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Microbiology 701 Part 2
Midterm Exam Material
213
Biology
Graduate
10/27/2007

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Term
MHC restriction is generated in which organ?
Definition
Thymus
Term
T cells from animal A will only recognize MHC from what animal?
Definition
A
Term
Foreign peptide + foreign MHC or self peptide + foreign MHC generate what response?
Definition
None
Term
Analysis of lysed target cells (MHC experiments) was performed with what compound?
Definition
Cr-51
Term
If AxB BM cells are injected into an irradiated mouse with thymus of type A, what will the T cells recognize? How about with thymus type AxB?
Definition
MHC A; MHC AxB
Term
How was activation of Th cells analyzed?
Definition
Pulsing mac's with Ag and mixing them with Ag-primed Th cells; Activation was measure by Th cell proliferation (Same strain and hybrids containing the original strain = activation)
Term
Alloreactivity is what?
Definition
Response to self-Ag in foreign MHC molecule (problem in transplants)
Term
CD4 T cells recognize what type of Ag?
Definition
Extracellular
Term
CD8 T cells recognize what type of Ag?
Definition
Intracellular
Term
If a self-peptide cannot be inserted into the MHCI molecule, what will happen?
Definition
The MHC molecule won't make it to the surface
Term
Ubiquitin does what with proteins in the cytoplasm?
Definition
Targets them to a proteasome
Term
What are sources of cytosolic Ag's?
Definition
Viruses, escaped microbes, tumors
Term
What is the proteasome?
Definition
A multiprotein enzyme complex with proteolytic activity in cytoplasm (degrade damaged/misfolded proteins)
Term
Structure of proteasome
Definition
Large cylinder (four rings of proteins with central channel); channel is degradation site
Term
Three subunits of proteasome (activity)
Definition
Chymotrypsin, trypsin, caspase
Term
Three subunits of proteasome (Names)
Definition
LMP-2/7/10, change predominant activity to chymotrypsin
Term
What mediates peptide transport from proteasome to ER?
Definition
TAP1/2
Term
What kind of transporters are TAP1/2?
Definition
ATP-binding complex (ABC)
Term
What does calnexin do?
Definition
Assists folding of alpha chain of MHC I and association with beta2M
Term
What does calreticulin do?
Definition
Stabilized newly formed EMPTY CI molecule
Term
What does tapasin do?
Definition
Tethers new CI molecules to TAP on lumenal side of ER, waiting for peptide
Term
Which receptors are higher in immature DC's?
Definition
Fc/Mannose (not MHC)
Term
How are Ag's internalized?
Definition
Receptor mediated phago and endocytosis
Term
At what pH are proteases optimally active?
Definition
Low, like 4.5 to 5
Term
What are the most abundant endocytic proteases?
Definition
Cathepsins (Cys/Asp proteases with broad specificities)
Term
Most Ag processing and CII loading occurs where?
Definition
In MHC II containing compartments
Term
After synthesis in the ER, what happens to CII alpha/beta chains?
Definition
They associate to form a heterodimer and then 3 of these a/b complexes assoc. with a homotrimer of the invariant chain
Term
What does the invariant chain do?
Definition
Promote assembly/proper folding of a/b CII dimer, prevents CII molecules from binding peptides in ER, targets the full structure to endocytic compartments
Term
How is the invariant chain removed from CII molecules?
Definition
Degradation through the endocytic pathway, the RLS of this is cleavage of Iip10 into CLIP
Term
What cathepsins cleave Iip10 to form CLIP?
Definition
Cat S and Cat L
Term
CII peptide loading is mediated by what?
Definition
DM (targeted to endo. pathway by itself, kicks CLIP out of cleft and waits for peptide with higher affinity to kick it out again; then recycles to load another CII molecule)
Term
Where are CD1 molecules loaded?
Definition
Endocytic pathway
Term
What do CD1 molecules present?
Definition
Nonprotein Ag's
Term
Where is Ab not found?
Definition
Immunologically sterile environs (CSF, eyes, urine)
Term
Antiserum is...
Definition
Serum with Ab
Term
What is titer?
Definition
Relative concentration of Ab (1/dilution)
Term
What is a hapten?
Definition
A molecule that won't generate an immune response by itself, but coupled with a carrier protein will generate Ab's for the protein, the hapten and the complex of carrier/hapten
Term
What shape is IgM?
Definition
Pentamer
Term
What shape is IgA?
Definition
Dimer
Term
3 phases of humoral immune response
Definition
Recognition, activation, effector
Term
Changing a proline to a serine causes what in Ig?
Definition
Loss of rigidity through loss of S-S binding and gain of intrachain S-S binding
Term
Alternative splicing causes what?
Definition
Change from membrane bound to soluble form of Ab; dual expression of IgM/IgD
Term
Papain cleaves where?
Definition
Above S-S bonds in Ig molecule (generates Fc and 2x Fab)
Term
Pepsin cleaves where?
Definition
Below S-S bonds in Ig molecule (generates Fab2 and chewed-up Fc)
Term
Ig domains are composed of what?
Definition
antiparallel beta sheets
Term
Ig domains (Variable domain, constant domains) are what size?
Definition
~110 aa
Term
What angle does a beta strand have?
Definition
120°
Term
Size of Ig domain
Definition
2 beta sheets (3+4 constant, 4+5 variable antiparallel)
Term
How large are complementarity determining regions in Ig's?
Definition
~10 aa
Term
What shape do CRD's have in Ig's?
Definition
Loop outside of overall structure, allows variability to be concentrated in specific locations
Term
What is the dissociation constant?
Definition
The concentration of Ag required to bind 1/2 of Ab binding sites at equil
Term
What is an allotype?
Definition
Difference in a few amino acids in the same isotype (Small difference in IgM Fc portion from one person to the next)
Term
What is an idiotype?
Definition
The sum of the Ag-binding sequences on an Ig molecule
Term
Lack of S-S bonds holding the two chains together in some IgG molecules causes what?
Definition
Hybrid (and quite often less effective) IgG molecules
Term
Polyclonal?
Definition
The sum of a humoral immune response, based on multiple B cells involved, multiple specificites, affinities, etc.
Term
Monoclonal?
Definition
A single Ab type from a single B cell, with specific affinity, binding site, etc.
Term
Functions of Fab
Definition
Neutralization of infectious agents/toxins and Ag entry into blood
Term
Functions of Fc (Aggregated)
Definition
Removal of Ag, Killing of infectious agents/abnormal cells, driving inflammation
Term
Best function of IgM
Definition
Activation of complement
Term
Antibody mediated neutralization does...
Definition
Interferes with microbial infectivity by blocking recognition sites/adhesion sites, inducing conf. changes; interferes with toxin activity, interferes with Ag transport across mucosal tissue
Term
Ig Opsonization occurs through what receptor?
Definition
Crosslinked Fcgamma
Term
How is activation signal sent into phago?
Definition
Through ITAM (immunoreceptor tyr-based activation motif) located on cyto. tail
Term
Activating Fc's
Definition
I, II-A, III, ERI, ARI
Term
Inhibitory Fc's
Definition
RII-B1/2
Term
What happens when mac's are activated through FcR's?
Definition
Release of RO's, degradative enzymes, prostaglandins
Term
What happens when NK cells are activated through FcR's?
Definition
Release of IFNgamma, perforin, granzymes
Term
What happens when allergic/parasitic defense cells are activated through FcR's?
Definition
Release of histamine, proteases, toxic proteins, etc.
Term
What happens when platelets are activated through FcR's?
Definition
Release of histamine, thrombi (clotting)
Term
Ab-dependent cell mediated cytotoxicity means what?
Definition
NK cells recognize Ig-coated cells through FcR's; Parasitic defense recognizes IgE coated parasites through FcR's
Term
What are natural Ab's?
Definition
Present without overt immunization, limited specificity (based on polysacc's), innate-like immunity
Term
What do natural Ab's block?
Definition
Xenografts (complement can be suppressed, but not natural Ab's)
Term
How does complement enhance B cell signaling?
Definition
Through interaction with CR2 receptor (while bound to BCR)
Term
Besides the B cell receptor, where does an Ag-Ab complex bind a B cell?
Definition
Fc receptor
Term
What is the major Ig produced daily?
Definition
IgA(60%)
Term
What is the major immunity function of IgA?
Definition
Mucosal
Term
How is IgA transported across the epithelium?
Definition
It is secreted with a J chain, bound to a poly-Ig receptor on the endo cells, endocytosed into endo cells, transported to opposite membrane where it is cleaved before release as active secreted IgA
Term
What does the secretory component of IgA do?
Definition
Protects it from breakdown in the lumen
Term
What Ab is responsible for neonatal immunity?
Definition
IgG
Term
What Ab is present in breast milk?
Definition
IgA
Term
What receptor allows IgG transport across placenta?
Definition
Brambell receptor
Term
What is type II hypersensitivity?
Definition
Tissue injury caused by anti-tissue Ab
Term
What is type III hypersensitivity?
Definition
Immune complex mediated tissue injury (Mainly vasculitis/deposition)
Term
What is lupus?
Definition
Multisystem disease caused by IC deposition (both Ab/complement types) on various tissues
Term
4 symptoms of lupus?
Definition
Inability to regulate production of auto-Ab, Dysfunctional clearance of Ag-debris/IC, Polymorphic complement proteins/Fc receptors protect against diseased tissue while mediating healthy tissue damage, defective complement/Fc receptors responsible for this situation
Term
Differences between mouse/human Ig's?
Definition
Mouse IgG2alpha/beta fix complement, IgG1/3 don't; Human IgG1/3 fix complement, 2/4 don't
Term
What are the four major classes of Ag?
Definition
Carbos, Lipids, NA's, Proteins (Only Carbos/usually and proteins/always are immunogens, the other two are rare... lupus is characterized by anti-DNA Ab)
Term
A greater degree of protein complexity causes what?
Definition
A more vigorous immune response
Term
What structural features of a protein can an Ab recognize?
Definition
All 4 (Primary, secondary, etc.)
Term
Are all antigens immunogenic?
Definition
No
Term
What is an antigen?
Definition
A particle/sequence which has the ability to combine specifically with Ab/cell surface BCR/TCR
Term
What is an epitope?
Definition
A specific site on a macromolecule where an immune cell will recognize and initiate a reaction
Term
What type of amino acids are typically part of a B cell epitope?
Definition
Hydrophilic (outside of protein complex)
Term
What type of aa are typically part of a T cell epitope?
Definition
Hydrophobic (inside protein complex, linear, etc.)
Term
What regions have B cell epitopes?
Definition
Flexible regions
Term
What type of B cell epitopes do complex proteins have?
Definition
Overlapping, some are immunodominant (larger response)
Term
Hen egg-white lysozyme makes how many nonsequential epitopes?
Definition
One
Term
If an S-S bond is reduced, will the same Ab bind this epitope?
Definition
No
Term
What are the four types of Ab-Ag interactions?
Definition
Ionic, H-bonds, hydrophobic, van der Waals
Term
What is the agretope?
Definition
The part of an Ag-peptide that binds to the MHC molecule
Term
A given MHC molecules has what type of specificity?
Definition
Broad but selective
Term
What are the factors in determining immunogenicity?
Definition
Foreignness, high MW, chemical complexity, degradability, dosage/route of administration, genetic composition, adjuvants (coupled with Ag simply increase immune response, not same as haptens)
Term
Which would generate an immune response in the same animal, sperm or collagen?
Definition
Sperm
Term
Which molecule would not generate an immune response in very distant animals, cytochrome C or corneal tissue?
Definition
Cytochrome C
Term
What is the cutoff for usual non-immunogenic MW?
Definition
1kDa
Term
If a homopolymer of aa is injected into a mouse, will there be a response?
Definition
Not likely, not complex enough
Term
If a peptide is composed of D-aa, will it be degraded?
Definition
No, resistant to enzymes
Term
Too high of a dosage of an Ag causes what?
Definition
Tolerance (also caused by numerous low doses)
Term
What is the only human adjuvant currently in use?
Definition
Alum (causes precipitation of Ag = higher response)
Term
4 effects of adjuvants
Definition
Prolong Ag persistence, Enhance co-stim signals, Induce granuloma formation (large mass of granulocytes), Stim lymphocyte proliferation
Term
Adjuvants used in animals?
Definition
Freund's complete (M. tb), BCG (Mycobact, C. parvum, B. pertussis) = slow continuous release of Ag, Bacterial endotoxins (LPS, MDP)
Term
What is the mechanism of alum?
Definition
Delayed release of Ag = enhanced uptake by APC
Term
How are epitopes determined?
Definition
Protein sequence analysis (compare with databases, check for HLA-binding peptides, look for coils, transmembrane segments, etc.)
Term
What do consensus predicted epitopes show?
Definition
High values for antigenicity, flexibility, surface location
Term
Heavy chain = how many domains?
Definition
1 variable and 3-4 constant
Term
Light chain = how many domains?
Definition
1 variable and 1 constant
Term
Structure of variable domains
Definition
3 hypervariable regions (HV1/2/3) flanked by four framework regions (FR1/2/3/4) with less variable sequences
Term
What does IgA do?
Definition
Provide mucosal immunity and defense against microbes
Term
Where is IgA made?
Definition
By plasma cells in mucosal lymphoid tissues
Term
What do IgG and IgE do?
Definition
Perform effector functions (Ab-mediated cytotoxicity); IgG bind to infected cells and Fc receptors on NK cells; IgE bind to parasites (worms) and FcE receptors on eosinophils
Term
Ig expressed during B cell development
Definition
Stem cell = no Ig, pre-B = IgH only (surrogate IgL), immature B = IgM only, Mature B = IgM/D
Term
Ig alterations
Definition
VDJ recombination/somatic hypermutation, secreted vs. membrane-bound, isotype switching
Term
On what chromosomes are the Ig genes located?
Definition
H = 14, kappa = 2, lambda = 22
Term
How many V/J/C segments does lambda have?
Definition
30V, 4J, 4C
Term
How many V/J/C segments does kappa have?
Definition
35V, 5J, 1C
Term
How many V/D/J/C segments does IgH have?
Definition
45V, 23D, 6J, numerous C's
Term
How is membrane/soluble form determined?
Definition
Polyadenylation of specific sites in the mRNA (upstream = secreted, downstream = membrane-bound), same as IgM/D
Term
How is class switching mediated?
Definition
Switch regions cross and intervening DNA is cut out (5'-3') = only remaining DNA transcribed, intervening = lost
Term
Somatic hypermutation selects for what?
Definition
Higher affinity Ig (after Ag stimulation)
Term
Mutations increase or decrease with multiple exposures?
Definition
Increase, attempting to better match the Ag and create stronger response
Term
Where does somatic hypermutation occur?
Definition
Germinal centers
Term
What are the 2 differences between BCR/TCR?
Definition
TCR is monovalent/BCR is bivalent, TCR has no secreted component
Term
What is the structure of a TCR?
Definition
Variable region, constant region, Transmembrane region, Tail piece
Term
TCR is similar to what of the Ig?
Definition
Fab fragment
Term
Can the TCR class switch?
Definition
No
Term
How was TCR cDNA isolated?
Definition
Obtaining fragments from Tcells and subtracting B cell DNA to isolate unique sequences
Term
How was TCR cDNA analyzed?
Definition
Southern blotting
Term
On what chromosomes are TCR genes located?
Definition
beta=7, alpha/delta=14, gamma=7
Term
Which TCR genes are located adjacent to each other?
Definition
alpha and delta (delta is within alpha)
Term
How many VDJ segments does alpha have?
Definition
45J, 55J, 1C
Term
How many VDJ segments does delta have?
Definition
10V, 3D, 4J, 1C
Term
How many VDJ segments does beta have?
Definition
50V, 2D, 12 J, 2C (DJC are repeated, so only 1D/6J/1C per repeat)
Term
How many VDJ segments does gamma have?
Definition
5V, 2J-C repeats
Term
What is the structure of the surrogate light chain?
Definition
VpreB and lambda5
Term
How does the VDJ work?
Definition
D to J and then V to DJ
Term
When are RAG1/2 turned on?
Definition
During H-chain rearrangement and kappa/lambda rearrangement
Term
When is TdT turned on?
Definition
During H-chain rearrangement
Term
What is allelic exclusion?
Definition
Expression of a single allele (kappa only or lambda only), also called light chain isotype exclusion
Term
Which chains are rearr first in T cells?
Definition
delta then gamma; beta then alpha
Term
Which chains are rearr first in B cells?
Definition
Heavy, then kappa/lambda
Term
What are recombination signal sequences?
Definition
Conserved sequences which mediate joining between variable region segments
Term
What is the structure of RSS's?
Definition
Palindromic heptamer and AT rich nonamer separated by 12 or 23 bp
Term
What is the 12/23 bp rule?
Definition
RSS's with same spacing cannot combine
Term
How do RSS's work?
Definition
RSS with 12 bp combines with RSS of 23 bp, etc.
Term
What does 12/23 bp rule prevent?
Definition
Direct combination of VH-JH (causes VDJ)
Term
Which VDJ recombination proteins are resistant to ionizing radiation?
Definition
RAG1/2, TdT
Term
Where is Artemis involved in VDJ recombination?
Definition
Nicks DNA at hairpins and allows insertion of palindromic P nucleotides (template dependent)
Term
What type of nucleotides does TdT add?
Definition
N nucleotides (template independent) (at the same time, exonucleases can cut away nt's)
Term
What aa's are present in the transmembrane region of the TCR to give positive charge?
Definition
Lysine and Arginine
Term
What function do the transmembrane proteins of the TCR serve?
Definition
Signal transduction
Term
When cDNA was added to T cells which coded for a portion of the TCR, did it allow for recognition of peptides previously recognized by that cell?
Definition
No, only the specific combination of original chains codes for that peptide recognition
Term
How many CDR's are present on TCR's?
Definition
3 on each (alpha/beta) chain, a 4th on the outside of the beta chain (used by super-Ag's)
Term
Which CDR's interact with what molecules (TCR)?
Definition
III with Ag, I/II with MHC
Term
What molecule do TCR's need for signal transduction?
Definition
CD3
Term
What chains compose the CD3 molecule?
Definition
epsilon/gamma (44-81aa), epsilon/delta (44-81aa), zeta/zeta or zeta/eta (113aa)
Term
How are zeta/zeta CD3 chains linked?
Definition
S-S bond
Term
What are ITAMs composed of?
Definition
Tyr-XX-Leu (Tyr is substrate for Tyr kinases)
Term
If CD3 is not expressed, what is prevented?
Definition
Expression of the TCR at the cell surface
Term
What is the structure of CD4 molecules?
Definition
4 domains, top two bind to beta2 domain of CII molecule
Term
What is the structure of CD8 molecules?
Definition
Heterodimer of single domains, either domain binds to alpha3 of CI molecule
Term
What is a common accessory molecule interaction bet. T cells and target cells/APC's?
Definition
LFA-1 to ICAM-1
Term
What molecules bind B cells to Th cells?
Definition
B-7 to CD28
Term
What is the signaling dimer needed by BCR's?
Definition
Igalpha/beta
Term
What is the preTCR?
Definition
beta chain with preTalpha
Term
What are cytokines?
Definition
Soluble proteins produced by leukocytes that regulate the intensity/duration of an immune response and bind to specific receptors/trigger signal transduction
Term
What effects do the signals from IL's have?
Definition
Growth/differentiation of lymphocytes, activation of effector cells, devel. of stem cells
Term
Some things about cytokine secretion?
Definition
Brief timing, not pre-formed, synth'd in response to cell activation, transient transcriptional activation, highly unstable mRNA, posttranslationally modified, rapid secretion after synthesis
Term
3 types of cytokines
Definition
autocrine (self), paracrine (neighboring cells), endocrine (systemic)
Term
Pleiotropism
Definition
Affect multiple cell populations (cytokines)
Term
Redundancy
Definition
Multiple cytokines with same effects
Term
Synergy
Definition
Multiple cytokines work together for specific response
Term
Antagonism
Definition
Cytokines inhibit each other
Term
Cascade
Definition
Cytokines affect a large number of cells in a cycle
Term
Cytokine categories
Definition
Mediate innate (from mac's), mediate adaptive (from T cells), stim hemato (from stromal cells, leukos)
Term
What are actions of TNFalpha?
Definition
Mediate acute inflammatory response (block O2 and nutrients to tumor area), systemic complications of severe infections
Term
What stimulates TNFalpha?
Definition
LPS/TLR4/CD14, enhanced by IFNgamma
Term
TNFalpha structure
Definition
Intracell N terminus, large extracell C terminus
Term
How is TNFalpha expressed in the membrane?
Definition
Homotrimer, cleaved to release polypeptides which trimerize and bind receptors at the base of the pyramid
Term
2 major TNF functions
Definition
Stimulate recruitment of PMN's and monocytes to sites of infection (Induce adhesion cascade, chemotaxis, etc.) and Activate cells to eradicate microbes (stimulate PMN's/mac's to kill more efficiently)
Term
Low to moderate TNF
Definition
Adhesion, activation, fever, microbicidal proteins, more PMN's
Term
High TNF
Definition
Septic shock, low cardiac efficiency, vessel clotting, liver problems, lack of glucose replenishment, loss of weight from low appetite
Term
What other cytokines work with TNFalpha to generate septic shock?
Definition
IL-1/12, IFNgamma (prevent lowering of shock by blocking TNFalpha)
Term
What is IL-1 cleaved by?
Definition
Caspase-1
Term
What are the actions of IL-1?
Definition
Mediate local inflammation (low), systemic responses like fever, BM production up, etc. (high), no septic shock
Term
Monocytes produce a natural agonist of IL-1 that does...
Definition
Binds receptor in competitive fashion
Term
What does IL-12 do?
Definition
Mediator of early innate immune response to intracellular microbes/induction of cell-mediated immunity, stim IFNgamma production (T/NK cells), diff. of CD4 T cells to TH1, enhance active NK cells/CD8 T cells
Term
IL-12 subunits
Definition
p40/p35 = activates or p40/p40 = inhibits
Term
IL-23 subunits
Definition
p40/p19
Term
What does IL-23 do?
Definition
Mac's produce during infection, contributes to autoimmune diseases, causes diff/maintenance of Th17 cells
Term
Th1 cells work with what kind of pathogens?
Definition
Intracellular
Term
Th2 cells work with what kind of pathogens?
Definition
Extracellular
Term
IL-12 deficiencies caused what in all 3 patients?
Definition
Recurrent opportunistic infections, some from immunizations
Term
IL-12 receptor deficiency led to what in patients?
Definition
Lack of IFNgamma (treated with IFNgamma injections)
Term
IL-12 component deficiency led to what in patients?
Definition
Lack of IFNgamma (treated with IL-12 injections)
Term
IFN-1 family does...
Definition
Mediates early innate immune responses to viral infections/intracellular microbes (up MHCI regulation, devel Th1 cells, sequester lymphos in LN)
Term
What stimulates IFN-1 family?
Definition
Viral NA that bind receptors/sensors and stimulate IRF transcription factors
Term
What is the range of IFN-1 family?
Definition
Paracrine/autocrine
Term
What does IFN-1 do to target cells?
Definition
Tell infected ones to die, tell uninfected to secrete enzymes which block viral replication
Term
TNFalpha/IL-1 control what pathogens?
Definition
Extracellular
Term
IL-12 controls what pathogens?
Definition
Intracellular bact/fungal
Term
IFN-1 controls what pathogens?
Definition
Viral
Term
What does IL-10 do?
Definition
Inhibits mac's/DC's (from mac's = negative feedback/reg T cells)
Term
How does IL-10 work?
Definition
Inhibits IL-12 from mac's/DC's, inhibits costim molecules/MHC II molecules in mac's/DC's
Term
IL-10 KO mice develop inflammatory bowel syndrome from what?
Definition
Inability to turn off inflammation from intestinal microbes
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