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NRSC 333 > 4. Bioenergetics > Flashcards

4. Bioenergetics Flashcards

1
Q

What is ATP? (loosely)

A

chemical energy

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2
Q

What are the two sets of reactions within metabolism?

A

Catabolic and anabolic reactions

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3
Q

What does TEA stand for?

A

Terminal electron acceptor

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4
Q

What are the electron donors for eukaryotes?

A

Organic compounds

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5
Q

What is the terminal electron acceptor for eukaryotes?

A

O2

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6
Q

What are the electron donors for lithoautotrophic prokaryotes?

A

H2, H2S, …

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7
Q

What is the terminal electron acceptor for lithoautotrophic prokaryotes?

A

Fe(OH)3

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8
Q

What does litho mean?

A

The electron source (donors) are inorganic

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9
Q

What does auto mean?

A

Doesn’t require organic carbon, it fixes its own CO2 to assemble it into organic molecules for itself

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10
Q

How do microbes obtain energy? (Get ATP)

A

By doing a complex set of redox reactions (redox = oxidation reduction reactions)

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11
Q

What is anabolism?

A

Biochemical reactions involved in the synthesis of compounds and macromolecules such as proteins and nucleic acids

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12
Q

What is catabolism?

A

Biochemical reactions that break down compounds, mostly to allow the cell to generate chemical energy

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13
Q

What are examples of catabolism? (2)

A
  • oxidation of carbohydrates (sugars) during respiration (aerobic or anaerobic)
  • fermentation
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14
Q

What happens if glucose is the main nutrient for a bacterium?

A

It will first be transported across the membrane, and then it will be oxidised to CO2

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15
Q

Which is related to biodegradation, anabolism or catabolism?

A

Catabolism

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16
Q

What is mineralization?

A

Conversion of organic compounds to CO2 and water

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17
Q

What are the three main steps of mineralization?

A
  1. Glycolysis
  2. Krebs Cycle or Citric Acid Cycle (ticarboxylic acids cycle; TCA)
  3. Oxidative phosphorylation (creating the proton motive force)
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18
Q

What is glycolysis?

A
  • Breaking down of glucose into 2 molecules of pyruvate.
  • Reactants = glucose
  • Products = pyruvate, ATP (energy), NADH, and water
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19
Q

What is the Krebs cycle / tricarboxylic acids cycle

A
  • The complete combustion of pyruvate to CO2 through a cyclic set of reactions (which are the TCA).
  • During this cycle, the pyruvate will be decarboxylated, leading to the production of CO2
  • Reactant = pyruvate
  • Products = ATP, NADH
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20
Q

What is oxidative phosphorylation?

A
  • The reduction of coenzymes (NADH, FADH) that will be further oxidized in the respiratory chain (electron transport system, ETS)
  • This produces the proton motive force
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21
Q

What is the electron transport chain / system? (ETC / ETS)

A

Electrons flow from reduced coenzymes (NAD, FAD) to a terminal electron acceptor such as O2

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22
Q

What does the ETC cause?

A

The flow of electrons down the chain causes some of the ETC complexes to pump protons (H+) out of the cell resulting in a protein gradient, also known as the Proton Motive Force (PMF)

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23
Q

What is the proton gradient?

A

A form of electrical energy used by the cell to synthesize ATP.
(it can also allow the cell to do membrane transport, etc)

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24
Q

Why do microbes biodegrade pollutants? (2)

A
  • Because it produces ATP and NADH, so the pollutants are important sources of energy
  • They also use the elements that they strip off to build structures
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25
Q

Can bacteria have different types of terminal electron acceptors besides O2?

A

Yes e.g. nitrate

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26
Q

What is cellular respiration?

A

Process by which cells release energy by breaking down organic or inorganic molecules

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27
Q

What are the two types of cellular respiration?

A

Aerobic and anaerobic

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28
Q

What is aerobic respiration?

A
  • Cells break down the glucose molecule and convert it to ATP in presence of O2.
  • Is the primary energy-yielding process of all living organisms
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29
Q

What is anaerobic respiration?

A
  • Cells break down the glucose molecule and convert it to ATP in absence of O2.
  • Most primitive form of respiration on Earth
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30
Q

What is aerobic respiration in more details and steps? (6 points)

A
  • Uses O2 as terminal electron acceptor
  • Reducing power (NADH etc) generated by oxidation of energy source
  • Electrons transferred to ETC, then to terminal electron acceptor (TEA) O2 → H2O
  • Results in proton (H+)/pH gradient
  • H+ gradient fuels processes like ATP synthesis
  • The overall process is called oxidative phosphorylation
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31
Q

What is anaerobic respiration in more detail?

A
  • Electrons transferred to compounds other than O2
  • Dissimilatory nitrate reduction (denitrification): NO3 -
  • Dissimilatory sulfate reduction: SO4 -
  • Complex membrane-bound enzymes
  • Reduction of the TEA may occur in periplasm rather than cytoplasm, but the effect is the same (electrons transferred, protons pumped, PMF created…)
  • Some organic compounds may serve as terminal electron acceptors in anaerobic respiration
    *Fumarate → succinate via fumarate reductase
    *Membrane-bound enzyme (part of ETC)
    *This is not the same as fermentation
  • Methanogenesis is similar
  • Transfer of electrons to CO2 yielding waste CH4
32
Q

Why are there different electron acceptors besides O2

A
  • Because different TEA are available in different niches
  • Their availability can differ with depth
33
Q

Are the use of different TEA in energy generation key parts of major biogeochemical cycles (C,N,S)?

A

yes

34
Q

What is an example of TEA many organisms use

A

Many organisms utilize metallic terminal electron acceptors (i.e., MnO2, Fe(OH3)), which also vary with depth

35
Q

Can organisms use more than one compound as TEA?

A

Some organisms may only be able to utilize one compound, others may be able to utilize more than one, but usually from adjacent zones only

36
Q

Why are aerobic and anaerobic respiration important to biodegradation? (5 points)

A
  • Most organic pollutants are better degraded aerobically
  • Aerobic respiration is generally faster and more efficient and results in more complete oxidation to CO2
  • However, anaerobic degradation steps are also very important in the biodegradation of some pollutants
  • The ability of bacteria to do this in the absence of O2 makes them extremely useful for biodegradation as many contaminated environments quickly become anaerobic
  • Thus, pollutant biodegradation is not limited by O2 as long as there is an alternative terminal electron acceptor and lots of it!
37
Q

How is the soil a heterogenous microbial habitat? (5 points)

A
  • Contains both aerobic and anaerobic zones, varies greatly, even within a soil aggregate
  • Different micro-habitats and food sources
  • O2 concentration decreases with depth in a soil
  • O2 concentration decreases towards the center of a soil particle due to diffusion, and utilization of O2 on the surface (before it can diffuse in).
  • And thus becomes anaerobic!
38
Q

Environmental heterogeneity (6 points)

A
  • Environmental systems are not homogenous: soil or sediment
  • Development of O2 microelectrodes in the 1980’s → became obvious that microgradients were important in nature
  • i. e. the use of these microelectrodes in sediment demonstrated that O2 may be completely depleted within 1 mm
  • Similar observations were obtained in soil granules, where the centers of such granules are severely depleted in O2
  • This rapid decrease of O2 may be explain by a consumption greater than the amount provided through diffusion, since no O2 is produces in sediment or soil below the surface
  • Depletion of O2 lead to anaerobic conditions, where a number of other bacterial populations become active
39
Q

What are some examples of bacteria that use different TEAs? (6)

A
  • denitrifers
  • iron-reducing bacteria
  • manganese-reducing bacteria
  • sulfate-reducing bacteria
  • methanogenic archaea
  • fermenters
40
Q

What do denitrifers use as a TEA?

A

NO3-

41
Q

When denitrifers reduces NO3-, what products does it make (e.g.) (2)

A

N2O and N2

42
Q

What are two examples of names of bacteria that are denitrifiers?

A

Pseudomonas and Alcaligenes

43
Q

What do iron-reducing bacteria use as TEA?

A

Iron lol

44
Q

What do manganese-reducing bacteria use as TEA?

A

Manganese lol

45
Q

What is an example of an iron reducing bacteria (name)?

A

Geobacter metallireducens GS15

46
Q

What do sulfate-reducing bacteria use as TEA?

A

Sulfate! (SO₄²-)

47
Q

What are some examples of sulfate reducing bacteria? (3)

A

Desulfovibrio, Desulfuromonas, Desulfosarcina

48
Q

What do methanogenic archaea use as TEA?

A

CO2

49
Q

What do methanogenic archaea use as energy or electron source (2 options)

A

H2 or ferment acetate

50
Q

What do fermenters use as TEA? (general)

A

organic molecules

51
Q

What are some products of fermentation (5)

A

Acetate, formate, butyrate, lactate, succinate, caproate, …

52
Q

What is an example of a fermenting bacteria?

A

Clostridium

53
Q

What is so interesting about Shewanella oneidensis?

A
  • It is a supermicrobe that is extremely versatile in regard to electron acceptors (TEA)
  • Indeed it can use, O2, NO3-, NO2-, Mn(IV), Mn(III), Fe(III), Fumarate, DMSO, TMAO, S0, S2O3 2-, U(VI), Cr(VI)
54
Q

What can the geobacter species be used to bioremediate?

A

Uranium

55
Q

How does uranium bioremediation work? (2 points)

A
  • Uranium in its highly soluble form is reduced to its highly insoluble form, which will allow it to precipitate out.
  • To stimulate geobacters you can add acetate, ethanol, glucose
56
Q

How to bioremediate arsenic contaminated groundwater by lithotrophic bacteria? (3 points)

A
  • Water cycles through oxygenation tanks back to the source, where aerobic bacteria oxidize Arsenite, iron and Manganese (electron donors)
  • Oxidized form of Arsenic (Arsenate), precipitates with iron and manganese for convenient removal
  • the TEA is oxygen
57
Q

Mercury transformations (6 points)

A
  • Mercury has tendency to concentrate in living tissues and it is highly toxic
  • Major form of Mercury in the atmosphere is elemental mercury (Hg0), which is volatile and oxidized to mercuric ion (Hg2+) photochemically
  • Most mercury enters aquatic environments as Hg2+
  • Hg2+ readily absorbs to particulate matter, where it can be metabolized by microorganism
  • Under anaerobic conditions, microorganisms form methylmercury (CH3Hg+): an extremely soluble and toxic compound
  • Several bacteria can also transform toxic methyl mercury to nontoxic forms, which is being explored to bioremediate mercury contaminated sites
58
Q

What are the 3 categories used to define microbial nutritional categories?

A
  • source of energy (e.g. light, chemical)
  • source of electrons (reducing equivalents) (organic or inorganic)
  • source of carbon (itself or other organisms)
59
Q

Energy sources categories (2)

A
  • Photo-: Light absorption captures energy and excites electron
  • Chemo-: Chemical electron donors are oxidized
60
Q

Electron source (donors) categories (2)

A
  • Litho-: Inorganic molecules donate electrons
  • Organo-: Organic molecules donate electrons
61
Q

Carbon source categories (2)

A
  • Auto-: CO2 is fixed and assembled into organic molecules
  • Hetero-: Preformed organic molecules are acquired from outside, broken down for carbon, and the carbon reassembled to make biomass
62
Q

Chemolithoautotrophs

A

Bacteria able to oxidize reduced inorganic compounds, such as NH4 +, H2S or H2 to synthesize ATP for biosynthesis

63
Q

Examples of chemolithoautotrophs

A
  • Ammonium-oxidizing nitrifying bacteria
  • Nitrite-oxidizing nitrifying bacteria
64
Q

Examples of Ammonium-oxidizing nitrifying bacteria

A

Nitrosomonas sp., Nitrovibrio sp.

65
Q

Ammonium-oxidizing nitrifying bacteria: energy source and what they do with it

A

Use NH4 + as sole energy source and oxidize it to NO2 -

66
Q

Why are Ammonium-oxidizing nitrifying bacteria interesting in terms of bioremediation?

A

Because they have a monooxygenase (ammonia monooxygenase, AMO), which may attack some pollutants such as trichloroethylene (TCE)

67
Q

What is an example of Nitrite-oxidizing nitrifying bacteria

A

Nitrobacter sp.

68
Q

What energy source do Nitrite-oxidizing nitrifying bacteria use and what do they do with it?

A

They use NO2 - as sole energy source and oxidize it to NO3

69
Q

How do ammonium-oxidizing nitrifying bacteria and nitrite-oxidizing nitrifying bacteria play a critical role in the nitrogen cycle?

A

by converting NH4 + to NO3 - which is often the rate-limiting step in nitrogen cycle

70
Q

Electron acceptors in marine sediment: their order in terms of depth (from surface to deepest) (4)

A
  • O2
  • NO3 -
  • SO4 2-
  • CO2
71
Q

Common sources of ground water contamination (5)

A
  • fertilizers
  • pesticides
  • road salt
  • surface water runoff
  • excavations, mining
72
Q

Summary Microbial physiology basics: Electron donors (what do they do)

A
  • Reduces organic compounds: carbohydrates, CH4
  • Reduced inorganic compounds: H 2S
72
Q

Summary Microbial physiology basics:
Electron acceptors what are they for aerobic and anaerobic respiration?

A

Terminal electron acceptor during respiration
* Aerobic respiration: O 2 (to H 2O)
* Anaerobic respiration: NO 3- (to NH 4+)

72
Q

How would you stimulate oil biodegradation in a contaminated aquifer?

A
  • In terms of remediation, it is important to know what is in the aquifer! (e.g. oxygen…
  • What can you do bc rn there is missing TEA
  • The aerobic lack oxygen
  • 2 choices:
  • Start pumping oxygen into the system to stimulate aerobic organisms
  • If Other organisms, pump what is limiting their biodegrative activity
72
Q

Sequential reduction of terminal electron acceptors in contaminated sediments and aquifers (4 points)

A
  • A profile of sediment show that after the depletion of O2 , NO 3- is depleted, and then depletion of SO 4- results in sulfide accumulation
  • Finally, utilization of CO2 results in CH 4 accumulation, as all the other potential electron acceptors have been depleted
  • After the flooding of a soil, a similar succession of reductions occurs, often leading to the production of methane
  • The sequential reduction of different electron acceptors indicates a succession of heterotrophic bacterial populations:
  • Denitrifiers
  • Iron reducers
  • Sulfate reducers
  • Methanogens
72
Q

Summary – Microbial bioenergetics / thermodynamics (5 points)

A
  • Needed to energize cytoplasmic membrane via proton gradient
  • Proton gradient interconverted with ATP, NAD(P)H pools
  • NAD(P)H = reducing power required for some biochemical reactions
  • Microbes use energy ATP, NAD(P)H for cellular functions such as biosynthesis: nucleic acids, proteins, lipids …
  • Also used for CO 2-fixation and initiation of some catabolic pathways, depending upon the species
72
Q

Summary Microbial physiology basics:

A
  • Organic compound during fermentation
  • Temperature, pressure, pH, salt
  • Surfaces to colonize (biofilms)

NRSC 333 (23 decks)

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