First things first. Distinguish between the innate and adaptive immune systems.

Antibody diversity. What are the mechanisms used by B cells to generate antibody diversity?

Hang in there. Explain the difference between affinity and avidity. For which immunoglobulin class might avidity be particularly important in antigen recognition?

Innate abilities. A strain of mice has been identified that does not respond to LPS. This lack of response is due to a single amino acid change in the intracellular domain of mouse TLR4. Propose an explanation for the lack of response.

TLR ligands. The PAMP recognized by TLR3 is double-stranded RNA (dsRNA). Against which pathogens would TLR3 be an effective immune receptor?

Energetics and kinetics. Suppose that the dissociation constant of an F_ab–hapten complex is 3 × 10⁻⁷ M at 25°C.

A brilliant emitter. Certain naphthalene derivatives, such as the dansyl group, exhibit a weak yellow fluorescence when they are in a highly polar environment (such as water) and an intense blue fluorescence when they are in a markedly nonpolar environment (such as hexane). The binding of ε-dansyl-lysine to specific antibody is accompanied by a marked increase in its fluorescence intensity and a shift in color from yellow to blue. What does this finding reveal about the hapten–antibody complex?

Miniantibody. The F_ab fragment of an antibody molecule has essentially the same affinity for a monovalent hapten as does intact IgG.

Turning on B cells. B lymphocytes, the precursors of plasma cells, are triggered to proliferate by the binding of multivalent antigens to receptors on their surfaces. The cell-surface receptors are transmembrane immunoglobulins. Univalent antigens, in contrast, do not activate B cells.

An ingenious cloning strategy. In the cloning of the gene for the α chain of the T-cell receptor, T-cell cDNAs were hybridized with B-cell mRNAs. What was the purpose of this hybridization step? Can the principle be applied generally?

1010

Pathogen susceptibility. Patients carrying specific mutations in the gene encoding the TLR4 protein are susceptible to infections from Gram-negative bacteria. Why are these patients vulnerable to this particular type of pathogen?

Matchmaker, matchmaker. Why is it important to match HLA alleles between donor and recipient in organ transplantation?

Instruction. Before the mechanism for generating antibody diversity had been established, a mechanism based on protein folding around an antigen was proposed, primarily by Linus Pauling. In this model, antibodies that had different specificities had the same amino acid sequence but were folded in different ways. Propose a test of this model.

Dealing with nonsense. Cells, including immune cells, degrade mRNA molecules in which no long open reading frame is present. The process is called nonsense-mediated RNA decay. Suggest a role for this process in immune cells.

Down, but not out. To understand the genes responsible for growth and infectivity in a disease-causing bacterial strain, you perform chemical mutagenesis on a culture of these bacteria. In the course of your investigation into the properties of the resulting mutants, you identify a set of mutant bacteria that is still viable but their virulence is significantly impaired. How might these mutants be useful for vaccine development?

Presentation. The amino acid sequence of a small protein is

MSRLASKNLIRSDHAGGLLQATYSAVSS-IKNTMSFGAWSNAALNDSRDA

Predict the most likely peptide to be presented by the class I MHC molecule HLA-A2.

Catalytic antibody. Antibody is generated against a transition state for the hydrolysis of the following ester.

Some of these antibodies catalyze the hydrolysis of the ester. What amino acid residue might you expect to find in the binding site on the antibody?

Signaling. Protein tyrosine phosphatases, such as the molecule CD45 expressed in both B cells and T cells, play important roles in activating such protein tyrosine kinases as Fyn and Lck, which are quite similar to Src. Suggest a mechanism for the activation of such protein kinases by the removal of a phosphoryl group from a phosphotyrosine residue.

Affinity maturation. A mouse is immunized with an oligomeric human protein. Shortly after immunization, a cell line that expresses a single type of antibody molecule (antibody A) is derived. The ability of antibody A to bind the human protein is assayed, with the results shown in the graph below.

After repeated immunizations with the same protein, another cell line is derived that expresses a different antibody (antibody B). The results of analyzing the binding of antibody B to the protein also are shown. From these data, estimate

Comparison of the amino acid sequences of antibody A and antibody B reveals them to be identical except for a single amino acid. What does this finding suggest about the mechanism by which the gene encoding antibody B was generated?