Unit 2 Flashcards
phototrophy
use of light energy
photosynthesis
metabolic process where light is used to drive metabolism
- energy of light converted to chemical
where does chemical energy come from in photosynthesis?
ATP and NADH
what is ATP and NADH used for?
fix CO2
autotrophic organisms
can fix CO2
photoautotrophic organisms
use light energy to start metabolism and fixes CO2
photoheterotrophic organisms
organisms that use light energy but CANNOT fix CO2
what do photoheterotrophic organisms use?
organic carbons sources
what do photoautotrophic organisms use?
co2 carbon source (inorganic)
kinds of photoautotrophic organisms
purple and green sulfur bacteria
cyanobacteria
kinds of photoheterotrophic organisms
purple and green NON sulfur bacteria
kinds of photosynthetic pigments
chlorophylls
bacteriochlorophylls
helper proteins
phycobiliproteins
carotenoids
antennae pigments
phycobiliprotein + carotenoids
- light harvesting center or chlorosomes
where are chlorosomes found?
green sulfur bacteria
where are antennae pigments found?
cyanobacteria
purple sulfur bacteria
what is a photocomplex made of?
chlorophylls/bacteriochlorophylls + helper proteins
what is a reaction center made of?
a few photocomplexes
what do antennae pigments surround?
reaction center
characteristics of purple sulfur bacteria?
- anoxygenic photosynthesis
- H2S oxidized (e donor)
- S2 byproduct (deposited inside cell)
- quinone based rxn center (P870)
- runs reverse e flow
what does reverse electron flow do?
helps purple sulfur bacteria in energy generation
- form ATP and NADH
what is the light harvesting structure in purple sulfur bacteria?
- bacteriochlorophylls a and b
- photosynthetic membrane - lamellae/stacks
- helper pigments (antennae pigments)
- pigments embedded in stacks
green sulfur bacteria
- anoxygenic photosynthesis
- H2S oxidized (e donor)
- S2 byproduct (deposited outside cell)
- ferredoxin based reaction center (P840)
light harvesting strucutre for green sulfur bacteria
- bacteriochlorophylls c,d,e
- photosynthetic membrane - lamellae/stacks
- helper pigments in chlorosomes
- pigments in stacks
cyanobacteria
- oxygenic photosynthesis
- H2O oxidized (e donor)
- O2 byproduct ( deposited outside cell)
- quinone and ferredoxin based rxn center
- PSII (P680)- quinone based (similar to purple sulfur)
- PSI (P700)- ferredoxin based (similar to green sulfur)
cyanobacteria light-harvesting structure
- chlorophyll a
- photosynthetic membrane - thylakoids
- helper pigment - organized as antennae pigment
- pigment in thylakoids
which bacteria uses the lowest light?
green
who is exposed to the light gradient?
green
what kind of sensory structures evolved in green bacteria?
chlorosomes
whats the function of carotenoids?
photoprotective agents
- absorb harmful light to prevent dangerous photooxidations
what colour are phycoerythrin?
red
what colour are phycocyanin?
blue
what are phycobilisomes?
phycobiliproteins organized into assemble into aggregates
what to phycobilisomes facilitate?
energy transfer to cyanobacterial reaction centers
what do phycobiliproteins allow cyanobacteria to do?
grow at lower light intensities
what happens to PSI if PSII is blocked in oxygenic phototrophs?
PSI takes role in cyanobacteria
what do cyanobacteria resemble?
anoxygenic photosynthesis
- uses H2S like green and purple sulfur bacteria
name a filamentous cyanobacteria
Oscillatoria limnetica
- lives in anoxic salt ponds
- oxidize H2S and create S
- along with purple and green sulfur
what kind of bacteria preceded cyanobactera?
purple and green sulfur bacteria
what was the first form of photosynthesis?
anoxygenic
what did the key evolutionary inventions of cyanobacteria connect?
- connect 2 forms of reactions centers
- evolve ability to use H2O as photosynthetic e donor
autotrophy
highly oxidized form of CO2 is reduced and assimilated into cell material
what are autotrophs
all phototrophs and chemolithotrophs
what do autotrophs do?
fix CO2
what kinds of bacteria use Calvin cycle?
- cyanobacteria
- purple sulfur
what bacteria uses hydroxypropionate cycle?
Chloroflexus
what was the earliest phototrophs?
Chloroflexus
what bacteria’s used reverse TCA cycle?
thermoproteus (Archaea)
sulfolobus
aquifex
what bacterias used wood-ljungdahl?
acetogens
methanogens
what are the autotrophic pahtways?
calvin
hydroxypropionate
reverse tca
wood-ljungdahl
what was one of the first autotrophic metabolisms?
hydroxypropionate
what was the most efficient pathway?
wood-ljungdahl
what was the youngest co2 fixation?
calvin
what was the most energetically expensive path?
calvin
carboxysomes
polyhedral structures or cell inclusions produced by autotrophs that operate with Calvin
what’s the function of carboxysomes?
concentrate CO2 in cell so its immediately available for RUBISCO
chemolithotrophs
use inorganic compounds to obtain energy for metabolic processes
what was the first form of energy conservation?
chemolithotrophy
how do we know chemolithotrophy was one of the first?
widespread among lineages near base of tree of B and A
what are the energy sources for chemolithotrophs?
H2S
NH4+
H2
Fe2+
what is the carbon source for chemolithotrophs?
CO2
what was one the oldest metabolic processes?
chemolithotrophy
hydrogen oxidation
B and A couple oxidation of H2 with reduction of various e acceptors
what are the e acceptors in H2 oxidation?
NO2
SO4
Fe3+
CO2
what do aerobic H2 oxidizing bacteria do?
H2 oxidizing bacteria that use O2 as terminal e acceptor
what did chemolithotrophs that use H2 develop?
enzyme hydrogenase
what did chemolithotrphs develop?
cytoplasmic hydrogenase-soluble enzyme
membrane-integrated hydrogenase
what organism modelled aerobic H2 oxidation?
Raistonia eutropha
what did colorless sulfur bacteria do?
reduced sulfur compounds as e donors
- anoxygenic photosynthesis
what are the reduced sulfur compounds used by colorless sulfur bacteria?
H2S
S
what do chemolithotrophic iron bacteria oxidize?
ferrous iron
what is the process of iron oxidation?
- ferric iron spont produced forming insoluble ferric hydroxide
- precipitates formed in aquatic enviro
- reaction drives pH down
why did iron bacteria become acidophilic?
acidification because of iron oxidation
what are the best known iron bacteria?
Acidithiobacillus ferrooxidans
Leptospirillum ferrooxidans
in nitrification aerobic conditions what do B and A oxidize?
- oxidize NH3 to NO2-
what is AOB and AOA
ammonia oxidizing bacteria
ammonia oxidizing archaea
what do NOBs do?
full process of nitrification
what do NOB oxidize?
nitrite to nitrate
what do anammox do?
in anoxic condition they oxidize ammonia
who performs anaerobic ammonia oxidation?
anammox
what is a major anammox organism?
Brocadia anammoxidans
what are characteristics of anammox?
- lack peptidoglycan
- cytoplasm contains membrane-enclosed compartments
what is anammoxosome?
- cells of B. anammoxidans in compartment
- membrane-enclosed structure surrounded by ladderane lipids- prevent leakage of toxic metabolic products from structure
- from ammonium and nitrite toxic hydrazine produced
what do fermentative organisms create?
ATP and NADH
whats the process fermentative organisms do?
substrate level phosphorylation
primary fermenters
microbes that ferment sugars to make acids or alcohol as primary product
secondary fermenters
use products of primary fermenters to generate gases important for other microbes (methanogens, sulfidogens, acetogens)
what do fermentative organisms not do?
respire and run ETC
homolactic fermentation
- product is lactate
- some have ethanol dehydrogenase and reduce pyruvate to ethanol
- net gain = 2 ATP
2 lactate per glucose molecule fermented
heterofermentative
no aldolase
6C to 5C molecule
gain glyceraldehyde 3P, acetyl phosphate, lactate, ethanol
stickland reaction formation
prevents dental caries
amino acid 1 - e donor (alanine)
amino acid 2 - e acceptor (glycine)
proline in saliva
- promoted between free proline and amino acids made by plaque bacteria
- product is delta- NH2 valeric acid- degraded to ammonia
peptostreptococci
plaque bacteria
complete glucose fermentation to produce free amino acids
what is anaerobic respiration?
cell breaks down sugars to generate energy in absence of oxygen
what molecule is the most efficient electron acceptor for respiration and why?
oxygen bc of high affinity for electrons
what are the alternatives for oxygen in respiration?
no3
no2
so4
co2
h
what is the worst compound for energy?
co2
what is the mild-bad compound for energy?
s and h2s
what is the best compound for energy?
o2
what is a good compound for energy?
no3-
in early earth was were the available energy sources?
h2s
h2
fe2+
what did microorganisms do to the energy souces?
extract electrons and delivered it to alternative electron acceptors
nitrate respiration
nitrate is electron acceptor
energy is oxidized
assimilative reduction of nitrate
create organic compound
dissimilative reduction of nitrate
create energy
what is the process of nitrate respiration?
Nitrate - nitrite - nitric oxide - nitrous oxide - dinitrogen
what enzyme is used for nitrate respiration?
reductases
what is denitrification detrimental for?
agriculture
what is denitrification beneficial for?
sewage treatment
- bacteria reduces nitrate to help remove toxic nitrogen compounds from sewage
denitrifying microogranisms
proteobacteria- phylogenetically
facultative aerobes - physiologically
Benthic foraminifer
eukaryotic denitrification
- foraminifers store large amounts of nitrate inside cell
- produce N2 from NO3-
- no associated denitrifying prokaryotes
- in mitochondria
- no oxygen
what is fusarium
fungus
eukaryotic organism
- hybrid respiration
what organisms perform nitrite reduction?
Anammox
Candidatus
what are the characteristics of anammox?
- nh4+ is the energy source - oxidized
- no2- respiration - reduced
- n2 and n2h2 is produced (toxic hydrazine)
- pseudoorganelle anammoxosomes (surrounded by ladderane lipids)
what are ladderane lipids?
cyclobutene ring attached to glycerol via ether and ester bond
what are the characteristics of Candidatus?
- methane is energy source - oxidized
- no2- respired -reduced
- produces n2 and o2
- o2 used to activate methane oxidation
- belongs to NC10 Phylum of Bacteria
what does the fuel source have to be to respire sulfate?
highly energetic
which 2 things are above sulfate?
organic substrates
H2
what is created when oxidizing fuel source and reducing sulfates?
microbes create sulfides (H2S)
microbes that create sulfides are called _____
sulfidogens or sulfate-reducing bacteria (SRB)
sulfidogenesis
reduction of sulfate to create sulfide
- areas with highly concentrates organic matter
ancient process of detox
add iron in area with sulfidogenesis
H2S reacts with ferric iron to form FeS2
what are the characteristics of SRB?
energy source is organic or H2
sulfate is respired
h2s is produced
compete with methanogens for H2 as fuel source
what is the process of sulfate reduction corrosions?
- assimilative: satisfy sulfur needs
- dissimilatory metabolism: create H2S
- microbes consume O2 at metal surface
- metal surface become O2 depleted
- SRB occupy anaerobic area
- SRB reduces SO4 and creates H2S
- H2S reacts with metals forming metal-sulfides
- metal sulfides create corrosions
- coating constructions prevent microbial biofilms to reduce corrosion
what are ANME?
anaerobic methane-oxidizing archaea
- consume methane
what do ANME do?
use methane as energy source and respire sulfate
use NADH made by SRB
- electrons transferred to SRB - sulfate reduction results in H2S forming
what do SRB do?
use organics and respire sulfate
creates energy
what is oxidized in acetogenesis?
H2
sulfur cycle
DMSP molecule made by marine algae
- microorganisms degrade DMSP and create DMS
- DMS highly produced in ocean
- DMS e donor
- photooxidation of DNS creates aerosols with SO2, SO4, methane-sulfonate
- compounds contribute to global cooling
what is fixed in acetogenesis?
co2 is respired
what is hydrogenase?
extracts energy from H2 fuel that helps in CO2 fixation
what is CO2 dehydrogenase?
reduces fixed CO2 and creates acetate
what is methanogenesis?
- consumes H2 and CO2
- generate methane
what category to methanogens belong to?
archaea
what are the 2 important metals respired in metal reduction?
ferric iron and manganic iron
what are the 2 famous iron reducers?
shewanella
geobacter
what do metal reducers use?
organic energy source and H2
nanowires are made of what?
cytochrome that protrude membrane and respire solids outside
Shewanella and Geobacter are what?
nanowires
who carries out the simplest anaerobic respiration?
Pyrococcus furiosus
at what temp to Pyrococcus furiosus grow at?
100
what do Pyrococcus furiosus respire?
H+
- modified glycolytic pathway
what does Desulfotomaculum perform?
arsenate and sulfate reduction
what does the process of arsenate and sulfate reduction generate?
As2S3 (orpiment)
hydrocarbons
organic compound consisting of hydrogen and carbon
- crude oil, natural gas and coal
- highly combustible and main energy source
- great electron donors
what do hydrocarbons need to be activated with?
o2
what enzymes are used in oxygenation?
monooxygenase
dioxygenase
how does monooxygenase work?
incorporates one atom of oxygen in organic compound
how does dioxygenase work?
incorporates both o2 atoms into molecule
what is the metabolic product of aliphatic hydrocarbons?
fatty acids
examples of aliphatic hydrocarbons
alkanes (methane)
alkenes
alkines
what are aromatic hydrocarbons?
aromatic hydrocarbons that go through initial stage of catechol formation
what are the carbon and energy source for bacteria methylotrophs?
methane and other C1 compounds
methanotrophs
bacteria that use methane
t or f: oxidation of methane/methanol by methanotrophs is aerobic?
true
what is the key enzyme in methane metabolism?
methane monooxygenase (MMO)
2 groups of formaldehyde methanotrophs
Gammaproteobacterial methanotrophs - Ribuloso monophosphate cycle (RuMP)
Alphaproteobacterial methanotrophs - Serine cycle
what is a special type of methanotroph?
Verrucomicrobia methanotrophs
- low pH, high temp, assimilate CO2 via Calvin
what 2 organisms work together in anaerobic methane degradation?
SRB and ANME
what can ANME utilize?
Sulfate
Nitrate
what do Candidatus Methanoperedens nitroreducens do?
respire nitrate
produces nitrite
feeds Anammox with nitrites
Methylomonas denitrificans sp. strain FJG1
gammaproteobacterial methanotrophs
uses nitrate (respiration)
produce N2O if respiring nitrate
if sulfate, nitrate and nitrite aren’t available what do methanotrophs respire?
iron 3+
manganese Mn4+
Winogradsky column
prokaryotic are very diverse
recycle all mineral elements for life support
- Winogradsky and Beijerinck
who studied pure culture?
Pasteur and Koch
what’s the order of bacteria in column
bottom:
Clostridium
Desulfovirbrio
purple and green sulfur bacteria
non sulfur purple and green bacteria
cyanobacteria
what promotes rapid microbial growth?
cellulose
- microbes degrade and consume all oxygen
process in Clostridium
cellulose to glucose to organic acid/CO2
process in Desulfovibrio
organic acid from 1 as energy
respires sulfate
creates sulfides (H2S)
- use fermentation products as energy source and respires sulfate on the bottom
process in purple/green sulfur bacteria
light to start anoxygenic photosynthesis
uses H2S made by Desulfovibrio
fixes CO2
- non sulfur
process in non sulfur purple and green bacteria
light from top
uses organics from 1
no co2 fixation
process in cyanobacteria
oxygenic photosynthesis
how is life on earth categorized into?
phototrophs- energy from light
chemotrophs - organic or inorganic
autotrophs- carbon for cellular synthesis from co2
heterotrophs - carbon for cellular synthesis from organic compounds
hydroxylase
c5-c16, fatty acids, alkyl benzenes and cycloalkanes
- pseudomonas
