15 April 2005

Lecture 38

Reading, Chapter 12

A. Prokaryotes (and viruses)

You will recall that prokaryotes (bacteria) have fundamentally different cells than do eukaryotes. For a review of prokaryotes, please refer to lecture 9.

The bacteria have been recently divided into two kingdoms: archebactera and eubacteria. Gene sequences and other molecular information show that these groups of bacteria are fundamentally different and belong in separate kingdoms. The ribosomes and RNA polymerases of archebacteria are similar to those of eukaryotic cells while the ribosomes and RNA polymerase of eubacteria are similar to those of mitochondria and chloroplasts. These similarities, combined with other evidence, have given rise to the hypothesis that an archebacterium was the original host cell that took up a eubacterium capable of aerobic respiration and kept it as the first mitochondrion. Subsequently, a photosynthetic eubacterium was taken up by cell with a mitochondrion and kept as the first chloroplast. This view of the ancestry of eukaryotes has caused some systematists to divide life into three "domains": the archebacteria, the eubacteria, and the eukaryotes that are a combination of both.

1. Kingdom Archebacteria

The archebacteria are associated with harsh living conditions. Hostile environments such as hot springs, very salty ponds, and very acidic waters are places that often have dense populations of archebacteria that can be easily cultured in the laboratory.

Interestingly, archebacteria are now known to occur in many less hostile environments. In the past, bacteria were known to live in a certain environment if they grew when samples of soil or water from that environment were put in a laboratory culture dish. Samples from non-hostile environments apparently had archebacteria in them but they did not grow well under laboratory conditions. Now, DNA can be extracted from soil or water samples and the presence of archebacteria can be determined from their distinctive gene sequences in the DNA. Through application of this method, archebacteria are now known to live in many environments alongside the more easily cultured eubacteria.

Some groups of archebacteria include the following:

Methanogens

These archebacteria are sensitive to oxygen and cannot perform aerobic respiration. Instead, they oxidize hydrogen and use its electrons to reduce carbon dioxide to methane (natural gas). The electron flow occurring from these reactions is used to make ATP. The methane is released as a waste product.

Methanogens are found in cow stomachs, swamp sediments, sewage, and buried landfills. In the future, they could be used to produce methane for energy as a byproduct of sewage treatment or landfill operation.

Halophiles

These are salt-loving bacteria that grow in places like the Great Salt Lake of Utah or the salt ponds in San Francisco Bay. Large numbers of certain halophiles can turn these waters a dark pink. The pink halophiles contain a pigment very similar to the rhodopsin in the human retina. They use this visual pigment for a type of photosynthesis that does not produce oxygen. Halophiles are not oxygen-sensitive, however, and perform aerobic respiration.

Thermophiles

These are bacteria from hot springs and other high temperature environments. Some can grow above the boiling temperature of water. They perform anaerobic respiration and are sensitive to oxygen. Thermophiles are interesting because they contain genes for heat-stable enzymes that may be of great value in industry and medicine. An example is "taq polymerase". The gene for this protein was isolated from a collection of Thermus aquaticus in a Yellowstone Park hot spring. Taq polymerase is used to make many copies of DNA sequences in a DNA sample. It is invaluable to medicine, biotechnology, and biological research. Annual sales of taq polymerase are roughly half a billion dollars.

2. Kingdom Eubacteria

These are the "true" bacteria. Two examples include Eschericia coli and the cyanobacteria.

a. Eschericia coli (E. coli)

This bacterium lives in your intestines, among other places. It can use oxygen for aerobic respiration and grows rapidly in the presence of oxygen and food (glucose and other biomolecules).

E. coli is mostly good for you. It helps digest your food, produces Vitamin K, and tends to keep out other bacteria that could make you sick. Some kinds of E coli can be "pathogenic" however (make you sick), causing diarrhea and cholera. These illnesses are major killers of young children in the developing world and are contracted by drinking water contaminated with human feces. (When drinking water is tested for "coliform bacteria", it is being tested for the presence of E. coli and its relatives.)

E. coli is also a workhorse of biotechnology and molecular biology. "Tame" laboratory strains of E. coli can be used to produce large amounts of DNA sequence or valuable proteins. An example of such a "recombinant" protein made in E. coli is human insulin. The gene for human insulin was combined with other genes in a small circle called a plasmid. This plasmid was put in a strain of E. coli that could then be made to produce large amounts of relatively pure human insulin for use in treating diabetes. Before insulin could be made in this way, it had to be extracted from pig pancreas tissue delivered from the slaughterhouse. "taq polymerase" is another example of a valuable protein that is produced in E. coli . The gene from Thermus aquaticus was put into E. coli on a plasmid controlled by a promoter that can't be turned off. The E. coli strain makes large amounts of the protein.

Most proteins needed in medicine and industry these days are produced by putting their genes into laboratory organisms that can make large amounts of the needed protein in very pure form. E. coli is often the organism of choice for doing this. After inserting the foreign gene for the needed protein, huge cultures of the E. coli are grown in vats. When the culture is nice and thick, the E. coli cells are separated from the culture liquid and the proteins extracted using a chemical extraction process.

Foreign genes are "added" to E. coli by chemically splicing them into plasmids and then forcing an E. coli strain to take up the plasmid and make large amounts of the protein coded for by the gene. Part of doing this requires connecting the foreign gene to a promoter that the E. coli cell cannot control before the gene is spliced into the plasmid. If such a promoter is used, the foreign gene cannot be turned off and the E. coli cells accumulate large amounts of the protein for which the gene codes.

Normally, bacteria use plasmids for a kind of bacterial sex. A bacterium with a plasmid will inject it into another, nearby bacterium. This gives the recipient bacterium some of the genes present in the donor bacterium. Genetic diversity in the population is increased by this process. Genetic engineers have "borrowed" plasmids as natural tools for putting genes of their choosing into bacteria.

b. Cyanobacteria

Cyanobcteria are a large and diverse group of eubacteria. Some are single cells, some are chains of cells. You may have seen them as "green slime" in your aquarium or in a pond. Cyanobacteria can do "modern photosynthesis", which is the kind that makes oxygen from water. All plants do this kind of photosynthesis and inherited the ability from the cyanobacteria. Cyanobacteria were the first organisms on Earth to do modern photosynthesis and they made the first oxygen in the Earth's atmosphere. They are also believed to be the ancestor of all chloroplasts.

 Adding oxygen to the Earth's atmosphere was a major event in the history of life. The oxygen killed many Archebacteria and many of these are now limited to places where there is no oxygen, e.g. sediments under bodies of water. Oxygen also set the stage for the appearance of aerobic respiration of the sort that you do. Aerobic respiration occurs in mitochondria, requires oxygen, and is a very efficient way to make energy from food. Without it, complex multicellular organisms would not be possible.

 In the present day, cyanobacteria can "bloom" and turn rivers or lakes green, killing fish and poisoning animals that drink the water. These blooms often result from addition of nitrates and/or phosphates to natural waters. Nitrates are present in sewage. Phosphates were present in many detergents until such detergents were largely outlawed. Both nitrates and phosphates are present in fertilizers that may wash off farmland and run into streams and lakes.

Additional information on Archebacteria and Eubacteria can be found on the following web pages at the University of California's Museum of Paleontology:

http://www.ucmp.berkeley.edu/archaea/archaea.html

http://www.ucmp.berkeley.edu/bacteria/bacteriamm.html

http://www.ucmp.berkeley.edu/bacteria/cyanointro.html

3. Viruses

Viruses are not cells at all. They are molecular parasites that consist of a few genes and enzymes enclosed in a protein casing. Viruses use other cells to reproduce themselves.

Viruses are a special case. They appear to be descended from both prokaryotic and eukaryotic ancestors. We know this by comparing the DNA sequences of genes from viruses with those of genes from other organisms. Having genes of similar sequence means that two organisms are related, since there has not been time for a lot of changes in the gene sequences to accumulate since they descended from a common ancestor. This same principal is used to analyze DNA evidence at crime scenes. It can identify one person from millions of suspects because of that person's unique DNA sequences.

Viruses are very small, 1/10 to 1/30 of the size of a bacterial cells. They are not cells but they are parasitic on cells.

 Viruses are composed of three basic elements:

1. A tough protein coat.

2. A chromosome inside the coat that is composed of DNA or RNA (genes made of RNA are very rare in the living world but many viruses have them).

3. A few tough enzymes that help the virus infect its host.

Viruses are parasites of cells and, like many parasites, they are simplified in comparison to their free-living ancestors. Viruses are so simple that they can only use energy to maintain organization and reproduce by pirating host cells for this purpose. They need a cell to perform these living functions and thus cell theory, which states that cells are the basic unit of life, is validated.

In general, viruses exhibit two kinds of life cycles: lytic and lysogenic.

The lytic cycle:

Virus attacks host cell and injects its DNA or RNA chromosome. The virus attaches to the host by binding to a particular surface protein, which is why a particular virus only infects specific cell types of specific host organisms.

Viral genes take over the cell, causing it to reproduce viral chromosomes, coat proteins, and other virus components.

The viral components are assembled into new viruses.

The host cell bursts, releasing the new viruses to infect other cells.

The virus that causes polio in humans exhibits an aggressive lytic cycle.

The lysogenic cycle:

Virus attacks host cell and injects its DNA or RNA chromosome.

Viral genes enter the host chromosome and stays there for a certain period of "latency".

Viral genes are reproduced every time the host cell replicates its chromosomes and divides.

At some time, often in response to some environmental change, the viral genes become active and begin producing new viruses in the host cell. This can cause the host cell to lyse, as in the lytic cycle, or the new viruses can be released slowly over time without killing the host cell.

The viruses that cause herpes and AIDS exhibit lysogenic cycles. For people infected with the herpes virus, a sunburn, illness, or emotional stress can activate latent viruses and cause cold sores.