Term
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Definition
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Term
| Basis of pressure effects |
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Definition
1. Motility
2. Cell division
3. Substrate Transport
4.DNA replication
5. Growth
6. Translation
7. Transcription
8 Viability |
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Term
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Definition
1. PUFAs
2. DNA Replication
3.Motility adaptations
4.Membrane protein adaptations
5. Larger membrane channels |
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Term
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Definition
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Term
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Definition
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Term
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Definition
Hot Springs
Hydrothermal vents
Deep earth |
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Term
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Definition
| Openings in earth where hot steam and gases are expelled |
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Term
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Definition
| Cool fumaroles that give off hydrogen suflide that react w/ O2 to produce sulfur deposits |
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Term
| Black smoker Gas composition and chimney composition |
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Definition
Gas: Sulfur
Chimney: Calcium sulfate and metals |
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Term
| White smoker Gas composition and chimney composition |
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Definition
Gas: Ca, Si, and Barium
Chimney: Calium carbonate |
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Term
| Thermophile temp divisions |
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Definition
1. Mesophiles -20 - 45ºC
2. Thermophiles -45 - 80ºC
3. Hyperthermophile - >80ºC |
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Term
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Definition
| Green thumb for microbes and appreciation of anaerobic microbiology |
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Term
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Definition
| Extensively sampled Yellowstone and isolated thermophilic microbes |
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Term
| Protein stability adaptations to high temperatures |
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Definition
a)Held together by Van der Waals interaction
b)Electrostatic interactions
c)Hydrogen bonds
d)Hydrophobic interactions |
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Term
| General adaptations to high temperatures |
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Definition
1. Protein stability
2. Fewer asparagines and glutamine
3. More weak bonds than normal
4. Chaperones - Protein chaps. which prevent folding and chemical chaperones
5. Reverse gyrase - Wind DNA up into positive superhelix
6. Archaea
a) tetra-ether linkage
Hydrocarbon w/ isoprene units
b) Very strong at high temp. |
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Term
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Definition
| Oxidize methane (CH4) as electron donor and source of cell carbon. |
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Term
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Definition
| Use one-carbon donor as electron donor and source of cell carbon |
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Term
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Definition
| Methane forms solid ice w/ water at low temp and high pressure. |
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Term
| Anaerobic methane equation |
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Definition
| CH4 +SO4-2 -> HCO3- + HS- +H2O |
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Term
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Definition
Type I
a)Gammaproteobacteria use RuMP, pMMO
b)Some live as symbionts in mussels
Type II
a)Alphaproteobacteria use Serine, pMMO and sMMO
b)Can fix nitrogen
c)Have serine pathway |
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Term
| Making ethanol w/ methanotrophes |
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Definition
| Methane combined w/ water at high temps to make synthesis gas that is converted to methanol |
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Term
| Optimization of ethanol w/ methanotrophes |
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Definition
(1)Use thermophilic methanotrophs
(2)Explore volume change of reaction
(3)Use heterologous expression system
(4)Use organic solvent tolerant host strain
(5)Use genetics to better control MDH activity
(6)Remove product inhibition
(7)Selectively evolve strains for greater production
(8)Use MMO enzymes in vitro |
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Term
| Growth and temperature effects |
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Definition
1.Minimum - Membrane gelling; transport processes so slow that growth cannot occur
2.Increasing - Enzymatic reactions occurring at increasingly rapid rates
3.Optimum - Enzymatic reactions occuring at maximal possible rate
4.Maximum - Protein denaturation; collapst of cytoplasmic membrane; thermal lysis |
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Term
| Enzymes adaptations to low temperatures. |
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Definition
1.Km - Reflect of how well bind to substrate. Very low Km values in psychrophiles
2.Kcat - How fast enzyme works [Higher in psychrophiles]
3.Stability - Psychrophiles less stable.
4.PUFAs keep membranes liquid. |
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Term
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Definition
When it is high, fewer substances are dissolved in it. When low, has many substances dissolved in it.
Microbes cope w/ low water activ |
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Term
| Microbes cope w/ low water activity by: |
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Definition
1. Pumping inorganic ions from the environment into the cell
2. By concentrating organic solutes. |
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Term
| Preferential hydration theory |
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Definition
Compatible solutes cannot penetrate the water layer (hydration layer) on the surface of proteins.
This decreases the entropy of the system. |
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Term
| Adaptations to low water activity |
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Definition
1.Salt in: Hold a lot in
a)Keep internal concentration of inorganic salts that are osmotically equivalent to their external environment
(1)K in; Na out
(2)Primarily used by Archaea
b)Need to evolve each protein to adapt
2.Salt out: Compatible solute
a)Definition: Cells keep low concentration of salt in their cytoplasm by balancing osmotic potential with organic, compatible solutes |
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Term
| Five classes of compatible solutes |
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Definition
(1)Methylamines (TMAO)
(2)Alcohols and carbohydrates
(3)DMSP
(4)Urea
(5)Free amino acids and their derivatives |
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Term
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Definition
| Need pyruvate medium to grow |
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Term
| Definitions of Neutrophiles, Acidophiles, and Alkaliphies |
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Definition
1.Acidophiles: <6 pH
2.Neutrophiles: 6-8 pH
3.Alkaliphiles: >9 pH |
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Term
| Define ChemotrophLithotroautotroph |
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Definition
| Autotrophic microorganism that obtains energy by oxidizing inorganic compounds. |
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Term
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Definition
| Microbial oxidation of sulfur in caves |
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Term
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Definition
a)Membranes resistant to proton movement around them
b)Positive membrane potential due to potassium
c)Resistant to many toxic metals |
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Term
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Definition
| Formed in basis w/ river inlet and no sea outlet. Evaporation of water leads to salt buildup. |
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Term
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Definition
(1)Protons are pumped across a membrane as electrons flow through the respiratory chain.
(2)Chemical component and charge component |
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Term
| Alkalophile protein adaptations |
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Definition
a)Modified ATPases
b)Sodium powered motility
c)H+ concentrators
d)Dicarboxylic acid transporters
e)Use antipodes that bring protons into the cell
f)Special F1ase
g)Sodium powered flagellum |
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Term
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Definition
| Kerry Mullis received the Nobel Prize for coming up with the polymerase chain reaction. However, the microbial source of the thermostable DNA polymerae used (Taq) came from Prof. Tom Brock who isolated from a hot spring in Yellowstone National Park. |
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Term
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Definition
a)Starch to Fructose
b)Could improve yield of fructose in HFCS |
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Term
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Definition
| Hydrogen as a energy source. Feed thermophilic Thermococcus species carbon monoxide. Make hydrogen and CO2. CO is waste product during steel production. |
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Term
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Definition
| Could treat Alzheimer's disease. Found in coconuts, sharks and locusts. |
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Term
| Dark Matter paper summary |
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Definition
1. Sequenced uncultivated archea and bacteria cells
2. Found metabolic features that were unexpected
3. Found some single-cell genomes that anchored up to 20% of metagenomic reads in some habitats
4. Could lead to better phylum classifications
5. New insights provided into the characteristics of 29 major B/A lineages
6. Super Phyla described
7. Interesting examples of lateral gene
transfer
8. Found many Bacteria and several Archaea are heterotropic |
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Term
| Dark Matter paper figures |
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Definition
1.Figure 1
a)Upper panel - Sampling sites
b)Middle panel - Describes how samples were processed
c)Lower panel - Shows taxonomy of of gene sequences grouped by phyla
2.Figure 2
a)Shows phyla containing SAGS from this study
b)Shows phylogenetic tree based on 38 conserved genes present in Bacteria and Archaea.
3.Figure 3
a)Shows interesting metabolic features determined from this study.
4.Figure 4
a)Shows geographic location of the metagenomic sample sites |
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Term
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Definition
The great plate anomaly refers to the fact that usually one can count one hundred times more microbes in a microscope than one can culture on a Petri Dish.
Cultures can be adapted
a. Diffusion chambers
b. Microbial traps |
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Term
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Definition
| Need methionine, glycine, and pyruvate to grow well. |
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Term
| Types of mineral precipitates |
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Definition
A.Five areas
1.Calcium phosphate bones
2.Silicon dioxide shells of diatoms
3.Calcium carbonate plates of coccolithophores
4.Manganese encrustation
5.Iron oxidation |
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Term
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Definition
1. Bacteria contain magnetosomes made by reducing iron to magnetite
2. Applications: Visualization of magnetic domains, Cells as magnetometers, contrast agent for MRI. |
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Term
| Diatomic silica cell creation |
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Definition
| Polymerise silicic acid during reproduction. Extrude to cell exterior as a wall |
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Term
Olitotroph characteristics
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Definition
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Term
Oliotroph gene
complement |
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Definition
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