All living organisms can be placed into one of three different Superkingdoms or ¡§Domains¡¨ of life: Eubacteria (the ¡§true¡¨ bacteria, for example: E. coli), Eukarya (e.g. humans, plants, and a large variety of other, mostly multicellular, organisms) and Archaea (very unusual bacteria that tend to live in extreme environments, such as hot springs, deep sea vents where temperatures can exceed 100 degrees Celsius, salt marshes, etc.).



Until the early 1970¡¦s, it was believed that there were only two superkingdoms or domains of life, namely, the Prokaryotes and Eukaryotes. Organisms lacking a nucleus and membrane-enclosed organelles were classified as prokaryotic. On the other hand, eukaryotes were usually larger and contained both a nucleus and membrane-enclosed organelles, such as mitochondria and chloroplasts. Then the archaebacteria were discovered. Structurally, the archaebacteria resemble eubacteria (which for the rest of this tutorial will be referred to simply as ¡§bacteria¡¨), in that they are very small, and have no nucleus or membrane-enclosed organelles. However, by comparing informational genes (that is, those genes involved in DNA replication, transcription, and translation), Carl Woese et al. discovered that, molecularly, archaebacteria are more closely related to eukaryotes than to the ¡§true¡¨ bacteria. One goal of this tutorial is to reproduce the findings of Woese et al. by using a subunit of the RNA polymerase enzyme (called rpoK) and the transcription factor TFIID to compare eukaryotic, bacterial and archaebacterial sequences. RNA polymerase is the enzyme responsible for making RNA copies of our genes. RNA polymerase hooks onto a specific part of the DNA called a promoter and ¡§transcribes¡¨ the DNA into RNA. Transcription factors (TFs) are proteins that also bind to promoter sequences. In eukaryotes, transcription is very inefficient if transcription factors are not present because they help the RNA polymerases to localize promoter sequences.

In this tutorial, you will use the sequences of these informational genes (rpoK and TFIID) to determine how closely related the three Domains of life are to one another at the molecular level. You will use a program designed for researchers, namely, the Biology Workbench, to search for and compare sequences. In order to become familiar with this comprehensive program, we have outlined the basic tools of the Workbench in the following tutorial. You will now become the researcher and begin to untangle the web of life.