3.2 Metabolic diversity Flashcards
describe general catabolism in chemoorganotrophs
- ie what pathways? (schéma!)
from glucose:
- glycolysis to 2 pyruvates –> than TCA cycles (intermediates go towards anabolism) –> 6 CO2
- glycolysis and TCA produce ATP (substrate level phos.) + [H] which reduce NAD+ into NADH
- NADH goes to respiratory chain, produces pmf which converts ADP to ATP (oxidative phosphorylation
- glucose can also to pentose phosphate pathway and make NADPH (reducing power for anabolism)
- can also form many C3, C4, C5, C6, C7 substances –> anabolism
metabolism of microorgs can be used to classify them into groups:
1. __________ requirement: 3 types
2. classify by 3 different things
OXYGEN REQUIREMENT
- aerobe: require O2 for growth (ie Legionella)
- anaerobe: oxygen NOT required for growth (Clostridium –> cannot live in presence of O2)
- facultative aerobe: O2 is not required but enhances growth rate (ie E.coli = versatile)
ENERGY: chemicals (chemotrophy) OR light (phototrophy)
ELECTRONS: organic compounds (ie glucose) (organotrophs) OR inorganic compounds (ie H2S) (lithotrophs)
CARBON: organic compounds (ie glucose) (heterotrophy) or inorganic compounds (ie CO2) (autotrophy)
describe what source of energy, electrons and carbon:
CHEMOORGANOHETEROTROPHS
CHEMOLITHOHETEROTROPHS
CHEMOLITHOAUTOTROPHS
PHOTOHETEROTROPHS
PHOTOAUTOTROPHS
- do they do aerobic or anaerobic respiration or photosynthesis?
- electron acceptors?
CHEMOORGANOHETEROTROPHS
- organic chemicals as source of E
- organic compounds as electron source/donor & carbon source
- both aerobic and anaerobic
- S^0, NO3-, SO4^2-, organic e- acceptors, O2
*ie protozoa, funghi, animal cells, most nonphotosynthesis bacteria
CHEMOLITHOHETEROTROPHS
- inorganic chemicals as source of E
- inorganic compounds (H2, H2S, Fe2+, NH4+) as electron source/donor
- organic chemical as carbon source
- both aerobic and anaerobic
- S^0, NO3-, SO4^2-,O2
*ie limnobacter thiooxidans
CHEMOLITHOAUTOTROPHS
- inorganic chemicals as source of E
- inorganic compounds (H2, H2S, Fe2+, NH4+) as electron source/donor
- inorganic chemical (CO2) as carbon source
*ie nitrifying bacteria, sulfur bacteria
PHOTOHETEROTROPHS
- light as E source
- organic or inorganic compound as e- donor
- organic chemical as C source
- e- donor: H2O, H2S
*purple non-sulfur bacteria
PHOTOAUTOTROPHS
- light as E source
- inorganic chemical as e- donor
- CO2 as C source
*ie algae, cyanobacteria, purple sulfur bacteria, green sulfur bacteria
what type of metabolism/energy, electron and carbon source/donor do they have:
SULFUR BACTERIA
PURPLE NONSULFUR BACTERIA
PURPLE SULFUR BACTERIA
SULFUR BACTERIA
- chemolitoautotroph:
- E: inorganic chemical
- e- donor: inorganic chemical
- C: CO2
PURPLE NONSULFUR BACTERIA
- phototheretotroph
E: light
e- donor: organic or inorganic chemical
C: organic chemical
PURPLE SULFUR BACTERIA
- photoautotroph
E: light
e- donor: inorganic chemical
C: CO2
what happens when your environment doesn’t contain oxygen? –> which type of respiration? explain how
anaerobic conditions: fermentation or anaerobic respiration
anaerobic respiration: used of other terminal electron acceptors than O2
- respiratory chain has specific cytochromes and proteins to allow use of specific terminal electron acceptors
which will make a bacteria/cell grow faster? –> put them in order from slowest to fastest (EXAM!)
- sulfate respiration (SO4^2-)
- denitrification
- aerobic respiration
- nitrate respiration (NO3-)
- sulfur respiration
higher up you’re on the tower, the worst/least amount of E you can get!
- sulfur respiration (highest up = lowest E)
- sulfate respiration
- nitrate respiration
- denitrification
- aerobic respiration (lowest on tower)
DENITRIFYING BACTERIA
- what are its sources of carbon, energy and electrons
- what are the most common terminal e- acceptors under anaerobic conditions
- what is denitrification? –> detrimental to what processes? vs beneficial for what?
- describe 4 reactions from nitrate to dinitrogen. which are gases?
- organic compounds!
- nitrogen compounds!
- NO, N2O and N2 are gasses –> lost to the environment = denitrification
- loss of nitrate to atmosphere = detrimental to agricultural processes; plants use nitrate as a source of nitrogen!
- beneficial for sewage treatment to remove nitrate –> nitrate stimulates algal growth in receiving water
nitrate (NO3-) –> nitrite (NO2-) –> nitric oxide (NO) –> Nitrous oxide (N2O) –> dinitrogen (N2)
NO, N2O and N2 are gases
how many protons can they pump if O2 vs no O2 present
- E.coli VS pseudomonas
E. COLI
- O2 as final e- acceptor –> 8 H+
- NO3- as final e- acceptor –> 6 H+ (less protons bc NO3- is higher on the tower) (from NO3- to NO2-)
PSEUDOMONAS:
- 8 H+ for O2 or NO3- (but very complicated denitrification system! –> from NO3- to N2)
SULFATE AND SULFUR REDUCTION
- source of C, E and e-?
- desulfovibrio can use (2) as terminal e- acceptor
- desulfovibrio can use (2) as an electron donor. when _________ is produced, more ATP is produced
- desulfuromonas uses WHAT as terminal e- acceptor and use (3) as e- donors
- what gives rotten egg smell? –> what doe sit also do?
- organic copounds!
- sulfate (SO4^2-) or sulfite (SO3^2-)
- organic (lactate) or inorganic (H2) as e- donor –> lactate! –> strip e- from lactate to pump H+ across membrane!
- use sulfur (S^0) as terminal e- acceptor and use acetate, ethanol and other organic compounds as e- donors
- H2S (sulfide) = egg small –> can turn mud flats black due to formation of metal sulfides
what are sources of sulfur compounds in environment? (4)
- volcanoes
- deep sea
- mining
- industry
H2S, S, S2O3^2-, SO4^2-, SO3^2-
PHOTOTROPHS
- all use ______ as E source
- who uses CO2 as C source? vs glucose/organic C?
- which bacteria as anoxygenic? vs oxygenic?
- what substance gives e- to make NADH (ie what substance is the reducing power) for anoxygenic vs oxygenic?
- what is something special about anoxygenic?
- what is used to generate pmf?
- light!
- photoautotrophs: CO2 VS photoheterotrophs: organic C
ANOXYGENIC:
- purple and green bacteria
- H2S (sulfide) and S^0 = e- donor! –> reduced to SO4^2-
- sulfate and sulfur reducers (ie reduce sulfate and sulfur to sulfide (H2S) allow anoxygenic phototrophs to have reducing power! so they live happily together!
OXYGENIC:
- cyanobacteria, algae, green plants
- H2O = e- donor –> reduced to 0.5 O2
- light energy!
- _____A______ are required for photosynthesis?
- how to differentiate ____A______?
light-sensitive pigments!
- each has a different absorption spectrum! and a different peak!
- ie chlorophyll a: peak at 680nm
- bacteriochlorophyll a: peak at 805 and 870nm
you have a sediment
- light shines on its top surface –> than there is a layer of green, than of purple, than sediments
- explain what type of bacteria are present on the sediment
GREEN LAYER:
- green bacteria (740 nm) + cyanobacteria (680nm, O2) –> both cannot absorb green, that’s why they look green
PURPLE LAYER:
- purple bacteria (830 nm) –> absorb wavelength that goes through the green rock
SEDIMENTS:
- there’s H2S produced by sulfate reducers –> used by phototrophs as reducing power
- also chemoheterotrophs and chemoautotrophs (don’t need light!)
- Chlorophyll or bacteriochlorophyll molecules are arranged in _________
containing (2) (not always). - do all pigments participate in photosynthesis?
- pigments that surround the _____________ act as ___________ to harvest light (LH) and ________ the energy to WHERE –> explain
- in photocomplexes –> other photosensitive pigments and proteins (not always).
- ponly a small fraction of the pigments participate directly in the photosynthesis reaction: the pigments in the reaction center (RC). Ex. P680, P700, P840.
- that surround reaction center act as antennae (light harvesting complex) –> funnel energy to the RC
*light harvesting complexes “exchange” the energy until one has enough high energy electron to become the reaction center (RC)
*RC –> than goes to electron transport system –> pmf to make ATP
Carotenoids are ___________, _______ –
sensitive _________ firmly embedded in the _____________ membrane.
- primary role?
Phycobilins form complexes with
_________ that are the main _________ in which bacteria? –> complex is called what?
- do they harvest light of same wavelengths than chlorophyll?
- hydrophobic, light sensitive pigment, embedded in photosynthetic membrane
- protect the system against bright light, which may lead to production of toxic forms of oxygen.
- proteins that are the main light-harvesting systems in cyanobacteria –> phycobilisomes
- harvest light of other wavelengths than chlorophyll –> complement each other yay!
SITE OF PHOTOSYNTHESIS
- in plants, algae (eukaryotes)?
where are chlorophylls? where is the pmf?
- in bacteria: where are photosynthetic pigments? –> 4 types ish
PLANTS/ALGAE:
- chloroplast!
- chlorophylls (+ light harvesting complex) are attached to membrane of thylakoid
- pmf is generated across thylakoid membrane: stroma (alkaline, negative) and intrathylakoid space (acid, positive bc H+)
BACTERIA:
- integrated into internal membranes!
a) in cytoplasmic membrane itself: heliobacteria
b) in intracytoplasmic membrane systems: purple bacteria (vesicles, lamellae) –> have vesicles!!!
c) in thylakoid membrane: cyanobacteria, prochlorophytes –> have thylakoid but no chloroplast
d) chlorosome: present in green sulfur bacteria (chlorobium) and green nonsulfur bacteria (chloroflexus)
what are chlorosomes?
- it is the best photosystem to do what?
- present in which bacteria?
giant antenna systems (proteins that hold lots of chlorophyll): Bchl c,d,e are arranged in rod like arrays in the chlorosome and transfer light energy to Bchl a in the reaction center
- it is the best photosystem to capture energy at very low light intensity
- present in green sulfur bacteria (chlorobium) and green nonsulfur bacteria (chloroflexus)
- green bacteria can colonize niches of very low light intensity, such as deep, anoxic aquatic habitat
anoxygenic photosynthesis: purple bacteria
- describe how ATP is produced
- which side of membrane is acid/alkaline and positive/negative?
- through cyclic photophosphorylation!: light is energy to renergize electrons! but e- are recycled!
- light shines on the membrane: antennaes funnel E to chlorophyll
- chlorophyll P870 (reaction center) is a good e- acceptor, until it accumulates so much energy that it becomes a good e- donor!
- once chlorophyll is a good e- donor (high on tower) –> gives e- to Q + H+ from cytoplasm –> shuttle e- to bc1 and pumps 2 H+ across membrane
- eventually, e- are shuttle back to P870 (low energy state now) = recycling of electrons!
- pumped protons across membrane create pmf which powers ATPase to make ATP!
periplasm/out = acid and positive bc H+ accumulation
cytoplasm = alkaline, negative
anoxygenic photosynthesis: green sulfur bacteria
- describe how ATP is produced?
- 2 systems run in parallel?
- consequence? reducing power electron source?
- cyclic photophosphorylation –> no need for e- donor, e- cycles through the system. produce pmf for ATP synthase (just like purple bacteria)
1. PMF –> ATP (electrons cycle and are recycled)
2. reduce NAD+, oxidize H2S - reducing power = need e- donor –> electrons are used to reduce NAD+ to NADH by ferredoxin –> because NAD+ steal e- to become NADH –> electron source becomes = oxidation of reduced sulfur compounds (H2S, S, S2O3)
ANOXYGENIC PHOTOSYNTHESIS: purple bacteria
- need electron source to do what (A)?
- that source is what for purple sulfur vs purple nonsulfur
- in purple bacteria, is energy of P870 enough to do (A) –> what happens then?
- consequence?
- to reduce NAD+!
purple sulfur: H2S
purple nonsulfur: succinate (organic compounds, photoheterotrophs, also used as a carbon source) - NOT enough to reduce NAD+ (bc too low on the tower)
- NADH is produced by REVERSE ELECTRON FLOW
1. pmf supply energy (less ATP will be produced) - pump so much H+ so that e- dont go to cytbc1 (bc pipe is blocked) –> so e- go up the tower to reduce NAD+ (ie pipe bursting)
2. electrons are transferred to complex 1 of respiratory chain (NADH dehydrogenase) which reduces NAD+ to NADH –> involves reversal of its normal function –> most enzymes are reversible - very low yield! many complexes will produce pmf, a few will produce NADH consuming pmf in the process (bc it requires a lot of energy to maintain pmf so high = bacteria will grow slowly)
what type of photosynthesis does purple bacteria vs green sulfur bacteria?
PURPLE bacteria; anoxygenic photosynthesis –> cyclic photophosphorylation + reverse electron flow
GREEN SULFUR bacteria: anoxygenic photosynthesis –> cyclic photophosphorylation
- sulfate reducer: sulfate = electron what?
- denitrifier: nitrate = electron what?
- in nitrate and sulfate reducers: how do you make NADPH for anabolic reactions?
- electron acceptors!
- electron acceptors!
- using pentose phosphate pathway!
- what type of photosynthesis does algae and cyanobacteria do?
- use what energy to oxidize WHAT?
- explain steps ish (5)
- oxygenic photosynthesis –> noncyclic photophosphorylation! pair of e- is used to produce PMF and NADPH
- light energy to oxidize H2O
H2O –> O2 + 2H+ + 2e-
1. H2O donates electron to P680 –> light energizes electron so they increase E (in photosystem II)
2. electrons (high energy now) go down electron transfer chain) –> through quinone pool –> pumps H+ = makes PMF
3. electrons go from photosystem II to photosystem I (a bit higher E than PSII), where light energizes electron
4. e- high energy now (higher than at 2)) –> go down ETC –> quinone –> makes PMF
5. e- fall down and produces NADH and NADPH
*PMF drives ATP synthase
oxygenic photosynthesis of algae and cyanobacteria:
- is it cyclic?
- what happens when reducing power is sufficient for cell’s needs? (ie enough NADH)
- better energy yield than purple and green bacteria?
- source of electron?
- usually noncyclic when electrons don’t come back to RC bc e- go to NADH VS
- when enough NADH, e- return to cytbf (part of PSII) –> no need to e- source –> cyclic phosphorylation!
- e- are then shuffled to PSI
- yes!
- water! –> produces H+ and O2 –> oxygenic phtosynthesis
oxygenic photosynthesis: which side is alakaline/negative vs acid and positive?
thylakoid lumen = accumulation of H+ = acid and positive
cyanobacteria = cytoplasm, –> chloroplast stroma –> alkaline and negative
what do some cyanobacteria have to do anoxygenic photosynthesis?
- source of e-?
- explain pathway steps (3 ish)
- cyclic or noncyclic?
- higher or lower yield than oxygenic photosynthesis?
- because sulfide (produced by sulfide reducers) inhibits photosystem II! so only PS I left
- oxidized H2S = electron source –> modified electron chain
- H2S donates e- to cytbf –> P700 of PSI
- light energizes electron –> goes down e- chain –> leads to the creation of PMF that drives ATP synthase
- cyclic if e- goes back to cyt bf (if enough reducing power)
- non-cyclic if NADPH accepts final electron
- lower! bc less pmf bc only PSI
what are chemoautotrophs?
- 2 examples
- electron acceptors?
- primary producers (bc can fix C)
- use inorganic compounds as source of E and e- + CO2 as carbon source
1) nitrifying bacteria (nitrosomonas and nitrobacter)
2) sulfur bacteria (thiobacillus - anaerobic: S^0, SO4^2-, NO3-
- aerobic: O2
NITRIFYING BACTERIA
- organisms that use WHAT (2) as electron donors –> which bacteria uses what?
- define nitrification
- what is a better source of N for plants?
- nitrification only occurs in what conditions?
- what are the benefits if low low yield?
- use inorganic N as e- donnors:
a) one group (nitrosomonas) oxidizes AMMONIA to nitrite
b) another group (nitrobacter) oxidizes nitrite to nitrate - nitrification = complete oxidation of ammonia to nitrate: NH3 –> NO2- –> NO3-
- nitrate is a better source! nitrite is toxic
- only in aerobic conditions! requires O2 bc nitrate is very low on tower –> O2 = only thing low enough to have enough difference to yield energy
- use something that nobody wants, don’t need to compete with other organisms, happy/content how they are
Nitrosomonas spp.
- final e- acceptor?
- ammonia monoxigenase needs # e- to oxidize ____________. supplied by WHAT?
- what is oxidized vs reduced?
- for every 4 e- generated from oxidation of NH3 to NO2- –> only # reach the cyt aa3, the proton pump
- NADH is produced by WHAT?
- high or low yield?
- O2
- 2e- to oxidize ammonia –> supplied by Q
- ammonia is oxidized. O2 is reduced
- 2 reach cytaa3
- reverse electron flow! Q –> back to complex 1 of respiratory chain. PMF is the energy source!
- very low yield! (2 ammonia = 1 ATP) –> 12 h for 1 duplication (vs 20min for E.coli)
nitrobacter spp.
- final e- acceptor?
- what is oxidized vs reduced?
- NADH is produced through what?
- high or low yield
- O2!
- nitrite (NO2-) is oxidized. O2 is reduced
- reverse electron flow! Q –> back to complex 1 of respiratory chain. PMF is the energy source!
- very low yield
SULFUR bacteria: thiobacillus sppl.
- source of e-?
- e- acceptor?
- produces (2) –> responsible for what?
- NADH is produced how?
- __________ oxidation occurs in steps, the first step yielding _____ –> stored in what?
- H2S, S^0, S2O3^2- –> bacteria oxidizes sulfur compounds!
(don’t confuse with sulfur reducers where sulfur compounds are electron acceptors!) - O2 = e- acceptor
- SO4^2- and protons (sulfuric acid) –> responsible for acidic run-off from coal mines
- by reverse electron flow
- sulfide (H2S) oxidation –> yields S^0 –> stored in cell inclusions and used as energy/e- source if bacteria is starving
- what is a methanogen?
- strict aerobes/anaerobes?
- found where? (4)
- 2 reactions
- microbes that produce methane!
- strict ANAEROBES! hate O2
found in marshes, anaerobic sediments, landfill sites, intestinal tract of animals (ie cows)
*don’t do fermentation or respiration!
source of e- and E: H2 and CO2
4 H2 + CO2 –> CH4 + 2H2O + E
CH3COOH (small organic acids) –> CH4 + CO2 + E
what are methanotrophs? are they chemoorganotrophs or chemolitotrophs?
- are strict aerobe/anaerobe?
- use what as source of C, E and e-?
- present where?
- reaction
microbes that burn methane! neither! bc methane is not organic (bc no O2)
- strict AEROBE!
- use CH4 as source of C, E and E (strip e- from CH4 –> e- go through ETC –> produce PMF –> ATPase)
- present in aerobic zones overlying anaerobic sediments (where methanogens live)
CH4 + 2O2 –> CO2 + 2H2O + E
fixation of CO2 –> what cycle?
- name photoautotrophs that do it
- name chemoautotrophs that do it
- where are enzymes found in eukaryotes vs prokaryotes?
- which enzyme?
- how much ATP and NADH do you need for 1 calvin cycle?
- CALVIN cycle!
- photoautotrophs: algae, cyanobacteria, purple sulfur and green sulfur bacteria
- chemoautotrophs: nitrifying bacteria, sulfur bacteria, some methanogens
- eukaryotes: stroma of chloroplast
- prokaryotes: cytoplasm
ribulose biphosphate carboxylase! –> convert 5C into 2 x 3C
- 12 NAD(P)H and 18 ATP –> need lots of energy and reducing power!
