S

Numbers below the diagonal line are similarities.

26.2 Amino Acid Sequence Alignment Insertion of a gap allows us to align two homologous amino acid sequences so that we can compare them. Once the alignment is established, sequences from more organisms can be added and compared. A similarity matrix sums similarities and differences between each pair of organisms.The larger the number of similarities, the more recent the presumed common ancestor of the organisms.

different, they would become similar if we were to insert a gap after the first amino acid in sequence 2 (after the leucine residue). In fact, these sequences then differ only by one amino acid at position 6 (serine or phenylalanine). Insertion of a single gap—that is, correcting a deletion—aligns these sequences. Longer sequences and those that have diverged more extensively require more elaborate adjustments.

After we have aligned the sequences, we can compare them by counting the number of nucleotides or amino acids that differ between them. If we add more sequences to our original example and sum the number of similar and different amino acids in each pair of sequences, we can construct a similarity matrix (Figure 26.2), which gives us a measure of the changes that have occurred during the divergence of the organisms.

The longer molecules have been evolving separately, the more differences they should have. Enough analyses of mammalian genes have been performed to show that the rate of nonsynonymous nucleotide substitution varies from nearly zero to about 3 x 10-9 substitutions per locus per year. Synonymous substitutions in the protein-coding regions of genes have occurred about five times more rapidly than nonsyn-onymous substitutions. In other words, substitution rates are highest at nucleotide positions that do not change the amino acid being expressed (Figure 26.3). The rate of substitution is even higher in pseudogenes, duplicate copes of genes that have undergone one or more mutations that eliminate their ability to be expressed. Why are these rates of substitution so dissimilar?

Rates of nucleotide substitution vary because the roles of molecules differ

The observation that rates of substitution are highest at sites and in molecules where they have no functional significance is consistent with the hypothesis that substitution rates at these sites are driven primarily by a combination of mutation and genetic drift. The much slower rates of substitution at sites that do affect molecular function is consistent with the

Pseudogenes

Synonymous substitutions

Nonsynonymous substitutions

Pseudogenes

Synonymous substitutions

Nonsynonymous substitutions

.and are low where they change the amino acid being expressed.

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