Microbiology Exam 2
Which of these can accept only electrons during respiration? a) NAD b) flavoprotein c) cytochrome d) quinone
NAD, flavoprotein, quinones take electrons and protons c) cytochrome (iron) only take electrons
What are common features in electron transport systems?
NADH oxidase, quinones, cytochromes
What is denitrification (basic)?
NO3 reduced down to NH4+
What class of chemicals includes ethylene oxide gas? a) alkylators b) alcohols c) oxidizers d) phenolics
a) alkylators good sterilizer
What type of microbes perform methanogenesis? a) archaea b) bacteria c) fungi d) algae
a) archaea nitrogen fixation -> bacteria (use enzyme nitrogenase to fix nitrogen)
What term refers to the air/water interface in an aquatic environment? a) neuston b) thermocline c) photic zone d) O horizon
a) neuston
Which of these is a way that glycolysis and Entner Doudoroff are the same? a) produce pyruvate as the end products b) use NADP to accept electrons c) partially reduce glucose d) make 2 net ATP per sugar
a) produce pyruvate as the end products
What separates the epilimnion and hypolimnion in a body of freshwater? a) thermocline b) benthos c) atmosphere d) oxygen
a) thermocline
What is bacteriorhodopsin in phototrophy?
absorb light, excites electrons, electron returns to ground state, releases energy, generates proton gradient
What is chlorophyll in phototrophy?
absorbs light; different chlorophyll absorbs wavelengths that determine where organisms grow purple bacteria, green bacteria, cyanobacteria, chloroplast in plants
What uses oxygen abundance?
aerobes, microaerophiles, anaerobes, facultative anaerobes, aerotolerant
What is secondary wastewater treatment?
aerobic: uses digestive reactions carried out by microbes under aerobic conditions to treat wastewater with low levels of organic materials activated sludge and trickling filter most common decomposition processes
What are the most abundant microbes in freshwater?
alpha and beta proteobacteria
What is fully reduced nitrogen used for?
amino acid synthesis, fixed nitrogen often limiting for cell growth
What are surfactants?
amphiphilic compounds that disrupt membranes; quaternary ammonium compounds with a charged nitrogen with 4 hydrophobic groups attached; example: cepacol, roccal
What are trichodesmium?
an abundant phototroph in tropical/subtropical oceans
How can chlorinated xenobiotics be degraded?
anaerobically by reductive dechlorination or aerobically by aerobic dechlorination; reductive more important because anoxic conditions develop quickly in polluted environments
What is antibiotic?
antimicrobial compound made by one living organism that affects other organisms
What exist in the deep subsurface?
archaea/bacteria in variable concentrations depending on nutrient availability; archaea closely related to eukaryotes called lokiarchaeota subsurface microbial life grows in extremely nutrient limited environments
What are deep sea sediments?
archaeal and bacterial population as deep as 1600 m; core samples taken from drilling into ocean floor; sub-seafloor ecosystems estimated to contain about 4x10^15 grams microbial cellular carbon
How do methanogens use CO2?
as a terminal electron acceptor reducing CO2 into CH4 with H2 as an electron donor
What is the most rapidly transferred carbon reservoir?
atmosphere
What does the carbon cycle include?
atmosphere, land, oceans, sediments, rocks, and biomass
Which of these is LEAST likely to result in sterilization of an aqueous solution? a) freezing b) gamma irradiation c) autoclaving d) UHT pasteurization
autoclaving really good; gamma would do it, but not nicely; UHT can do it, like with milk a) freezing (stops growth but cells do not die)
Which portion of the soil has the highest concentration of microbial growth? a) O horizon b) A horizon c) B horizon d) C horizon
b) A horizon
Which type of pasteurization can result in sterilized products? a) none b) UHT c) HTST d) VAT
b) UHT (ultra high temp) (121 C for second or two) UHT milk can be stored in cabinet because there is nothing to grow inside it
What term refers to metabolically related groups of microbes (like methanogens)? a) niche b) guild c) ecosystem d) community
b) guild
Which of these element cycles does not have a gas phase? a) carbon b) phosphorous c) nitrogen d) sulfur
b) phosphorus
What is metabolism?
balance between catabolism and anabolism; has a central biochemical pathway used for both; TCA cycle, glycolysis, pentose phosphate shunt
What are active sites in enzymes?
binds substrates; facilitates reaction
What are the techniques for physical moist heat?
boiling will not kill endospores tyndallization: discontinuous boiling pasteurization: high heat, short time autoclaving: very high heat advantages: cheap and easy disadvantages: materials must withstand high temperatures
What is the anoxic zone?
bottom tube; anaerobic -> colorless
What is stage 3 of entner-doudoroff?
break-even point using SLP
What is stage 3 of glycolysis?
break-even point using substrate level phosphorylation (SLP)
What is catabolism?
breaking down molecules for energy
How do microbes accelerate corrosion?
by change in pH and redox producing corrosive metabolites/microenvironments like biofilms which lead to a loss in structural integrity in stone/cement
What type of microbes grow best at pH 9.0? a) acidophiles b) psychrophiles c) alkalinophiles d) mesophiles
c) alkaniophiles not as likely to be a pathogen, won't live in us well; can still be a pathogen and make us sick
What process is being performed here? NH3+ -> NO3 a) nitrogen fixation b) assimilation c) nitrification d) denitrification
c) nitrification (oxidizing nitrogen)
What term refers to the microbial growth inhibition exerted by some metals? a) chemotaxis b) eutrophication c) oligodynamic effect d) antisepsis
c) oligodynamic effect
What group of bacteria predominates in nearly all environmental locations? a) firmicutes b) archaea c) proteobacteria d) cyanobacteria
c) proteobacteria archaea are there, but not dominating
What process is most important for removal of xenobiotics like pesticides from the environment? a) nitrogen fixation b) methanogenesis c) reductive dechlorination d) oxidative decarboxylation
c) reductive dechlorination (takes off the halogens)
What is the main purpose of primary wastewater treatment? a) remove excess nutrients to prevent eutrophication b) reduce number of pathogens present c) remove large materials that are not easily biodegradable d) reduce amount of oxygen in the water
c) remove large materials that are not easily biodegradable (settling/screening in BR) d -> most oxygen is taken up from bacteria before it reaches treatment center b -> tertiary a -> secondary
Where is the most carbon on earth located? a) atmosphere b) living organisms c) rocks and sediments d) oceans
c) rocks and sediments
What stage of endospore formation involves making the cortex? a) stage II b) stage III c) stage IV d) stage V
c) stage IV
How many ATP can be maximally formed from one NADH during chemiosmosis? a) one b) two c) three d) four
c) three pump out 10 protons, need 3 to synthesize ATP -> about 3 ATP for NADH needed
What are hydrocarbons in regards to bioremediation?
can completely be degraded to CO2; prokaryotes are used commonly in crude oil spills; gas/crude oil tanks are potential habitats for hydrocarbons; sulfate-reducing bacteria can grow and consume hydrocarbons
Why do Anabaena (cyanobacteria) produce heterospores? a) to survive amino acid starvation b) to perform oxygenic photosynthesis c) to disseminate to new locations when dry d) to fix nitrogen
can do b and d, but can not use nitrogen gas as a nitrogen source; the oxygen is a competitive inhibitor in nitrogenous; N2 reduced down to NH4+ which can fix nitrogen
What is a major element in ALL classes of macromolecules? Which microbe uses this organically?
carbon; heterotrophs use organic carbon
What device is used to grow bacteria in continuous culture? a) cell sorter b) chemostat c) incubator d) autoclave
cell sorter fractionate cells and label b) chemostat used for continuous culture autoclave sterilizes, no growth
What is a biofilm?
cells secrete material to hold on to a surface; cells act together and signal to each other (quorum sensing); protects against dispersion and antibiotics from infiltrating
What is methanogenesis?
central to carbon cycling in anoxic environments
What is the source of energy in chemotrophs?
chemicals are electron donors a) oxidation: donating electrons b) reduction: accepting electrons
How can xenobiotics be partially/completely degraded?
co-metabolism: another organic material is present as a primary energy source for a microbe and the microbe would breakdown the xenobiotic and organic molecule
What are flavoproteins?
common proteins, flavin cofactor, FAD/FMN, carry 2 protons and 2 electrons
What is autoclaving?
commonly used in labs; temperature higher than boiling, use steam pressure ~ 15 psi; 121 C for 20 minutes kills all endospores; home pressure cookers do the same thing
What is the hypolimnion layer in freshwater?
cooler, denser water at the bottom of lakes and ponds; decreasing oxygen levels, increasing hydrogen sulfide levels
What is stage 4 of endospore formation?
cortex; peptidoglycan between 2 membranes; sporulation
What is the petroff-hause chamber?
counts cell directly and gives an accurate number; down fall is it can not tell if cells are dead/alive so we use a stain to distinguish living cells
What are viable counts?
counts cells only able to reproduce and form colonies; downfall is it requires time for colonies to form (at least overnight)
What is thioglycollate?
created oxygen gradient?
What is the proton motive force used for?
creates ATP (synthase at cell membrane), drives flagellar rotation (motors = base, pushes ions in/out)
Which of these reactions is a simulation (think that is the word)? a) N2 -> NH3 b) NH3 -> NO3 c) NO3 -> N2 d) NH3 + pyruvate -> alanine
d) NH3 + pyruvate -> alanine
Where would you find an extreme piezophile? a) the moon b) dead sea c) yellowstone hot springs d) bottom of the ocean
d) bottom of the ocean
Which of these does not perform photorespiration? a) purple sulfur bacteria b) green sulfur bacteria c) cyanobacteria d) euryarchaeota
d) euryarchaeota oxygenic photosynthesis = cyanobacteria (algae/plants) purple/green = anoxygenic photosynthesis (could make nothing as end products or elemental sulfur)
Which element has the most possible redox states? a) phosphorus b) sulfur c) carbon d) nitrogen
d) nitrogen carbon has quite a few, but nitrogen has more nitrogen cycle most important in nature
Cyanobacteria use light for energy and carbon dioxide as a carbon source. Therefore they are .... a) chemoheterotrophs b) photoheterotrophs c) chemoautotrophs d) photoautotrophs
d) photoautotrophs
What term refers to the area around plant roots where water and nutrients are absorbed? a) rhizoid b) rhizopus c) rhizome d) rhizosphere
d) rhizosphere
What are oxidizers?
damage proteins and lipids (halogens); chlorine: disinfectant (added to H2O) iodine: antiseptic (betadine, tincture of iodine) hydrogen peroxide: 3% weak antiseptic -> body and many bacteria can break down this enzymatically
More carbon is found in ______ organic material than _____ organisms.
dead, living
What are the 2 states iron exist as?
ferrous (Fe2+) and ferric (Fe3+)
What is a chemostat in continuous culture?
flow controls growth rate, food is added constantly; no toxic end products and nutrient conditions control culture density
What are myxospores?
form inside fruiting body; not an endospore; insemination with starvation; multicellular structure
What are actinomycetes?
form spores; when food runs out that produce aerial hyphae that protect against bad conditions; disseminated cells
What are methane hydrates?
form when high levels of methane are under high pressure and low temperature; fuel deep sea ecosystems called cold seeps
What is pentose phosphate pathway?
forms 6-phosphogluconate and is converted to ribulose-5-phosphate which produces sugars (3-7 carbons) produces 1 ATP, no NADH, 2 NADPH using biosynthesis
What are the techniques of physical cold?
freezing -> kills some cells due to ice crystal formation refrigeration -> preservation advantages: many products tolerate cold more disadvantages: very little killing and is expensive
What are characteristics of rivers?
freshwater; may be well mixed from rapid water flow but can still suffer from oxygen deficiencies from large inputs of organic matter from sewage and agricultural/industrial pollution
What is the secondary purpose of fermentation?
generate additional energy; energy yields are very small
What is tertiary wastewater treatment?
get rid of excess phosphate, additional organic matter/suspended solids, reduces levels of inorganic nutrients (phosphate, nitrite, nitrate); most complete method of treating sewage, but is costly so not adapted widely; BR uses FeCl3
What is transamination regarding nitrogen assimilation?
glutamine donates NH3 to make other amino acids a) pyruvate + glutamine -> alanine + a-ketoglutarate b) oxaloacetate + glutamine -> aspartate + a-ketoglutarate
How is NAD+ regenerated?
glycolysis = 2 NADH ED = 1 NADH + 1 NADPH kreb's = 4 NADH + 1 FADH2
What are the 3 pathways of glucose metabolism?
glycolysis, entner-doudoroff, pentose phosphate
What environments lack O2?
gut, deep soil, deep ocean
What is a niche?
habitat shared by a guild; supplied nutrients and conditions for growth
What is occurring in the log phase of the growth cycle?
"exponential growth"; bacteria are growing at a fast rate
What does respiration do in regards to the carbon cycle?
(CH2O) + O2 -> CO2 + H2O oxidizes organic carbohydrates to inorganic CO2
What are the 3 cell differentiation?
heterocyst, myxospores, actinomycetes
What are characteristics of freshwater environments?
highly variable in resources and conditions available for microbial growth balance between photosynthesis / respiration controls the oxygen and carbon cycles layers vary greatly in temp, oxygen availability, and chemical composition
Deep soil subsurface can extend for several ______ below soil surface
hundred meters
What is the major volatile sulfur gas produced by bacteria via sulfate reduction or emitted from geochemical sources?
hydrogen sulfide
Where do electron transport systems occur?
in membranes; inner membrane of bacteria/archaea and mitochondria/chloroplast
Where does the bulk of sulfur on earth occur? As what is the form?
in sediments and rocks as sulfate or sulfide minerals such as gypsum/pyrite
What are the physical (dry heat) techniques?
incineration: flaming our loops baking: requires long periods advantages: cheap, easy, fast disadvantages: materials have to withstand high temperatures and can not be water
What is the oligodynamic effect?
inhibition by metals such as silver, copper, mercury, or gold
What is occurring in the lag phase of the growth cycle?
initially add bacteria to culture; no net growth, bacteria are adapting to environment
What are the ultimate electron acceptors in inorganic and organic molecules?
inorganic: respiration organic: fermentation
What is the nuston in an ocean?
interface between the surface of the water and atmosphere where most phototrophs are on the surface
What is the most abundant element in earth's crust, but limiting for microbial growth?
iron
What is a pelobacter?
oligotroph; most abundant marine heterotroph; contain proteorhodopsin oligotroph: organism that grows best at very low nutrient concentrations proteorhodopsin: form of rhodopsin that allows cells to use light energy to drive ATP synthesis
What can run the nitrogen cycle alone?
only bacteria
Which of these would be the terminal electron acceptor for fermentation? a) nitrate b) pyruvate c) oxygen d) carbon dioxide
oxygen = aerobic respiration nitrogen = anaerobic respiration CO2 = inorganic need carbon-hydrogen bond / organic c) pyruvate
What are phytoplankton in freshwater?
oxygenic phototrophs suspended freely in water; include algae and cyanobacteria
What are the techniques of physical filtration (air/liquid)?
pass liquid or gas through a filter with sufficiently small pore size; HEPA filter advantages: no thermal damage disadvantage: viruses not eliminated and must be either gas or liquid
What are the two ways of nutrient uptake?
passive diffusion and facilitated diffusion
What are the 3 ways of counting bacteria?
petroff-hauser chamber, viable counts, and spectrophotometer
What are 5 chemical treatments?
phenolics, alcohols, oxidizers, surfactants, alkylators
How is carbon dioxide removed from the atmosphere?
photosynthetic land plants and marine microbes
What are the deep sea microbes?
piezophilic: pressure loving psychrophilic: cold loving adaptations for growth under high pressure likely seen for a few key proteins that are adapted to cold (short chain fatty acids/increased alpha helices in proteins)
What is a habitat?
portion of an ecosystem where a community could reside (an ecosystem contains many different habitats)
What are ostreococcus?
small phototrophic eukaryotes that inhabit coastal and marine waters; likely important primary producers
Description of pelagic bacteria
small planktonic heterotrophic prokaryotes abundant in pelagic marine waters; prokaryotes decrease with depth; bacterial species dominate surface waters; bacteria & archaea equal in deeper waters
What are cytochromes?
have heme groups, electron carriers only, Heme A/B/C, heme D (in oxidase), heme O (in oxidase)
What are hydrothermal vents?
thriving animal and microbial communities are associated with deep sea hydrothermal vents chemolithotrophic: bacteria predominates the vent that utilizes inorganic materials from the vents thermophiles/hyperthermophiles are present as well
What is the d-value in microbial death rate? What is it effected by?
time required to kill 90% of cells; affected by temperature, type of microorganism, physiological state, and other substances
What is the purpose of materials in microbial life?
to make cell parts (nutrients)
What is the purpose of energy in microbial life?
to move electrons
What is the oxic zone?
top tube; aerobic -> pink/red
What are micronutrients?
trace elements necessary for enzyme function
What does the biogeochemical cycle define?
transformation of key element by biological and chemical agents -> typically preceded by oxi-red reactions microbes play critical role in energy transformations and biogeochemical processes that result in recycling of elements in living system
What is facilitated diffusion?
transported pass material into and out of cell; follows gradient of material
What is pasteurization?
used with juice, beer, milk, other dairy batch -> 63 C for 30 minutes HTST -> 72 C for 15-20 seconds UHT -> 121 C for less than 3 seconds (boxed/shelved milk)
What is primary wastewater treatment?
uses physical separation methods to separate solid and particulate organic and inorganic materials; screening and settling
What is anabolism?
using energy to build cell components; reducing entropy, creating order
What is anammox (basic)?
using nitrite and ammonia reduced to give N2 gas
What is stage 1 of endospore formation?
vegetative cycle; grow/medial division by binary fission; polar division
What is the epilimnion layer in freshwater?
warmer, less dense surface water; high in oxygen
What is "greywater"?
washing, bathing, cooking water
What is sewage?
water contaminated with human or animal fecal materials
What is the growth kinetics equation?
x = 2^y * Xo
If you begin with 1000 bacteria with a doubling time of 30 minutes, how many cells will you have after 2 hours of growth? a) 4000 b) 8000 c) 16000 d) 32000
x = number of cells y = number of doubling y = time / generation time Xo = start of number of cells x = 2^y * Xo y = 120/30 = 4 x = 2^4 * 1000 = 16000 c) 16,000
What sort of microbes grow best around 0 degrees celsius? a) xerophiles b) psychrophiles c) mesophiles d) barophiles
xero = like it dry, desert meso = middle temps (20-40 C) baro = like high barometric pressure (bottom of ocean) b) psychrophiles
What is soil composed of?
~40% inorganic mineral matter / ~5% organic matter / ~50% air and waste / ~5% living organisms
A typical bacterial cell is ______ carbon.
~50%
What represents the largest reservoir for sulfur?
oceans as sulfate
What are the interdependent physical, chemical, and biological processes that form soil?
1. CO2 formed by respiring organisms that form carbonic acid that breaks down rock 2. physical processes such as freezing/thawing break apart rock, allowing plant roots to penetrate and form an expanded rhizosphere 3. rhizosphere: area around plant roots where plants secrete sugars and other compounds; rich in organic matter and microbial life
What is the order of the growth cycle?
1. Lag phase 2. Log Phase 3. Stationary Phase 4. Death phase
Rank these phases of microbial growth from first (1) to last (4) 1. log phase 2. death phase 3. stationary phase 4. lag phase
1. Lag phase 2. Log phase 3. Stationary phase 4. Death phase
What are the 4 distinct layers of soil?
1. O horizon: at surface; undecomposed plant material (grass) 2. A horizon: black soil; most microbial growth; rich in organic material and nutrients 3. B horizon: lighter/sandy; subsoil where organic material leached from A horizon gathers; little microbial activity 4. C horizon: generates mineral particles; base directly above the bedrock; helps form bedrock oxygen decreases the further down the layers
Rank the stages of endospore formation from first to last. a) dehydration of cytoplasm b) asymmetric cell division c) peptidoglycan laid down in cortex d) engulfment of the forespore
1. asymmetric cell division 2. engulfment of the forespore 3. peptidoglycan laid down in cortex 4. dehydration of cytoplasm
Rank the layers of a bacterial endospore from inside (1) to outside (4) 1. cortex 2. exosporium 3. core 4. coat
1. core 2. cortex (primarily made of peptidoglycan) 3. coat 4. exosporium
What is the order from outside to inside of sporulation structure?
1. exosporium: outermost part 2. coat 3. cortex: peptidoglycan 4. core: inside; dipicolinic acid that stabilizes DNA ribosomes
What are the steps of drinking water purification?
1. sedimentation to remove particles 2. coagulation and flocculation form additional aggregates which settle out 3. filtration 4. disinfection with chlorine gas or UV radiation
What is stage 2 of endospore formation?
1st committed; septum off-center; asymmetric cell division; polar division
What are biofilms?
3D; assemblage of bacterial cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells matrix = mix of polysaccharides typically trap nutrients for microbial growth and help prevent detachment of cells in flowing systems; slower growing and antibiotic resistant example: pseudomonas aeruginosa
How many ATP are consumed for nitrogen fixation?
40; very costly for cell
What do autotrophs use instead of carbon?
CO2
What does photosynthesis do in regards to the carbon cycle?
CO2 + H2O -> (CH2O) + O2 reduces inorganic CO2 to organic carbohydrates
What is pyrite?
FeS2
Why must natural nitrogen fixation stay anaerobic?
O2 can be reduced by mistake to H2O which is a waste of resources; difficult for aerobic bacteria
What are the 3 cofactors of pyruvate dehydrogenase?
TPP, lipoamide, FAD
What are the forms of uranium that bacteria can covert?
U6+ to U4+ U6-> water soluble U4-> NOT water soluble
What are the techniques of physical radiation?
UV -> damages DNA with poor penetration Gamma -> very good penetration, very energetic X-ray -> less penetration advantages: very effective with little product damage; how band-aids are sterilized disadvantages: dangerous materials need shielding and lack public trust
What are characteristics about plastics and pesiticides?
degrade extremely slow because organisms lack enzymes to recognize new compounds
What are phenolics?
denature proteins and disrupt membranes; joseph lister; example: phenol, lysol, chlorhexidine; effective on surfaces but many are too toxic to apply to tissue
What are alcohols?
denature proteins and disrupt proteins; example: ethanol, isopropanol; most effective is 50-70%; increases plasmolysis after damage; commonly used for antisepsis
What results in loss of organic N from the biosphere?
denitrification and anammox
What is the Haber process?
dependent on natural gas; bacteria can't do artificially: N(g) + H(g) -> ammonia to make fertilizers
What are heterocysts?
different cells produce different nutrients vegetative cells -> energy heterocyst -> fixed nitrogen, thick cell wall, ATP/NAD
What is the most abundant sulfur compound in nature?
dimethyl sulfide (DMS); produced primarily in marine environments as degradation product of dimethylsulfoniopropionate which is associated with the unique smell of the ocean
What is wastewater?
domestic sewage or liquid industrial waste
In reduction potential what is the best electron donor and electron acceptor?
donor: NADH + H+ acceptor: 1/2 O2
What is electron flow in regards to microbial nutrition?
drive all life processes; drives ions into and out of cells used to create ATP
What uses mixed acid fermentation?
e.coli, acetic acid; has a metabolic flexibility which is dumping electrons vs ATP generation
What does all microbial life require?
electron flow, energy, materials
What is the important of fermentation in the cell?
electrons from metabolism are dumped; potential source of ATP for the cell
What is stage 1 of glycolysis?
energy is spent in the front end to get more later ("spend money to get money")
What is stage 1 of entner-doudoroff?
energy is spent in the front to get more later
What is stage 3 of endospore formation?
engulfment; prespores with 2 membranes; sporulation
What is the thermocline layer of freshwater?
epilimnion / hypolimnion separated; "in between"
Which of these microbes would need to perform reverse electron transport? a) purple sulfur bacteria b) green sulfur bacteria c) cyanobacteria d) euryarchaeota
eury = do not even need electron transport cyan = can make as much NADH they want purple = can not make enough NADH themselves green = can make NADH, but have to replace electrons a) purple sulfur bacteria
What are quinones?
isoprenoid lipids (chains), embedded phospholipid of bacteria, variant structures are known (UQ, MQ, PQ), and carry protons & electrons
What is sterilization?
kill all vegetative cells and spores
What is antisepsis?
killing microbes on living tissue
What does prochlorococcus account for in marine environments?
less than 40% of the biomass of marine phototrophs and ~50% of the net primary production
Description of the deep sea
less than 75% of all ocean water is the deep sea; an organism that inhabits has to deal with low temperature, high pressure, and low nutrient levels
What is the source of energy for phototrophs?
light energy excites electrons; excited molecules are electron donors
Why is phosphorus typically a limiting nutrient?
limits growth of aquatic photosynthetic autotrophs
What are the source of electrons for lithotrophs and organotrophs?
lithotrophs: inorganic molecules are electron donors organotrophs: organic molecules are electron donors
What are soils?
loose outer material of Earth's surfaces
What is biodeteriation?
loss of structural integrity of stone/concrete caused by microorganisms microorganisms can colonize surface of stone and row within certain stones (bacteria, archaea, fungi, algae, cyanobacteria)
What is the thermal death point?
lowest possible temperature that will achieve complete killing within 10 minutes
What are the two nutrients?
macro and micro
What are macronutrients?
major elements in cell macromolecules; C, O, H, N, P, S and ions that are necessary for protein function such as Mg, Ca, Fe, K
What is decontamination?
makes contaminated surfaces safe to handle by reducing the number of microbes present (sanitation)
What is stage 6/7 of endospore formation?
maturation/cell lysis; dehydrate cytoplasm; mother cell dies
What is the importance of fermentation for humans?
means of classifying bacteria; important source of solvent
What is a guild?
metabolically related microbial populations; sets of guilds form microbial communities that interact with macroorganisms and abiotic factors in the ecosystem
What are cofactors in enzymes?
metals and vitamins
What are the major end products of decomposition?
methane (CH4) and CO2
What is the biochemical oxygen demand (BOD) in freshwater?
microbial oxygen-consuming capacity of a body of water; increases with an influx of organic material then decreases over time
All ______ cycles are linked to the carbon cycle. Why?
nutrient; nitrogen and carbon are macronutrients
What is an overview of microbes in homes/public spaces?
microbiota inhabit air, dust, surfaces, ventilation/H2O systems that may expose us to pathogens but decrease overall exposure leading to allergies microbiota are very predictive in a family and changes within days due to a change of occupancy; flushing a toilet -> releases 100,000 bacteria into air; STD are unlikely to transmit through air because they are sensitive to dryness
What does water treatment include?
microorganisms that identify, remove, degrade pollutants
What is thermal death time?
minimum time to achieve complete killing in a liquid solution at a given temp
What is occurring in the death phase of the growth cycle?
more cells are dying than growing; cell number declines; doesn't enter 0
Description of viruses in oceans
most abundant microorganisms in oceans; concentration 10^8 in some areas; proteobacteria dominates
What is spectrophotometer?
most common; measures optical density, but still can not tell if cells are dead/alive; shines a red light through and measures how much can go through; solution must be 10^7-10^10 cells/mL
What are alkylators?
most toxic; damage proteins and DNA by adding carbon adducts; examples: formalin, glutaraldehyde, ethylene oxide; highly noxious; ethylene oxide used to sterilize products via gas
What uses lactic acid fermentation?
muscles, yogurt, sourdough bread (yeast and bacteria)
What is the choice of chemical treatment based on?
nature of object, microbes targeted, desired effect
What are emerging concerns needing tertiary water treatment?
new biological active pollutants released in treated/untreated sewage 1. pharmaceuticals 2. personal care products 3. household products 4. sunscreen new treatment systems have to degrade these chemicals
What are the 4 major nitrogen transformations?
nitrification, denitrification, anammox, and nitrogen fixation
What terminal electron acceptors are used for anaerobic respiration?
nitrogen compounds, sulfur compounds, metals (manganese/iron)
Which of these reactions is catalyzed by nitrogenase? a) N2 -> NH3 b) NH3 -> NO3 c) NO3 -> N2 d) NH3 + pyruvate -> alanine
nitrogenase is how we fix to make biologically available a) N2 -> NH3
What is occurring in the stationary phase of the growth cycle?
no net growth; cells are growing and dying; can be brief or long
What are iron sulfur proteins?
non-heme iron, cellular proteins, acid labile (ruins protein with acid), iron coordinated by Cys, electron carrier only
What are major marine phototrophs?
primary productivity in open oceans due to photosynthesis by prochlorophytes
What are endospores?
protect against bad conditions; disseminates cells; forms inside mother cell
Nearly all enzymes are _____, some ____
proteins, ribosomes
What is the most abundant microbe in the deep sea?
proteobacteria
What is the most abundant microbe in soil?
proteobacteria (gram-negative)
What is the equation for pyruvate dehydrogenase?
pyruvate + NAD+ + CoA -> acetyl CoA + CO2 + NADH + H+
What is the intracellular communication like in biofilms?
quorum sensing is critical in the development and maintenance of a biofilm; major intracellular signalling molecules are acylated homoserine lactones; intraspecies and interspecies signalling occurs
What is sulfide?
reacts with numerous metals; toxic to plants and animals
What is nitrification (basic)?
reduced NH3+ and oxidizes it to NO3
What is disinfection?
reduces number of pathogens on an inanimate surface
What is the primary purpose of fermentation?
regenerate NAD for reuse; the electron acceptor is an organic molecule
What are oxygen minimum zones (OMZ) in marine environments?
regions of oxygen-depleted waters at intermediate depths; high oxygen demand with nutrient rich areas; high levels of denitrification and anammox; these zones are expanding
What is enzyme nitrogenase?
related to natural nitrogen fixation; has atom of molybdenum which is linked to FeS cluster; transfers electrons to a needed electron donor
What is an overview of wasterwater treatment?
relies on industrial scale use of microbes for bioconversion; after treatment water to suitable for release into surface waters and released to drinking H2O purification facilities; primary/secondary/advanced tertiary
What does drinking water purification consist of?
removes pathogens, eliminates taste/odor, reduces chemicals, decreases turbidity
How is carbon dioxide returned to the atmosphere?
respiration and decomposition
What are reservoirs for calcium?
rocks and oceans
Compared to freshwater, marine environments are ____
saline and low in nutrients such as nitrogen, sulfur, and iron
What is the largest carbon reservoir?
sediments and rocks
Why do bacteria form biofilms?
self defense: allow cells to remain in favorable niches and bacterial cells to live in close association with one another biofilms resist physical forces that sweep away unattached cells, phagocytosis by immune system cells, penetration of toxins (antibiotics)
What is passive diffusion?
some gases such as O and CO2 pass freely through membranes; follows gradient of material
What does electron flow require?
source of electrons and an ultimate electron acceptor
What are benthic in freshwater?
species are attached to the bottom or sides of lakes and streams
What are 2 ways of distribution of microbes in their ecosystem?
species richness: total number of different species present species abundance: proportion of each species in an ecosystem microbial species richness and abundance are function of the kinds and amounts of nutrients available in a habitat
What is stage 2 of glycolysis?
splitting into 2 molecules double the reactant
What is stage 2 of entner-doudoroff?
splitting into 2 molecules gives one reactant
What is stage 5 of endospore formation?
spore coat; spores visible and become heat resistant; sporulation
What are the 2 cell types in the Caulobacter life cycle?
swarmer cell: motile, no division stalked cell: non-motile, cell division
What are the two movements of flagellar rotation?
symport (same direction as proton movement) antiport (opposite direction)
What are xenobiotics?
synthetic chemicals that are not naturally occurring; pesticides, polychlorinated biphenyls, munitions, dyes, chlorinated solvents
What do methanogens team up with?
syntrophs: supply them with necessary substrates such as hydrogen
What is nitrogen fixation (basic)?
taking N2 gas from the atmosphere and reducing it to form NH3 (only performed by bacteria)
What is stage 4 of entner-doudoroff?
the pay-off -> net yield of ATP by SLP
What is stage 4 of glycolysis?
the payoff -> net yield of ATP by SLP = 2 ATP
What is microbial leaching?
the removal of valuable metals such as copper from sulfide ores by microbial activities
What is biogeochemistry?
the study of biologically mediated chemical transformation
What is an ecosystem?
the sum of the total of all organisms and abiotic factors in a particular environment