Part I is worth a total of 270 points and is to be completed in class. Points are in parentheses for each question. If you don't finish these in class, you can hand in the rest, or revisions, at the part II deadline for additional points, up to 25% or 68 points (of the 270 total for Part I). Part II is to be done at home. It is worth 150 points, and your answers are due at 1:25 PM on Monday October 26 at the beginning of class in Fernald Hall Room 11. During part II, you may refer to your textbook and notes, and you may discuss general approaches with your classmates. If asked for help, avoid giving complete details of your answer. Each of you must work out the details of your own answer; copying or paraphrasing an answer given to you by someone else is prohibited. Part III is worth 30 points and will be group answers prepared between 1:25 and 2:40 on Monday October 26 during class in Fernald Hall Room 11. In Part III your group will answer (again) questions assigned from Parts I or II. The same questions will be assigned to all groups. One set of answers will be handed in per group, and one grade given to all members of each group. The format of these immunology exams is called a "pyramid" exam. The goal of education includes enabling the student to solve problems independently, and to understand new developments in the field, after the class is over. Traditional exams don't allow time for thought or problem solving. Real world jobs require teamwork, but traditional exams don't involve teamwork. Pyramid exams provide more opportunities for problem solving and teamwork.

Portions of answers in (parentheses) are not necessary for full credit.

1. List the names of the professional phagocytes. (10 points)

   Macrophages (and their immature blood precursors, monocytes) and neutrophils.

2. Which leukocytes are professional APC? (And what does APC stand for?) Do these cells deal primarily with endogenous or exogenous antigens? What surface protein must these cells express which other cell types need not express (at least not normally). (25 points)

   Macrophages, B cells, and (interdigitating) dendritic cells. Exogenous. MHC Class II.

3. If antigen enters a break in the skin, where does the primary immune response occur? How does the antigen get there?
   (20 points)

   In the draining lymph node. It is carried (either alone or in a Langerhans cell) by the flow of lymph fluid. (A Langerhans cell in the lymph is called a "veiled cell".)

4. List the names of the granulocytes. Which one has red granules in an ordinary stained blood smear? What is the purpose of granules? Why do some cells have them and some don't? Give one example of each situation (two situations: cell functions with and without granules). (40 points)

   Neutrophils, eosinophils (granules stain red), and basophils. (Mast cells are granulocytes. NK and CTL cells have a few small granules but are not usually called granulocytes. Monocytes/macrophages are NOT granulocytes.) Granules store pre-manufactured materials which are needed very quickly. Cells have granules when their function requires releasing large quantities of defense substances immediately upon encounter with microorganisms. Examples are the release of worm-killing substances by eosinophils, or the release of vasoactive amines by mast cells or basophils.

   Cells which lack granules can produce what they need more slowly and release it as produced. Examples are plasma cells which make lots of antibody, but release it into the circulation as it is made, or T cells which release cytokines as they are made. (In neither case do these cells need to store up the product.)

5. How does recirculation of naive lymphocytes ensure a prompt primary adaptive immune response? What problems does recirculation solve? (40 points)

   When an antigen comes into the body for the first time, there are very few lymphocytes in the body which can recognize it with high specificity. (These lymphocytes occurred by random diversification of antigen receptors, in the absence of antigen.) The problem is to make sure these rare lymphocytes physically come into contact with the antigen quickly. The problem is compounded because both specific T and B cells are needed, so two separate rare events must occur in order for Th to be delivered to B cells which have found antigen. Recirculation moves large numbers of naive lymphocytes (all with different receptor specifities) past antigen, which is trapped in a secondary lymphoid tissue. This ensures that the rare specific lymphocytes encounter the antigen quickly.

6. List these numbers in the order in which these events or locations occur in the recirculation of naive immunocompetent lymphocytes. Three of the events/locations are irrelevant -- leave their numbers out of your answer! Start in the heart, so the first number in your answer should be the location immediately after the heart. (25 points)
   1. Lymphatic vessel going out of secondary lymphoid tissue.
   2. Post-capillary venule with high endothelium.
   3. Post-capillary venule with thin flat endothelium.
   4. Crossing the endothelium.
   5. Thoracic duct.
   6. Blood vessel entering the thymus.
   7. Wandering, "looking" for antigen.
   8. Artery, arterioles.
   9. Vein returning to heart.
   10. Capillary in muscle tissue.
   11. Capillary in secondary lymphoid tissue.
   12. Entering secondary lymphoid tissue.

   8 11 2   4 12 7   1 5 9
   (Omitting 3 6 10)
   

7. List numbers 1-4 bluebook. Then write DNA or mRNA next to each number, indicating whether the responsible rearrangement or splicing occurs in DNA or mRNA. (10 points)
   1. IgG to IgA
   2. mIg to sIg
   3. IgM vs. IgD
   4. VJ
   5. DDDJ

   1 DNA
   2 RNA
   3 RNA
   4 DNA
   5 DNA
   

8. Are all the amino acids in the CDR's of the TCR of a naive T cell coded for by the genome? If yes, briefly explain the mechanisms which guarantee this. If no, briefly explain how this happens and where in the V domain structure these amino acids end up. (30 points)

   No. During V(D)J rearrangement and splicing, some noncoded or "N" nucleotides can be added randomly by terminal deoxynucleotidyl transferase. These end up in the V(D)J joint which codes for CDR3. (Palindromic nucleotides are not coded for in the sequence in which they end up, but they are in one sense coded for in the DNA.)

9. Why do we need antibody isotypes? Give a few specific examples. Where do antibody isotypes differ in structure? Where do antibodies of identical specificity, but different isotypes, have identical structures? What induces change in isotype? What kinds of antigens generate primarily one isotype of antibody? Which isotype? Briefly describe the mechanism by which isotypes change. (40 points)

   We need antibody isotypes because different antibody isotypes perform different defense functions. For example, only IgA is transported to mucosal surfaces, only IgG activates complement by the classical pathway, and only IgE triggers mast cells and basophils. Antibody isotypes differ in the constant regions of the heavy chains, Antibodies of identical specificity but different isotype have the same variable domains. Change in isotype, called "class switching", is induced by T cell help for B cells. (This help includes both T cell cytokines, and signals through receptor interactions during contact between the T and B cells.) T cell-independent antigens are so-named because they trigger B cells to produce antibody without T cell help. Such antigens are ineffective at inducing class switching, and mostly IgM is produced. Class switching occurs by DNA recombination, splicing the V(D)J adjacent to the desired downstream C regions. This eliminates DNA for upstream C regions making the switch irreversible.

10. Give two examples of how innate immune defenses are increased in strength by the adaptive immune system. Briefly explain each example. (30 points)

    First, macrophages and neutrophils have innate ability to phagocytose and kill microorganisms. However, the coating of microorganisms by specific antibodies opsinizes them. Phagocyte Fc receptors bind to the antibody coat and stimulate the phagocyte, increasing its activity by over one thousand fold.

    Second, complement proteins in the blood have an innate ability to react with microorganisms, coating them with opsonins and/or lysing them. This is called the alternate complement pathway. However, antibody bound to microorganisms greatly accelerates the reaction with complement proteins and the consequences. This is called the classical pathway of complement activation.

End of Part I.