Phylogenetic Trees STUDENT ACTIVITY 1 Find the protein sequences of cytochrome c from two different organisms. One way to achieve this is through the NCBI website: perform a pair wise alignment using the online tool called “BLAST” (the website also contains an excellent tutorial). Protein sequences may be copied and pasted directly into the BLAST template, or an identification number (referred to as an accession number) may be entered. Explain how the positions of disulfide bonds within a protein are experimentally determined. Discuss reasons why the same protein from two different species, such as mouse and human, may display a significantly different mutation rate. How would this complicate the use of molecular clocks? STUDENT ACTIVITY 2 The chain-termination method of DNA sequencing includes a low concentration of a dideoxynucleotide in the reaction mix. Draw the structure of a dideoxynucleotide and describe its purpose. How are the sequences of introns distinguishable from exons? The five kingdom system of classification was defined in 1969 and is increasingly under scrutiny as new taxons are characterized. The three most widely accepted systems of classification are (1) the five-kingdom system, (2) the eight-kingdom system, and (3) the three-domain system. Contrast the three systems by considering how prokaryotes and eukaryotes are classified in each. STUDENT ACTIVITY 3 Construct a hypothetical phylogenetic tree according to the guidelines outlined above. In a small group setting, one group decides the relatedness of hypothetical organisms and another group translates that information into a phylogenetic tree.