Term
| Faculative Intracellular Pathogens |
|
Definition
| can live in host or freely |
|
|
Term
|
Definition
| seek refuge by invading host |
|
|
Term
| Pollutants that cause eutrophication |
|
Definition
|
|
Term
|
Definition
| microbial communities at unheated benthic where methane and petroleum seep out |
|
|
Term
|
Definition
| one species harms another (nonspecific) |
|
|
Term
|
Definition
| mutualism, but both species can thrive separately |
|
|
Term
|
Definition
| feeding together of two species on something that wouldn't otherwise be digestable |
|
|
Term
|
Definition
| sequencing of genomes in an environmental community |
|
|
Term
|
Definition
| core genome and accessory genes present in isolates |
|
|
Term
|
Definition
| genes present in all sequenced genomes of species |
|
|
Term
|
Definition
| steroid-like molecules of bacteria membranes |
|
|
Term
|
Definition
| identifying variations within subspecies of pathogen |
|
|
Term
| How technology spreads disease |
|
Definition
colonization of woods and rainforests
transplants and transfusions
modern meat-processing
transportation |
|
|
Term
|
Definition
|
|
Term
|
Definition
| epidemic where infected spread disease to healthy |
|
|
Term
|
Definition
outbreak, high frequency over short period
from one source; little transmission by infected |
|
|
Term
|
Definition
| low frequency of disease; normally present |
|
|
Term
|
Definition
| study of factors affecting illness and health of populations |
|
|
Term
| Survival strategies for pathogens of of cell, but still in host |
|
Definition
secretion of capsule
manufacturing of proteins that bind to antibodies
cause apoptosis of phagocytes
alter cell surface
(all to avoid detection and attachment of antibodies) |
|
|
Term
| Survival strategies for pathogens in cell |
|
Definition
use hemolysin to break out of phagosome
secrete proteins to prevent fusion of phagosome with lysosome
mature in acidic lysosome |
|
|
Term
|
Definition
| intermediates for pathogen transmission |
|
|
Term
|
Definition
| inanimate objects that relay pathogens |
|
|
Term
|
Definition
| cause disease in compromised host |
|
|
Term
|
Definition
| cause disease in otherwise healthy host by breaching defenses |
|
|
Term
| Signature-tagged mutagenesis |
|
Definition
mutate pathogen and tag it
inoculate host
recover pathogen and determine which mutations prevented growth in host |
|
|
Term
| in vivo expression technology |
|
Definition
| identify promotors that transcribe only when infecting a host |
|
|
Term
|
Definition
| endotoxin that activates inflammatory response that can also cause toxic shock |
|
|
Term
|
Definition
5 B subunits surround A and delivers A to host
A subunit is toxic |
|
|
Term
| 5 types of toxin function |
|
Definition
1. causes host cell membrane leakage
2. block protein synthesis
3. block 2nd messenger pathways
4. superantigens overactivate immune system
5. proteases cleave host proteins |
|
|
Term
|
Definition
protein secreted into periplasm
secreted to site of assembly
subunits strung together
tips of pili bind to host |
|
|
Term
|
Definition
hollow fibrils made of pilin with tips that bind to host
prevents expulsion from host |
|
|
Term
| Pathogenicity island characteristics |
|
Definition
multiple genes associated with pathogenicity transferred as block from other organisms
flanked by phage or plasmid genes
different base ratio than other parts of genome |
|
|
Term
| Examples of virulence factors |
|
Definition
| toxins, attachment proteins, capsules |
|
|
Term
|
Definition
| number of organisms to kill 50% of hosts |
|
|
Term
|
Definition
| frequency of lethal infections |
|
|
Term
|
Definition
number of organisms to colonize 50% of host
measure pathogenicity |
|
|
Term
|
Definition
| nonprotein; hyperactivates immune system |
|
|
Term
|
Definition
| toxic proteins; kills host to unlock nutrients |
|
|
Term
|
Definition
|
|
Term
|
Definition
1. encounter
2. entry
3. establish infection
4. cause damage |
|
|
Term
| Benefits of biofilms to microbes |
|
Definition
protection from:
predators
phages
biocides
antibiotics
immunophagocytes
antibodies |
|
|
Term
|
Definition
| community of bacteria enclosed in ECM |
|
|
Term
|
Definition
oligopeptides (gram +)
n-acyl homoserine lactones (AHLs) (gram -)
Al-2 INTER species communication (gram +/-) |
|
|
Term
|
Definition
adapt to availability of nutrients
defense
avoidance of toxins
coordination of virulence to escape
immune response and establish infection |
|
|
Term
|
Definition
| ability of bacteria to communicate and coordinate behavior via small molecules (inter and intra species) |
|
|
Term
|
Definition
| protists, viruses, bacterial predators |
|
|
Term
|
Definition
worm takes up CO2 and H2S
microbes must oxidize to make organic matter |
|
|
Term
| Metabolism of deep sea ocean vents |
|
Definition
producers oxides H2S for energy
methanogens and methanotrophs prevent CO2 buildup
hydrogen oxidizers convert H2 and S --> H2S |
|
|
Term
|
Definition
host for bioluminescent bacteria
bacteria emit light to match moonlight to eliminate shadow on ocean floor
undetectable by predators |
|
|
Term
|
Definition
| bacteria and algae help coral fix N2, photosynthesis, protection against pathogens |
|
|
Term
|
Definition
| break down cellulose in anaerobic environment |
|
|
Term
| Arbuscular mycorrhizal fungi |
|
Definition
improve acquisition of phosphate, nitrogen, water
reduce incidence of root disease |
|
|
Term
|
Definition
| region of soil surrounding rocks |
|
|
Term
|
Definition
|
|
Term
|
Definition
| fungal infection in plants that increase ability to absorb nutrients |
|
|
Term
| Rhizobium infection cycle |
|
Definition
legumes secrete flavanoids
rhizobia express nod genes and enter cortical cells
remains in symbiosome
Rhizobia fix nitrogen; plant provides nutrients |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| both organisms combine metabolic capabilities to catabolize substances they couldn't alone |
|
|
Term
| Cycle leading to acid rain |
|
Definition
phytoplankton produce DMSP to protect against UV
other bacteria convert DMSP-->DMS (volatile, acts as nuclei for cloud formation)
DMS is hydrated to sulfuric acid, which falls as acid rain |
|
|
Term
| Characteristics of phosphorus cycle |
|
Definition
same oxidation state
no gas intermediate
soluble in oceans |
|
|
Term
|
Definition
| used as and e- acceptor in e- transport chain |
|
|
Term
|
Definition
|
|
Term
|
Definition
| anaerobic formation of N2 from ammonia and nitrite |
|
|
Term
|
Definition
cascade of anaerobic respirations converting nitrate-->N2
nitrate-->nitrite-->nitric oxide-->nitrous oxide-->nitrogen gas |
|
|
Term
|
Definition
ammonia-->nitrite-->nitrate
oxidation
makes nitrogen available to plants |
|
|
Term
|
Definition
nitrogen gas-->ammonia
nitrogenase reduces nitrogen
complex cofactors make it oxygen sensitive |
|
|
Term
|
Definition
oxidize methane to CO2
CH4 + SO4 --> CO2 + H2S + OH-
CH4 + H2O --> CO2 + 4H2
removal of H2 drives rxn to right |
|
|
Term
|
Definition
| break down trapped carbon compounds in anaerobic environments to CH4 |
|
|
Term
| Why viruses aren't "living" |
|
Definition
no cellular integrity
only a protein and nucleic acid
depend on host for survival and replication |
|
|
Term
|
Definition
alveolate
2 long flagella
red algal chloroplast
secrete neurotoxins via extrusome |
|
|
Term
|
Definition
|
|
Term
|
Definition
| growth material is secreted at hyphal tips |
|
|
Term
|
Definition
| must absorb as individual molecules |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| amoebas, alveolates, heterokonts, euglenozoa, excavates |
|
|
Term
|
Definition
| circular, similar to bacteria |
|
|
Term
| Protein chemistry for increased stability |
|
Definition
| ion pairs, acidic/basic residues, disulfide bridges, hydrogen bonds, hydrophobic interactions |
|
|
Term
|
Definition
| ether-linked, making it more resistant to acid and heat |
|
|
Term
| Gram-negative proteobacteria |
|
Definition
light-supplemented heterotrophs
adaptable metabolisms |
|
|
Term
|
Definition
specialized pore cells
survive desiccation and then germinate at better conditions |
|
|
Term
|
Definition
| short chains of motile cells |
|
|
Term
|
Definition
| used for buoyancy to maintain position |
|
|
Term
|
Definition
| carbon dioxide fixation location |
|
|
Term
|
Definition
| photosynthetic apparatus separate from plasma membrane |
|
|
Term
|
Definition
| cell part specialized in nitrogen fixing |
|
|
Term
|
Definition
oxygenic phototrophs
photolyze water to make oxygen
photolyze hydrogen
reduce sulfur compounds
only bacteria producers |
|
|
Term
|
Definition
phototrphic, filamentous
moderate thermophiles
lots of membrane-bound chlorophylls |
|
|
Term
|
Definition
| have little water activity |
|
|
Term
|
Definition
| live at low temperature environments |
|
|
Term
|
Definition
| live in low carbon environment |
|
|
Term
|
Definition
| live in high temperature environments |
|
|
Term
|
Definition
| lives in high salt environments |
|
|
Term
|
Definition
| live within rock crystals |
|
|
Term
|
Definition
| basic components from abiotic factors infused with electricity formed biomolecules |
|
|
Term
|
Definition
| idea that life came from other planets |
|
|
Term
| Metabolism of early microbes |
|
Definition
sulfur-based
anaerobic metabolism
reduction of nitrate and sulfate |
|
|
Term
|
Definition
| CH4, CO2, N2, NH4+, H2S, FeS, CO, H2 |
|
|
Term
|
Definition
| infectious single strand RNA |
|
|
Term
|
Definition
microbe found in all cases, but not healthy
microbe isolated and grown
induce disease by introducing microbe
can obtain microbe from diseased |
|
|
Term
|
Definition
RNA can:
store info
duplicate
catalyze (ribosomes)
later, DNA and proteins took over these roles |
|
|
Term
|
Definition
structure and form
catalytic activity
self-replication
membrane compartmentalization
metabolism of energy |
|
|
Term
|
Definition
| live in high pressure environment |
|
|
Term
|
Definition
| live in basic environments |
|
|
Term
|
Definition
| live in acidic environments |
|
|
Term
|
Definition
components of metabolism arose from self-sustaining abiotic rxns
proteins and metabolism formed first |
|
|
Term
|
Definition
| species that grow in extreme environments |
|
|
Term
|
Definition
| thrive at cold temperatures |
|
|
Term
|
Definition
| gene duplication and independent mutation of two protein lines |
|
|
Term
|
Definition
| proteins that diverge from one another in different species |
|
|
Term
| Proteobacteria resemble... |
|
Definition
|
|
Term
| Endosymbiosis example: sea slug & chloroplasts |
|
Definition
sea slugs engulf chloroplasts
chloroplasts perform photosynthesis |
|
|
Term
| Endosymbiosis example: aphids |
|
Definition
| have symbionts that make essential amino acids for them |
|
|
Term
| Endosymbiosis example: amoeba and cyanobacteria |
|
Definition
cyanobacteria provides food
amoeba provides protection |
|
|
Term
|
Definition
| help establish organism that can alter host functions to cause disease |
|
|
Term
|
Definition
| when immune response to pathogen is contributing cause to pathology |
|
|
Term
|
Definition
group of genes transferred together horizontally frequently
linked to tRNA
abnormal base-pair ratio
flanked by genes similar to phage/plasmid |
|
|
Term
|
Definition
DNA transfer via plasmids, transposons, bacteriophages
with genes coding for metabolism, stress response, pathogenicity |
|
|
Term
|
Definition
|
|
Term
|
Definition
| loss or mutation of DNA encoding for unselected traits |
|
|
Term
| Shared ancestor (progenote) characteristics |
|
Definition
genetic code
fueling pathways
protein synthesis
very inefficient |
|
|
Term
|
Definition
|
|
Term
| Requirements for phylogenetic marker study |
|
Definition
gene must be present in organisms studied
gene can't be horizontally transferred
gene must have conservation
must be large enough |
|
|
Term
|
Definition
| redox reactions of e- transport chain store energy in proton gradients in mitochondria |
|
|
Term
|
Definition
| feed on only inorganic minerals |
|
|
Term
|
Definition
| can survive extreme pH and temperatures |
|
|
Term
|
Definition
algae live in fungus
algae provides food
fungus provides protection |
|
|
Term
|
Definition
| layers of earliest microorganisms |
|
|
Term
|
Definition
bacteria
archaea
eukaryotic microbes: yeasts, protists, algae |
|
|
Term
|
Definition
live in hot water
branched off early |
|
|
Term
|
Definition
| carbon & energy sources, storage material, adhesives, parts of other structures, virulence factors, signaling |
|
|
Term
| Stabilizing forces of proteins |
|
Definition
| hydrophobic interactions, hydrogen bonds, ionic interactions, disulfide bonds |
|
|
Term
|
Definition
| glycerol backbone with hydrophilic phosphate group and two fatty acid side chains |
|
|
Term
|
Definition
| planar, rigid structure within phospholipid bilayer; improves membrane stability |
|
|
Term
| Linkage in bacterial and eukaryotic membranes |
|
Definition
|
|
Term
| Linkage in archaeal membranes |
|
Definition
| ether-linked; more stable |
|
|
Term
| Membrane structure is stabilized by |
|
Definition
| hydrophobic interactions, hydrogen bonds, negative charges on proteins and cations |
|
|
Term
|
Definition
| passive transport through membrane from high to low concentration |
|
|
Term
|
Definition
| passive transport flowing down concentration gradient via protein |
|
|
Term
|
Definition
| transport of two molecules through same protein in same direction |
|
|
Term
|
Definition
| transport of two molecules through same protein in opposite direction |
|
|
Term
| ATP-binding cassette transporter |
|
Definition
active transporter
hydrophobic channel and two proteins that bind ATP for uptake of particular molecule |
|
|
Term
|
Definition
| active transport; intake of one molecule affects the uptake of others nearby via different proteins |
|
|
Term
|
Definition
| generates ATP through flowing of H+ ions |
|
|
Term
| periplasm location in gram+ |
|
Definition
| between cytoplasm and peptidoglycan |
|
|
Term
| periplasm location in gram- |
|
Definition
| between cytoplasm and outer membrane |
|
|
Term
| Functions of the periplasm |
|
Definition
| has protein-folders, hydrolytic enzymes, used to adjust osmotic stress, transport, chemoreception, detoxification |
|
|
Term
|
Definition
| forms contractile ring for cytokinesis |
|
|
Term
|
Definition
| encircles cell; involved in cell division |
|
|
Term
|
Definition
| involved in shaping, strength, transport, movement, chromosome separation, cell division, organization |
|
|
Term
|
Definition
| CO2 concentrator that contains RubisCO that fixes CO2 |
|
|
Term
|
Definition
| catabolizes nutrients via TCA cycle to make ATP |
|
|
Term
|
Definition
| contains thylakoids (folds) where photosynthesis takes place; converts light to ATP & reducing power |
|
|
Term
|
Definition
| bacteria that move along magnetic fields in order to maintain proper spacing in water column to live in environment with right amount of oxygen |
|
|
Term
|
Definition
| filled by cell to manage level in water column |
|
|
Term
|
Definition
| cell structure that is resistant to heat, radiation, chemicals, dessication |
|
|
Term
|
Definition
| adds protection especially against phagocytes of immune system |
|
|
Term
|
Definition
| contains porins to allow passage of small molecules |
|
|
Term
|
Definition
| cross-linked glycopeptides; amide bonds between strings of amino acids and glucose derivatives |
|
|
Term
| location of peptidoglycan |
|
Definition
| in bacteria; one molecule that surrounds entire cell |
|
|
Term
|
Definition
| stabilizes cell wall in gram+ bacteria |
|
|
Term
|
Definition
| lots of disulfide bonds, but function unknown |
|
|
Term
|
Definition
polysaccharides and S-layer (protein)
thick cell wall with peptidoglycan cross-links; thin periplasm; contains membrane |
|
|
Term
|
Definition
| some have capsule of polysaccharide; outer membrane of lipopolysaccharide in outer leaflet; thin cell wall with fewer crosslinks; thick periplasm, plasma membrane |
|
|
Term
|
Definition
made of lipopolysaccharides
contains O-polysaccharide antigen that determines virulence and can be altered
endotoxin |
|
|
Term
|
Definition
| made of peptidoglycan and sugar chains linked by amino acid polymer cross-links |
|
|
Term
|
Definition
| made of peudomurien (like peptidoglycan); may have S-layer, ether linked |
|
|
Term
| Polar arrangement of flagella |
|
Definition
|
|
Term
| Lophotrichous arrangement of flagella |
|
Definition
| many flagella on one end of cell |
|
|
Term
| Peritrichous arrangement of flagella |
|
Definition
| multiple flagella at different places |
|
|
Term
| Difference between prokaryotic and eukaryotic flagella |
|
Definition
prokaryotic flagella rotate to move cell
eukaryotic flagella whip to move cell |
|
|
Term
|
Definition
| movement across solid surface by hyperflagellated cells |
|
|
Term
|
Definition
| movement through liquid medium with flagella |
|
|
Term
|
Definition
|
|
Term
| Mechanisms of cell movement |
|
Definition
| swarming, swimming, type IV pili, excretion of surface slime to slide across, rotary motors |
|
|
Term
|
Definition
| cell wall-less bacteria; must live in host; tough membrane w/sterols |
|
|
Term
|
Definition
| cell wall-less; low pH and high temperature environment; rigid membrane with tetra-ether lipids |
|
|
Term
|
Definition
distinguishes gram+ and gram- bacteria
add crystal violet to bacteria
precipitate dye with I-
extract precipitated dye
this removes all dye from gram-
gram positive still contains crystal violet due to the peptidoglycans that are present |
|
|
Term
| Macronutrients for microbes |
|
Definition
| carbon, oxygen, nitrogen, hydrogen, phosphorus |
|
|
Term
|
Definition
| CO2, sugar, organic acids, fatty acids, amino acids |
|
|
Term
|
Definition
| amino acids, nucleic acids, peptidoglycan layer |
|
|
Term
|
Definition
| amino acids, nucleic acids, nitrate, ammonia, nitrogen gas |
|
|
Term
|
Definition
| phospholipids, nucleic acids, ATP synthesis |
|
|
Term
|
Definition
| phosphate, degraded organics |
|
|
Term
| Micronutrients for microbes |
|
Definition
| sulfur, potassium, magnesium, calcium, iron |
|
|
Term
|
Definition
|
|
Term
|
Definition
| sulfate, elemental sulfur, dihydrogen sulfide |
|
|
Term
|
Definition
|
|
Term
|
Definition
stabilizes ribosomes, cell membranes, nucleic acids
required for ATP-dependent enzymes (forms complex w/ATP) |
|
|
Term
|
Definition
| stabilizes walls and spores |
|
|
Term
|
Definition
| maintenance of osmotic balance |
|
|
Term
|
Definition
|
|
Term
| Trace elements needed by microbes |
|
Definition
|
|
Term
|
Definition
| used by cell to make coenzymes |
|
|
Term
|
Definition
|
|
Term
| Function of tetrahydrofolate |
|
Definition
| synthesis of nitrogenous bases |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| Decarboxylation of keto acids |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Coenzyme form of nicotinic acid |
|
Definition
|
|
Term
| Function of nicotinic acid |
|
Definition
|
|
Term
| Coenzyme form of pyridoxine |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Function of adenosylcobalamin |
|
Definition
|
|
Term
|
Definition
energy source: light
carbon source: CO2
reducing power source: inorganics |
|
|
Term
|
Definition
energy source: light
carbon source: organics
reducing power source: organics |
|
|
Term
|
Definition
energy source: chemicals
carbon source: CO2
reducing power source: inorganics |
|
|
Term
|
Definition
energy source: organics
carbon source: organics
reducing power source: organics |
|
|
Term
|
Definition
| gets energy from chemicals and organic compounds |
|
|
Term
| Process of division in spherical bacteria |
|
Definition
|
|
Term
| Division in Gram- rod-shaped bacteria |
|
Definition
Z ring forms when both nucleoids are present
pulls membranes inward
synthesizes new peptidoglycan |
|
|
Term
| Division in Gram+ rod-shaped bacteria |
|
Definition
Z-ring forms at middle
peptidoglycan forms down middle |
|
|
Term
|
Definition
determines location of Z ring
MinE depolymerizes MinCD, causing both proteins to oscilate back and forth
when MinE runs out, MinCD complex reforms and causes Z-ring to form |
|
|
Term
| Influences on growth rate |
|
Definition
| rate of catalysis, metabolism speed, nutrient availability, temperature, pH, gases available |
|
|
Term
|
Definition
| rate of exponential growth |
|
|
Term
|
Definition
| final # cells= initial # cells * 2^(# generations) |
|
|
Term
|
Definition
| lives in -5-10 degrees Celsius |
|
|
Term
|
Definition
| lives in 10-45 degrees Celsius |
|
|
Term
| What temperature classification of bacteria infect humans? |
|
Definition
|
|
Term
|
Definition
| lives in 40-80 degrees Celsius |
|
|
Term
|
Definition
| lives in 80+ degrees Celsius |
|
|
Term
| How do cells adjust to cold temperatures? |
|
Definition
| incorporate unsaturated fatty acids to increase membrane fluidity; express enzymes that are effective at low temperatures |
|
|
Term
| How do cells adjust to hot temperatures? |
|
Definition
| incorporate saturated fatty acids, more sterols and hopanoids to decrease membrane fluidity; express enzymes resistant to denaturation; use chaperones to stabilize proteins |
|
|
Term
|
Definition
|
|
Term
|
Definition
| don't use oxygen and are killed by it |
|
|
Term
|
Definition
| can use oxygen, but can grow without it |
|
|
Term
|
Definition
| can survive in oxygen, but don't use it |
|
|
Term
|
Definition
| require oxygen, but can't survive in atmospheric conditions |
|
|
Term
| How do cells adjust to acidic conditions? |
|
Definition
| seal off membrane to prevent H+ ions from entering |
|
|
Term
| How do cells adjust to basic conditions? |
|
Definition
| utilize other monovalent ions for cell processes; use antiport to expel ion and take up H+ ions |
|
|
Term
| Membrane-permeant organic acids |
|
Definition
| weak acids that can enter cell membrane in uncharged form and then dissociate to cause decrease in pH |
|
|
Term
|
Definition
|
|
Term
| What pH classification of microbes are pathogens? |
|
Definition
|
|
Term
|
Definition
grow best in pH 0-5
tetraether lipids in membrane decrease H+ permeability |
|
|
Term
|
Definition
grow best 9-11
diether lipids that prevent proton linkage
expel Na+ ions to take up H+ |
|
|
Term
| How do cells prevent water loss? |
|
Definition
| synthesize compatible solutes |
|
|
Term
| How do cells prevent water gain? |
|
Definition
|
|
Term
|
Definition
| process where living cells, spores, viruses, are destroyed on an object |
|
|
Term
|
Definition
| killing or removal of disease-producing organisms from inanimate surfaces |
|
|
Term
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Definition
| removal of pathogens from surface of living tissues |
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Term
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Definition
| reducing microbial population to safe levels |
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Term
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Definition
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Term
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Definition
| chemical substances that kill microbes and pathogens |
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Term
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Definition
| heating food to temperature long enough to kill most heat resistant nonspore pathogens |
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Term
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Definition
| length of time it takes agent to kill 90% of population |
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Term
| Decimal reduction time is affected by |
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Definition
| population size, population composition, agent concentration, duration of exposure |
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Term
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Definition
| cross-link assembly in membrane, protein synthesis, nutrient synthesis, gene expression, DNA replication |
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Term
| How microbes resist drugs |
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Definition
| add group to antibiotic to inactivate it, pump out antibiotic, lack molecular target of antibiotic, modify receptors so it is unrecognizable |
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Term
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Definition
| treatment of radioactive waste using genetically engineered bacteria |
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Term
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Definition
oxidize iron, making it insoluble (Fe2+-->Fe3+)
gets carbon from CO2 |
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Term
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Definition
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Term
| How to drive a reaction by altering concentrations |
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Definition
| increase reactants; decrease products |
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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
| Sign of redox potential that means oxidized form is more stable |
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Definition
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Term
| Sign of redox potential that means reduced form is more stable |
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Definition
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Term
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Definition
| accepts 2e- at once and 2H+ |
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Term
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Definition
| accepts 1e- or 2e-, can also accept H+ |
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Term
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Definition
| transition metal complexes that cannot accept protons |
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Term
| Characteristics of energy carriers |
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Definition
| phosphorylated compounds or compounds with high energy bonds |
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Term
| Types of high energy bonds |
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Definition
| anhydride bond, thioester bond, ester bond |
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Term
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Definition
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Term
| What does catabolism achieve? |
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Definition
| chemical energy, reducing power, building blocks for biosynthesis |
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Term
| oxidative phosphorylation |
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Definition
synthesis of ATP by ion-driven ATPase; respiration
substrate is passed from carrier to carrier to be reduced and eventually combines O2 and H+ to make water; generates proton motive force |
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Term
| substrate level phosphorylation |
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Definition
| synthesis of ATP from ADP coupled with breakdown of bonds; fermentation |
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Term
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Definition
| energy carrier that donates and accepts 2-3 times more energy than ATP |
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Term
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Definition
| ADP attached to stable ring; ring has N base and sugar phosphate |
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Term
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Definition
| aromatic ring is disrupted by addition of 2 electrons and H+; must transfer electrons to another carrier or substrate to reduce it |
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Term
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Definition
| accepts 2e- and 2H+ to form FADH2 |
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Term
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Definition
| extracts energy from electron by pushing protons out of cell; must tolerate/avoid oxygen |
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Term
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Definition
1. protons & electrons brought to flavoprotein
2. electrons passed to Fe/S
3. Proton extruded to make PMF
4. electrons from Fe/S enter quinine pool
5. protons picked up from cytosol
6. electrons are brought to heme and Fe/S clusters of cytochromes
7. electrons from Fe/S centers are brought to heme
8. cytochrome oxidase transfers electrons to final acceptor and consumes protons from cytoplasm |
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Term
| F0 mechanism of ATP synthase |
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Definition
a-subunit port of entry for protons
interacts with c unit to deprotonate amino acid residue
neutralized c subunit can rotate and bring neutral c to exit where proton is lost, and then reprotonated |
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Term
| F1 mechanism of ATP synthase |
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Definition
active site on beta unit where ADP and phosphate loosely bind
rotation of F0 drives this rotation
rotation switches binding to tight state forming ATP
Another rotation brings to open state to release ATP |
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Term
| Proton motive force-driven ATP synthesis |
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Definition
| splits hydrogen to create protons and provide energy to make NADH and ATP |
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Term
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Definition
| oxidize sulfur to pump out H+ and drive production of ATP and NADH |
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Term
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Definition
| oxidize iron to pump out H+ and drive production of ATP |
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Term
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Definition
| less efficient than aerobic respiration; still involves ETS, but O2 is not terminal acceptor |
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Term
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Definition
nitrate-->nitrite, nirate-->nitrogen gas
ineffective, toxic
only used when oxygen is scarce |
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Term
| hydrogenotrophic methanogenesis |
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Definition
CO2-->CH4
CO2 is activated and then reduced by methanofuran
Methanopterin reduces it twice more
then forms CH4 |
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Term
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Definition
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Term
| light-drive energy generation |
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Definition
| use light to make ATP & reducing power |
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Term
| Light-driven proton motive force |
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Definition
light hits compound to bring electron up an energy level
electron flows down transport system to make NADPH or NADH
enters a second photosystem to repeat and recycle electrons |
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Term
| Capture of light in archaea |
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Definition
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Term
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Definition
| drive archaeal cell away from damaging light and towards optimal absorbing light |
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Term
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Definition
| gets reducing power from sulfur containing compounds (anaerobic) or water (aerobic) |
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Term
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Definition
| organic compounds donate electrons |
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Term
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Definition
| catabolism with inorganic or small organic electron acceptor using glycolysis, TCA cycle, ETS |
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Term
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Definition
| inorganic compounds donate electrons |
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Term
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Definition
| anaerobic with inorganic donor and CO2 acceptor |
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Term
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Definition
| photolysis of water (aerobic) or others (anaerobic) using photosystems |
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Term
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Definition
| catabolism with light absorption supplements |
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Term
| What do obligate fermenters lack? |
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Definition
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Term
|
Definition
1. activate substrate
2. rearrange C skeleton
3. oxidize activated substrate
4. couple reaction to synthesize ATP
5. balance oxidation with reduction
6. excretion of products |
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Term
| What glucose breakdown yields |
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Definition
| two 3-carbon sugars + 4H+ on NADH |
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Term
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Definition
| glucose 6-phosphate-->fructose 6-phosphate-(phosphorylation)->2 pyruvates, 2 net ATP, 2 net NADH |
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Term
| Entner-Duodoroff (ED) pathway |
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Definition
| glucose 6-phosphate-(oxidation)->6-phosphogluconate-->1 pyruvate + 1 G3P-->G3P enters glycolysis , 1 net ATP, 1 net NADH, 1 net NADPH |
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Term
| Pentose-phosphate shunt (PPS) |
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Definition
glucose 6-phosphate-(oxidation)->6-phosphogluconate-(decarboxylation)->ribulose 5-phosphate (used for biosynthesis, or converted to pyruvate)
makes 1 ATP and 2NADPH |
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Term
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Definition
| can participate in both catabolism and anabolism, simply by reversing process |
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Term
| Steps that regulate glycolysis |
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Definition
| involves steps that are not reversible |
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Term
| How fermentation completes catabolism |
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Definition
| recycles e- carriers by transferring H's back to pyruvate products |
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Term
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Definition
| forms various products depending on pH |
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Term
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Definition
| esterified coenzyme A to acetyl group |
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Term
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Definition
| uses lipases to generate acetyl-CoA that feeds into TCA cycle by dehydrating, then adding water and oxidizing to ketone |
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Term
| Catabolism of aliphatic hydrocarbons |
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Definition
| addition of oxygen, then two oxidations |
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Term
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Definition
| attach CoA, removal of aromaticity, break ring, then oxidize |
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Term
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Definition
| broken down to peptides then amino acids to feed into TCA cycle |
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Term
| Cycles involved in CO2 fixation |
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Definition
| Calvin cycle, reductive TCA cycle, reductive acetyl-CoA pathway, methylotrophic strategy |
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Term
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Definition
1. 3CO2-->G3P
2. 1CO2-->rubisco-diphosphate -->6-carbon product-->2 G3Ps
each cycle yields 1 G3P and spends 9ATP |
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Term
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Definition
| TCA cycle in reverse, but some enzymes are replaced because they can't run in reverse |
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Term
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Definition
| pick up CO2 to detoxify formaldehyde |
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Term
| Biosynthesis of fatty acids |
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Definition
| CO2+acetyl-CoA-->malonyl CoA that then progresses to form fatty acid and kick off CO2 |
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Term
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Definition
| fixes CO2, housed in carboxysome |
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Term
| Where does nitrogen fixation occur? |
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Definition
| in cells that have differentiated into heterocysts so that O2 isn't there because nitrogen fixation is toxic in presence of oxygen |
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Term
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Definition
fix nitrogen in symbiosis with legumes
make leghemoglobin that binds to oxygen and prevent it from reacting with nitrogen fixation; also don't let ammonia freely float around |
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Term
| Why do ensymes require metal cofactors? |
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Definition
| bind to active sites of enzymes; play structural roles |
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Term
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Definition
| take up iron for bacterial cells; used by pathogens to survive and cause disease |
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Term
| What's the difference between cofactors and coenzymes? |
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Definition
coenzymes: organic, required by some enzymes for catalysis
cofactors: inorganic, required for or increase rate of catalysis |
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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
| adenine and guanine; double-ring |
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Term
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Definition
| thymine, cytosine, uracil; single-ring |
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Term
| Difference between RNA and DNA sugar |
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Definition
| ribose has 2' -OH group, so it's more easily cleaved |
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Term
| What does double-stranding of DNA accomplish? |
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Definition
| protection from chemical attack; information redundancy; repair mechanisms |
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Term
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Definition
| RNA that catalyzes reactions |
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Term
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Definition
| mRNA with a UTR that binds to metabolite in order to hide a ribosome binding site, creating a terminator |
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Term
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Definition
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Term
|
Definition
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Term
|
Definition
| adds nucleotides during replication |
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|
Term
| Sigma subunit of RNA polymerase recognizes what? |
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Definition
| -35 and -10 regions and binds to promoter |
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Term
| Rho-independent termination |
|
Definition
| G-C rich stem-loop forms, followed by a series of A's, causing the polymerase to fall off |
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Term
| Rho-dependent termination |
|
Definition
| polymerase stalls and Rho protein cleaves it off |
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Term
|
Definition
| 3rd nucleotide of a codon can bind to something else; G can bind to U or C; U can bind to A or G |
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Term
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Definition
| block translation, causing a stoppage in downstream transcription, since both occur at the same time |
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Term
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Definition
| conversion of a purine to another purine or pyrimidine to another pyrimidine |
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Term
|
Definition
| conversion of purine to pyrimidine or vice versa |
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Term
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Definition
| cause pyrimidine dimers to form |
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Term
| Effects of X-rays and Gamma rays |
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Definition
| double-stranded breaks in DNA |
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Term
| Effects of oxidation on DNA |
|
Definition
| deamination, depurination, methylation |
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Term
| Mismatch repair mechansim |
|
Definition
repairs base substitutions
substitution is recognized by MutS; Excision is performed by MutL and MutH; repair is performed by Pol I |
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Term
|
Definition
| removal of damaged bases, and then a separation of that gap |
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Term
|
Definition
| plasmid has a long-lived poison and a short-lived antidote; daughter cells that inherit the plasmid will survive because they have the antidote code, but ones that don't will die because the poison lingers from the parental cells |
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Term
| Uncoating of Eukaryotic viruses |
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Definition
| can be uncoated upon attaching to membrane; can be uncoated once inside cell into an endosome (derived from cell membrane); can be uncoated upon attaching to nuclear membrane |
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Term
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Definition
| involved in replication of RNA of viruses; doesn't proofread |
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Term
|
Definition
| has ribosome that makes RNA-RNA polymerase |
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Term
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Definition
| needs to bring an RNA-RNA polymerase with it because it doesn't have a ribosome to transcribe RNA-RNA polymerase |
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Term
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Definition
| naked nucleic acid molecules that act as plant pathogens |
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Term
|
Definition
| single protein molecules that infect |
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Term
|
Definition
| senses stimulus; phosphorylates itself and transfers phosphate to response regulator |
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Term
|
Definition
| removes phosphate from response regulator |
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Term
| What does membrane curvature control? |
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Definition
| where lipids are positioned and localization of some proteins |
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|
Term
| What shapes membrane curvature? |
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Definition
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|
Term
| Cardiolipin (CL) structure |
|
Definition
| 2 phosphate groups with side chains on each |
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|
Term
| Where is cardiolipin found? |
|
Definition
| found in bacteria and membranes related to mitochondria and chloroplasts at poles of septum |
|
|
Term
| What does cardiolipin do? |
|
Definition
| destabilizes planar lipid bilayers |
|
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Term
|
Definition
| use lysozyme to turn it into a sphere then confine them to microchambers; sphere membranes will then conform to curvature of the chambers |
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Term
|
Definition
| protein that inhibits division plane formation |
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