In the 18th Century, organisms were considered to belong to one of two kingdoms, Animalia or Plantae. As biologists gathered more information about the diverse forms of life on Earth, it became evident that the two-kingdom system did not accurately reflect relationships among different groups of organisms, and the number of kingdoms increased. In 1969, Robert Whittaker proposed a five-kingdom system consisting of monerans, protists, fungi, plants and animals. In the last few years, comparative studies of nucleotide sequences of genes coding for ribosomal RNA and other proteins have allowed biologists to recognize important distinctions between bacteria and archaebacteria. The graphic on this slide illustrates the phylogenetic relationships drawn from this information using a three-domain and a six-kingdom arrangement, compared to the traditional five kingdom system.

In our previous presentation about phylogenetic classification, we introduced classifying organisms under a broad three-domain system versus classifying organisms using a five, six, or more kingdom approach. For the purpose of this discussion, we will refer to the traditional five-kingdom system.  Organisms are divided into each of five kingdoms based on defining characteristics, such as: cell type; cell structures; whether the organism is unicellular, multicellular, or has both forms; and nutrition.  As new information is gathered, classifying approaches are constantly being refined.

There are two domains of prokaryotes: bacteria and archaea. Members of these groups do not have a cell nucleus or organelles bounded by membranes. Although there are exceptions, bacterial genomes do not typically have introns. On the other hand, the genes of organisms in the domain Archaea are sometimes a bit more complex and can have introns and other structural and regulatory elements similar to those found in eukaryotes. Prokaryotic genome sizes can vary widely. Some may be as small as a a few hundred thousand base pairs or as large as several million base pairs.

Like the extensive diversity in life forms within the eukaryote domain, the genomes of eukaryotes also vary greatly in size and composition. For example, the yeast Saccharomyces cerevisiae genome is ~12.5 million base pairs in size, while the fern Psilotum nudum genome is ~250 billion base pairs in size. Further, most eukaryotic genomes encode complex genetic elements that preserve and maintain the structure of the genome, and regulate the transcription (expression) of eukaryotic genes.

Genomes of eukaryotes contain regions known as introns. Introns are non-coding segments of DNA, of variable size, that separate the coding segments, or exons, of the genes of eukaryotic organisms. During RNA processing, the introns are removed from RNA molecules in a complex process called splicing. In addition, the genetic material of eukaryotes is organized into one or more linear structures called chromosomes.

The RNA molecules made within eukaryotic cells must be processed before they can be used as messengers of the DNA code. Eukaryotic genes contain introns that must be removed. Introns are non-coding segments of DNA, of variable size, that separate the coding segments, or exons, of the genes of eukaryotic organisms. During RNA processing, the introns are removed from RNA molecules in a complex process called splicing. In addition, a methyl group called a 5' cap is attached to the 5' end of the RNA, and a polyA tail is added to the 3' end of the RNA in a process called polyadenylation. The resulting processed RNA is called a messenger RNA (mRNA). Processed mRNAs migrate from the nucleus (the site of their transcription and modification) to the cytoplasm for translation by ribosomes.

Prokaryotic genes typically do not contain introns, although there are some exceptions. As such, there is usually no splicing of RNA molecules in prokaryotic cells. Prokaryotic RNAs also are not capped or polyadenylated as are eukaryotic RNAs. Further, in prokaryotic cells, there is no nucleus to separate the processes of transcription and translation, so transcription and translation often occur simultaneously, with RNA molecules being translated into proteins as they are being transcribed from the prokaryotic DNA. A newly discovered branch of the tree of life is the domain Archaea. Members of the domain Archaea are prokaryotes, as are bacteria. However, some genes of members of the domain Archaea have introns and share other structural and functional similarities with eukaryotes (organisms with a cell nucleus surrounded by a membrane).

Edited Transcript from “The Pathway to Genomic Medicine,” Richard Gibbs, PhD*
So what we are able to do, and Amy designed this data flow, was to make it clear that the submission to the public databases would be from the individual whose sequence was obtained. So here, we’re able to do the analysis and validation of the data, and it was passed back to him [Dr. Watson] for his release to the public domain. Actually, someone sent me a link. You can actually download it right now if you want from the NCBI. It’s very accessible.

* Notes in this slide presentation are adapted from the transcript of “The Pathway to Genomic Medicine,” a presentation by Richard Gibbs, PhD, given in August 2007, as part of Baylor College of Medicine’s Department of Medicine Grand Rounds Human Genetics Symposium.

In this activity, students will observe the bacteria in yogurt (Lactobacillus* and others), which are rod-shaped. Other types of bacteria can be spherical or spiral-shaped. Bacteria are examples of prokaryotes, which are almost always microscopic and single-celled (unicellular).

Typically, prokaryotes are surrounded by a cell wall and lack internal compartmentalization. In the Five Kingdom system of classification, all prokaryotes are assigned to the Kingdom Monera. More recent classifications, however, separate the prokaryotes into two different Domains: Domain Bacteria and Domain Archaea. A third Domain, Eukarya, consists of all Eukaryotic organisms, such as plants, animals, fungi and protists. Learn more about recent classification of prokaryotes at http://www.tigr.org/tol/.

Most bacterial cells are 1-5µm in diameter, but there are exceptions. (Thiomargarita namibiensis, for example, is 750µm in diameter and is visible to the naked eye.) Because most bacteria are so small, their internal structures are not visible through most classroom microscopes. Instead, students will see rod shapes, such as those above, distributed throughout the yogurt on the slides they prepare.

*Lactobacilli are found in the intestines of humans and generally are beneficial. They convert lactose and other sugars to lactic acid. Some species produce vitamin K and anti-microbial substances.

Viewing this presentation fulfills part of the requirements for completing the short course on The Science of Microbes, offered on BioEd Online for professional development contact hours. The Science of Microbes Teacher's Guide may be obtained in its entirety from the Center for Educational Outreach, Baylor College of Medicine (1-800-798-8244).

You can download a PDF of this lesson, including the pre-assessment, from BioEd Online or K8 Science.

The Science of Microbes and accompanying online professional development were supported, in part, by Science Education Partnership Award number 5R25RR018605 from the National Center for Research Resources of the National Institutes of Health (NIH) to Baylor College of Medicine. The unit was developed in partnership with the Baylor-UT Houston Center for AIDS Research, an NIH-funded program (AI036211). The opinions, findings, and conclusions expressed in this presentation are solely those of the authors and do not necessarily reflect the views of Baylor College of Medicine or the sponsoring agencies.