is labeled with the same fluorochrome
322
What are the pros/cons for using a color density dot plot to analyze the flow cytometry results?
Pros: - good for showing two differently labeled antibodies to overlap Cons: - dots can get too dense - heat map help tell you relative amount
323
What is the purpose of cell sorting using flow cytometry?
to sort cells based on either: 1) how much of a surface protein they're expressing 2) what combination of surface proteins are the cells expressing
324
How does cell sorting work using flow cytometry?
- do set up similar to flow cytometry - as cells are falling, have an ionizing region to pull/sort cells based on charge - if the cell is fluorescently labeled, drops will have a negative charge - if the cell isn't labeled, it will have a positive charge - colors can also be given different charge to be sorted
325
What are the types of regions present in the variable domains of immunoglobulins?
- hypervariable - framework
326
what are the 3 hyper variable regions in the variable domain?
- CDR1 - CDR2 - CDR3
327
What do the hypervariable regions do in the variable domain?
- give the specificities to antibodies
328
what is the GOD problem?
- generation of diversity - questions how to fit in all the genes needed to create limitless array of Ig seqs
329
What allows Ig molecules to have limitless combination possibilities?
- somatic recombination in every B cell
330
On the southern blot that is trying to look at recombination in organ tissues, what genomic region yields the same constant band every time?
- there is a long and short fragment fro both cell lines and tissue samples - a consistent band between every sample is the shot fragment of the Ck region - the long fragment changes every cell and tissue.
331
why is there a smear on a southern blot for spleen samples?
- because there are many different types of Cells present that it picks up all the different long fragments from their antibodies
332
What types of segments make up the variable domain that causes them to change in the heavy chain?
- Vh (~100) kinds, v = variable - Dh (~12 kinds), d = diversity - Jh (~4 kinds) j = joining
333
What is the general process of VDJ rearrangement?
- 1 V to D - D to J - D to J happens first - there can still be leftover upstream V segments and downstream J segments - contains the 3 hyper variable regions
334
Where are the 3 hyper variable regions in VDJ recombination?
- HV1 and HV2 is in the V segment - HV3 is in the D segment
335
What hyper variable region has most of the antibody variation?
- HV3 - has most contact with epitope on the antigen
336
How do you get rid of the leftover downstream J segments next to the constant domain when the gene is transcribed?
- through RNA splicing
337
T/F: somatic recombination occurs in Both the heavy and light change loci.
true
338
What is different between somatic recombination in the heavy and light chain loci?
- the light chain doesn't have D segments
339
Where is the most hyper variable region in the light chain rearrangement?
- V to J junction
340
Why aren't there infinite antibodies actually in existence?
- some of the rearrangements have messed up reading frames - won't produce antibody at all or produces a non-functional antibody
341
What does RSS stand for?
- recombination signal sequence
342
Where are RSSs present in the DNA?
- flanked on V, D, J, or other rearranging gene segments - directly next to the coding segment of the gene
343
What is the structure of an RSS?
- Heptamer region closest to the gene coding segment (7nts) - spacer of 12 or 23 nucleotides - nonamers (9nts) - all segments of the same type will have the same RSS type - cis-acting element
344
What are some characteristics of the heptamer in RSSs?
- always contiguous with the coding segment - very conserved - touches the DNA that will code for the immunoglobulin
345
Is the nonamer region of the RSS conserved or not conserved?
- kinda-conserved
346
What types of RSSs are present near Vh segments?
RSS-23s - downstream
347
What types of RSSs are present near Dh segments?
- RSS-12s - present both up and downstream of the segment because it gets rearranged 2x
348
What types of RSSs are present near Jh segments?
RSS-23 - upstream
349
What is the 12/23 Rule?
- gene segments with opposite RSSs can undergo V(D)J recombination
350
Do some segments have preferences to which ones they will recombine with?
- yes, RSSs closest to the D segments have a slight preference - some other certain RSSs show preferential rearrangement with one another for other reasons
351
What are the products of Recombination between segments?
- A coding joint - Signal joint
352
What is a coding joint?
- the combine segments of VDJ/VJ recombination that will encode for a protein - it's imprecise
353
Why is a coding joint considered imprecise?
- between coding segments there can be and insertion or deletion of nucleotides during recombination
354
What is a signal joint?
- a circular deletion of DNA from the chromosome - precise: no nucleotides are lost or added because it forms blunt ends when excised - RSSs are fused together with a blunt fusion/ligation: heptameters fuse together
355
Why does the cell bother to make the circular signal joint instead of leaving it linear?
- Repair machinery doesn't like free, linear DNA - could become an insertional mutagen if left linear
356
How often are productive rearrangements made in VDJ/VJ recombination?
- 1/3 of the time - since there are 3 nts in a codon, there is 1 way out of 3 to maintain the reading frame
357
How often are nonproductive rearrangements occurring?
- 2/3 times the product is in the wrong reading frame
358
How does a V(D)J transfection assay work for recombination?
- transfect the pJH200 plasmid into pre-B cells that encourage recombination activity for antibody production - recover plasmids from pre-B cells - transform them into bacteria - drug-select bacteria to see which ones have Amp only resistance (no recombination) and which ones have amp and cloro resistance (recombination occurred)
359
What is the high conserved part of the heptamer in RSSs?
- CAC, touches the coding region - typically the heptamer is CACAGTG
360
True or false: both RAG-1 and RAG-2 proteins are required for recombination to occur.
true
361
What are the unusual features of the RAG locus?
- they are physically linked because theyr are so close together - they get transcribed at the same time - they are in a single, large coding exon
362
Due to RAG proteins unusual locus features, what is the hypothesis of these proteins?
- VDJ recombinase is a descendent of a transposon
363
Why were the people who discovered the RAG protein locus so lucky?
- needed 2 genes to be transferred on the same portion of DNA to allow for recombination - it was popped into a region of the genome that allowed it to be expressed
364
What cell types are RAG proteins specific for?
B and T cells - the only essential factors that are lymphocyte specific, others are found in most cell types
365
What is the job of the RAG-1 and 2 complex?
- recognizes pairs of RSSs - makes precise dsDNA breaks at the heptamer coding segment junction
366
What are the roles of nonamer binding domains in RAG proteins?
- NBD bind to nonamers
367
How many times does Rag 1 and 2 touch the coding joints?
- 2x - this is why it is important for there to be a 23 and 12 RSS, 23s allow for bending to get segments close enought to form coding joints and signal joints
368
T/F: RSS-12s and 23s are looped in different directions.
true
369
What are the early steps of V(D)J recombination?
- RAG1/2 complex is formed and RAG1 Knicks (single strand break) the top strand in between the coding segment and the hepatmer region - this will end up yielding hairpin formation and another segment of blunt ends (5' phosphorylated) - 3'OH attacks the phosphorus of the attached strand to form the hairpin loop = covalently attached
370
What happens to the hairpins formed by RAG proteins?
- complex breaks the hairpin open - can either be blunt end if it breaks at the tip or it could be asymmetrical with a 5' or 3' overhang
371
How does P-nucleotide addition occur?
- every early step of Recombination until the hairpin is broken open - Repair enzymes can add nucleotides that are complementary to the coding segments of overhangs - this creates palindromic sequences
372
How does N-nucleotide addition occur?
- every early step of Recombination until the hairpin is broken open - TdT adds random nucleotides to open coding ends (only expressed in developing B and T cells) - they end up in the middle of the variable domain exon - could be responsible for creating frame reading issues
373
What does TdT stand for?
- terminal deoxynucleotidyl transferase
374
Do RAG proteins paste/make joints?
no - polymerases + ligases
375
What are characteristics of SCID mice?
- no mature lymphocytes or serum Ig - Attempts VDJ recombination but makes large deletions instead of coding joints - signal joints form normally - can't process coding-end hairpins - defective in dsDNA repair - loss of DNA-PK
376
What is DNA-PK?
- a dsDNA-repair enzyme - important for coding joint formation - activates Artemis for hairpin opening
377
What would happen if you tried to use a transfection assay with pJH200 and cells with DNA repair defects an added RAG proteins?
- there would be no chlorophenicol resistance
378
What is Artemis?
- breaks the hairpins - gets activated by DNA-PK
379
What does Ku proteins do in VDJ recombination?
- binds to broken ends - a scaffold for DNA-PK to hold onto and activate Artemis
380
What are the 5 mechanisms that contribute to antibody diversitye B cells?
- multiple V, D, and J segments at each locus - combinatorial joining - Heavy chain and light chain combinatorial diversity - P-nt addition: templated nt addition between joints that results from asymmetrical cleavage of hairpins - Exonuclease trimming: occurs at junctions resulting in loss of nts and changes in reading frames - N-nt addition: non-templated, TdT-mediated, adds random nucleotides between joints
381
How to capture and sequence entire B cell Igs from individual or populations of cells?
1) single-cell emulsification: allows for the isolation of a single cell per drop in a high-pressure dropper 2) cell lysis and mRNA capture 3) make cDNA from mRNA 4) combine all Igs from all cells 5) sequence the combined samlpe to see the VDJ and VJ repertoire
382
Where were the RAG proteins transposed to during evolution as a transposase?
- in between V-type segments
383
Does VDJ recombinase have transposase activity?
- yes
384
How was VDJ recombinase tested for transposase activity?
- took a tet-resistant piece of DNA with RSS ends that is radioactively labeled - mix it with an amp-resistant plasmid - transduce into bacteria to see if they are tet-resistant - if they are = has transposase activity
385
true or false: the VDJ recombinase can accidentally casue chromosomal translocation
true
386
What types of cancers commonly arise from VDJ recombinase-mediated translocations?
- leukemias
387
Where are hematopoietic stem cells found?
- fetal liver - adult bone marrow
388
What are the two stages of B cell development?
- Antigen independent (first) hematopoietic stem cell to B cell - Antigen dependent (second) B cell to plasma cell
389
What events occur during the antigen independent stage of B cell development?
- VDJ recombination - Allelic exclusion - gene regulation
390
Where are B cells found in the body?
- spleen - lymph nodes
391
What happens if a B cell doesn't recognize an antigen for the weeks/months it circulates around the body?
- will die after some time
392
What are the events that occur during the antigen dependent stage of B cell development?
- Clonal selection - Class-switching - somatic mutation
393
Where are plasma cells found in the body?
- tissues - bone marrow
394
What is clonal selection?
- there are many types of B cells with different antigen receptors - antigen binds to one of those B cells' antibodies - causes the cell to proliferate a bunch and out compete the other B cells - forming multiple clones - each clone has an identical antigen receptor
395
396
What is allelic exclusion?
- one copy of HC and LC loci focuses making a good protein, one at a time. - if one copy of the chromosome can't make a good, functioning HC or LC, the first copy is excluded - the second copy tries to make good HC and LC proteins - if first copy makes a good protein, second copy is excluded
397
What are the benefits to allelic exclusion?
- allows for clonal selection due to mono-specificity of B cells - Avidity for antigens depends on antibodies have a valence of at least two
398
What are the 2 characteristics of a cell to be considered a stem cell?
1) give rise to differentiated progeny 2) have to be able to copy itself
399
What do early B cell progenitors depend on?
- stromal cells - IL-7
400
Why do early B cell progenitors need to be in physical contact with stroll cells?
- bind via VCAM and VLA-4 ( adhesion molecules) - stromal cells spit growth and stem cell factors at the B cells - keeps the B cell alive
401
What is C-kit in stromal cell and IL-7 dependence?
- a proto-oncogene receptor
402
WHen does a B cell no longer depend on IL-7 and stromal cells?
- when it can produce a function immunoglobulin Heavy chain
403
What determines the cell type that hematopoietic stem cells will differentiate into?
- sequential regulation of transcriptions factors
404
What does Notch1 signaling cause?
- T-cell progenitor differentiation
405
What does PU.1, Pax5, and EBF signaling cause?
- B cell progenitor differentiation
406
How does IL-7 drive B cell development?
- signaling activated specific sets of transcription factors in B cells to drive development
407
What are the E2A and EBF transcription factors important for?
- surrogate light chain gene transcription - helps B cell to know its made a good HC protein by synthesizing LC surrogates
408
How do E2A and EBF work together or transcribe light chain surrogates?
- they both bind in a series of locations of surrogate chains genes - each gene has a unique relative combination positions of these factors to turn on transcription
409
True or False: there is stage-specific gene expression
true
410
What does FACS stand for?
- Fluoresence activated cell sorting
411
What is flow cytometry and FACS used for?
- can be used to see which cell-surface proteins are present on a population or type of cells
412
How can different stages of B cell development be distinguished?
- differential expression of various cell surface markers
413
What is B220/CD45?
a cell surface protein expressed on all B-lineage cells
414
What is CD43?
a surface protein expressed on early B cells and other non-BCs
415
What stages of development are IgM and IgD characteristically found in?
- immature BCs - mature BCs
416
What causes inverse expression of IgM and IgD?
- they are on the same long exon - alternative splicing produces each of the Igs
417
Typically in an immature B cell, what are the expression levels of IgM and IgD?
- High IgM - no IgD
418
In a mature B cell, what are the expression levels of IgM and IgD?
- low IgM - High IgD
419
in germinal center B cells, what are the expression levels of IgM and IgD?
-high IgM - no IgD
420
How do RAG proteins know which genes to rearrange at what stage in B cell development?
via the accessibility hypothesis
421
What is the accessibility hypothesis?
chromatin structure dictates recombinase targeting 1) germline transcripts: transcripts from unrearranged gene-segments 2) treatments which activate transcription also activate rearrangement 3) mutations preventing transcription also prevent rearrangment
422
what are the potential mechanisms of the accessibility hypothesis?
- the open chromatin structure allowing for the movement of RNA polymerase makes RSSs accessible - Binding of transcription factors to enhancers and promoters allows more accessibility - TFs recruit RAGs to rearranging loci via protein-protein contact - chromosomes folding brings gene segment into proximity
423
True or False: there is stage-specific reorganization of IgHC locus.
true: progenitor: no reorganization pro-B cell: yes reorganization pre-B cell: no reorganization
424
What is the purpose of transgenesis and targeted mutation?
- techniques for altering the mouse genome/germline
425
What are the 4 techniques used to modify the germline?
1) transgenesis 2) gene targeting using homologous recombination 3) gene targeting using CRISPR/Cas9 4) Conditional gene disruption
426
What is the process of making a transgenic mouse?
1) collect fertilized eggs 2) inject synthetic/cloned DNA into one of the pronuclei 3) implant injected eggs into the oviduct of a psuedopregnant female 4) 10-30% of the offspring contains the trnsgene 5) test for the presence of the transgene, can breed from there on
427
What is the origin of embryonic stem cells?
- fertilized egg > 2 cells > morula/8 cells > 16 cells > blastocyst (inner cell mass are stem cells)
428
How does CRISPR/Cas9 system cause genomic changes?
- load Cas9 with a specific guide RNA for region of interest - cause a double strand break - DSB can cause insertion or deletion via DNA repair machinery - DSB can also cause gene replacement using homologous recombination
429
What is the process of blastocyst injection?
- select target ES cells - hold blastocyst with suction pipette - inject ES cells into blastocyst - implant embyo into foster mother - develops into a chimeric mouse ( some tissues from ES cells some from embryo host)
430
What does a difference in coast colors in different blastocyst injected mice tell you?
- how much injected pluripotent cells there were
431
What stage of development do RAG-null B cells get arrested in?
- Pro-B cell stage - prior to making HC protein
432
What is the definition of a pre-B cell?
- expressed cytoplasmic HC - lacks surface IgM - divides a lot - allelic exclusion - rearrangement of LC locus is turned on
433
What is the definition of a Pro-B cell?
- tries to make rearrangements, but hasn't made a successful HC protein yet - once it does, becomes a pre-B cell
434
What events occur between the pro-B cell and pre-B cell stages ?
- IgHC rearrangement - Allelic exclusion
435
What event occurs between Pre-B cell and Immature B cell Stages?
- activation of IgLC rearrangement
436
What signals are sent/told to developing B cells expressing HCs?
- proliferate (3-4 cycles) - shut off HC rearrangement - Turn on Germline LC transcription - start LC rearrangement - turn down TdT gene - alterations in gene expression - diminish IL-7 dependence - don't die
437
T/F: you can use flow cytometry to assess cell cycle activity/states.
true
438
What is required for early pre-B cell proliferation?
HC expression
439
What promotes the pro-to-pre-B cell transition?
- HC expression
440
What can rescue BCD in RAG-null cells?
- adding HC protein to cells
441
What is the membrane-associated form of IgHC in early BCD required for?
1) LC gene germline transcription and rearrangement regulation 2) allelic exclusion, stopping rearrangement 3) cause proliferation of pre-B cells, selects for productive rearrangements 4) prevent apoptosis of developing cells
442
How does a pre-B cell know it's a pre-B cell?
- being able to assemble pre-B cell complexers like IgHC as a receptor
443
What makes up the pre-BCR?
- IgHC - VpreB - lambda 5 - Iga -Ig-B
444
What are Iga and Ig-B?
- signaling molecules between the BCR and the cell
445
What is VpreB and lambda5?
- surrogate LCs - chaperone proteins expressed in pro-B but goes away in pre-B cell from pre-BC signal - don't rearrange
446
How long does a cell have to make a good LC in order to not die?
- VpreB and lambda5 expression is shut off
447
What is the pre-BC signal that shuts off expression of VpreB and lambda5?
- aggregation of pre-BCR on the surface via ionic interactions of charged VpreB and lambda5 interactions - a ligand signal is not required for this to happen
448
What stage is central tolerance imposed in BCD?
- immature B cell stage
449
What happens when a BCR crosslinks with a self protein?
- apoptosis occurs, not activation - causes receptor editing
450
What happens when a BC produces a self-tolerant receptor?
- inactiviation of RAG genes
451
What is receptor gene editing?
- happens when an IMBC has made a good HC/LC, but it binds to a self protein - LC rearranges to fix this - upstream V segment rearranges with a downstream J segment - this deletes the previous VJ combination - creates a different LC
452
When is an LC permanent?
when a cell is tolerant of self proteins
453
T/F there are self-tolerance mechanisms in periphery tissues when a BC becomes mature.
true
454
Can igHC undergo receptor gene editing?
no
455
What are the two clonal selection steps during BCD?
- cell makes a good HC (Pre-BC) - makes a good LC (IMBC)
456
What is the process of IMBC self tolerance and development?
- IMBC moves through the blood into the spleen - gets checked constantly for self-tolerance - if it is self-tolerant, receives signaling from a survival cytokine, BAFF - becomes a mature BC - IMBC > T1 (lymphoid sheath in spleen)>T2 (Follicle) > MBCs T = transitional cells
457
What is BAFF?
- a cytokine that binds to self-tolerant IMBCs to mature - a survival signal - found in the follicle
458
What are B-1 B cells?
- innate-like - produced during fetal life - limited BCR diversity - IgM only - no CSR or SHM - spontaneous secretion (always making antibody) - responds to many carb antigens - don't require much help from TCs - found in peritoneal and other bodily fluids - normally all antibodies produced by B-1 cells are the same between people - no N regions in VDJ junctions - don't rely on BAFF
459
What are B-2 B cells?
- continuously made - contribute to immune responses - produced after birth - circulate the body for a few months then die
460
What are natural antibodies?
- produced without immunization - poly-specific IgM - produced by B-1B cells in the absence of infection - responsible for a significant fraction of IgM in serum of healthy humans - provides an innate-like response to infection (pre-existing) - activates the complement system
461
What happens when you inject an IgM-null mouse with IgM?
- is rescued from infection death compared to just IgM-null untreated mice - shows that serum IgM is essential for the function of the innate immunity
462
What are characteristics of BCD and tumors/cancers?
- status of Ig Gene rearrangement = developmental stage of tumor cell - many tumors have unusual VDJ recombination
463
What is X-linked Agammaglobulinemia?
- mutation in B-cell tyrosine kinase = activation of PLC-gamma - BCs fail to mature past pre-B cells; essentially no mature BCs - patients lack serum antibody but has normal TCs - high rate of infections in early life due to disappearance of maternal antibodies
464
What are characteristics of primary responses?
- has an initial lag period - IgM precedes IgG - IgG will continue to persist at the same low lvl after first infection
465
What are characteristics of secondary responses?
- no lag phase - IgG>IgM - increased affinity to antigen - has IgA present
466
What is the T cell independent type 1 B cell response to an antigen?
- B cells express and can also be activated via toll-like receptors and other PRRs (type 1) - activates when the cell sees PAMPS - will secrete antibody without worrying about the specificity - bound TLRs can activate naive B cells - secretes antibodies that it is specifically programmed for
467
What is the T cell independent type 2 B cell response to an antigen?
- simple, repetitive antigens (like carbs) - activate B cells by direct BCR cross linking and BCR aggregation - directly activates B cells - seems like a holding mechanism to wait until T cell mechanism kicks in - cross linking activates protein tyrosine kinases
468
What are characteristics of both types of T cell independent B cell responses?
- mostly IgM - modest affinity - no memory
469
What do the M1 and M2 regions in the Ig HC gene do?
- exon coding for transmembrane domain of the Ig receptor
470
T/F: secreted and membrane form of Ig comes from the same transcript and genome location.
true - RNA splicing determines if Ig is in membrane or secreted form
471
How does splicing occur to allow for the secreted or membrane form of an Ig molecule in the HC gene?
- signals received by the BC will shift transcription depend on if it wants the membrane form or not - If it wants the membrane form, the first polyadenylation site is skipped and transcribes the membrane exons - if the cell wanted the secreted form, first poly-A site ends transcription without membrane exon domain
472
what two antibodies are produced through different RNA splicing and transcriptional termination?
- IgM and IgD - can be co-expressed in the same cell - cannot be produced at the same time
473
What is the order of IgM and IgD exons?
- VDj joints/ segments - IgM exons - IgD exons
474
How does a cell transcribe/produce an IgD molecule?
- skips over the IgM exon
475
What is the process of the T cell dependent B cell response?
1) Macrophages/DCs activate TCs 2) BC and TC physically interact 3) clonal expansion for plasma cell development 4) other set of cells undergo class switching 5) some cells undergo SHM in GC 6) other cells become memory cells
476
What type of antigen does the TC recognize?
- processed antigen - a foreign part of the antigen that wasn't accessible before processing
477
What are the characteristics of the TCR that recognizes processed antigen?
- TCR is an aB heterodimer -aB genes generated by VDJ recombination - assembled in the membrane with CD3 complex - CD4 is a co-receptor
478
How is an antigen processed and presented to a TC?
- an antigen presenting cell (APC) ingests antigen - APC digest antigen into peptides - peptides form a complex with MHC class 2 - MHC=peptide complex transported to cell surface
479
What types of cells are APCs?
- macrophages - DCs - B cells
480
How does TC recognized processed antigen?
- TCR recognizes the MHC complex on the APC - this triggers and activates the TC - the co receptor (CD4) increases the avidity of the reaction - epitopes recognized by TCs are often buried in the antigen - T and BCs don't need to recognize the same part of an antigen
481
How do TCs help BCs to respond appropriately to an antigen?
- TC secretes cytokines that can cause BCs to undergo SHM and increase their binding affinity for the antigen
482
What is the process of a B-T cell interaction?
- BC takes up and processes the antigen - MHC complex is transported to the membrane - TCR and CD4 recognize the MHC complex and binds - CD28 receives a signal from the BC B7 = TC activation - CD40 receptor on BC receives a signal from TC gp39 - TC secretes cytokines as another activation signal for the BC (does this after receiving both activation signals) - BC activates
483
What are the 2 signals from the BC that activate the TC?
- MHC from BC to TCR and CD4 on TC - B7 from BC to CD28 on TC (second activation signal)
484
What are the 3 activation signals that BCs receive from TCs?
1) antigen, not from TC 2) gp39/CD40L from TC to CD40 receptor on BC 3) cytokines from TC
485
What type of TCs activate antigen-specific B cells?
- T follicular helper cells
486
How do Ig isotypes change after being coming mature and having Ig on the surface already?
- through Class-switch recombination (CSR)
487
Where is a switch sequence in reference to the constant region exons?
upstream
488
Does CSR happen in a T-cell dependent or independent immune response?
dependent
489
How does CSR occur?
- switch sequences undergo regulated transcription and RNA recombination -transcription through switch region is initiated at 2 different switches by activation of upstream promoter - different cytokines received from TCs (info relayed from DCs) turn on different TFa = turning on different switch promoters - there are breaks in the DNA that are introduced - causes repair machinery to join two switch regions together - excises DNA in-between switch regions - new constant exon is downstream of joined switch regions - no reading frame issues because CSR happens in the intron between VDJ and constant exons
490
Are RAG proteins required for CSR?
- no - this is happening in mature B cells not in the bone marrow
491
Does CSR require Ku70, Ku80?
- yes - bind to broken ends on knocked or broken DNA prior to switch sequence recombination
492
What is affinity maturation?
- antibody affinity increases during the course of an immune response or with multiple immunizations/infections - happens only in T-cell dependent immune responses
493
Why does affinity maturation only occur in TC dependent BC immune responses?
- only response pathway that allows for the formation of memory of the infection
494
What regions do somatic hypermutation normally occur?
- in the hypervariable regions of the variable domain (in CDRs = increased mutations on the same allele) - increases as immune response progresses - from downstream of V gene promoter and upstream of constant enhancer
495
What does AID stand for?
- Activation-induced Cytidine Deaminase
496
What is AID most structurally homologous to?
- RNA editing enzymes
497
What are the characteristics of AID?
- lymphocyte-specific enzyme - responsible for CSR and SHM - changes a nucleotide in RNA transcript - catalyzes a reaction to change C residues to U in DNA - requires ssDNA to work - causes UDG activity which is required for SHM
498
How was AID discovered by subtractive cDNA cloning?
- adding a specific cytokine would cause clonal cell lines to change Ig Isotype production
499
What causes Human Inherited immunodeficiency Hyper IgM syndrome 2 (HIMS2)?
- AIDS cause patients to only produce IgM because it is dysfunctional
500
What happens after AID catalyzes cytosine deamination?
- a protein will most likely remove the deoxyuridine because it doesn't belong in DNA - happens via base excision repair - removing base makes an open spot for mutation recombination
501
What mechanism and protein removes the deoxyuridine from DNA caused by AID?
- base excision repair - uridine D-glycosylase
502
What happens in AID-null mice?
- IgM levels stay the same - all other isotypes are completely gone or significantly decreased - shows that it's important for CSR
503
How does AID work with transcription R-loops?
- transcription starts on one of the strands of dsDNA - RNA being formed on the strand transiently forces the other strand to bubble up = R-loop becasue of RNA/DNA hybrid - increases AID activity, replaces Us for Cs
504
How are the Knicks in ssDNA created during CSR?
- uracil placed by AID in DNA attracts various DNA repair enzymes - they create the Knicks by excising the deoxyuridine
505
How can AID cause SHM?
- changes Cs to Us in DNA - causes U-G mismatch - can be repaired by several pathways - depending on the mechanism, can result in transitions, transversions, or random nucleotide insertions
506
What processes are involved in regulated Ig gene expression?
- VDJ recombination - transcription - polyadenylation - RNA splicing - CSR -SHM
507

MCDB 436: Immunology (2 decks)

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