1. The innate immune system responds rapidly to common features present in many pathogens. The genes for the innate immune system’s key molecules are expressed without substantial modification. In contrast, the adaptive immune system responds to specific features present only in a given pathogen. Its genes undergo significant rearrangement and mutation to enable specific recognition of a vast number of potential binding surfaces.

2. VJ and V(D)J recombination; variability in segment joining by the action of terminal deoxyribonucleotidyl transferase; somatic mutation.

3. Affinity refers to the strength of a single interaction; avidity refers to the cumulative strength of multiple independent binding interactions. Avidity may play a significant role in the interaction between IgM and antigen because this immunoglobulin class features 10 binding sites.

4. The intracellular signaling domain common to each of the TLRs is responsible for docking other proteins and reporting that a targeted pathogen-associated molecular pattern (PAMP), such as LPS, has been detected. If a mutation within this domain interfered with the intracellular docking and signal transduction, then TLR4 would not respond to LPS.

5. Viruses that contain dsRNA genomes would be expected to stimulate a TLR3-mediated immune response.

6. (a) ΔG°′ = −37 KJ mol⁻¹ (−8.9 kcal mol⁻¹)

(b) K_a = 3.3 × 10⁶ M⁻¹

(c) k_on = 4 × 10⁸ M⁻¹ s⁻¹. This value is close to the diffusion-controlled limit for the combination of a small molecule with a protein. Hence, the extent of structural change is likely to be small; extensive conformational transitions take time.

7. The fluorescence enhancement and the shift to blue indicate that water is largely excluded from the binding site when the hapten is bound. Hydrophobic interactions contribute significantly to the formation of most antigen–antibody complexes.

8. (a) An antibody combining site is formed by CDRs from both the H and the L chains. The V_H and V_L domains are essential. A small proportion of F_ab fragments can be further digested to produce F_v, a fragment that contains just these two domains. C_H1 and C_L contribute to the stability of F_ab but not to antigen binding.

(b) A synthetic F_v analog 248 residues long was prepared by expressing a synthetic gene consisting of a V_H gene joined to a V_L gene through a linker. [J. S. Huston et al., Proc. Natl. Acad. Sci. U.S.A. 85:5879–5883, 1988.]

9. (a) Multivalent antigens lead to the dimerization or oligomerization of transmembrane immunoglobulins, an essential step in their activation. This mode of activation is reminiscent of that of receptor tyrosine kinases (Section 14.2).

(b) An antibody specific for a transmembrane immunoglobulin will activate a B cell by cross-linking these receptors. This experiment can be carried out by using, for example, a goat antibody to cross-link receptors on a mouse B cell.

10. B cells do not express T-cell receptors. The hybridization of T-cell cDNAs with B-cell mRNAs removes cDNAs that are expressed in both cells. Hence, the mixture of cDNAs subsequent to this hybridization are enriched in those encoding T-cell receptors. This procedure, called subtractive hybridization, is generally useful in isolating low-abundance cDNAs. Hybridization should be carried out by using mRNAs from a closely related cell that does not express the gene of interest. [See S. M. Hedrick, D. I. Cohen, E. A. Nielsen, and M. M. Davis, Nature 308:149–153, 1984, for an interesting account of how this method was used to obtain genes for T-cell receptors.]

11. TLR4 is the receptor for LPS, a toxin found specifically in the walls of Gram-negative bacteria. Mutations that inhibit the function of TLR4 impair an affected person’s defenses against this class of bacteria.

12. If the HLA alleles are not matched, then the recipient’s T cell receptors will identify the MHC proteins of the transplanted tissue as nonself and transplant rejection is likely.

13. Purify an antibody with a specificity to one antigen. Unfold the antibody and allow it to re-fold either in the presence of the antigen or in the absence of the antigen. Test the re-folded antibodies for antigen-binding ability.

14. In some cases, V–D–J rearrangement will result in combining V, D, and J segments out of frame. mRNA molecules produced from such rearranged genes will produce truncated molecules if translated. This possibility is excluded by degrading the mRNA.

15. The mutant bacteria may still stimulate an immune response without causing disease. Hence, they may be valuable starting points for the design of a live attenuated vaccine for the original pathogenic strain.

16. The peptide is LLQATYSAV (L in second position, V in last).

17. Catalysis is likely to require a base for removing a proton from a water molecule. A histidine, glutamate, or aspartate residue is most likely. In addition, a potential hydrogen-bond donor may be present and will interact with the negatively charged oxygen atom that forms in the transition state.

18. A phosphotyrosine residue in the carboxyl terminus of Src and related protein tyrosine kinases binds to its own SH2 domain to generate the inhibited form of Src (Section 14.5). Removal of the phosphoryl group from this residue will activate the kinase.

19. (a) K_d = 10⁻⁷ M; (b) K_d = 10⁻⁹ M. The gene was probably generated by a point mutation in the gene for antibody A rather than by de novo rearrangement.