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Bio 322 > Unit 2 > Flashcards

Unit 2 Flashcards

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1
Q

phototrophy

A

use of light energy

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2
Q

photosynthesis

A

metabolic process where light is used to drive metabolism
- energy of light converted to chemical

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3
Q

where does chemical energy come from in photosynthesis?

A

ATP and NADH

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4
Q

what is ATP and NADH used for?

A

fix CO2

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5
Q

autotrophic organisms

A

can fix CO2

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6
Q

photoautotrophic organisms

A

use light energy to start metabolism and fixes CO2

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7
Q

photoheterotrophic organisms

A

organisms that use light energy but CANNOT fix CO2

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8
Q

what do photoheterotrophic organisms use?

A

organic carbons sources

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9
Q

what do photoautotrophic organisms use?

A

co2 carbon source (inorganic)

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10
Q

kinds of photoautotrophic organisms

A

purple and green sulfur bacteria
cyanobacteria

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11
Q

kinds of photoheterotrophic organisms

A

purple and green NON sulfur bacteria

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12
Q

kinds of photosynthetic pigments

A

chlorophylls
bacteriochlorophylls
helper proteins
phycobiliproteins
carotenoids

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13
Q

antennae pigments

A

phycobiliprotein + carotenoids
- light harvesting center or chlorosomes

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14
Q

where are chlorosomes found?

A

green sulfur bacteria

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15
Q

where are antennae pigments found?

A

cyanobacteria
purple sulfur bacteria

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16
Q

what is a photocomplex made of?

A

chlorophylls/bacteriochlorophylls + helper proteins

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17
Q

what is a reaction center made of?

A

a few photocomplexes

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18
Q

what do antennae pigments surround?

A

reaction center

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19
Q

characteristics of purple sulfur bacteria?

A
  • anoxygenic photosynthesis
  • H2S oxidized (e donor)
  • S2 byproduct (deposited inside cell)
  • quinone based rxn center (P870)
  • runs reverse e flow
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20
Q

what does reverse electron flow do?

A

helps purple sulfur bacteria in energy generation
- form ATP and NADH

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21
Q

what is the light harvesting structure in purple sulfur bacteria?

A
  • bacteriochlorophylls a and b
  • photosynthetic membrane - lamellae/stacks
  • helper pigments (antennae pigments)
  • pigments embedded in stacks
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22
Q

green sulfur bacteria

A
  • anoxygenic photosynthesis
  • H2S oxidized (e donor)
  • S2 byproduct (deposited outside cell)
  • ferredoxin based reaction center (P840)
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23
Q

light harvesting strucutre for green sulfur bacteria

A
  • bacteriochlorophylls c,d,e
  • photosynthetic membrane - lamellae/stacks
  • helper pigments in chlorosomes
  • pigments in stacks
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24
Q

cyanobacteria

A
  • 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)
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25
Q

cyanobacteria light-harvesting structure

A
  • chlorophyll a
  • photosynthetic membrane - thylakoids
  • helper pigment - organized as antennae pigment
  • pigment in thylakoids
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26
Q

which bacteria uses the lowest light?

A

green

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27
Q

who is exposed to the light gradient?

A

green

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28
Q

what kind of sensory structures evolved in green bacteria?

A

chlorosomes

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29
Q

whats the function of carotenoids?

A

photoprotective agents
- absorb harmful light to prevent dangerous photooxidations

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30
Q

what colour are phycoerythrin?

A

red

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31
Q

what colour are phycocyanin?

A

blue

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32
Q

what are phycobilisomes?

A

phycobiliproteins organized into assemble into aggregates

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33
Q

what to phycobilisomes facilitate?

A

energy transfer to cyanobacterial reaction centers

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34
Q

what do phycobiliproteins allow cyanobacteria to do?

A

grow at lower light intensities

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35
Q

what happens to PSI if PSII is blocked in oxygenic phototrophs?

A

PSI takes role in cyanobacteria

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36
Q

what do cyanobacteria resemble?

A

anoxygenic photosynthesis
- uses H2S like green and purple sulfur bacteria

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37
Q

name a filamentous cyanobacteria

A

Oscillatoria limnetica
- lives in anoxic salt ponds
- oxidize H2S and create S
- along with purple and green sulfur

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38
Q

what kind of bacteria preceded cyanobactera?

A

purple and green sulfur bacteria

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39
Q

what was the first form of photosynthesis?

A

anoxygenic

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40
Q

what did the key evolutionary inventions of cyanobacteria connect?

A
  • connect 2 forms of reactions centers
  • evolve ability to use H2O as photosynthetic e donor
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41
Q

autotrophy

A

highly oxidized form of CO2 is reduced and assimilated into cell material

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42
Q

what are autotrophs

A

all phototrophs and chemolithotrophs

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43
Q

what do autotrophs do?

A

fix CO2

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44
Q

what kinds of bacteria use Calvin cycle?

A
  • cyanobacteria
  • purple sulfur
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45
Q

what bacteria uses hydroxypropionate cycle?

A

Chloroflexus

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46
Q

what was the earliest phototrophs?

A

Chloroflexus

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47
Q

what bacteria’s used reverse TCA cycle?

A

thermoproteus (Archaea)
sulfolobus
aquifex

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48
Q

what bacterias used wood-ljungdahl?

A

acetogens
methanogens

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49
Q

what are the autotrophic pahtways?

A

calvin
hydroxypropionate
reverse tca
wood-ljungdahl

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50
Q

what was one of the first autotrophic metabolisms?

A

hydroxypropionate

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51
Q

what was the most efficient pathway?

A

wood-ljungdahl

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52
Q

what was the youngest co2 fixation?

A

calvin

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53
Q

what was the most energetically expensive path?

A

calvin

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54
Q

carboxysomes

A

polyhedral structures or cell inclusions produced by autotrophs that operate with Calvin

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55
Q

what’s the function of carboxysomes?

A

concentrate CO2 in cell so its immediately available for RUBISCO

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56
Q

chemolithotrophs

A

use inorganic compounds to obtain energy for metabolic processes

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57
Q

what was the first form of energy conservation?

A

chemolithotrophy

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58
Q

how do we know chemolithotrophy was one of the first?

A

widespread among lineages near base of tree of B and A

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59
Q

what are the energy sources for chemolithotrophs?

A

H2S
NH4+
H2
Fe2+

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60
Q

what is the carbon source for chemolithotrophs?

A

CO2

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61
Q

what was one the oldest metabolic processes?

A

chemolithotrophy

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62
Q

hydrogen oxidation

A

B and A couple oxidation of H2 with reduction of various e acceptors

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63
Q

what are the e acceptors in H2 oxidation?

A

NO2
SO4
Fe3+
CO2

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64
Q

what do aerobic H2 oxidizing bacteria do?

A

H2 oxidizing bacteria that use O2 as terminal e acceptor

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65
Q

what did chemolithotrophs that use H2 develop?

A

enzyme hydrogenase

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66
Q

what did chemolithotrphs develop?

A

cytoplasmic hydrogenase-soluble enzyme
membrane-integrated hydrogenase

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67
Q

what organism modelled aerobic H2 oxidation?

A

Raistonia eutropha

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68
Q

what did colorless sulfur bacteria do?

A

reduced sulfur compounds as e donors
- anoxygenic photosynthesis

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69
Q

what are the reduced sulfur compounds used by colorless sulfur bacteria?

A

H2S
S

70
Q

what do chemolithotrophic iron bacteria oxidize?

A

ferrous iron

71
Q

what is the process of iron oxidation?

A
  • ferric iron spont produced forming insoluble ferric hydroxide
  • precipitates formed in aquatic enviro
  • reaction drives pH down
72
Q

why did iron bacteria become acidophilic?

A

acidification because of iron oxidation

73
Q

what are the best known iron bacteria?

A

Acidithiobacillus ferrooxidans
Leptospirillum ferrooxidans

74
Q

in nitrification aerobic conditions what do B and A oxidize?

A
  • oxidize NH3 to NO2-
75
Q

what is AOB and AOA

A

ammonia oxidizing bacteria
ammonia oxidizing archaea

76
Q

what do NOBs do?

A

full process of nitrification

77
Q

what do NOB oxidize?

A

nitrite to nitrate

78
Q

what do anammox do?

A

in anoxic condition they oxidize ammonia

79
Q

who performs anaerobic ammonia oxidation?

A

anammox

80
Q

what is a major anammox organism?

A

Brocadia anammoxidans

81
Q

what are characteristics of anammox?

A
  • lack peptidoglycan
  • cytoplasm contains membrane-enclosed compartments
82
Q

what is anammoxosome?

A
  • 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
83
Q

what do fermentative organisms create?

A

ATP and NADH

84
Q

whats the process fermentative organisms do?

A

substrate level phosphorylation

85
Q

primary fermenters

A

microbes that ferment sugars to make acids or alcohol as primary product

86
Q

secondary fermenters

A

use products of primary fermenters to generate gases important for other microbes (methanogens, sulfidogens, acetogens)

87
Q

what do fermentative organisms not do?

A

respire and run ETC

88
Q

homolactic fermentation

A
  • product is lactate
  • some have ethanol dehydrogenase and reduce pyruvate to ethanol
  • net gain = 2 ATP
    2 lactate per glucose molecule fermented
89
Q

heterofermentative

A

no aldolase
6C to 5C molecule
gain glyceraldehyde 3P, acetyl phosphate, lactate, ethanol

90
Q

stickland reaction formation

A

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

91
Q

peptostreptococci

A

plaque bacteria
complete glucose fermentation to produce free amino acids

92
Q

what is anaerobic respiration?

A

cell breaks down sugars to generate energy in absence of oxygen

93
Q

what molecule is the most efficient electron acceptor for respiration and why?

A

oxygen bc of high affinity for electrons

94
Q

what are the alternatives for oxygen in respiration?

A

no3
no2
so4
co2
h

95
Q

what is the worst compound for energy?

A

co2

96
Q

what is the mild-bad compound for energy?

A

s and h2s

97
Q

what is the best compound for energy?

A

o2

98
Q

what is a good compound for energy?

A

no3-

99
Q

in early earth was were the available energy sources?

A

h2s
h2
fe2+

100
Q

what did microorganisms do to the energy souces?

A

extract electrons and delivered it to alternative electron acceptors

101
Q

nitrate respiration

A

nitrate is electron acceptor
energy is oxidized

102
Q

assimilative reduction of nitrate

A

create organic compound

103
Q

dissimilative reduction of nitrate

A

create energy

104
Q

what is the process of nitrate respiration?

A

Nitrate - nitrite - nitric oxide - nitrous oxide - dinitrogen

105
Q

what enzyme is used for nitrate respiration?

A

reductases

106
Q

what is denitrification detrimental for?

A

agriculture

107
Q

what is denitrification beneficial for?

A

sewage treatment
- bacteria reduces nitrate to help remove toxic nitrogen compounds from sewage

108
Q

denitrifying microogranisms

A

proteobacteria- phylogenetically
facultative aerobes - physiologically

109
Q

Benthic foraminifer

A

eukaryotic denitrification
- foraminifers store large amounts of nitrate inside cell
- produce N2 from NO3-
- no associated denitrifying prokaryotes
- in mitochondria
- no oxygen

110
Q

what is fusarium

A

fungus
eukaryotic organism
- hybrid respiration

111
Q

what organisms perform nitrite reduction?

A

Anammox
Candidatus

112
Q

what are the characteristics of anammox?

A
  • nh4+ is the energy source - oxidized
  • no2- respiration - reduced
  • n2 and n2h2 is produced (toxic hydrazine)
  • pseudoorganelle anammoxosomes (surrounded by ladderane lipids)
113
Q

what are ladderane lipids?

A

cyclobutene ring attached to glycerol via ether and ester bond

114
Q

what are the characteristics of Candidatus?

A
  • methane is energy source - oxidized
  • no2- respired -reduced
  • produces n2 and o2
  • o2 used to activate methane oxidation
  • belongs to NC10 Phylum of Bacteria
115
Q

what does the fuel source have to be to respire sulfate?

A

highly energetic

116
Q

which 2 things are above sulfate?

A

organic substrates
H2

117
Q

what is created when oxidizing fuel source and reducing sulfates?

A

microbes create sulfides (H2S)

118
Q

microbes that create sulfides are called _____

A

sulfidogens or sulfate-reducing bacteria (SRB)

119
Q

sulfidogenesis

A

reduction of sulfate to create sulfide
- areas with highly concentrates organic matter

120
Q

ancient process of detox

A

add iron in area with sulfidogenesis
H2S reacts with ferric iron to form FeS2

121
Q

what are the characteristics of SRB?

A

energy source is organic or H2
sulfate is respired
h2s is produced
compete with methanogens for H2 as fuel source

122
Q

what is the process of sulfate reduction corrosions?

A
  • 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
123
Q

what are ANME?

A

anaerobic methane-oxidizing archaea
- consume methane

124
Q

what do ANME do?

A

use methane as energy source and respire sulfate
use NADH made by SRB
- electrons transferred to SRB - sulfate reduction results in H2S forming

125
Q

what do SRB do?

A

use organics and respire sulfate
creates energy

126
Q

what is oxidized in acetogenesis?

A

H2

127
Q

sulfur cycle

A

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

128
Q

what is fixed in acetogenesis?

A

co2 is respired

129
Q

what is hydrogenase?

A

extracts energy from H2 fuel that helps in CO2 fixation

130
Q

what is CO2 dehydrogenase?

A

reduces fixed CO2 and creates acetate

131
Q

what is methanogenesis?

A
  • consumes H2 and CO2
  • generate methane
132
Q

what category to methanogens belong to?

A

archaea

133
Q

what are the 2 important metals respired in metal reduction?

A

ferric iron and manganic iron

134
Q

what are the 2 famous iron reducers?

A

shewanella
geobacter

135
Q

what do metal reducers use?

A

organic energy source and H2

136
Q

nanowires are made of what?

A

cytochrome that protrude membrane and respire solids outside

137
Q

Shewanella and Geobacter are what?

A

nanowires

138
Q

who carries out the simplest anaerobic respiration?

A

Pyrococcus furiosus

139
Q

at what temp to Pyrococcus furiosus grow at?

A

100

140
Q

what do Pyrococcus furiosus respire?

A

H+
- modified glycolytic pathway

141
Q

what does Desulfotomaculum perform?

A

arsenate and sulfate reduction

142
Q

what does the process of arsenate and sulfate reduction generate?

A

As2S3 (orpiment)

143
Q

hydrocarbons

A

organic compound consisting of hydrogen and carbon
- crude oil, natural gas and coal
- highly combustible and main energy source
- great electron donors

144
Q

what do hydrocarbons need to be activated with?

A

o2

145
Q

what enzymes are used in oxygenation?

A

monooxygenase
dioxygenase

146
Q

how does monooxygenase work?

A

incorporates one atom of oxygen in organic compound

147
Q

how does dioxygenase work?

A

incorporates both o2 atoms into molecule

148
Q

what is the metabolic product of aliphatic hydrocarbons?

A

fatty acids

149
Q

examples of aliphatic hydrocarbons

A

alkanes (methane)
alkenes
alkines

150
Q

what are aromatic hydrocarbons?

A

aromatic hydrocarbons that go through initial stage of catechol formation

151
Q

what are the carbon and energy source for bacteria methylotrophs?

A

methane and other C1 compounds

152
Q

methanotrophs

A

bacteria that use methane

153
Q

t or f: oxidation of methane/methanol by methanotrophs is aerobic?

A

true

154
Q

what is the key enzyme in methane metabolism?

A

methane monooxygenase (MMO)

155
Q

2 groups of formaldehyde methanotrophs

A

Gammaproteobacterial methanotrophs - Ribuloso monophosphate cycle (RuMP)
Alphaproteobacterial methanotrophs - Serine cycle

156
Q

what is a special type of methanotroph?

A

Verrucomicrobia methanotrophs
- low pH, high temp, assimilate CO2 via Calvin

157
Q

what 2 organisms work together in anaerobic methane degradation?

A

SRB and ANME

158
Q

what can ANME utilize?

A

Sulfate
Nitrate

159
Q

what do Candidatus Methanoperedens nitroreducens do?

A

respire nitrate
produces nitrite
feeds Anammox with nitrites

160
Q

Methylomonas denitrificans sp. strain FJG1

A

gammaproteobacterial methanotrophs
uses nitrate (respiration)
produce N2O if respiring nitrate

161
Q

if sulfate, nitrate and nitrite aren’t available what do methanotrophs respire?

A

iron 3+
manganese Mn4+

162
Q

Winogradsky column

A

prokaryotic are very diverse
recycle all mineral elements for life support
- Winogradsky and Beijerinck

163
Q

who studied pure culture?

A

Pasteur and Koch

164
Q

what’s the order of bacteria in column

A

bottom:
Clostridium
Desulfovirbrio
purple and green sulfur bacteria
non sulfur purple and green bacteria
cyanobacteria

165
Q

what promotes rapid microbial growth?

A

cellulose
- microbes degrade and consume all oxygen

166
Q

process in Clostridium

A

cellulose to glucose to organic acid/CO2

167
Q

process in Desulfovibrio

A

organic acid from 1 as energy
respires sulfate
creates sulfides (H2S)
- use fermentation products as energy source and respires sulfate on the bottom

168
Q

process in purple/green sulfur bacteria

A

light to start anoxygenic photosynthesis
uses H2S made by Desulfovibrio
fixes CO2
- non sulfur

169
Q

process in non sulfur purple and green bacteria

A

light from top
uses organics from 1
no co2 fixation

170
Q

process in cyanobacteria

A

oxygenic photosynthesis

171
Q

how is life on earth categorized into?

A

phototrophs- energy from light
chemotrophs - organic or inorganic
autotrophs- carbon for cellular synthesis from co2
heterotrophs - carbon for cellular synthesis from organic compounds

172
Q

hydroxylase

A

c5-c16, fatty acids, alkyl benzenes and cycloalkanes
- pseudomonas

Bio 322 (11 decks)

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