MBI - 414 Immunology Principles
The full text of the new withdrawal policy that goes into effect this term, excerpted from Registration Proceedure: Sections 01.203.E and 01.203.F in the Student Handbook, is reproduced here:
Q: How important is it to know the names of the various people
your outlines. There are an awful lot of people, and I am struggling trying
to remember specific people and the specific activity that they did.
A: There will be at least one question that relates to major advances in the field of immunology and the names of the people involved will, at the very least, be important clues to which advance you need to discuss. My aim in presenting the experiments and telling you who did them is to help you see how the field developed.
Q: I am a PhD student at Iowa State. I was just browsing
and chanced on your immunology class notes. I have a question on
antigen-antibody interactions. In specific antigen-antibody
interaction for the formation of the various noncovalent bonds how
much time is needed? Or in other words what is the time scale of
A: Formation of the initial interactions between antibody binding sites and the antigenic determinants for which they are specific is diffusion rate controlled (sensitive to variations in temperature, viscosity and, molecular weight, especially in gels). Therefore, they occur on the time-scale of seconds, perhaps faster (since the experiments to determine this were done a long time ago (Heidelberger and Kendall. 1935. J. Exp. Med. 61:563-591) and the sophisticated equipment we have now was not available to do the reactions more quickly). Formation of stable precipitable antigen-antibody complexes for soluble antigens is, however, a two-step process, and the second step takes hours (we usually incubate 1-2 hr at 37C, then overnight at 4C to allow for this). December 9 Q: I was wondering if B7.1 and B7.2 were just parts of the whole B7 molecule that interacts with CD28, or if only one portion of the B7 (like just B7.1) interacted with CD28?
A: If you check out page 39 of your textbook, you will see that B7.1 and B7.2 are alternative forms of B7
Q: When we discussed the
spleen, I think that I may have interpreted your drawing wrong. The
notes I took indicate that antigen travels through
the splenic artery and is dumped into the red pulp where it
encounters a dendritic cell and is presented to a T-cell which
releases cytokines and triggers a b cell to divide and differentiate
into ab producing plasma cells and memory cells. My confusion is that
figure 2-19 in the book shows the red pulp surrounding the B-cell
rich marginal zone, and the T-cell rich PALS at the center of the
spleen. So does antigen get dumped into the red pulp, taken up by a
dendritic cell, then the dendritic cell travels through the marginal
zone to the PALS(in the center) and presents it to a T cell and the T
cell travels back out to the marginal zone to release cytokines to
the B cells? I am confused about the path of this process.
A: The antigen diffuses from the red pulp into the white pulp, where it:
1) gets phagocytized, processed and presented to T cells
2) diffuses into the B cell rich area of the PALS (follicles) and is bound to BCRs with appropriate specificity.
Q: Okay, the first question is based on antibody/antigenic
binding. For some reason I had thought that the binding of these two
was a collection of noncovalent interactions, but in the book it
describes the affinity labeling experiment as AA covalently bonded to
the residues on the antibody binding site. If they are covalent, does
that make this question false: Using affinity labeling techniques,
Kabat (and others) showed that the hypervariable regions of antibody
molecules contain contact residues (amino acids that actually form
NONCOVALENT bonds with the antigenic determinants) and are therefore
considered to be the CDRs.
A: The way all antibodies interact with determinants is via noncovalent interactions. Kabat and others capitalized on this to localize their ligands in antibody combining sites. Once the ligand was bound to the combining site, they photoactivated a reactive center in the ligand so it would also form a covalent bond with one of the amino acids in its vicinity. The assumption that an amino acid that was located close to (within?) the three-dimensional location of the bound ligand was one that was involved in binding the ligand was the basis for the idea that this experiment would determine the location of the CDRs.
Q: Okay, the next question I have is just nomenclature
type... The effector cell of cytotoxic cells is CTLs right? then what
do just plain old Tc cells do? are they merely a step in the
maturation of CTLs?
A: Tc are the precursors of CTLs ... Tc cells will become CTLs when they are activated.
Q: In the notes I have Neutrophils, Basophils and
Eosinophils as being in the bone marrow and only mast cells in the
tissues, yet in the book they often talk about them migrating from
the blood to the tissue?? do these become mast cells when they reach
A: The granulocytes (Neutrophils, Basophils and Eosinophils) are all cells found primarily in the blood. They do, however, migrate into the tissues during inflammatory episodes ... where they die within a couple of days. In contrast, mast cells do not mature until their precursor cells migrate into the tissues ... and they live in the perivascular tissues for years (not just hours-to-days).
Q: B cells bind to soluble antigen right? does this mean
that if an antigen is insoluble, that B cells will not recogonize it
at all? and thus they cannot become APCs?
A: B cells can bind to either soluble or insoluble antigen. They don't "care" about it's form, just as long as there are determinants available for their BCRs to bind in a specific manner.
Q: i just had a quick question about T cell response, i
understand why T cells would respond to denatured antigen because
they recognize antigen that is processed into antigenic peptides, but
don't B cells typically present the antigen.. so if the antigen was
denatured, how does the MHC get on the antigen for the T cells to
A: You're right when you say that B cells can present antigen to T cells. However, they only do that after they have specifically recognized the native form of the antigen via their BCR (the antibody molecules on their surface). BCR recognition is what we refer to when we say that B cells only respond to native antigen ... since native antigen (whatever is present in the extracellular fluids) is what they bind with their BCR and that is what stimulates them to make and secrete antibody molecules. Binding of processed antigen to MHC-2 for presentation is only done during antigen processing ... when partially degraded antigen is being generated for that purpose. That's not a response to the antigen per se.
Q: The figure with the apple and the 6 fingers around it
that you showed in class I had some questions to clear it up. Is the
apple represent the antigentic determinats?
A: The apple represents a single antigenic determinant.
Q: ... and 3 of the 6 fingers represent the light chain
complementarity determing regions, and the other 3 represent the
heavy chain complementarity determing regions?
A: Yes, that's exactly right!
Hello. I was reading about the different classes of antibodies,
and I have a few questions about IgE.
Q: In humans, does IgE play a role in any immune response besides hypersensitivity associated with allergic reactions?
A: Yes ... it is involved in mediating immunity against anti-parasites (intestinal protozoa, worms, etc.). It binds to surface receptors on eosinophils and "arms" them to deal with these parasites.
Q: Is IgE a more prominent antibody type in other species
A: Other animals have immunoglobulins that serve the same purposes, but most do not have Ig molecules with similar enough structure to be called IgE.
Q: What advantages (if any) does IgE bring to an
A: See the answer about arming eosinophils (above).
Q: Since it is significantly less abundant than the other
classes and it is responsible for harmful allergic reactions, would
an organism potentially be better off without it?
A: It is actually not less abundant than the other Ig classes ... unless one only looks in the fluid phase of the blood. Remember, it is mostly found attached to surfaces of basophils and mast cells throughout the body. People who have few or no intestinal parasitic infections might actually be "better off" without IgE ... as long as they could guarantee that they would never get these infections. It appears that IgE-mediated allergies in developed countries are such a problem precisely because we don't have the parasites to contend with. It's a long story (and it's mostly conjecture) but the "gist" of it is that people who have few or no intestinal parasitic infections are destined to have more type-I hypersensitivities (than those who have the infections) because most of their IgE antibody molecules are specific for allergens, rather than parasites. To trigger histamine release from basophils or mast cells (via IgE mediation), you need two adjacent surface IgE molecules with ability to bind to determinants on the same allergen molecule. If you think about the probability of this happening, you can immediately see that "diluting out" the anti-allergen IgE molecules with anti-parasite IgE molecules (i.e., increasing the specificity heterogeneity of the IgE population) would decrease the tendency to get allergic reactions when exposed to the allergen after sensitization. How about that?
Q: I'm still having trouble with the idea that MHC class 1
molecules present our own proteins to other cells and can't seem to
understand how this brings on an immune response. Are these not host
proteins no matter how you look at them. It shouldn't matter if a
virus is "telling" us to make it, it is still a host protein. Maybe
it's that we would not normally present these proteins on our
A: Presentation of peptides derived from our own proteins on our MHC class 1 molecules does *not* bring on an immune response. This is because our own proteins are not recognized - i.e., they are not foreign. The key to foreignness is *not* being present in the thymus during development of T cells. When T cells are formed, we first develop a large population of T cells representing a very broad spectrum of TCRs, then we eliminate all those cells whose TCRs recognize processed antigens being presented to them by APCs in the thymus. The antigens that are presented during this time are self antigens (provided the host is not infected at the time). So . . . the only T cells able to respond are those that recognize things that were *not* present while the T cells were being formed, and these are non-self proteins. Peptides from a viral protein (one that was not being synthesized during development of T cells) would, then, be recognized and an immune response would be induced.
Overall, this approach was used to show that (a) the variability
in antibody molecules (as one looks at molecules with differing
specificity) occurs in three restricted areas of the N-terminal ~110
amino acids of both light and heavy chains, and that (b) this
variability is in the same areas (amino acid residues) that bind
antigenic determinants (i.e., are contact residues).