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Biology of extremophiles
Biology of extremophiles midterm UCSD
50
Biology
Undergraduate 4
10/28/2013

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Term
Temperature limits
Definition
-20 - 122C
Term
Basis of pressure effects
Definition
1. Motility
2. Cell division
3. Substrate Transport
4.DNA replication
5. Growth
6. Translation
7. Transcription
8 Viability
Term
Adaptations to pressure
Definition
1. PUFAs
2. DNA Replication
3.Motility adaptations
4.Membrane protein adaptations
5. Larger membrane channels
Term
pH limits
Definition
0.7-11.5
Term
Pressure limit
Definition
120 MPa
Term
Thermophile environments
Definition
Hot Springs
Hydrothermal vents
Deep earth
Term
Fumaroles
Definition
Openings in earth where hot steam and gases are expelled
Term
Solfataras
Definition
Cool fumaroles that give off hydrogen suflide that react w/ O2 to produce sulfur deposits
Term
Black smoker Gas composition and chimney composition
Definition
Gas: Sulfur
Chimney: Calcium sulfate and metals
Term
White smoker Gas composition and chimney composition
Definition
Gas: Ca, Si, and Barium
Chimney: Calium carbonate
Term
Thermophile temp divisions
Definition
1. Mesophiles -20 - 45ºC
2. Thermophiles -45 - 80ºC
3. Hyperthermophile - >80ºC
Term
Steter culturing
Definition
Green thumb for microbes and appreciation of anaerobic microbiology
Term
Brock
Definition
Extensively sampled Yellowstone and isolated thermophilic microbes
Term
Protein stability adaptations to high temperatures
Definition
a)Held together by Van der Waals interaction
b)Electrostatic interactions
c)Hydrogen bonds
d)Hydrophobic interactions
Term
General adaptations to high temperatures
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.
Term
Methanophiles
Definition
Oxidize methane (CH4) as electron donor and source of cell carbon.
Term
Methyltrophs
Definition
Use one-carbon donor as electron donor and source of cell carbon
Term
Methanohydrates
Definition
Methane forms solid ice w/ water at low temp and high pressure.
Term
Anaerobic methane equation
Definition
CH4 +SO4-2 -> HCO3- + HS- +H2O
Term
Methanophile types
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
Term
Making ethanol w/ methanotrophes
Definition
Methane combined w/ water at high temps to make synthesis gas that is converted to methanol
Term
Optimization of ethanol w/ methanotrophes
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
Term
Growth and temperature effects
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
Term
Enzymes adaptations to low temperatures.
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.
Term
Water activity
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
Term
Microbes cope w/ low water activity by:
Definition
1. Pumping inorganic ions from the environment into the cell
2. By concentrating organic solutes.
Term
Preferential hydration theory
Definition
Compatible solutes cannot penetrate the water layer (hydration layer) on the surface of proteins.

This decreases the entropy of the system.
Term
Adaptations to low water activity
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
Term
Five classes of compatible solutes
Definition
(1)Methylamines (TMAO)
(2)Alcohols and carbohydrates
(3)DMSP
(4)Urea
(5)Free amino acids and their derivatives
Term
Haloquadratum walsbeyi
Definition
Need pyruvate medium to grow
Term
Definitions of Neutrophiles, Acidophiles, and Alkaliphies
Definition
1.Acidophiles: <6 pH

2.Neutrophiles: 6-8 pH

3.Alkaliphiles: >9 pH
Term
Define ChemotrophLithotroautotroph
Definition
Autotrophic microorganism that obtains energy by oxidizing inorganic compounds.
Term
Define Snotties
Definition
Microbial oxidation of sulfur in caves
Term
Acidophile Adaptations
Definition
a)Membranes resistant to proton movement around them

b)Positive membrane potential due to potassium

c)Resistant to many toxic metals
Term
Soda lakes
Definition
Formed in basis w/ river inlet and no sea outlet. Evaporation of water leads to salt buildup.
Term
Protein motive force
Definition
(1)Protons are pumped across a membrane as electrons flow through the respiratory chain.

(2)Chemical component and charge component
Term
Alkalophile protein adaptations
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
Term
Talk about Taq
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.
Term
Glucose asomage
Definition
a)Starch to Fructose
b)Could improve yield of fructose in HFCS
Term
Biohydrogen production
Definition
Hydrogen as a energy source. Feed thermophilic Thermococcus species carbon monoxide. Make hydrogen and CO2. CO is waste product during steel production.
Term
Skylophalophiles
Definition
Could treat Alzheimer's disease. Found in coconuts, sharks and locusts.
Term
Dark Matter paper summary
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
Term
Dark Matter paper figures
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
Term
Great plate anomaly
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
Term
Plagobacter ubique
Definition
Need methionine, glycine, and pyruvate to grow well.
Term
Types of mineral precipitates
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
Term
Magnetite production
Definition
1. Bacteria contain magnetosomes made by reducing iron to magnetite

2. Applications: Visualization of magnetic domains, Cells as magnetometers, contrast agent for MRI.
Term
Diatomic silica cell creation
Definition
Polymerise silicic acid during reproduction. Extrude to cell exterior as a wall
Term

Olitotroph characteristics

 

 

Definition
[image]
Term

Oliotroph gene

complement

Definition
[image]
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