Chapter 6: Exploring Evolution & Bioinformatics

Exploring Evolution & Bioinformatics begins by defining homology, distinguishing between paralogs, which are homologs present within a single species that often diverge in function, and orthologs, which are homologs found across different species that typically retain the same function. A major focus is placed on sequence alignment techniques used to detect these relationships, employing statistical methods like sequence shuffling to determine if alignments are significant or merely due to chance. The text explains the sophistication of modern scoring systems, such as the Blosum-62 substitution matrix, which accounts for evolutionary divergence by scoring conservative substitutions (replacing amino acids with chemically similar ones) differently than nonconservative substitutions. The utility of database search tools like BLAST is highlighted for identifying homologous sequences and estimating the likelihood of random matches. The chapter further argues that three-dimensional tertiary structure is more evolutionarily conserved than primary sequence, illustrated by the structural similarities between diverse globins and the unexpected paralogy between actin and heat shock protein 70 (Hsp70). Concepts of convergent evolution are introduced using serine proteases as a case study, showing how chymotrypsin and subtilisin evolved distinct structures but settled on the same catalytic triad mechanism. The discussion extends to nucleic acids, describing how RNA secondary structures can be predicted by analyzing conserved Watson-Crick base-pairing in homologous sequences. Furthermore, the construction of evolutionary trees based on sequence divergence is explained, along with the calibration of these trees using fossil records. The summary also covers complex evolutionary mechanisms such as horizontal gene transfer, exemplified by the red alga Galdieria sulphuraria acquiring bacterial genes to survive extreme environments. Finally, the chapter details modern experimental techniques, including the polymerase chain reaction (PCR) amplification of ancient DNA from Neanderthals to map human ancestry, and combinatorial chemistry methods like SELEX that generate aptamers (specific binding RNA molecules) to simulate molecular evolution in the laboratory.