Iahi: 01 - Podcasts On Antigen Processing And Presentation

Front 1

In the case of a viral infection, what neutralizes the extracellular virus particles? What produces this?

Back 1

Antibodies (made by B cells)

Front 2

In the case of a viral infection, what eliminates the source of the virus?

Back 2

T cell response
(Humoral B cell response cannot do this)

Front 3

Where are viral proteins made?

Back 3

Within the host cell, by the host's own protein synthesis machinery

Front 4

Why must an effective immune system test both vacuolar and cytoplasmic compartments?

Back 4

- Viral fragments (red) are in cytoplasm
- Bacterial fragments (green) are in vacuolar compartments

Front 5

Through what process do viral and bacterial proteins get degraded?

Back 5

Routine protein turnover - all proteins in a cell (both cellular and foreign) are degraded to fragments/peptides via this process

Front 6

What happens to the peptide fragments of viral and bacterial origin after being degraded by routine protein turnover?

Back 6

Peptide fragments are presented to T cells on Class I (viral) or Class II (bacterial) MHC molecules = Antigen Presentation

Front 7

What is the inside of a vacuole equivalent to?

Back 7

Outside of the cell

Front 8

What is the primary difference between Class I MHC and Class II MHC molecules?

Back 8

- Class I - sample inside of a cell (cytoplasm)
- Class II - sample outside of a cell/vacuoles

Front 9

What is the process of a molecule being presented on a Class I MHC antigen?

Back 9

1. Proteins must be tagged for destruction
2. Proteolysis must occur to generate peptides of 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 context of class I MHC molecules

Front 10

How are proteins tagged for proteolysis?

Back 10

- Ubiqutin (small 8 kDa protein) added to protein destined for degradation (on Lysine residues)
- Forms a Ub chain (polyubiquitination)

Front 11

How are peptides generated?

Back 11

- Protein that is labeled w/ Ubiquitin is recognized by Proteasome
- Proteasome cuts up protein to release peptides

Front 12

What are some characteristics of the peptides that are presented on Class I MHC molecules?

Back 12

- 9 peptides long
- End w/ a hydrophobic residue (L, I, V, F)

Front 13

If a cell is infected with a virus, how does it enrich for peptides that are suitable for loading onto class I MHC molecules?

Back 13

- Proteasomes have 3 types of protease activity that are suitable for producing peptides that are presented on class I MHC molecules
- Chymotrypsin-like proteases, Trypsin-like proteases, and Caspase-like proteases
- Chymotrypsin-like proteases cleave proteins so that they end w/ a hydrophobic residue (L, F, I, V)

Front 14

Which type of proteases cleave proteins to generate peptides that end with hydrophobic residues? What is the significance of this?

Back 14

Chymotrypsin-like proteases (end w/ L, F, I, or V) - these peptides are suitable for binding to Class I MHC molecules

Front 15

What must happen to a protein before it can be processed by the proteasome? Why?

Back 15

- Ubiquitin must be removed by isopeptidases
- Protein must be unfolded by unfoldases
- The diameter of the center of the proteasome is only 13A (so can't fit a folded protein w/ ubiqutin on it)

Front 16

What size of peptides does the proteasome generate?

Back 16

4-20 AA residues

Front 17

What happens to peptides after they are cleaved by the proteasome?

Back 17

TAP: Transporter associated w/ Antigen Processing transports peptides into the ER

Front 18

What is the preferred substrate of the TAP (Transporter associated w/ Antigen Processing)?

Back 18

- Only peptides
- Favors peptides ending w/ L, I, V, or M (hydrophobic)
- 6-15 AA residues

Front 19

What are the molecular sieves that limit the size of peptides that are presented onto Class I MHC molecules?

Back 19

- Proteolysis by proteasomes generates peptides 4-20 residues
- TAP transporter selects for subset ending w/ L, I, V, or M that are 6-15 residues long
- Binding to class I MHC molecule has strict size restrictions of 8-10 residues (image shows that many are 9 AA long)

Front 20

Which proteins help keep the TAP transporter in close proximity to the Class I MHC molecule? Why?

Back 20

- Tapasin and light chain β2m
- Makes sure that Class I MHC molecules are close to the incoming peptides

Front 21

When does this process happen?

Back 21

At all times, regardless of whether foreign proteins are present

Front 22

What happens when a virus infects a cell?

Back 22

1. Protein tagged for destruction (ubiquitin)
2. Proteolysis (peptides ending in L, I, V, or M)
3. Delivery of peptide (selection for L, I, V, or M enders)
4. Binding of peptide (chaperone-mediated)
5. Transport to cell surface and presentation to T cells (which proceed to kill the cell presenting the peptide)

Front 23

What is the structure of the Class I MHC molecule?

Back 23

- Heavy chain makes peptide-binding cleft on its own (α1, α2, and α3)
- Light chain (β2-microglobulin) is much smaller
- Peptide is critical to structure (without it molecule falls apart)

Front 24

In which kind of MHC molecule does a single heavy chain form the entire peptide-binding cleft?

Back 24

Class I MHC

Front 25

What is the structure of the Class II MHC molecule?

Back 25

- 2 Heavy chains contribute equally to peptide-binding cleft (α1/α2 and β1/β2)
- No light chains
- Peptide is critical to structure (without it molecule falls apart)

Front 26

In which kind of MHC molecule do two heavy chains form the peptide-binding cleft?

Back 26

Class II MHC

Front 27

What happens if there is no peptide bound to a MHC molecule?

Back 27

MHC molecules fall apart, therefore the peptide is considered a subunit of the MHC molecule

Front 28

What secondary structures form the peptide binding cleft of MHC Class I molecules?

Back 28

α1 and α2 both contribute α helices and β pleated sheets (both from heavy chain)

Front 29

What secondary structures form the peptide binding cleft of MHC Class II molecules?

Back 29

- α1 and β1 each contribute α helices and β pleated sheets
- α1 and β1 are from separate heavy chains

Front 30

Class I MHC molecules hold what length of peptides in their binding cleft?

Back 30

8-10 residues

Front 31

Class II MHC molecules hold what length of peptides in their binding cleft?

Back 31

10-16 residues, but can be longer, up to 30+

Front 32

How does tagging of proteins differ for Class I vs Class II MHC molecules?

Back 32

- Class I - proteins must be tagged (ubiquitination)
- Class II - no tagging of proteins

Front 33

How does delivery of peptides differ for Class I vs Class II MHC molecules?

Back 33

- Class I - Peptides must be delivered to MHC molecules
- Class II - No topological barriers, delivery not an issue

Front 34

How does the location of binding of peptides to MHC Class I vs Class II molecules differ?

Back 34

- Class I - in ER
- Class II - in endocytic compartment (not ER)

Front 35

Class I vs Class II MHC molecules bind to which T cells?

Back 35

- Class I - CD8 T cells
- Class II - CD4 T cells

Front 36

In the Class II MHC molecule pathway, how do you know what is going to be lysed?

Back 36

Anything that is delivered to the lysosome - does not have to be tagged

Front 37

How are antigens lysed into peptides for the Class II pathway?

Back 37

Lysosomal Proteases (Cathepsins - cystein proteases)

Front 38

What is the concentration of Cathepsin / Lysosomal proteases in the lysosome?

Back 38

On the order of mM (this is very concentrated)

Front 39

What is the pH in a lysosome?

Back 39

pH = ~5

Front 40

How do Class II MHC molecules get into the lysosome (where they load peptides)?

Back 40

- Start at ER
- Pass through Golgi
- Lysosome (where they load peptides)
- Plasma membrane

Front 41

How do you prevent peptides in ER destined for Class I molecules from binding to class II molecules?

Back 41

Invariant chain (Ii) sits in peptide groove and blocks binding of peptides in ER

Front 42

What is Invariant chain (Ii)?

Back 42

- Scaffold, stabilizer
- Barrier to peptides in ER (sits in peptide groove)
- Contains zip code to MIIC (MHC Class II Compartment)

Front 43

What part of the Invariant chain (Ii) peptide sends the MHC Class II molecules to the lysosome? What is the name of this compartment?

Back 43

- LL sorting signal (two lysine residues)
- Sends MHC Class II to MHC Class II compartment (MIIC)

Front 44

What is the structure of Invariant Chain (Ii)?

Back 44

Trimer w/ 3 class II molecules and 3 invariant chains

Front 45

How do you remove the Invariant Chain (Ii) from the MHC class II groove?

Back 45

- Cathepsin initially cleaves Ii to leave a fragment bound to the molecule and the mebrane
- Further cleavage leaves peptide fragment, CLIP in groove
- HLA-DM catalyzes exchange of CLIP and antigenic peptide

Front 46

What is the function of HLA-DM?

Back 46

Catalyzes exchange of CLIP (peptide remaining in Class II MHC groove) for an antigenic peptide

Front 47

Is the groove of a Class II MHC molecule usually empty or full?

Back 47

Usually full - only empty when HLA-DM catalyzes the removal of CLIP (before binding of antigenic peptide)

Front 48

Why must a peptide almost always be found in the groove of the Class II MHC molecule?

Back 48

Without the peptide in the groove the Class II molecule is destabilized (black), it unfolds, and is destroyed by proteases in the lysosome

Front 49

Can self-peptides be presented by Class II MHC molecules?

Back 49

Yes

Front 50

What are the specialized antigen presenting cells for Class II MHC molecules?

Back 50

- B cells
- Dendritic cells
- Macrophages

Front 51

On what kind of cells are Class I MHC molecules expressed?

Back 51

All nucleated cells

Front 52

On what kind of cells are Class II MHC molecules expressed?

Back 52

Only on specialized antigen presenting cells (B cells, Dendritic cells, and Macrophages)