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