Adaptive Immunity

Question 1

Production of viral proteins

Answer 1

Viral proteins are made within the host cell, by the hosts own protein synthesis machinery

Question 2

An effective immune system has to do what?

Answer 2

Devise a system to sample both vacuolar and cytoplasmic compartments

Question 3

All proteins in a cell - both ____ and ____ are degraded into _____

Answer 3

Cellular; Foreign; Fragments (peptides)

Question 4

Antigen presentation

Answer 4

Peptide fragments of proteins are “presented” to T cells on Class I or Class II MHC molecules

Question 5

Concepts underlying class I MHC antigen presentation to T Cells

Answer 5

1) Proteins must be tagged for destruction
2) Protelysis must occur to generate peptides of the appropriate size
3) Peptides must be delivered to class I MHC molecules
4) Peptides must bind to class I MHC molecules
5) Peptides must be displayed to T cells in the context of class I MHC molecules

Question 6

How are proteins tagged for proteolysis

Answer 6

Ubiquitin (small 8 kDa) added to protein destined for degradation - Ub on lysine residues
If a protein is destined for degradation, ubiquitin molecules are added to the ubiquitin to form a Ub chain

Question 7

3 types of protease activity associated with proteasome

Answer 7

Chymotrypsin-like (The important one)
Trypsin-like
Capsase-like

Question 8

IFN-γ

Answer 8

IFN-γ - protective cytokine usually associated with virus infection
Induces expression of 3 replacement of β proteasome subunits called LMPs, which increase the production of peptides suitable for antigen presentation (chymotrypsin activity)

Question 9

Immunoproteasome

Answer 9

Proteasome once replacement subunits are encoded in the MHC

Question 10

How many subunits in the proteasome

Answer 10

7

Question 11

Actions of the proteasome

Answer 11

The ubiquitin must be removed before entry into the proteasome - done by isopeptidases
Unfoldases (associated with proteasome) stretch out the protein
Proteasome generates peptides of 4-20 amino acid residues

Question 12

TAP (Peptide delivery)

Answer 12

Transporter associated with antigen processing - transports peptides into ER

Question 13

TAP characteristics

Answer 13

Encoded in MHC
12 membrane spanning domain integral membrane proteins
One substrate: peptides
Peptides ending in L,I,V,M favored substrates
Size range:6-15 amino acid residues

Question 14

What types of amino acids do degraded peptides end in

Answer 14

Hydrophobic (Leucine, Isoleucine, Valine, methionine)

Question 15

Peptide generation and loading onto class I molecules (3 steps)

Answer 15

1) proteolysis of proteins - not totally random, but diverse (4-20 residues)
2) TAP transporter - selects for subset ending with L, I, V, M (6-15 residues)
3) Binding to class I MHC molecule - strict size restrictions and anchor residues (8-10 residues)

Question 16

Class I MHC antigen processing and presentation (5 steps)

Answer 16

1. Proteins tagged for destruction
2. Proteolysis (peptides ending in L,I,V,M)
3. Delivery of peptide (selction for L, I, V, M - enders)
4. Binding of peptide (chaperone-mediated)
5. Transport to the cell surface and presentation to T cells

Question 17

Why don’t T cells recognize all cells as foreign

Answer 17

T cell receptors (TCR) recognize the combination of self MHC + peptide

Question 18

How does a T cell know whether it is seeing self or foreign peptide?

Answer 18

During development, we generate a population of newborn T cells that have the capacity to recognize everything, including self peptide +MHC
Then we eliminate the T cells that recognize self peptide in complex with self-MHC

Question 19

Alloreactivity

Answer 19

Some of the positively selected TCRs that bind weakly to self MHC + self peptide may bind strongly to non-self MHC and peptide

Question 20

Thymic education (3 possibilities)

Answer 20

“Education” of T cells in the thymus

1) NO affinity - T Cell dies (death by neglect)
2) High affinity - T cell dies
3) Weak/moderate affinity - T cell lives to leave the thymus and populate the periphery

Question 21

What causes rejection of transplanted tissue

Answer 21

Alloreactivity - reactivity of T cells to non-self (allogenic) MHC class I or class II molecules

Question 22

Class I MHC chains (1 gene)

Answer 22

β2 Microglobulin, α1, α2, α3

Question 23

Class II MHC chains (2 genes)

Answer 23

α1, α2, β1, β2

Question 24

How do peptides contribute to MHC molecules

Answer 24

Considered a subunit of these MHC molecules - if no peptide bound, the MHC molecules fall apart

Question 25

Class I molecules

Answer 25

Proteins must be tagged for destruction Proteolysis must occur to generate peptides of the appropriate size Peptides must be delivered to MHC molecules Peptides must bind to MHC molecules (occurs in the ER) Peptides must be displayed to CD8 T cells in the context of MHC molecules

Question 26

Class II molecules

Answer 26

``` No tagging of proteins for destruction Proteolysis for antigen into peptides mediated by lysosomal proteases No topological barriers - delivery not an issue Loading of peptide occurs in endocytic compartment NOT in ER Peptides displayed to CD4 T cells in the context of MHC class II molecules ```

Question 27

Why don't Class II molecules face the problem of crossing the topological barrier of a lipid bilayer

Answer 27

Class II molecules present peptides that are derived from the outside of the cell i.e. endocytic pathway

Question 28

How do we get class II molecules to the lysosome and how do we prevent peptides in the ER destined for class I molecules from binding to class II molecules

Answer 28

Invariant chain (Ii) - Scaffold, stabilizer - Barrier to peptides in ER - Zip code to MHC class II compartment

Question 29

Invariant chain

Answer 29

Forms a trimer with 3 class II molecules and 3 invariant chains

Question 30

CLIP

Answer 30

``` Invariant chain binds in the groove of MHC class II molecule Cleavage results in a short peptide fragment (CLIP) bound to the class II molecule ```

Question 31

HLA-DM

Answer 31

catalyzes the exchange between CLIP and the antigenic peptide DM destabilizes peptide bound in the cleft

Question 32

Class II antigen processing and presentation

Answer 32

1) No tagging of proteins for destruction 2) Proteolysis of antigen into peptides 3) Deliver to MHC 4) Loading of peptide 5) Peptides displayed to CD4 T cells

Question 33

Can self peptides be presented by class II MHC molecules

Answer 33

Yes

Question 34

How can extracellular peptides access class I MHC molecules (both CD4 and CD8 T Cells are critical to preventing viral infection)

Answer 34

``` Cross presentation - Occurs only in specialized antigen-presenting cells Can present engulfed materials to class I MHC (don't know why this happens) ```

Question 35

Possibilities to explain Cross presentation (3)

Answer 35

1) ER fuses with endosome or phagosome 2) Antigen crosses phagosome membrane into cytoplasm 3) ER-derived phagosomes contain TAP and export machinery

Question 36

What presents lipid moieties (antigens) to T-Cells

Answer 36

CD1 molecules - strikingly similar to class I and class II MHC molecules

Question 37

Antigen presentation by CD1

Answer 37

CD1 assembles with β2m (like Class I) NK-T Cells express classical T-Cell receptors that recognize lipid antigens held in the groove of CD1 Travels with invariant chain (like Class II) - expressed in antigen-presenting cells

Question 38

Specialized antigen presenting cells

Answer 38

B cells Dendritic cells Macrophages

Question 39

Peptide binding pocket

Answer 39

External domains of MHC I and MHC II molecules fold to form a peptide binding pocket