Most disease-causing organisms, or pathogens, are too small to be seen without a microscope. Some (e.g., most viruses) are even too small to be visible under a light microscope and must be viewed with the more powerful electron microscope. Because of their microscopic size, these minute organisms often are referred to as microbes or microorganisms. The study of these organisms is called microbiology, and scientists who study these organisms are microbiologists. Not all microbes cause disease; many are beneficial and even essential. Bacteria, in the digestive system, for example are important partners in digestion. Microbes that cause disease are sometimes informally referred to as “germs” or “bugs”.

The five main groups of pathogens are bacteria, viruses, protozoa, fungi, and helminths. Bacteria are simple, single-celled organisms that lack an organized nucleus or membrane enclosed organelles. They often have a cell wall (prokaryotes), and their cells usually are rod-shaped or spherical. Commonly known diseases caused by bacteria are diarrheal diseases, pneumonia, strep throat, tuberculosis, and anthrax. 

Viruses are particles of nucleic acid (DNA or RNA) surrounded by a protective coat that replicate within specific host cells and can spread from cell to cell. Infectious diseases caused by viruses include the flu, the common cold, AIDS, chickenpox, and hepatitis. 

Protozoa are single-celled, motile, eukaryotic organisms, found in the Kingdom Protista, that can be human parasites. A protozoan known as Plasmodium (over 170 species), causes malaria, an infectious disease that is one of the world’s top killers.

Fungi are made of eukaryotic cells (organized nucleus and membrane enclosed organelles). All fungi, with the exception of the yeast group, are multi-cellular organisms that absorb nutrients from the environment. Fungi can cause athlete’s foot, sinusitis, skin diseases, and vaginal infections.

Helminths (worms and flukes) are invertebrate animals, some of which are parasitic. Wuchereia bancrofti is transmitted to humans by way of the mosquito. The mature adults pass into lymphatic glands, obstructing lymphatic drainage and resulting in a disfiguring condition, known as elephantiasis.

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.

Bacteria are the most numerous and ancient life forms found on Earth.  They can live in places normally found inhospitable to other organisms (too cold, too dark, too hot, etc.).  Bacteria are unicellular organisms that do not contain a nucleus or internal compartments, and their genome does not contain introns.  Most species of bacteria can be assigned to two groups, based on the amount of peptidoglycan found in their cell walls.  Bacteria with a thick layer of peptidoglycan in their cell walls are called "gram-positive" because they retain a blue color after staining (following a technique developed by Christian Gram.)  Bacteria with a thin layer of peptidoglycan sandwiched between other layers stain orange-red following the same procedure and are called "gram-negative."  The three most common shapes of bacteria are spherical (cocci), rod (bacilli), and helices (spirilla).

The number of ways that bacteria can obtain nutrition and respire contributes to their ability to inhabit so many diverse places on Earth.  To obtain energy and carbon, bacteria can be photoautotrophic- harness light energy to drive metabolic processes and use CO2 as a carbon source, while others are chemoautotrophic- oxidize inorganic substances for energy and use CO2 as a carbon source, photoheterotrophic- use light to generate energy but obtain carbon from other organic molecules, or chemoheterotrophic- consume organic molecules for both energy and carbon.   The chemoheterotrophs include saprobes, decomposers that absorb their nutrients from the body fluids of living hosts.  Bacteria also form many diverse symbiotic relationships with other organisms.

Bacteria exhibit wide variation in their use of oxygen and can be classified based on their dependence upon it.  Obligate aerobes must have oxygen for cellular respiration; facultative anaerobes use oxygen if it is present, but also can grow by fermentation in an anaerobic environment.  Obligate anaerobes can not tolerate oxygen at any level. 

Bacterial reproduction normally occurs asexually by binary fission.  Bacteria do have the ability to transfer genes or segments of genes, and they do so using three mechanisms: conjugation, transformation and transduction.  Conjugation involves the direct transfer of genetic material between prokaryotes.  In transformation, the cells absorb fragments of DNA from the surrounding environment (even from other species).  Transduction occurs when bacterial viruses play a role in transferring genetic material between prokaryotes. 

These abilities, along with a rapid reproductive rate, leaves little surprise as to why bacteria are "masters" of change and adaptation.

A research team led by Carl Woese at the University of Illinois, first recognized the distinction between bacteria and archaea, also known as archaebacteria.  By analyzing RNA in subunits of ribosomes, they defined the early branching of the prokaryotes into Archaea and Eubacteria.  In addition to their unique composition of ribosomal RNA, archaea also are distinguished by the lack of peptidoglycan in their cell walls and their unusual membrane lipids not found in other organisms.  Unlike traditional bacteria, archaebacterial genes contain introns similar to those found in eukaryotes.

Archaea live in the most extreme or harsh environments on Earth and are classified based on the environment in which they can be found.  Methanogens produce energy from organic compounds in the presence of carbon dioxide, nitrogen and water.  They produce methane and can not live in an oxygen-containing environment.  Thermophiles live in very hot water found in areas around hot springs and ocean hydrothermal vents, and Halophiles are found in water with a high saline content, like the Great Salt Lake in Utah.

The majority of bacteria are not harmful and, in many cases, are beneficial to survival.  Prokaryotes are the decomposers of the Earth.  Many prokaryotes obtain energy by breaking down organic molecules and, in the process, make nutrients available for use by other organisms. Prokaryotes are the only organisms to metabolize inorganic nutrients such as sulfur, iron and nitrogen.  Nitrogen recycling, or nitrogen fixation, is unique to Prokaryotes and is the only biological mechanism that makes atmospheric nitrogen available for the production of organic compounds.  Mutualistic bacteria live inside our intestines aiding in digestion while other bacteria suppress the growth of yeasts and other microbes by altering pH levels in our body.
  
In the late 1800s, Louis Pasteur and other scientists linked bacteria to disease.  Robert Koch was the first to identify the organisms that cause tuberculosis and anthrax.  Since then, other pathogenic prokaryotes have been identified and linked to diseases, such Lyme's disease, tetanus, cholera, diarrhea, botulism and syphilis. In industry, bacteria have been used in bioremediation and as metabolic "factories" that produce acetone as well as pharmaceuticals like insulin and antibiotics.  Bacterial metabolic abilities are useful in separating sulfur compounds from copper and uranium in mining low grade ores.

In this slide set, we will explore the structures and functions of genomes, including the genomes of eukaryotes, prokaryotes and viruses. We also will explore the human genome in depth and learn how changes in the structure or number of chromosomes in the human genome lead to certain genetic disorders.

Illustration:
The image on this slide is a photograph of the model of the DNA molecule built by Drs. James Watson and Francis Crick in 1953. Drs. Watson and Crick used this model to depict their proposed structure for the DNA double helix. The hypothesized structure was derived from X-ray diffraction data produced by Drs. Maurice Wilkins and Rosalind Franklin. The model was constructed from metal scraps obtained from a machine shop.

Drs. Watson and Crick published their proposed DNA structure in the journal, Nature, on April 2, 1953 (Volume 171, page 737). For their work, Drs. Watson, Crick and Wilkins were awarded the Nobel Prize in Physiology or Medicine in 1962. Dr. Franklin died before 1962. Since Nobel Prizes are awarded only to living individuals, she could not be honored.

Each chromosome of a living cell is a DNA double helix. The atoms that make up DNA are organized into two primary molecular components: bases and pentose sugars with attached phosphate groups. The bases are the key informational components of DNA, the letters of the DNA alphabet. The bases of DNA include adenine (A), cytosine (C), guanine (G), and thymine (T). Each base consists of a nitrogen-containing component called an amine. The side groups attached to the amines differ among the bases. The pentose sugars and phosphate groups serve as the links that connect the bases in a string, or strand, of DNA. When DNA strands form a double-stranded molecule, two strands of DNA are joined together through hydrogen bonds that form between the bases. In the double-stranded DNA molecule, an A base always pairs with a T base and a C base always pairs with a G base. Once joined, the bases are referred to as base pairs.

Embedded within the DNA sequence of each chromosome are the organism’s genes. The chromosome can be thought of as the DNA scaffolding within which the genes reside. An organism’s set of chromosomes is called its genome. Genes are interspersed unevenly along the lengths of most eukaryotic chromosomes. Across the human genome, for example, there are gene-rich regions and gene-poor regions.

The genomes of most eukaryotes are fairly large and often complex. In addition to genes themselves, most eukaryotic genomes also contain a variety of non-coding structural and regulatory elements and introns. Some of the genetic material also serves as a fossil record, a history book written in biological terms and handed down from generation to generation.

In addition to the DNA inside the cell nucleus, eukaryotic cells have separate genetic material in certain organelles such as mitochondria and, in plants, chloroplasts. In general, organelles, prokaryotes and viruses have greater biological constraints than nuclei on the tolerable sizes of their genomes because of the small genome size that can be incorporated into the organelle, bacterial cell, or viral capsid. As such, the genes of mitochondria, bacteria and viruses typically lack many of the complex non-coding elements commonly found in the nuclear genes of eukaryotes.

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.

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).

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.