There is no time limit on this test, though I have tried to design one that you should be able to complete within 3 hours, except for typing. You are not allowed to use your notes, or any books, any electronic sources, nor are you allowed to discuss the test with anyone until all exams are turned in at 9:30 am on Monday February, 14. EXAMS ARE DUE AT CLASS TIME ON MONDAY FEBRUARY 14. You may use a calculator and/or ruler. The answers to the questions must be typed on a separate sheet of paper unless the question specifically says to write the answer in the space provided. If you do not write your answers on the appropriate pages, I may not find them unless you have indicated where the answers are.
-3 pts if you do not follow this direction.
Please do not write or type your name on any page other than this cover page. Staple all your pages (INCLUDING THE TEST PAGES) together when finished with the exam.
Name (please print here):
Write out the full pledge and sign:
Here is the honor code
"On my honor I have neither given nor received unauthorized information regarding this work, I have followed and will continue to observe all regulations regarding it, and I am unaware of any violation of the Honor Code by others."
How long did this exam take you to complete (excluding typing)?
I. Define these terms - 2 pts each. When the term is preceded by an asterisk (*), provide a specific example to further demonstrate your knowledge. These terms can be define succinctly so using a lot of words is not the best way to demonstrate your fluency with these terms.
1) b barrel
- two beta sheets on
one protein connected by disulphide bonds, cylindrical in shape.
2) MIIC- endosomal compartment, MHC II is found here and loaded with peptide as CLIP is produced and then removed.
3) * MHC restriction- TCR binds to peptide which is recognized only in the context of sitting in an MHC binding groove. Example = TCR cannot recognize the same peptide sitting in a different MHC allotype, even in the same person.
4) * sandwhich ELISA- a method where Ab is bound to well, antigen is added and binds, second Ab binds and is detected via enzymatic reaction to produce colored product. Example = quantification of the level of cytokine secretion by some cells.
5) RAG-1- half of the RAG1/RAG2 complex used during somatic recombination, cuts at the 3' end of the 7mer of the RSS, cuts only one strand of dsDNA.
6) CLIP- Ii chain is cut twice in MIIC to produce CLIP after MHCII a and b have assembled in ER and move on to MIIC. CLIP is located in the binding groove of MHCII and acts as chaperone to keep MHCII from unfolding until antigenic peptide is loaded.
7) immunohistochemistry- method for labeling proteins in tissue with antibody that is attached to an enzyme and produces a colored product which is visible when viewed through a microscope.
8) P-nucleotides- Variation produced during somatic recombination when the phosphodiester backbone of nucleotides on one strand near the hairpin loop is cut so that the nucleotides on this same strand are flipped over the hairpin "hinge". The exact number of P nucleotides produced is random and become a part of the coding joint.
9) somatic hypermutation- point mutations producted after B cells have produced a functional Ig and the B cells have been activated. The mutations occur randdomly but are concentrated in the hypervariable regions and change the affinity either higher or lower.
10) HLA-DM- MHCII-like instructure, this molecule stablelizes the a/b MHC II in the MIIC as CLIP is removed and peptide loaded by HLA-DM.
11) * hapten- small molecule two which you want to make an antibody. Hapten is bound to a larger carrier protein to stimulate an immune response since hapten is too small to. Example = cAMP bound to lysozyme.
12) * recombination signal sequence- RSS is used for somatic recombination and is comprised of a sequence of nucleotides in this pattern: 7mer - spacer of 12 or 23 - 9mer. Example = D segment - RSS (12)-intron - RSS(23) - J segment for H chain somatic recombination.
13) MHC haplotype- the specific allelic combination located in the MHC complex (includes about 200 genetic loci) on one chromosome
14) proteasome- always found in the cytoplasm of a cell, this structure is a protease that digests proteins in the cytoplasm. In lymphocytes, it can be modified by LMP's to produce peptide fragments that are optimized for loading in MHC I.
15) invariant chain- Chaperone that that helps in the assembly and folding of MHC II a/b in the ER. Ii is found as homotrimer and binds 3 MHC II heterodimers to forma a megacomplex as a 9mer. Once the 9mer is assembled, it leaves the ER and moves onto the MIIC. Ii also functions to prevent premature peptide binding in MHC II.
More thoughtful questions:
1) How many MHC molecules with different specificity does a human B cell express? Explain your answer.
3 MHC I genes and two chromosomes = 6 different MHC I on B cell.
4 MHC II genes (due to one a and two b in HLA-DR); two chromosomes = 8 different MHC II on B cell.
Plus, each of the MHC II a and b subunits can mix and match to produce more than 14 different combinations.
2) Explain the why one antibody can only bind one epitope but one MHC can bind many different peptides.
- On an antibody, the idiotype has a specific shape that binds to a particular epitope. Each shape fits the other perfectly.
On an MHC, the binding groove has certain constraints (length and anchor residues) but the rest of the peptide can vary, and even modify the shape of the MCH.
3) Using this diagram as a starting place, draw what has to happen in order to wind up with a functional immunoglobulin (your choice of specificity and effector function). You must draw each step that has to happen from DNA to protein. Keep your diagram at the level of boxes for exons. Do NOT draw anything at the nucleotide level for this question. Assume all the transciptional units have the same orientation in this diagram. Make sure your drawings take into account all the DNA before and after somatic recombination.
Figure taken from ImmunoBiology by Janeway et al., Forth Edition.
4) What are complementarity-determining regions? amino acid loops on Ig and TCR that determine the shape of the ligand that can be bound.
How many are there on a Fab fragment? 6
Then what is the valence of a Fab fragment? 1
On which immunoglobulin domain of a Fab fragment would you find a complementarity-determining region or regions?- Variable
5) Explain why it is impossible to predict the exact nucleotide sequence within a coding joint. Your answer should include the two major factors responsible for this unpredictability. Two main mechanisms:
Coding joint includes P nucleotides which are generated randomly and thus unpredictably. Variation produced during somatic recombination when the phosphodiester backbone of nucleotides on one strand near the hairpin loop is cut so that the nucleotides on this same strand are flipped over the hairpin "hinge". The exact number of P nucleotides produced is random and become a part of the coding joint.
Likewise, N nucleotides are added on randomly by TdT after P nucleotides. The sequence and number is unpredictable.
6) Is it possible for a B cell to make both membrane bound IgG and secreted IgG, or is the membrane bound form always IgM and IgD? Explain your answer.
- Yes, if the B cell is secreting IgG, then the membrane bound form must also be IgG. In order to make an IgG, the activated B cell must have undergone isotype switching which would result in the illimination of the Heavy chain M/D region. Therefore it is impossible to produce IgG and IgM at the same time.
7) Explain what aspect or aspects of the immune system is/are working under these two different conditions:
a. superantigen toxicity- This antigen is not processed and presented by MHC II, but rather binds to the more constant portions of MHCII and TCR. It does not see or interact with the peptide presented by the APC. It stimulates many CD4+ cells in a non-specific response to secrete cytokine and a non-productive immune response that can lead to death.
b. allogeneic organ transplant rejection- 5- 10% of the T cells respond to the foreign tissue. The exact mechanism is not clear but it is either due to strong binding of the peptide despite the unrecognized MHC allotypes, or strong binding to the allotypic MHC despite the lack of recognition of peptide.
8) As you may remember, CD3 is a marker for T cells and CD19 is a marker for B cells. A ficol gradient was used to purify lymphocytes.
a. In general terms, how were the data below produced?- By flow cytometry; all lymphocytes were labeled with antibodies of two different colors (e.g. anti-CD3 = green and anti-CD19 = red) and measured one by one. Each dot represents a different cell.
b. Interpret these data fully. Tell me what they mean.- Upper left indicates B cell, Upper right is non-existant CD3+/CD19+ cell, Lower left is NK cell, Lower right is T cell. More lymphocytes were measured on the left than right.
c. What would your conclusion be for the person on the left and right?- The person on the left is wt, and has more T cells than any other lymphocyte in circulation. The perons on the right lacks B cells but NK and T cells seem OK.
Figures taken from Case Studies in ImmunoBiology by Rosen and Geha, Second Edition.
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