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96 Cards in this Set

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How small are microbes?
10^-7 - 10^-3 M
Only visible by microscope.
What are the 6 major groupings of microbes? What categories do they fit into?
Prokaryotes: Bacteria and Archaea
Eukaryotes: Algae, Protists, and Fungi
Viruses
What is an organism's total genetic content called?
Genome
What is the name for infectious proteins? What do they do?
Prions: causes proteins to take a misshapen form
When was the light microscope invented? Who and when described the first cells?
1660s: microscope invented
1665: Robert Hooke describes fruiting structure of molds
Who was the first to describe microbes in detail? When?
1676: Anton von Leeuwenhoek (looked at the substances upon his teeth!)
What three scientists (and when) did experiments to disprove spontaneous generation?
Late 1600s: Redi - maggots /flies experiment
1700s: Spallanzani boils broth (no air)
1861: Pasteur uses swan-neck flask
How much of the planet's biomass is made up by microbes?
60% (5x10^31 microbial cells)
Can most microbes grow on typical mediums?
No - they are mainly unculturable!
What is a Winogradsky column? What occurs inside of one?
A clear bottle containing mud mixed with shredded news (organic carbon source) which ultimately zones into different layers of microbes when exposed to light for several weeks; layers go from oxygen-rich conditions to highly reduced conditions.
Microbes can be used to cycle many elements; name the four common cycles.
1) Nitrogen (fix N2 to NH4, nitrify NH4 to NO3)
2) Carbon (photosynthetic microbes fix it)
3) Sulfur
4) Phosphorus
What is the theory that many diseases are caused by microbes?
Germ Theory of Disease (Pasteur)
In Germ Theory, how can resistant individuals not only become resistant, but in essence, prevent the spread of the disease?
Vaccines
How did Edward Jenner develop the first vaccine for smallpox in 1798?
He used pustules from cattle as an innoculum based on observations from Lady Montagu and Turkish physicians.
Which scientist described the microbiology of lactic acid fermentation, coined the terms aerobic and anaerobic for alcohol production from yeast, made a vaccine for chicken cholera from attenuated strain, and came up with an emergency vaccine for rabies?
Louis Pasteur
How did Robert Koch validate the germ theory of disease in 1876?
He studied anthrax and determined that a bacterium was the cause of the disease.
Who discovered the cause of anthrax, tuberculosis, and cholera?
Robert Koch
What were the four criteria for Koch's postulates?
1) Microbe always present in diseased; absent in healthy
2) Microbe grown in pure culture with no other microbes present
3) Introduce pure microbe into healthy individual; they become sick
4) Same microbe re-isolated from new sick individual
Why did Robert Hooke come up with the name "cell"?
When he looked at a cork, the dead plant material in cork reminded him of a jail cell.
Who devised methods for staining bacteria, photographing, and preparing permanent visual records on slides in 1881?
Robert Koch
What is the name of the dye system for identifying bacteria? Who developed it in 1891?
Gram Stain - Hans Christian Gram
What are the two mediums that microbes (those that can, that is) can grow on?
Broth - liquid containing all the nutrients the microbe requires
Agar - solid media, useful for wide range of temperatures
What is an antiseptic?
A chemical that kills microbes.
What was the first antibiotic discovered? When? By whom?
Penicillin, 1929-1941, Alexander Fleming
What are three advantages to studying microbes?
1) Small - large populations easy to work with
2) Quick Growth - short generation times; easy to study life-cycle
3) Easy Growth - model microbes have simple requirements
Which experiment discovered the act of transformation in bacteria? By whom?
Frederick Griffith: smooth/rough bacteria killing mice.
What did the experiment by Avery and others that repeated Griffith's experiment but with various parts of the cell eliminated (protease, RNAse, DNAse...) prove?
DNA is the hereditary material
The first phylogenetic tree by Ernst Haeckel, 1866, had which three kingdoms?
1) Plants
2) Protists
3) Animals
What were the original molecules, as seen in the Prebiotic Soup Model?
H2O, NH3, CH4, H2
Although Oxygen has been around since 4bya in small quantities, when did it really increase? What happened after this sudden increase in O2?
2 bya; evolution of diverse life
What does the banded iron indicate?
Early life was attempting to use reduced iron and oxygen as an electron acceptor.
What transformed the original Prebiotic Soup molecules into amino acids?
Heat and Pressure and Energy (often in the form of lightning)
What are the four criteria for a molecular phylogeny marker?
1) Gene must be present in all organisms being compared
2) No gene transfer
3) Must have some sequence conservation
4) Large enough to have historical info
What is one of the best phylogenetic markers? Why?
Ribosomal RNA; required for translation of mRNA into protein and is therefore present in all bacterial, archaeal, and eukaryotic cells.
What two criteria must be met for changes in a sequence to constitute a molecular clock?
Neutral and Random; number of differences between homologous macromolecules in two organisms should be a measure of time since they share a common ancestor.
What occurs during vertical gene transfer?
Passage of genes from parents to offspring or transfer of genes by replication or division.
What occurs during horizontal gene transfer?
Passage of genes among microbial lineages; confounds phylogeny deduced from sequences.
What is the idea of the progenote?
There was a common ancestor "community" of primitive cells as opposed to a single common ancestor. Genes would have been shareable amongst these microbes.
==> UNIVERSAL ANCESTOR
What are the two types of microbial cooperation?
Symbiosis
Syntrophy
What is defined as the living together of two kinds of organisms?
Symbiosis
What is this circumstance: when one organism utilizes the by products from another organism?
Syntrophy
What is defined as analyzing ALL possible organisms/functions in a given environment based on DNA sequence; culture independent.
Metagenomics
What is mycorrhizae?
A symbiosis between plant roots and fungi; plant provide nutrients, fungi fixes nitrogen for plants.
What is the eukaryotic clade that contains fungi, multicellular animals, and some protist-like organisms?
Opisthokonta
Rhizopus is what kind of mold?
Bread; multicellular structures with spores.
What is a lichen a symbiosis between?
Fungi with green algae or cyanobacteria ("blue-green algae")
What are volvox? Porphyra?
Green algae; red algae.
What are red algae (porphyra) used for?
Wrap sushi; wrap around seaweed
What type of eukaryote is yeast?
Unicellular fungi
What do methanogens do?
Carry out methanogenesis: use of hydrogen to reduce CO2 and other single carbon compounds to methane, yielding energy.
Which type of archaea are important for waste-water treatment and nutrient cycling?
Methanogens (Euryarchaeota)
Which type of archaea live in intermediate temperatures but at extremely low pH's? What is interesting about them?
Thermpolasmatales - only have a plasma membrane; no cell wall to protect them
What distinguishes archaea from eukaryotes and bacteria?
Ether-linked lipids: Archaea (forms lipid monolayer)
Ester-linked lipids: Bacteria/Eukarya
Why is the ether-linked lipids so important for archaea?
They are much more stable in low pH's which is important since archaea live in extreme conditions.
How did some bacteria (deep-branching thermophiles) acquire their ability to live in such extreme temperatures?
Horizontal gene transfer
Which type of bacteria became chloroplasts in modern-day plants?
Cyanobacteria
What is the function of cyanobacteria?
Photosynthesis by day (produce oxygen)
Fix nitrogen by night
What are three key components of the cyanobacteria's cell structure?
Carboxysome
Thylakoids
Heterocysts
What is the function of a carboxysome in a cyanobacteria?
Fixes CO2 using rubisco
What is the function of the thylakoids in a cyanobacteria?
Responsible for photosynthesis
What is the function of the heterocysts in a cyanobacteria?
Site of nitrogen fixation (N2 --> NH4+) using nitrogenase (enzyme that is oxygen sensitive)
Which type of bacteria has two membranes with a small periplasm containing a very small layer of peptidoglycan?
Gram-Negative Bacteria
Which type of bacteria has one membrane bilayer with a large peptidoglycan layer and a S-layer protein "wall"?
Gram-Positive Bacteria
Which type of bacteria are well known for sporulation?
Bacillus
What is sporulation used for?
Used to survive unfavorable environmental conditions by forming a durable, inert, heat-resistant spore (endospore) that can remain viable for thousands of years.
Why is Bacillus thuriengensis used as an insecticide?
It makes a protein that is so concentrated it forms a crystalline inclusion which is toxic to mosquitos.
What is Bacillus antracis known for?
First microbe grown in pure culture; causes anthrax
Why is Epulopiscium fishelsoni special?
It is a very large bacteria (quarter mm long)! Visible by eye; grows in symbiosis with a fish.
Which bacteria is commonly used to make antibiotics?
Streptomyces
Which bacteria is a dangerous pathogen due to its waxy-coat? Why is it more dangerous? What does it cause?
Mycobacteriacae - the waxy layer is less sensitive to antibiotics; tuberculosis
Rhizobia, an alpha proteobacteria, is a symbiotic bacteria that does what?
Provides nitrogen fixation for legumes (via the roots)
What kind of bacteria are proteobacteria?
Gram-negative bacteria
Which Beta Proteobacteria lives in soil, is a dangerous pathogen to those with cystic fibrosis, is a powerful, metabolic organism and carries out degradation pathways?
Burkholderia
What kind of bacteria is E. coli?
Gamma Proteobacteria; gram-negative
Grows in the human intestine; some are beneficial, others are detrimental (0157:H7)
What is an opportunistic pathogen?
Most people are not affected by it; only causes infection or disease in an immune compromised host organism; wounds are susceptible.
Which Gamma proteobacteria is an opportunistic pathogen that grows in many environments and is harmful to those with cystic fibrosis?
Pseudomonas
Why do myxobacteria (delta proteobacteria), such as Myxococcus xanthus, form fruiting bodies?
When it runs out of nutrients (starvation) the cells aggregate to form a fruiting body so that it may disperse spores that may get to better suited environments.
Borrelia burgdorferi and Treponema pallidum are examples of which kind of Gram-Negative Bacteria? What do they cause?
Spirochetes:
Borrelia burgdorferi - Lyme's disease
Treponema pallidum - Syphilis
What are metagenomics used for?
Sequencing an entire community of microbes' genome without culturing them.
How do metagenomics work?
Extract DNA, use PCR to clone the sequence molecular phylogeny marker directly from the environment, sequence.
Where was the large community of uncultured species from that was sequenced via metagenomics?
Sargasso Sea by Bermuda
What is an accumulation of microbes on the teeth?
Biofilm: dental plaque
When does tooth decay occur?
When the wrong bacteria occur in too strong of a concentration.
Termites eat soil and "wood"... Who is really digesting the cellulose in the wood?
Microbes in the hind-gut (primarily bacteria, some eukaryotes, minimal archaea).
When the bacteria or protozoa digest the cellulose in wood for termites, what is released? What happens to this? What is this an example of?
Hydrogen is a by-product which is removed by methanogens (critical because otherwise it would build up to a high quantity). Synthrophy.
How are all cells alike? (5)
Double-stranded DNA
RNA Polymerase
rRNAs and elongation factors
Proteins - common functional domains
Cell structure - aqueous cell compartments have a membrane
How do Archaea and Bacteria resemble each other but not Eukaryotes? (6)
Smaller in size
Circular chromosome
Nucleoids (no nucleus)
Multigene operons (not single genes)
Denitrification, N2 fixation, lithotrophy, respiration, fermentation (vs. resp. and ferm.)
No complex multicellularity
How are bacteria and eukaryotes alike, different than archaea? (6)
No methanogenesis
Limited growth at high temps
Many species: photosynthesis
Red and Blue chlorophyll light absorption
Ester-linked fatty acids (vs. ether-linked)
Many pathogens (vs. none)
What are the two kinds of gram-positive bacteria? What two examples do we have for each of those categories? (What are these examples known for?)
Firmicutes: Bacillus (sporulation) & Epulopiscium fishelsoni (large)
Actinobacteria: Streptomyces (antibiotics) & Mycobacteria (thick cell wall; tuberculosis - waxy)
Steptomyces forms which cellular structure? What do they make? What is an example of that?
Mycelia (branched filaments)
Secondary metabolites --> Antibiotics
How are all cells alike? (5)
Double-stranded DNA
RNA Polymerase
rRNAs and elongation factors
Proteins - common functional domains
Cell structure - aqueous cell compartments have a membrane
How do Archaea and Bacteria resemble each other but not Eukaryotes? (6)
Smaller in size
Circular chromosome
Nucleoids (no nucleus)
Multigene operons (not single genes)
Denitrification, N2 fixation, lithotrophy, respiration, fermentation (vs. resp. and ferm.)
No complex multicellularity
How are bacteria and eukaryotes alike, different than archaea? (6)
No methanogenesis
Limited growth at high temps
Many species: photosynthesis
Red and Blue chlorophyll light absorption
Ester-linked fatty acids (vs. ether-linked)
Many pathogens (vs. none)
What are the two kinds of gram-positive bacteria? What two examples do we have for each of those categories? (What are these examples known for?)
Firmicutes: Bacillus (sporulation) & Epulopiscium fishelsoni (large)
Actinobacteria: Streptomyces (antibiotics) & Mycobacteria (thick cell wall; tuberculosis - waxy)
Steptomyces forms which cellular structure? What do they make? What is an example of that?
Mycelia (branched filaments)
Secondary metabolites --> Antibiotics
Which is the best-studied gram-positive organism; the model system for "firmicutes"?
B. subtilis