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IBI Test 4 > B3.061 Proteins in Immunity > Flashcards

B3.061 Proteins in Immunity Flashcards

(59 cards)

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1
Q

what are the major protein classes that are players in immunity?

A

Immunoglobulins/ Antibodies
MHC complexes/ TCRs
Lectins

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2
Q

which Ig classes are monomers?

A

IgD, IgE, IgG

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3
Q

which Ig class is a dimer

A

IgA

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4
Q

which Ig class is a pentamer

A

IgM

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5
Q

what makes up the binding sites of an immunoglobulin?

A

dynamic loops
Velcro-like mechanism
effective at binding a wide range of antigens

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6
Q

where are Ig binding sites on the Ig?

A

Fab regions (top parts of the Y shape)

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7
Q

what are some examples of antigens that can be bound by Igs?

A 
whole proteins
peptides
DNA/RNA
carbs
haptens
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8
Q

what is the Fc region of an Ig

A

the stem of the Y shape

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9
Q

what can bind to the Fc region of an Ig?

A

Fc receptors
complement
bacterial protein A (IgG)
other species antibodies (ELISA)

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10
Q

when does bacterial protein A bind to the Fc region of an Ig?

A

when it is fighting back against the immune system

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11
Q

how do we design ELISA tests?

A

raise Abs against the Fc region of human Igs to mark them

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12
Q

what is located at the bottom of the BCR

A

C-terminal transmembrane domain

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13
Q

discuss the physical structure of the MHC class 1 complex

A

heterodimer

alpha 1, 2, 3 and B microglobulin

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14
Q

what does MHC class 1 bind

A

cytosolic antigens

8-10 aa in length

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15
Q

discuss the physical structure of the MHC class 2 complex

A

heterodimer

B 1,2 and alpha 1,2

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16
Q

what does MHC class 2 bind

A

extracellular antigens after phagocytosis

15-24 aa in length

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17
Q

how are peptide antigens generated?

A

by the proteasome
takes in self and mutant/viral proteins
spits out chunks of proteins that are them displayed by class 1 MHC on cell surface

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18
Q

what part of the TCR interacts with an antigen/MHC complex?

A

complementarity determining region (CDR) loops

TCR binds composite surface of peptide and MHC protein

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19
Q

discuss the physical structure of the TCR

A 
heterodimer
a and B chains
V region, C region, hinge, transmembrane region (top to bottom)
coated with carbohydrates on outside
chains linked by disulfide bond
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20
Q

how does TCR discriminate MHC1/2?

A

CD4/8 co-receptors

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21
Q

what are lectins?

A

receptors that recognize carbohydrates

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22
Q

who expresses lectins?

A

hosts, microbes, plant toxins
allows for a wide range of binding combos
the carb or the lectin can be on either type of cell

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23
Q

describe the structure of lectins

A

extremely variable
grouped into 6 families
can be grouped into higher order structures with multiple binding sites

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24
Q

what are the 4 characteristic that are needed in an immune response

Study These Flashcards
A

diversity
specificity
high affinity
stability

25
diversity
body must be ready to encounter any of 1000s of antigens
26
specificity
discrimination among potential antigens
27
high affinity
must bind tightly to antigen (time vs equilibrium) | must be stable and persist
28
stability
must survive in circulation or on the cell surface
29
what are the 2 different options for protein engineering diversity
option 1: make thousands of different proteins option 2: a few proteins bind many ligands **either way must be ready to encounter thousands of antigens
30
how do Igs and TCRs achieve diversity?
option 1 combinatorial power -VDJ gene recombination -high frequency somatic mutations (only Igs) throw out self and amplify those that encounter antigens
31
how is alternative splicing in DNA utilized in Ig heavy chain?
as B cells mature, they start rearranging and changing their DNA sequence this process is deliberately error prone with varied domain boundaries and random insertions, deletions
32
lists the steps in Ig VDJ recombination within DNA
1. all genes in heavy chain locus 2. removal of unwanted D and J gene segments 3. recombination of D and J exons (DJ recombination) 4. removal of unwanted V and D gene segment
33
list the steps in Ig VDJ recombination done at the mRNA level
5. recombination of V and DJ exons | antibody transcript will also include constant domain gene
34
what is the function of alternative splicing in the mRNA utilized in the Ig heavy chain?
allows isotype switching while maintaining antigen specificity chosen chosen C region can code the membrane or the secreted form
35
how do MHCs achieve diversity?
option 2 more diversity across the human population than within an individual genetic cross over during meiosis leads to these polymorphisms
36
most polymorphic genes known
MHC every person possesses a set of MHC molecules with different ranges of peptide binding specificities evolutionary insurance??
37
MHC specificity
broad
38
how do MHC 1 molecules bind peptides
peptide stabilized by anchors at both ends
39
how do MHC 2 molecules bind peptides
``` peptide side chains protrude into pockets lined by polymorphic residues more permissive than class 1 no clear binding rules ```
40
TCR/Ig specificity
high/narrow | each variant has a reasonably strict specificity
41
can you predict a TCR/Ig's structure from its sequence?
nope, makes it hard to make targeted drugs
42
what is an example of cross reactivity leading to disease?
lonestar tick induced allergy to red meat body develops an immune response against ticks similar antigen present in meat which is then recognized by immune system following tick exposure
43
how can drugs mediate self vs non self mistakes?
HIV drug abacivir drug binds to self peptide leading to a 'new' self peptide that is not recognized as self causes and immune response
44
what proteins have some of the highest protein-protein binding affinities?
antibodies TCRs nearly permanent
45
how does lectin-carb binding affinity compare to antibodies/TCR?
relatively transient
46
how many biding sites are on 1 Ab?
2 identical and independent binding sites
47
do the 2 Ab binding sites act completely independently?
no | cooperativity arises through protein communication
48
discuss the concept of avidity
more binding sites increases avidity after the first binding event, subsequent binding events have high local concentration making binding affinity higher than a single Ab-Ag affinity would be
49
discuss the binding affinity of IgM molecules and the overall avidity
IgM antibodies are produced before B cells undergo hypermutation tend to have lower affinity than other isotypes 10 Ag binding sites can bind simultaneously to multivalent antigens high overall avidity
50
discuss the differences in complement activation by IgM and IgG
only 1 IgM required to activate | at least 2 IgGs required
51
what does multi-valency allow for?
clustering | different cluster formations can send different signals
52
why is having a high abundance of proteins important?
hard to inhibit Abs : 18% of total blood protein TCR: 30,000 on T cell surface cell surface carbs: clusters measured in um, there are so many
53
why is delivering drugs to target specific microbe receptors so difficult? i.e. flu hemagglutinin
need a HUGE concentration in body to have an effect
54
what are 2 key factors that provide protein stability?
glycosylation | disulfide bonds
55
where is the Ig molecule glycosylated
in the middle of the Fc region
56
how does the glycosylation act on the Ig
covalent osmolyte | helps the molecule to stay folded and block proteases
57
how are antibody drugs designed?
de novo design doesn't work (cant design an Ab for a specific Ag) make a huge library and screen for the one that works
58
discuss the stability requirements of Ab drugs
``` must survive on the shelf (refrigeration) delivery mode (infusion, don't survive GI tract) solubility (concentrated drug gets diluted in vivo, so has to be super concentrated at administration to avoid volume overload) ```
59
how are humanized antibodies used?
antibody template from some other organism constant regions/carb altered to resemble human diminishes chance of immune response to antibody drug

IBI Test 4 (21 decks)

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