1. There are 26 identities and two gaps for a score of 210. The two sequences are approximately 26% identical. This level of homology is likely to be statistically significant.

2. They are likely related by divergent evolution, because three-dimensional structure is more conserved than is sequence identity.

3. (1) Identity score = −25; Blosum score = 14; (2) identity score = 15; Blosum score = 3.

4. U. One possible structure:

5. There are 4⁴⁰, or 1.2 × 10²⁴, different molecules. Each molecule has a mass of 2.2 × 10⁻²⁰, because 1 mol of polymer has a mass of 330 g mol⁻¹ × 40, and there are 6.02 × 10²³ molecules per mole. Therefore, 26.4 kg of RNA would be required.

6. Because three-dimensional structure is much more closely associated with function than is sequence, tertiary structure is more evolutionarily conserved than is primary structure. In other words, protein function is the most important characteristic, and protein function is determined by structure. Thus, the structure must be conserved but not necessarily a specific amino acid sequence.

7. Alignment score of sequences (1) and (2) is 6 × 10 = 60. Many answers are possible, depending on the randomly reordered sequence. A possible result is

Alignment score is 4 × 10 = 40.

8. (a) Almost certainly diverged from a common ancestor. (b) Almost certainly diverged from a common ancestor. (c) May have diverged from a common ancestor, but the sequence alignment may not provide supporting evidence. (d) May have diverged from a common ancestor, but the sequence alignment is unlikely to provide supporting evidence.

9. Replacement of cysteine, glycine, and proline never yields a positive score. Each of these residues exhibits features unlike those of its other 19 counterparts: cysteine is the only amino acid capable of forming disulfide bonds, glycine is the only amino acid without a side-chain and is highly flexible, and proline is the only amino acid that is highly constrained through the bonding of its side chain to its amine nitrogen.

10. Protein A is clearly homologous to protein B, given 65% sequence identity, and so A and B are expected to have quite similar three-dimensional structures. Likewise, proteins B and C are clearly homologous, given 55% sequence identity, and so B and C are expected to have quite similar three-dimensional structures. Thus, proteins A and C are likely to have similar three-dimensional structures, even though they are only 15% identical in sequence.

11. The likely secondary structure is

12. To detect pairs of residues with correlated mutations, there must be variability in these sequences. If the alignment is over-represented by closely related organisms, there may not be enough changes in their sequences to allow the identification of potential base-pairing patterns.

13. After RNA molecules have been selected and reverse transcribed, PCR is performed to introduce additional mutations into these strands. The use of this error-prone, thermostable polymerase in the amplification step would enhance the efficiency of this random mutagenesis.

14. The initial pool of RNA molecules used in a molecular-evolution experiment is typically much smaller than the total number of possible sequences. Hence, the best possible RNA sequences will likely not be represented in the initial set of oligonucleotides.

A8

Mutagenesis of the initial selected RNA molecules allows for the iterative improvement of these sequences for the desired property.

15. 107 or 108 identities (depending on which annotated human sequence is chosen).