Fall 1997 Immunology Exam #1 - Chapters 1 - 5

There is no time limit on this test, though I have tried to design one that you should be able to complete within 2.5 hours, except for typing. You are not allowed to use your notes, or any books, nor are you allowed to discuss the test with anyone until all exams are turned in at 8:30 am on Monday October 6. EXAMS ARE DUE AT CLASS TIME ON MONDAY OCTOBER 6. 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.

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:

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) hematopoietic stem cells -
the cells that give rise to all other blood cells including RBCs, WBCs, and platelets.
*2) leukocytes-
also known as white blood cells, this includes B-cells, T-cells, natural killer cells, macrophages
*3) lymphocytes -
a subset of WBCs that is comprised of T-cells and B-cells and is responsible for adaptive immunity.
4) monocytes -
the precursor for macrophages. Monocytes circulate in the blood and differentiate as macrophages in the tissue.
5) plasma cells-
after a B-cell has been activated, it can differentiate into a type of effector cell called a plasma cells which mass produces and secretes antibodies.
6) germinal centers -
locations in secondary lymphoid organs where B-cells are proliferating after activation.
7) freebie - no term here (
Dr. Campbell is soooo nice!)
*8) combinatorial diversity -
this term describes how joining together different gene segments can produce antibodies or T-cell receptors that recognize every possible shape. It is generated by the large number of gene segments for each of the V, D, and J segments. Since there are a large number of each, the possible number of unique combinations is the product (i.e. multiply) of all the numbers of segments (e.g. 50V x 15D x 25J = 18750 combinations for VDJ). In addition, the combination of H + L chain variable regions adds to the diversity.
*9) apoptosis -
this term means programmed cell death and it means that a cell can commit suicide from within. An example is T-cells that are programmed to die unless they receive positive selection.
*10) antigen-presenting cell (APC) -
these cells are able to take up extracelluar pathogens, toxins, or self-proteins and process them so that they can be presented on the surface of an APC, such as macrophages, dendritic cells, or B-cells.
11) opsonization -
this is the process of binding a protein (e.g. antibody) to an antigen or bacterium so that the antigen or bacterium can be engulfed by a phagocyte
*12) hapten -
this is a small molecule that must be coupled to a carrier protein in order to elicit an immune response. An example would be cAMP since it is too small to be detected by the immune system.
13) adjuvant -
this is a mixture of oils and bacterial cellular debris that will stimulate the immune response to respond more vigorously to what is being injected to immunize an individual.
14) epitope -
this is the shape that is recognized specifically by the binding domain of an immunoglobulin
15) hybridoma -
this is a composite of two cells, a B-cell tumor that does not make any antibody and a B-cell isolated from an immunized individual. It is used to produce monoclonal antibodies.
*16) clusters of differentiation -
also known as CD, these are surface proteins that are expressed by cells (mostly lymphocytes) that allow us to follow the development of cells as they differentiate.
17) H-2 -
this is the name given to the mouse MHC locus. It includes several genes.
18) another freebie!
(Dr. Campbell is getting soft in his old age!)
19) haplotype -
this is the unique set of alleles on one chromosome at the MHC locus. Each person has one or two haplotypes (they could be homozygous).
*20) idiotype -
this term describes the the area on an antibody that recognizes the epitope. Every B-cell expresses a unique idiotype, for example and IgE anti-pollen is different from an IgE anit-cat hair.
21) allotype -
this describes the subtle differences between two amino acid sequences of the same constant region isotype (e.g. IgG2) and is due to inheritance of different alleles of constant regions.
22) TdT -
terminal deoxynucleotide transferase is an enzyme that adds extra nucleotides onto the 3' ends of DNA and does not need template DNA to read. It helps generate additional junctional diversity by inserting N-nucleotides.
23) affinity maturation -
this is a process where activated B-cells undergo somatic hypermutations and alter the amino acid sequences at the binding sites (thus altering their idiotypes). This generates new antibodies that will have different affinities for their epitopes and those B-cells with higher affinity will be selected for additional activation and thus produce more B-cells with the newer and higher affinity.
*24) tyrosine kinase -
this is a protein that can phosphorylate its substrate on a tyrosine residue. An example is Blk which is used in the signal transduction of B-cells.
25) anchor residues -
these are the amino acids of a processed peptide that directly interact with an MHC molecule and are critical to the binding of one to the other.
26) gene conversion -
this is a process to generate additional diversity in binding sites of antibody binding sites by substituting in a part of one gene segment into another gene segment, both of the same family of genes.
*27) superantigen -
these are proteins produced by viruses or bacteria that can bind to the non-specific portions of MHC and TCR so that every T-cell can be stimulated regardless of it specificity for a particular antigen peptide. It leads to catastrophic immune responses as seen in toxic shock syndrome toxin produced by a bacterium.

Short to medium answers:
4 pts.

1) What is the difference in function of T H 1 and T H 2 cells?
T H 1 activates macrophages to kill intracellular bacteria. T H 2 is required to activate B-cells once B-cells have bound antigen.

4 pts.
2) Define the clonal selection theory. Use a list or outline format to provide the major components of this very important concept.
1) Each lymphocyte has a single type of receptor with a unique specificity.
2) Receptor interaction with foreign antigen leads to activation of the lymphocyte.
3) All cells derived from an activated lymphocyte will have the same specificity as the parental cell.
4) Lymphocytes that recognize self-antigens will be deleted during lymphocyte maturation.

8 pts.
3) Name all the parts to the T-cell receptor complex and the main role played by each part. Limit yourself to integral membrane proteins.
alpha and beta chains of the TCR - these two chains make a heterodimer and provide the binding site that will recognize MHC plus peptide.
CD3 (including delta/ epsilon , and gamma/epsilon , and zeta/zeta dimers) - these molecules are closely associated with the TCR and are required for signal transduction.
Coreceptors CD4 and CD8 - these are required for TCR to recognize and bind to MHCII and MHCI, respectively.

4 pts.
4) What is HLA-DP and what is its function?
This is the term used to describe one of the three loci of a human MHCII molecule, and it includes one alpha subunit and one beta subunit genes. It is used to present antigens that originated outside the cell and are internalized by phagocytosis and processed before presentation on the surface of the cell.

8 pts.
5) If a B-cell is going to display an antigen that is derived from a protein that was made in the cytoplasm, describe what must happen in order for this protein to be displayed? Make sure you include all the players involved in antigen processing. I strongly encourage you to make a list of the steps rather than using a paragraph format and mention the major molecules involved at each step.
1) MHCI alpha subunit is made, is partially folded, and interacts with calnexin.
2) MHCI alpha subunit binds to b 2 microglobulin (though still not properly folded), releases calnexin, and binds to calreticulin.
3) The complex above binds to tapasin which is bound to the TAP1/2 complex.
4) TAP binds to peptides generated in the cytoplasm and imports them into the lumen of the ER.
5) Proteins are degraded in the cytoplasm by a multisubunit complex called the proteasome which has many subunits, including LMP2 and LMP7. The proteasome generates the peptides above.
6) MHCI binds to the imported peptides and becomes properly folded, lets go of tapasin, and is allowed to transport to the plasma membrane of the cell.

2 pts.
6) What process is RAG-1 involved in and what is its particular role?
This protein is a part of an endonuclease that cuts one strand of dsDNA at the ends of the heptamers in the signal sequences. It is involved in somatic recombination which is used to splice together different immunoglobulin and TCR gene segements.

10 pts.
7) Outline the steps required for a B-cell to generate an IgG. The starting place for your answer is a mature B-cell's DNA and wind up with the translation of IgG (do not worry about posttranslational modifications). Do not address how the B-cell knows that it should make IgG instead of an IgA, for example.
Once a B-cell "knows" that it needs to undergo isotype switching...
1) The switch signal for m is brought next to the switch signal for gamma.
2) Somatic recombination splices the new gamma constant region gene segment adjacent to the VDJ variable segments.
3) This newly recombined gene is transcribed.
4) The nacent RNA is spliced so that the introns are removed that were between the leader and the VDJ, and between the VDJ and the constant region.
5) The leader sequence causes the new protein to be translated on the rER and enter the ER.
6) The leader sequence is cleaved off and the heavy and light chains assemble to form a tetramer of two heavy and two light chains.

2 pts.
8) Go to the following URL using Netscape:
Click Here
Is the MHC molecule showing an MHC class I or II? To receive full credit, you must explain how you can tell. (The figure would not print well so I am trying a new method for this test.)
This is an MHCI with a peptide bound. You can tell for two reasons. 1) the binding domain is all of one subunit (the alpha) and 2) because the peptide is totally surrounded by MHCI (unlike MHCII binding sites).

6 pts.
9) There are four major steps in the process of B-cell development in the bone marrow. List these four steps and briefly describe the major event that is happening to the B-cell receptor and the B-cell at each of these steps. Your answer should begin with a bone marrow cell that will become a B-cell and should focus on more than just DNA rearrangements. This answer is not to be a reiteration of question #7 above.
pro-B cell: V- D-J rearrangement
pre-B cell: surface pre-B cell receptor (with CD3) is made with the surrogate light chain. This tells the pre-B cells to continue development and to rearrange the light chain gene segments (V-J).
immature B cell: heavy and light chain genes are rearranged and there is surface expression of an IgM
mature B cell: This cell has both IgM and IgD on its surface and it leaves the bone marrow.
If at any point the recombination is non-productive (no full-length protein is made), then the other homolog (including k and l for light chains) is rearranged. If all rearrangements fail, the B cell fails to develop further.

2 pts.
10) What is wrong with this patient? (Let's call her Sallie.)
Chronic bacterial infections - no problem with viral infections.
Normal white blood cell count (4200 cells / µl).
In her serum, there are very few IgG and IgA molecules, but elevated levels of IgM.
Lymph node biopsy shows no secondary follicles or germinal centers.
B-cell count in blood was normal (based on FACS analysis using CD19 as a marker).
It appears that Sallie can make B cells, but they cannot be activated (lack of germinal centers). That would explain why there is lots of IgM but no IgG or IgA.

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