Authors of original unit: Radomir Niewrzol, Saba J. Elderkin, Michael J. Darcy, John Sabo, and Deanna M. Raineri

Partner Projects: Biology Student Workbench

Grade Level: High school chemistry teachers

Subject Areas: Endosymbiotic Theory

This tutorial provides evidence for the Endosymbiotic Theory, using the Biology Workbench. We use bioinformatics tools in BW to search for sequences displaying a high degree of homology (similarity) to mitochondrial and chloroplast gene sequences from a basic eukaryote. The problem we are facing is that the eukaryotic and prokaryotic gene sequences that we will be comparing have been evolving separately for two billion years! Even if, originally, the mitochondrion was a prokaryotic cell, after two billion years the mitochondrial genome might have changed to the point where it no longer bears any similarity to the original prokaryotic genome. One solution to this problem is to pick a gene sequence that is absolutely indispensable for the cell¡¦s survival and, for that reason, is most likely to have been highly conserved (any mutation occurring in that gene being lethal to the cell). We will then use mitochondrial and chloroplast sequences from our basic eukaryote and the corresponding sequences from different types of prokaryotes to construct phylogenetic trees. Assuming that the earlier two organisms diverged from one another, the more different their sequences will be, by constructing a phylogenetic tree we should be able to determine whether mitochondrial and chloroplast sequences are more closely related to certain types of prokaryotes.

Intended for high school chemistry teachers, who wish to use computational tools in the classroom. Also suitable for introductory college chemistry. It could also be used directly by students for self-study.

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Introduction: Background information on Endosymbiotic Theory

Part 1: Opening An Account, Starting a new Session and Importing Sequences from Protein Databases

Part 2: Using the Ndjinn Tool: to Search Sequence Databases

Part 3: Using the BLAST Tool to Find Homologous (Similar) Sequences

Part 4: Using the BLAST Tool to Find Sequences Homologous to the Mitochondrial NADH Dehydrogenase, Subunit 8 Gene

Part 5: Looking at Chloroplasts

Part 6: Phylogenetic Tree