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.

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.

Members of the microbial kingdom Protista originally were defined by structure (mainly unicellular eukaryotes) and by the difficulty to classify them as either plant, fungi or animal.  More recently, the concept of protists was expanded to include certain multicellular organisms such as kelp (Copeland, 1956). Thus defined, members of Protoctista range from microscopic one-celled organisms like dinoflagellates, to multicellular organisms, like seaweed. To untangle this confusing kingdom, biologists now are turning to molecular analysis. 

When following the traditional five- or six-kingdom classification, the Protist group contains all eukaryotes that are not fungi, plants or animals. There are unicellular, colonial, and multicellular forms, some of which show cell specialization.  Protists groups include both autotrophs and heterotrophs, some of which function as detrivores.

Animal-like groups are often referred to as Protozoans.  The term Protozoa dates back to when members of this group were considered "first animals."  Plant-like forms are generally called algae.

Traits such as method of motility, presence or absence of a shell, manner of obtaining nutrition, and reproducing, are used to categorize and discuss this diverse group, but it is important to remember that these traits do not necessarily reflect evolutionary history.  Recent work suggests that green and red algae are more closely allied with land plants, and that slime molds are more closely allied to animals (Baldauf, et al. 2000).

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.

The genes within an organism's genome are generally not evenly distributed along the length of that organism's DNA. The genes of mitochondria, bacteria and viruses often are immediately adjacent to one another, and frequently overlap. In eukaryotes, there are gene-rich and gene-poor regions within the genome where non-coding spacer regions span the distance between gene-rich areas. Within the gene-rich areas, overlapping genes are common. Overlapping genes are different genes whose nucleotide sequences overlap along a segment of DNA. The nucleotide sequence of overlapping genes is read by RNA polymerases in two or more reading frames or from opposite strands of the DNA molecule, thereby encoding different proteins within the same segment of DNA. Overlapping genes are found throughout nature, from bacteria and viruses to mammals, including humans.

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.

Mitochondria are the power plants of cells: they provide cells with the chemical energy needed to perform the metabolic tasks associated with life. It is widely believed that mitochondria are the remnants of ancient energy-producing symbiotic bacterial cells that were assimilated into eukaryotic cells. Similarly, chloroplasts in green plants are believed to be remnants of photosynthetic bacteria.

The mitochondrial chromosome encodes 13 proteins, 2 rRNAs and 22 tRNAs. Mitochondria obtain many of their proteins from genes encoded in the nuclear genomes of cells. Nuclear encoded proteins are imported into the mitochondria after translation.