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115 Cards in this Set
- Front
- Back
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Nutrient
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any substance used in biosynthesis and or energy production and required for growth in mass or cell numbers
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Macroelements
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C, O, H, S, N, P: organic, proteins, lipids, carbs, and nucleic acids
K, Ca, Mg, Fe: cations serve in enzymes and biosynthesis, needed in large amounts |
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Micronutrients
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Mn, Zn, Co, Mo, Ni, Cu: trace amounts, supplied in water or media, enzymes and cofactors
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Heterotrophs
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use organic molecules as carbon sources which often also serve as energy source
can use a variety of carbon sources |
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Autotrophs
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use CO2 as their sole or principal carbon source, must obtain energy from other sources
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Prototroph
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makes all things it needs from basic raw building blocks, can grow on minimal media
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Auxotroph
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can't make all things it needs from basic building blocks, can't grow on minimal media unless you supplement it or provide the gene for synthesis on a plasmid
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Phototrophs
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use light as energy source
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Chemotrophs
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obtain energy from oxidation of chemical compounds
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Lithotrophs
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electron source is from reduced inorganic substances
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Organotrophs
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obtain electrons from organic compounds
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Photolithoautotrophs
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photoautotrophs= cyanobacteria
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Chemoorganoheterotrophs
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chemoheterotrophs = majority of pathogens
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Photoorganoheterotrophs
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ecological importance= purple/green bacteria polluted lakes/streams
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Chemolithoautotrophs
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ecological importance= acid rain
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Mixotrophs
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autotroph or heterotroph depending on environment
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Nitrogen
Phosphorous Sulfur |
needed for synthesis of molecules (amino and nucleic acids)
nitrogen supplied numerous ways phosphorous usually supplied as inorganic phosphate sulfur usually as sulfate via assimilatory sulfate reduction |
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Sources of Nitrogen
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organic molecules
ammonia nitrate via assimilatory nitrate reduction nitrogen gas via fixation |
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Sources of P and S
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Phosphorous- most use inorganic which is directly incorporated into cells
Sulfur- most use sulfate and reduce by assimilatory sulfate reduction |
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Growth Factors
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must be supplied by environment, organic, essential
-amino acids: protein synthesis -purines and pyrimidines: nucleic acid synthesis -vitamins: enzyme cofactors -heme |
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Passive Diffusion
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high to low concentration between cell's interior and exterior
-H2O, O2, and CO2 move this way |
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Facilitated Diffusion
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Not energy dependent, high to low, size of gradient impacts rate of uptake
-Uses carrier molecules: permeases -transports glycerol, sugars, amino acids -more prominent in eukaryotic than bacteria or archaea -low concentration= increased rate of transport -rate reaches plateau when carrier becomes saturated |
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Active Transport
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energy dependent process: ATP or proton motive force used
-move against gradient -concentrates molecules inside cell -involves carrier proteins (permeases) |
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ABC Transporters
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Example of Active Transport
use ATP -ATP-binding cassette transporters -2 hydrophobic membrane spanning domains -2 cytoplasmic associated ATP-binding domains |
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Secondary Active Transport
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MFS- major facilitator superfamily
-use ion gradients to cotransport substances -protons -symport- 2 things move in same direction -antiport- two things move in opposite |
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Group Translocation
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cell fools itself
-energy dependent transport that chemically modifies molecule as it is brought in -PTS: phosphotransferase system, best known, many anaerobic bacteria transport sugars while phosphorylating them using PEP (phosphoenolpyruvate) as the proton donor |
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Iron Uptake
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-Need iron
-Ferric iron is insoluble so uptake is hard -Siderophores- secreted by organism to help uptake they complex with ferric iron which is then brought in |
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Defined or Synthetic Media
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all components and concentrations are known
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Complex Media
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some ingredients are unknown in composition and/or concentration
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Media Components
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-peptones- protein hydrolysates, partially digested protein sources
-extracts- aqueous, beef or yeast -agar- sulfated polysaccharide used to solidify media, most cannot degrade it like they can gelatin |
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Supportive or General Purpose Media
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Support growth of many organisms
tryptic soy agar |
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Enriched Media
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General purpose supplemented by blood or other special nutrients
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Selective Media
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favor growth of some and inhibit growth of others
Ex: MacConkey agar, selects for gram-negative bacteria |
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Differential Media
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distinguishes between different groups of microorganisms
ex. blood agar: hemolytic vs. non ex. MacConkey agar: lactose fermenters vs. non |
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Bacteria and Archaea Reproductive Strategies
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Haploid Only
-asexual - binary fission, budding, filamentous -all must replicate and segregate the genome prior to division |
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Bacterial Cell Cycle
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formation of new cell >>> next cell division
Two Pathways: 1. DNA replication and partition 2. Cytokinesis- cell division |
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OriC
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-site at which replication of chromosome begins in bacteria
-most chromosomes are circular (bacteria) |
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Terminus
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site at which replication is terminated
located opposite of the origin |
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Replisome
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group of proteins needed for DNA synthesis
-DNApol molecular machine -replication is in both directions from origin |
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Replication
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5'>>>3'
leading: always going into fork lagging: Okazaki fragments coming out of fork Need RNA primer put down by primase DNA polymerase I cuts out primer Helicase- opens fork DNA pol II works at fork SSBP- single strand binding proteins topoisomerase- relieves supercoiling |
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Chromosome Partitioning
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-MreB: murein cluster B- actin homolog, plays role in cell shape, is a spiral inside cell, aids in chromosome segregation
-if mutated, chromosome does not segregate>> artificial diploid |
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Plasmid
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genetic material outside chromosome, F-plasmid, R-plasmid, cloning plasmid
-Have own origin of replication -Kept in cell through selection pressure |
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Plasmid Segregation
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replicate independently
-E.coli R1 plasmid produces three proteins essential for its inheritance: 1. ParM: actin homolog, long filaments 2. ParR, repressor and ParC centromere-like bind to origins and link to ParM 3. ParM filaments elongate and separate plasmids to opposite ends of cell |
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Cytokinesis, Septation
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Septation: formation of cross walls between daughter cells
Steps: 1. selection of site for septum 2. assembly of Z ring (FtsZ protein) 3. linkage of Z ring to cell wall 4. assembly of cell wall synthesizing machinery 5. constriction of cell and septum formation |
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Z ring and its role in septation
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FtsZ protein: tubulin homolog, in most bacteria and archaea; polymerization forms Z ring, meshwork
MinCDE system in E. coli limits Z ring to center of cell: oscillates from one side to other, link Z ring to membrane, Z ring constricts and cell wall synth forms a septal wall |
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Determination of cell shape
Growth |
determined by peptidoglycan synthesis in bacteria
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Penicillin binding proteins (PBPs)
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link peptidoglycan strands and catalyze controlled degradation for new growth
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autolysins
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PBP enzymes that degrade peptidoglycan and site where new units are added
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cocci divisome
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new peptidoglycan forms only at the central septum
-FtsZ determines site of growth, may recruit PBPs for synthesis of septum |
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rods cell wall growth/shape
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elongate prior to septation
-MreB determines cell diameter and elongation as Z ring forms in center |
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vibrio cell wall growth/shape
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-comma-shaped
FtsZ forms Z ring MreB helical polymerization throughout cell crescentin- intermediate filament causes curve shape, localizes to short curved side of cell, asymmetric cell wall sythesis forms curve |
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Growth Curve
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-increase in population not cell size
- batch culture -plotted as log of cell number vs. time -Four phases: 1. lag 2. exponential 3. stationary/ senescence 4. death |
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Lag Phase
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cell synthesizing new components to replenish and adapt to new media
varies in length |
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Exponential Phase
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log phase
rate of growth is constant and maximal population most uniform in terms of chemical and physical properties |
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Balanced Growth
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during log phase
cellular constituents manufactured at constant rates relative to each other |
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Unbalanced Growth
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rates vary relative to each other
occurs under a variety of conditions -change in nutrient levels- shift up/down media -change in environment |
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Stationary Phase
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closed system population growth eventually ceases total cell number remains constant
-substances are limiting, pathways being shut down Reasons: nutrient limitation, limited O2, toxic waste accumulation, critical population density |
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Starvation Response
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entry into stationary activates survival strategy
-morphological changes- endospore -decrease in size, protoplast shrinkage, nucleoid condensation -RpoS protein: assists RNA polymerase in transcribing genes for starvation proteins, it is a Sigma Factor |
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Starvation Proteins
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- increase cross-linking in cell wall
- Dps protein: protects DNA - Chaperone proteins: prevent protein damage: chaperonins, help refold misfolded proteins (heat-shock) - Cells are called persister cells: long term survival, increased virulence |
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Senescence and Death Phase
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1. cells are Viable But Not Culturable (VBNC) : cells alive but dormant, capable of new growth when conditions are right
2. Programmed cell death: some of cells are genetically programmed to commit suicide |
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Generation
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doubling time: time required for population to double
-varies depending on species 10 mins to several days E.coli double every 20 mins |
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Measuring Growth Rate and Generation Time
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If a pop goes from 10^3to 10^9 cells in 10 hours
1. Growth Rate constant u? u = log10^9 - log10^3 / (0.301)(10 hrs) = 9 - 3 / 3.01 = 2.0 gen/hr 2. What is generation time? g = 1/u g = 1/2 generations per hour or 30 mins per generation |
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Counting Chambers
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easy inexpensive quick
useful for counting eukaryotes and prokaryotes cannot distinguish between living and dead cells dye= tri-pam blue exclusion Hemocytometer |
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Direct Counts on Membrane Filters
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special membrane
stained with flourescent dyes- UV can distinguish between live and dead with certain dyes |
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Flow Cytometry
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-microbial suspension forced through small hole with a laser light
specific antibodies can be used to determine size and internal complexity -can sort cells neutrophils from monocytes |
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Measurement of Cell Mass
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-dry weight: some mass lost, humidity affects it
-quantity of a cell constituent: protein, DNA, ATP, chlorophyll -turbidometric measures- light scattering, absorbance and transmittance low absorbance = high transmittance = clear high absorbance = low transmittance = cloudy |
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Chemostat
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rate of incoming medium = rate of removal of medium from vessel
an essential nutrient is in limiting quantities |
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Turbidostat
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regulates the flow rate of media through vessel to maintain a predetermined turbidity or cell density
dilution rate varies no limiting nutrient |
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hypotonic solution
hypertonic solution |
water enters cell
cell may burst, (plasmoptysis) hyper- water leaves cell |
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mechanosensitive channels
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channels in plasma membrane that allow solutes to leave
increase internal solute concentration with compatible solutes to increase internal osmotic concentration in hypertonic solutions |
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halophiles
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grow in presence of NaCl or other salts
extreme: require salt 2M - 6.2 M (dead sea) |
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Water Activity (a_w)
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amount of water available to organisms
A_w = P_soln / P_water - low water activity means most water is bound |
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pH
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-log [H+]
acidophiles = pH 0 - 5 neutrophiles = pH 5.5 - 7 alkaliphiles = pH 8.5 - 11.5 |
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acidic tolerance response
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pump protons out of cell
some synthesize acid and heat shock proteins that protect proteins ATP synthase- protons come back in |
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temperature ranges
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psychrophiles = 0 - 20
psychrotrophs = 0 - 35 mesophiles = 20 - 45 thermophiles = 55 - 85 hyperthermophiles = 85 - 113 (TAQ polymerase producer) thermopilus aquaticus |
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Oxygen Concentration
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aerobe = grows in presence of O2 (20%)
obligate aerobe = requires O2, P. aeriginosa anaerobe = grows in absence of O2 obligate anaerobe = killed in presence of O2 microaerophiles = requires 2 - 10 % O2 facultative anaerobes = do not require O2 but grow better with it aerotolerant anaerobes = grow with or w/ out O2 |
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Aerobes Have:
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superoxide dismutase- protective enzymes, changes oxygen to a free radical
catalase peroxidase *strict anaerobes lack these enzymes |
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Pressure
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barotolerant = adversely affected by increased pressure, not severe as nontolerant orgs
barophilic = require or grow better with increased pressure, change fatty acids to adapt |
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Radiation
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UV, x-rays, gamma rays
mutations >>> death damage thymine dimers mutates DNA, polymerase doesn't know what to do |
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Deinococcus radiourans
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very resistant to DNA damage
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Biofilms
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attached to surfaces
complex slime enclosed communities formed on any conditioned surface artificial joints, iron pipes, plaque, implants EPS= extracellular polymeric substance |
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Quorum sensing
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AHL- acylhomoserine lactone- autoinducer molecule produced by many gram neg
-diffuses across membrane -induces expression of target genes -way for bacteria in biofilms to communicate - symbiosis with squid DNA uptake for antibiotic resistance genes |
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Metabolism
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total of all reactions divided into
1. catabolism 2. anabolism- build |
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Catabolism
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fueling rxns
energy-conserving rxns ready source or reducing power (electrons) generate precursors for biosynthesis |
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Anabolism
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synthesis of complex organic molecules from simpler ones
requires energy from catabolism Energy for -creating bonds, fighting entropy, bring pieces together and coordinate them |
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Work
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Chemical - synthesis of complex molecule
transport- in/out cell mechanical- getting around |
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Free Energy
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^G = ^H - T^S
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Redox Rxns
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transfer of electrons from donor to an acceptor
the more electrons a molecule has the more energy rich it is. Best e- acceptor = O2 Best e- donor = H+ |
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Electron Transport Chain
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electron carriers organized into ETC with first electron carrier having the most negative E_o
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Electron carriers
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plasma membranes of chemoorganotrophs in bacteria and archaea, mitochondria of eukaryotic cells
NAD >>>NADH = 3 ATP NADP FAD FMN Coenzyme Q Cytochromes- use iron nonheme iron-sulfur proteins |
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Enzymes
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protein catalysts
catalyst- increases rate substrates products |
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Enzymes 2
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apoenzyme= protein component of enzyme
cofactor = nonprotein component, prosthetic group, coenzyme (loose) holoenzyme= apoenzyme + cofactor |
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Ribozymes
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Thomas Cech and Sidney Altman discovered some RNA molecules also catalyze reactions
-catalyze peptide bond formation -self-splicing- tetrahymena |
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Post-translational Regulation of Enzymes
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1. allosteric regulation
2. covalent modification |
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Allosteric regulation
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most regulatory enzymes
small molecule binds to site, changes shape of enzyme, positive effect or increases activity negative effector inhibits the enzyme |
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Covalent Modification
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reversible on/off switch
addition or removal of a chemical group -respond to more stimuli, adds second level of regulation |
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Feedback Inhibition
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end-product inhibition, inhibits one or more critical enzymes
pacemaker enzyme= catalyzes slowest/ rate-limiting step in pathway |
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Respiration
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uses electron transport chain to final electron acceptor
Proton motive force is generated and used to make ATP Aerobic= final acceptor is oxygen Anaerobic = final is different: NO3- SO4, CO2, Fe3+ ATP made primarily by oxidative phosphorylation of ADP via PMF |
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Fermentation
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no electron transport chain
no PMF -oxidizes pyruvate or other organic source substrate level phosphorylation = makes ATP |
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Catabolic Pathways
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enzyme catalyzed
provide intermediates |
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Amphibolic Pathways
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can go forward or reverse depending on what is needed
Important: Embden-Meyerhof pentose phosphate TCA cycle |
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Aerobic Respiration
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can completely catabolize organic energy source to CO2 using:
glycolysis TCA cycle electron transport chain with O2 as final e- acceptor |
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Embden- Meyerhof Pathway
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cytoplasmic matrix
most common for glucose degradation to pyruvate function with or w/out O2 two phases : 6 carbon and 3 carbon |
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Summary of Glycolysis
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glucose + 2ADP + 2P + 2 NAD+ =
2 pyruvate + 2 ATP + 2 NADH +2H+ NET = 8 ATP (w/ETC) |
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Entner- Duodoroff Pathway
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soil bacteria and few gram negs
replaces first phase of E-M pathway produces 1ATP /glucose NET = 7 ATP with ETC |
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Pentose Phosphate Pathway
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hexose monophosphate pathway
can go same time as glycolytic path or E-D path No direct production of ATP- just a lot of NADH a lot of intermediates endless supply if ETC present transketolase transaldolase |
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Tricarboxylic Acid Cycle
TCA (Kreb's cycle) |
common in aerobic bacteria, free living protozoa, algae, fungi
-1 glucose = 2 pyruvates go through (1 pyruvate = 15 ATP) -1 glucose = 30 ATP (2 turns) -MAX = 38 ATP from TCA and glycolytic pathway |
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Bacterial/ Archaeal ETCs
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in plasma membrane
many different electron carriers may be branched may be shorter both directions stationary and log phases-- different aeration |
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Oxidative Phosphorylation
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ATP synthesized as a result of electron transport driven by the oxidation of a chemical source
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PMF drives ATP synthesis
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diffusion of protons back across membrane drives formation of ATP
ATP synthase: enzyme that uses PMF down gradient to catalyze ATP synthesis rotary engine with conformational changes |
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ATP Yield during Aerobic Respiration
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32-38 ATP
not maximally efficient, multi-tasking use PMF to move power flagella, continually sense environment |
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Anaerobic respiration
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electron carriers other than O2
yields less energy because acceptor is less positive than O2 Example: dissimilatory nitrate reduction- nitrate is terminal acceptor denitrification- nitrate > nitrogen gas, bad for soil Eutrophication of local water |
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Fermentation
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oxidation of NADH produced by glycolysis
pyruvate or derivative is used and endogenous electron acceptor o2 not needed ATP formed by substrate level phosphorylation |
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Other sources of energy
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monosaccharides
disaccharides, polysaccharides (cleaved by hydrolases) reserve polymers- glycogen, starch lipid catabolism- triglycerides, hydrolyzed by lipases (Beta-oxidation- oxidizes fatty acids: 2 carbons = 5ATP) -Protease: hydrolyzes proteins and amino acids |
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Chemolithotrophy
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electrons released from energy source which is inorganic
goes to terminal e- acceptor by ETC ATP synthesized by oxidative phosphorylation Chemolithotrophs- acid rain, sulfur oxidizing, nitrifying |
