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

B3.061 Proteins in Immunity Flashcards

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

A

diversity
specificity
high affinity
stability

25
Q

diversity

A

body must be ready to encounter any of 1000s of antigens

26
Q

specificity

A

discrimination among potential antigens

27
Q

high affinity

A

must bind tightly to antigen (time vs equilibrium)

must be stable and persist

28
Q

stability

A

must survive in circulation or on the cell surface

29
Q

what are the 2 different options for protein engineering diversity

A

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
Q

how do Igs and TCRs achieve diversity?

A

option 1
combinatorial power
-VDJ gene recombination
-high frequency somatic mutations (only Igs)
throw out self and amplify those that encounter antigens

31
Q

how is alternative splicing in DNA utilized in Ig heavy chain?

A

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
Q

lists the steps in Ig VDJ recombination within DNA

A
  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
Q

list the steps in Ig VDJ recombination done at the mRNA level

A
  1. recombination of V and DJ exons

antibody transcript will also include constant domain gene

34
Q

what is the function of alternative splicing in the mRNA utilized in the Ig heavy chain?

A

allows isotype switching while maintaining antigen specificity chosen
chosen C region can code the membrane or the secreted form

35
Q

how do MHCs achieve diversity?

A

option 2
more diversity across the human population than within an individual
genetic cross over during meiosis leads to these polymorphisms

36
Q

most polymorphic genes known

A

MHC
every person possesses a set of MHC molecules with different ranges of peptide binding specificities
evolutionary insurance??

37
Q

MHC specificity

A

broad

38
Q

how do MHC 1 molecules bind peptides

A

peptide stabilized by anchors at both ends

39
Q

how do MHC 2 molecules bind peptides

A 
peptide side chains protrude into pockets lined by polymorphic residues
more permissive than class 1
no clear binding rules
40
Q

TCR/Ig specificity

A

high/narrow

each variant has a reasonably strict specificity

41
Q

can you predict a TCR/Ig’s structure from its sequence?

A

nope, makes it hard to make targeted drugs

42
Q

what is an example of cross reactivity leading to disease?

A

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
Q

how can drugs mediate self vs non self mistakes?

A

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
Q

what proteins have some of the highest protein-protein binding affinities?

A

antibodies
TCRs
nearly permanent

45
Q

how does lectin-carb binding affinity compare to antibodies/TCR?

A

relatively transient

46
Q

how many biding sites are on 1 Ab?

A

2 identical and independent binding sites

47
Q

do the 2 Ab binding sites act completely independently?

A

no

cooperativity arises through protein communication

48
Q

discuss the concept of avidity

A

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
Q

discuss the binding affinity of IgM molecules and the overall avidity

A

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
Q

discuss the differences in complement activation by IgM and IgG

A

only 1 IgM required to activate

at least 2 IgGs required

51
Q

what does multi-valency allow for?

A

clustering

different cluster formations can send different signals

52
Q

why is having a high abundance of proteins important?

A

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
Q

why is delivering drugs to target specific microbe receptors so difficult? i.e. flu hemagglutinin

A

need a HUGE concentration in body to have an effect

54
Q

what are 2 key factors that provide protein stability?

A

glycosylation

disulfide bonds

55
Q

where is the Ig molecule glycosylated

A

in the middle of the Fc region

56
Q

how does the glycosylation act on the Ig

A

covalent osmolyte

helps the molecule to stay folded and block proteases

57
Q

how are antibody drugs designed?

A

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
Q

discuss the stability requirements of Ab drugs

A 
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
Q

how are humanized antibodies used?

A

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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