WEEK 5 MICB 302
Practice Questions (answers provided the following week).
1. What are the basic structures of the two types of MHC proteins that present
peptides? What part of the MHC protein binds the peptide, and what is/are the
source(s) of these peptides?
MHC 1 and MHC 2 are the different MHC's. And within MHC1 proteins, HLA-A, HLA-B,
and HLA-C present peptides. And within MHC2 proteins, HLA-DP, HLA-DQ, and HLA-
DR present peptides. MHC 1 consists of an alpha chain and a b2-microglobulin. The
alpha chain has 3 domains a1, a2, and a3. The alpha chain is within the HLA locus, the
B2 micro globulin is the same for everyone. The part of the MHC 1 protein that binds
the peptide is the a1 and a2, the a3 is a supporting domain along with the b2 micro
globulin. The source of peptides for MHC1 proteins are endogenous.
MHC 2 protein consists of an alpha and beta chain, both transmembrane, and the a1,
and b1 are what bind the peptide. the source of peptides are exogenous.
2. Are self-peptides loaded onto MHC I proteins or MHC II proteins? Why don’t
we generate fullblown responses against them?
Self peptides are loaded onto MHC 1 proteins and MHC 2 proteins. We don't generate
a full blown response against them because if the TCR binds to it, then that TCR can
get a signal of clonal deletion as it shouldn't be binding to a self peptide.
3. MHC proteins have been described to have promiscuous binding specificity.
What does this mean with respect to peptide binding?
MHC proteins are promiscuous in the respect that they will bind any type of peptide,
they don't distinguish between self and non-self peptide, they just bind any peptide that
shares some affinity. It means that any peptide can bind to an MHC protein.
4. How do the proteasome and TAP provide peptides that are optimal for MHC I
5. What is the CLIP? What is HLA-DM and what does it do? 6. What is meant by the term cross-presentation? Which cells does it occur in?
Why is it important for the initiation of immune responses to viruses? How does
7. Define allelic exclusion and how it differs from co-dominant expression. What
would be the
consequence of having allelic exclusion at the MHC locus?
WEEK 5 Tutorial Q/A
1. An MHC 1-containing vesicle might fuse with an endosome; why wouldn't the
MHC-1 then bind antigen peptides from the endosome?
At that point an MHC 1 has already bound a peptide so there wouldn't even be space
for a peptide from the endosome. Also MHC are pretty specific of what they bind, they
bind peptides that are 8-10 amino acids long with hydrophobic and basic residue at the
** Chaperone proteins held the MHC1 in place while it bound a peptide, and folded into
a stable conformation. The protein would have to unfold significantly for the peptide to
2. Suppose a mutation in the alpha chain gene alters the peptide-binding cleft of
MHC 1 so that it can't bind peptides. Now, suppose (although this is extremely
unlikely), that all six MHC 1 alleles of a particular individual had this mutation.
This person would have NO MHC 1 on the surface of the cell. They would be MHC 1
deficient, because fr the MHC 1 to leave the ER it has to bind an peptide, so it would
remain in the lumen of the ER.
3. A knock-out mouse is genetically engineered mouse in which researchers
have inactivated or "knocked out" an existing gene by replacing it or disrupting it
with an artificial piece of DNA. A particular strain of knock-out mice have had the
HLA-DM gene disrupted. What would the consequence of this mutation on the
MHC II peptide presentation pathway? The consequence would be that the MHC II protein would be unstable with no HLA-DM
to stabilize it. There would still be MHC 11 found on the surface of the cell, its just that
the CLIP would still be attached, and no peptide would be attached.
5. Draw the basic structure of the alphabeta T cell receptor and compare it with
the basic structure of a membrane bound immunoglobulin (IgM). How are they
similar and how are they different?
Both have Ig-like domains. TCR joined by 1 di sulfide bond ,BCR has di-sulfide
between H and L chain and between pair of HL chain.
TCR- 2 polypeptides, 1 abs
BCR - 4 polypeptides, 2abs
both have transmembrane domain
WEEK 6 Tutorial Q/A
1. The TCR beta chain locus can undergo successive gene rearrangements to
rescue unproductive V(D)J rearrangements.
A. What aspects of gene segment rearrangement at the TCRB locus make this
possible? (top cartoon)
B. Can the immunoglobulin heavy chain locus, which is also composed of V, D,
and J segments, undergo successive rearrangements? If not give reasons for the
difference. bottom cartoon
A. Successive gene rearrangement is possible at a TCRB locus because there are two
sets of D, J, and C gene segments downstream of the cluster of V gene segments:
V)n….D,1…(J,1)n…C,1…D,2…(J,2)n…C,2. If a first rearrangement involving D,1 and
J,1 segment is unproductive, an upstream V gene segment can rearrange to the second
D gene segment and an associated J segment. If this is unproductive , an upstream V
gene segment can rearrange to the second D gene segment and an associated J
segment. If this is unproductive, no more gene rearrangements can be made. B. The answer is no. The heavy-chain locus cannot undergo successive
rearrangements because it splices out the intervening D regions. No unarranged D
segments remain after the two rearrangement events (DJ and VDJ)
2. Discuss how TCR differ from immunoglobulins in the way that they recognize
antigen. Use the following terms in their answers: peptides, APC, MHC
molecules, antigen binding sites, CDRs, onrate/offrate.
TCR differ from IG in the way that they recognize antigen. TCR can only recognize
linear peptide presented by an MHC protein. Ig can recognize unprocessed, intact
antigens, that are not presented by MHC proteins. TCR can only bind peptides:MHC
complexes presented on APC, whereas Ig doesn't need to bind to peptides on APC.
The TCR has one antigen binding site, which is formed by the a1 and b1 on the
WEEK 6 Practice Questions
Practice Questions (answers provided the following week).
1. How is the structure of the TCR similar to the structure of the BCR (antibody
molecule)? How are
the two different?
- TCR similar to the structure of BCR as they both have variable and constant regions.
- TCR similar to structure of BCR is that they both have 3 CDR regions within the
- TCR similar to structure of BCR in that the variable regions make contact with the
- both have quaternary structures.
- Both have polypeptides attached by disulphide bonds.
- The V and C regions are Ig like domains
- TCR is different from BCR in that it is not a soluble molecule but it is a membrane
- TCR is different from BCR in that it has co-receptors CD8/CD4 and CD3.