Chapter #1 - The Evolutions Of Microorganisms and Microbiology Flashcards
Archaea
The domain of life containing anucleate cells that have unique lipids in their membranes, distinctive rRNA sequences, and cell walls that lack peptidoglycan.
Many are found in extreme environments, including those with high temperatures (thermophiles) and high concentrations of salt (extreme halophies).
Although some archae are members of a community of microbes involved in gum disease in humans, their role in causing disease hasn’t been clearly established.
Eukarya
The Domain of life that features organisms made of cells having a membrane-delimited nucleus and differing in many other ways from Archaea and Bacteria; includes protists, fungi, plants, and animals.
Fungi
A diverse group of eukaryotic microorganisms that range from unicellular to multicellular forms.
Molds and mushrooms are multicellular fungi that form thin, threadlike structures called hyphae.
They absorb nutrients from their environment, including the organic material molecules that they use as sources of carbon and energy.
Because of their metabolic capabilities, many fungi play beneficial roles, including making bread rise, producing antibiotics, and decomposing dead organisms. Other fungi cause plant and animal diseases.
Genome
The entire genetic makeup of an organism.
Genomic Analysis
An approach to studying organisms that involves sequencing the genome, identifying genes, and assigning functions to the genes.
Koch’s Postulates
A set of rules for proving that a specific microorganism causes a particular disease.
Still widely used, but their application at times is not feasible. When that is so, microbiologists sometime use molecular and genetic evidence.
Microbiology
The study of organisms that are usually too small to be seen with the naked eye; special techniques are required to isolate and grow them.
Microorganism
An organism that is too small to be seen clearly with the naked eye and lacks highly differentiated cells and distinct tissues.
Prions
Infectious agents, composed only of protein, that cause spongiform encephalopathies such as scrapie in sheep and “mad cow disease”.
Prokaryotic Cells
Cells having a type of structure characterized by the lack of a true, membrane-enclosed nucleus. All known members of Archaea and most members of Bacteria exhibit this type of cell structure.
Protists
Mostly unicellular eukaryotic organisms that lack cellular differentiation into tissues. Cell differentiation is limited to cells involved in sexual reproduction, alternate vegetative morphology, or resting states such as cysts.
Spontaneous Generation
An early belief, now discredited, that living organisms could develop from nonliving matter.
Viroids
Infectious agents of plants composed only of single-stranded RNA.
Viruses
Infectious agents having a simple acellular organization with a protein coat and a cucleic acid genome, lacking independent metabolism, and reproducing only within living host cells.
Simplest viruses composed of only proteins and a nucleic acid, and can be 10,000 times smaller than a bacterium.
Virusoids
Infectious agents composed only of single-stranded RNA. They are unable to replicate without the aid of specific viruses that coinfect the host cell. Cause some important human diseases.
Domains
The accepted sorting of organisms. Bacteria (sometimes referred to as true bacteria or eubacteria), Archaea (sometimes called archaeobacteria or archaebacteria), and Eukarya (all eukaryotic organisms).
Bacteria
The domain of life that contains anucleate cells having distinctive rRNA sequences and cell walls that contain the structural molecule peptidoglycan.
Usually single-celled. Most have cell walls that contain the structural molecule peptidoglycan.
Although most bacteria exhibit typical prokaryotic structure, a few members off the phylum Planctomycetes have their genetic material surrounded by a membrane.
Abundant in soil, water, and air, and are major inhabitants of our skin, mouth, and intestines. Some bacteria live in environments that have extreme temperatures, pH, or salinity.
Some bacteria cause disease, but many more play beneficial roles such as cycling elements in the biosphere, breaking down dead plant and animal material, and producing vitamins.
Enzymes
Catalytic proteins. They speed up the myriad of chemical reactions that occur in cells. They are the workhorses of the cell.
Tetrahymena
A protist that contained an RNA molecule that could cut out an internal section of itself and splice the remaining sections back together. Discovered by Thomas Cech in 1981.
Important discovery because at one point in evolution, there must have been a single molecule that could do both cellular work and replicate itself, the jobs of enzymes and DNA respectively.
Ribozymes
Catalytic RNA molecules. Can do both cellular work and replicate oneself.
RNA World
Coined by Walter Gilbert in 1986. Describes a stage in evolution when RNA was capable of storing, copying, and expressing genetic information, as well as catalyzing other chemical reactions.
However, for this precellular stage to proceed to the evolution of cellular life forms, a lipid membrane must have formed around the RNA. Easy to believe because lipids spontaneously from liposomes.
Liposomes
Lipids are major structural components of the membranes of modern organisms. They spontaneously form liposomes, vesicles bounded by a lipid bilayer.
RNA’s Function
Much of RNA exists in the ribosome, a structure that consists largely of rRNA and uses messenger RNA (mRNA) and transfer RNA (tRNA) to construct proteins. Also recall that rRNA itself catalyzes peptide bond formation during protein synthesis. RNA seems to be well poised for its importance in development of proteins.
ATP is a ribonucleotide and RNA can also regulate gene expression.
RNA Created DNA?
Because RNA and DNA are structurally similar, RNA could have given rise to double-standed DNA. It’s suggested once DNA evolved, it became the storage facility for genetic info because it provided a more chemically stable structure.
Evolution of Metabolism
Early Earth was a hot environment that lacked oxygen. The cells that arose there must have been able to use the available energy sources under these harsh conditions. Today there are heat-loving archael species capable of using inorganic molecules such as FeS as a source of energy. Some suggest this interesting metabolic capability is a remnant of the first form of energy metabolism.
Universal Phylogenetic Tree
Developed by Norman Pace. It’s based on comparisons of small subunit rRNA molecules, the rRNA found in the small subunit of the ribosome.
The sequences of the nucleotides in the genes that encode SSU rRNAs from diverse organisms are aligned and pair-wise comparisons are made. For each pair of SSU rRNA gene sequences, the number of differences in the nucleotide sequences is counted. This value serves as a measure of the evolutionary distance between organisms. This is a measure of relatedness, not time. We do not know when they diverged from each other.
At the center of the tree is a line labeled “Root”. This is where the data indicates the last universal common ancestor (LUCA) to all three domains. The root is on the bacterial branch, so it appears Archaea and Eukarya evolved independently, separate from Bacteria.
Following the lines of descent away from the root, toward Archaea and Eukarya, it is clear that they shared common ancestry but diverged and became separate domains.
Unfortunately, the nature of LUCA is not known at this time.
Endosymbiotic Hypothesis
The origin hypothesis of three eukaryotic organelles: mitochondria, chloroplasts, and hydrogenosomes.
Endosymbiosis is an interaction between two organisms in which one organism lives inside the other. This hypothesis proposes that over time a bacterial endosymbiotic of an ancestral eukaryote lost its ability to live independently, becoming either a mitochondrion, if the bacteria used aerobic respiration, or a chloroplast, if the bacteria was photosynthetic.
Hydrogen Hypothesis
Modifies the endosymbiotic hypothesis for mitochondria. This asserts that the endosymbiont was an anaerobic bacterium that produced H2 and CO2 as end products of its metabolism. Over time, the host became dependent on the H2 produced by the endosymbiont. Ultimately, the endosymbiont evolved into one of two organelles. If the endosymbiont could perform aerobic respiration, it evolved into mitochondrion. But if it did not develop this ability, it evolved into a hydrogenosome: an organelle found in some extant protists that produces ATP by a process called fermentation.
Horizontal Gene Transfer
SInce the bacteria and archaea do nor reproduce sexually, they must vary their genomes through HGT.
During HGT, genetic info from a donor organism is transferred to a recipient, creating a new genotype. Thus genetic info does not need to be passed to the next generation because it can be passed between the current generation. Maybe even different microbial species.
HGT still shapes their genomes today.
Taxonomist’s Definition of Species
Group of interbreeding or potentially interbreeding natural populations that is reproductively isolated from other groups. Definition is appropriate for plants, animals, and many eukaryotic microbes that reproduce sexually.
This definition does not apply for bacteria and archaea since they do not reproduce sexually.
Robert Koch
The first direct demonstration of the role of bacteria is causing disease came from his study of anthrax. He used the criteria proposed by former teacher Jacob Henle and others to establish the relationship between Bacillus anthracis and anthrax; he published his findings in 1876.
Koch injected healthy mice with material from diseased animals, and the mice became ill. After transferring anthrax by inoculation through a series of 20 mice, he incubated a piece of spleen containing the anthrax bacillus in beef serum. The bacteria grew, reproduced, and produced endospores. When isolated bacteria or their spores were injected into healthy mice, anthrax developed.
His criteria for proving the casual relationship between a microorganism and a specific disease are known as Koch’s postulates. Koch’s proof that B. anthracis caused anthrax was confirmed by Pasteur and his coworkers. They found out that after burial of dead animals, anthrax spores survived and were brought to the surface by earthworms. Healthy animals then ingested the spores and became ill.
After completing his anthrax studies, Koch fully outlined his postulates in his work on the cause of tuberculosis. In 1884 he reported that this disease was caused by the rod-shaped bacterium Mycobacterium tuberculosis, and he was awarded the Nobel Prize in Physiology or Medicine in 1905 for his work. Koch’s postulates were quickly adopted by others and used to connect many diseases to their causative agent.
Francesco Redi
Challenged idea of spontaneous generation. He made a series of experiments on decaying meat and its ability to produce maggots spontaneously.
Redi placed meat in 3 containers. One was uncovered, second covered with paper, 3rd covered with fine gauze that would exclude flies. Flies laid their eggs on the uncovered meat and maggots developed. The other two pieces of meat did not produce maggots spontaneously. However, flies were attracted to the gauze covered container and laid their eggs on the gauze; these eggs produced maggots. Thus, maggots came from flies, and meat did not spontaneously generate them.
John Needham
English priest. In 1748, he reported results of his experiments on spontaneous generation. He boiled mutton broth in flasks that he then tightly stoppered. Eventually many of the flasks became cloudy and contained microorganisms. He thought organic matter contained a vital force that could confer the properties of life on nonliving matter.
Lazzaro Spallanzani
Italian priest and naturalist. He improved on Needham’s experiment by first sealing glass flasks that contained water and seeds. If the sealed flasks were placed in boiling water for three quarters of an hour, no growth took place as long as the flasks remained sealed. He proposed that air carried germs to the culture medium but also commented that the external air might be required for growth of animals already in the medium. Supporters of spontaneous generation said that heating air in sealed flasks destroyed its ability to support life.
Theodore Schwann
Took Spallanzani’s experiment but allowed air to enter a flask containing a sterile nutrient solution after the air had passed through a red-hot tube. The flask remained steile.
Georg Friedrich Schroder and Theodor von Dusch
Took Spallanzani’s experiment but allowed air to enter a flask of heat sterilized medium after it had passed through a sterile cotton wool. No growth occurred in the medium even though the air had not been heated.
Felix Pouchet
French naturalist. Claimed in 1859 to have carried out experiments that proved that microbial growth could occur without air contamination.
Louis Pasteur Shoots Down Spontaneous Generation
Was provoked by Pouchet’s claim to settle matter of spontaneous generation.
He first filtered air through cotton and found that objects resembling plant spores had been trapped. If a piece of the cotton was placed in sterile medium after air had been filtered through it, microbial growth occurred.
Next he placed nutrient solutions in flasks, heated their necks in a flame, and drew them out into a variety of curves. The swan-neck flasks that he produced in this way had necks open to the atmosphere. Pasteur then boiled the solutions for a few minutes and allowed them to cool. No growth took place even though the contents of the flask were exposed to air.
He pointed out that no growth occurred because dust and germs had been trapped on the walls of the curved necks. If the necks were broken, growth commenced immediately. He had not only resolved the controversy by 1861, but also had shown how to keep solutions sterile.
Louis Pasteur’s Contribution to Disease
He also contributed to disease research. He was a trained chemist and spent many years studying the alcoholic fermentation that yield ethanol and are used int he production of wine and other alcoholic beverages. When he began his work, the leading chemists believed microorganisms weren’t involved in alcoholic fermentation. They were convinced fermentation was due to a chemical instability that degraded the sugars in grape juices and other substances to alcohol.
In 1856, M. Bigo, an industrialist in Lille, France, where Pasteur worked, requested Pasteur’s assistance. His business produced ethanol from the fermentation of beet sugars, and the alcohol yields had recently declined and the product had become sour. Pasteur discovered that the fermentation failed because the yeast normally responsible for it were replaced by bacteria that produced acid rather than ethanol. In solving this problem, Pasteur showed that all fermentations were due to the activities of the yeasts and bacteria, and he published several papers on fermentation between 1857 and 1860.
He was also called upon by wine and silk industries in France for help. The wine industry was having problems resulting in the production of poor quality wines. Pasteur referred to the wines as diseased and showed that particular wine diseases were linked to particular microbes contaminating the wine. He eventually suggested a method of heating wines to destroy the bad microbes. The process is now called pasteurization. The silk industry asked Pasteur to investigate the pebrine disease of silkworms. After years, he showed the disease was due to a protozoan paradist.
Joseph Lister
English surgeon. He indirectly discovered evidence for the germ theory of disease on the prevention of wound infections. Lister, impressed with Pasteur’s studies, developed a system of antiseptic surgery designed to prevent microbes from entering wounds. Instruments were heat sterilized, and phenol was used on surgical dressings and at times sprayed over the surgical area. The approach was remarkably successful and transformed surgery.
It also provided strong indirect evidence for the role of microbes in disease because phenol, which kills bacteria, also prevented wound infections.
Pure Culture
A culture containing only one type of microorganism.
Discovery of Viruses
Viral pathogens were being studied and methods of culturing them were being made.
Charles Chamberland, one of Pasteur’s associates, constructed a porcelain bacterial filter in 1994. Dimitri Ivanowski and Martinus Beijernick used the filter to study tobacco mosaic disease. They found that plant extracts and sap from diseased plants were infectious, even after being filtered with Chamberland’s filter. Being the infectious agent passed through a filter that was designed to trap bacteria, they thought the agent must be smaller than bacteria. Thus the discovery of viruses happened.
Culturing Role in Immunology
Culturing also played a role in immunological studies.
During studies of chicken cholera, Pasteur and Pierre Rous discovered that incubating the cultures for long intervals between transfers would attenuate the bacteria, which meant they had lost their ability to cause disease. If chickens were injected with these attenuated cultures, they remained healthy and developed the ability to resist the disease when exposed to virulent cultures.
Emil von Behring and Shibasaburo Kitasato
They discovered the role of soluble substances in preventing disease. After the discovering of diphtheria was caused by a toxin released by a bacterium, they injected inactivated diphtheria toxin into rabbits. The inactivated toxin induced rabbits to produce an antitoxin, which protected against the disease. Antitoxins are now known to be antibodies that specifically bind toxins, neutralizing them.
Elie Metchnikoff
Discovered the first immune system cells by finding that some white blood cells could engulf disease causing bacteria. He called these cells phagocytes and the process phagocytosis. (Greek phagein, eating).
Naming the Vaccine
Pasteur called the attenuated culture a vaccine in honor of Edward Jenner because, many years earlier, Jenner had used material from cowpox lesions to protect people against small pox. Shortly after this, Pasteur and Chamberland developed an attenuated vaccine.
Joseph Meister
Pasteur also prepared a rabies vaccine using an attenuated strain of Rabies virus. During the course of these studies, Joseph Meister, a 9 year old boy who had been bitten by a rapid dog, was certain to be dead in absence of treatment. Pasteur agreed to try to cure him with vaccination. Joseph was injected 13 times over ten days with increasingly virulent preparations of the attenuated virus. He survived.
In honor of this achievement, the Pasteur Institute of Paris was made in France.
What Koch First Used To Culture
Koch at first cultured bacteria on the sterile surfaces of cut, boiled potatoes, but the bacteria would not always grow well. Eventually he developed culture media using meat extracts and protein digests, reasoning these were similar to body fluids. Initially he tried to solidify the media by adding gelatin. Separate bacterial colonies developed after the surface of the solidified medium had been streaked with a bacterial sample. The sample could also be mixed with liquefied gelatin medium. When the medium hardened, individual bacteria produced separate colonies.
Fanny Eilshemius Hesse
Gelatin is not an ideal solidifying agent because it can be digested by many microbes and melts at temperatures above 28 degrees celcius. But Fanny Eilshemius Hesse proved a better alternative. She was the wife of one of Koch’s assistants. She suggested use of agar, which she used to make jellies, a solidifying agent. Agar wasn’t attacked by most bacteria. Furthermore, it didn’t melt until reaching a temperature of 50 degrees celcius; this eliminated the need to handle boiling liquid. Some of the media developed by Koch and his associates, such as nutrient broth and nutrient agar, are still widely used.
Richard Petri
Another important tool developed is Koch’s lab was a container for holding solidified media-the Petri dish (plate), named after Richard Petri (1852-1921), who devised it.These developments directly stimulated progress in all areas of microbiology.
