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BB10004 > Microbes and Metabolism > Flashcards

Microbes and Metabolism Flashcards

1
Q

Describe main features of prokaryotes

A
  1. Bacteria are prokaryotes
  2. Do not have a nucleus
  3. But some have organelles
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2
Q

What is the idea of endosymbiosis

A
  1. Mitochondria is an ancestor from bacteria
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3
Q

What is the main way bacteria are categorised

A
  1. Gram positive and Gram negative cells based on cell wall structure
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4
Q

How are prokaryotes diverse

A
  1. Catabolic diversity of prokaryotes greatly exceeds that in eukaryotes (although, arguably, fungi rival them)
  2. Diversity of substrates utilised
  3. Diversity of metabolic pathways
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5
Q

What are the two divisions of how the energy source is acquired

A
  1. Photo: Light energy excites e- to higher-energy state

2. Chemo: Chemical e- donors are oxidised

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6
Q

What are the two divisions based on electron source

A
  1. Organo: Organic molecules donate e-

2. Litho: Inorganic molecules donate e-

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7
Q

What are the two divisions based on carbon source of biomass

A
  1. Auto: CO2 is fixed and assembled into organic molecules

2. Hetero: Preformed organic molecules are acquired from outside and assembled

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8
Q

Give an example of a chemolithoautotroph

A
  1. Tube worms are packed of chemolithoautotrophs which eat inorganic molecules from geothermal vents
  2. Fix CO2 from water and turn it into themselves – organic structure- worm eats itself
  3. Can have ecosystems not based primarily on light
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9
Q

What is energy needed for

A
  1. Energy needed for anabolism and growth e.g.
  2. Growth and reproduction
  3. Maintenance – biosynthesis, transport, motility, etc.
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10
Q

How is energy converted to a usable form

A
  1. Redox- e- “float” from one compound to another
  2. Oxidation – loose e-
  3. Reduction – gain e-
  4. Energy conserved as energy-rich chemical bond or used directly for work
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11
Q

Describe the types of reaction relating to gibbs energy

A 
Exergonic reaction
1. ΔG is negative
2. Free energy leaves the system
3. Free energy is energy that can do work (available energy)
Endergonic reaction
1. ΔG is positive
2. Free energy is gained by the system
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12
Q

What does delta G depend on

A
  1. ΔG of reaction varies depending on concentrations, temperature and pressure
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13
Q

What are the main features of the electron transport chain

A
  1. The membrane is a boundary between the cytoplasm and the surroundings-semipermeable which allows an electrochemical gradient
  2. e- donor and e- acceptor (terminal)
  3. Acceptor from surroundings
  4. Respiration
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14
Q

Describe conditions with and without oxygen

A
  1. Aerobic – presence of O2 (aerobic conditions)
  2. Anaerobic – absence of O2 (anoxic conditions)
  3. O2 is the terminal e- acceptor in aerobic respiration
  4. Atmosphere ~21% O2
  5. Solubility is low in water
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15
Q

Where does the energy for Chemoorganotrophy come from

A
  1. Energy from organic compounds
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16
Q

Where does the energy for Chemilithotrophy come from

A
  1. Energy from inorganic compounds
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17
Q

Give examples of Chemolithotrophic e- donors

A
  1. Hydrogen (H2) e.g., Pseudomonas hydrogenovara
  2. Sulphur compounds (H2S, S0, thiosulfate (S2O32-)) e.g., Thiobacillus spp., Beggiatoa spp.
  3. Ammonia (NH3) e.g., Nitrosomonas europaea
  4. Nitrite (NO2-) e.g., Nitrobacter winogradskyi
  5. Iron (Ferrous iron (Fe2+)) e.g. iron pyrite FeS2 e.g., Thiobacillus spp.
  6. Arsenite (H3AsO3) e.g., Pseudomonas arsenitoxidans
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18
Q

Describe examples of electron acceptors in anaerobic respiration

A
  1. Anaerobic respiration use other molecules as terminal e- acceptor
  2. Facultative anaerobes- can use oxygen but don’t need it
  3. Often use nitrate (NO3-) or nitrite (NO2-)
  4. Obligate anaerobes- must live with no oxygen around
  5. Often use sulfate (SO42-)
  6. CO2 as terminal e- acceptor for methanogens
    - CO2 + 4H2  CH4 + 2H2O
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19
Q

What do chemolithotrophs still need

A
  1. Chemolithotrophs still need ATP and NAD(P)H
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20
Q

How do chemolithotrophs generate NAD(P)H

A
  1. Most inorganic e- donors have redox potentials higher than NAD(P)+ and NAD(P)H
  2. So e- are transferred to coenzyme Q or a cytochrome and then;
  3. Some generate a proton motive force when passed to a terminal e- acceptor- Forward e- transport
  4. Some are passed to NAD(P)+ to make NAD(P)H but uses the proton motive force- Reverse e- transport
  5. This takes 5x forward pathway to power 1x reverse pathway
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21
Q

What do Acidiothiobacillus ferrooxidans do

A
  1. Eat rock – FeS2 using H2O
  2. Have protein that makes FE2+ go to Fe3+ put electrons into transport chain
  3. Only works because external pH is acidic
22
Q

Describe the carbon sources of chemolithotrophs

A
  1. Most chemolithotrophs are autotrophs (chemolithoautotrophy)
  2. Most use the Calvin cycle
  3. Alternatives are reverse TCA cycle, acetyl-CoA pathway, and 3-hydroxypropionate cycle
  4. Some chemolithotrophs use organic carbon sources (chemolithoheterotrophs or mixotrophs)
23
Q

Describe Campylobacter jejuni

A
  1. Common cause of gastroenteritis
  2. Microaerophilic
  3. A chemoorganotroph with diverse metabolic pathways
  4. Can’t use glucose
  5. Can also use H2 and sulphite (SO32-) as an e- donor
  6. Has chemolithotrophic capability- not sure why as live in organic compound
  7. Sulphite released by neutrophils as part of immunity
24
Q

Give examples of anaerobic environments

A
  1. water,
  2. soil,
  3. food,
  4. plant and animal tissues,
  5. GI tract
25
Q

What are 3 methods of anaerobic metabolism

A
  1. anaerobic phototropy
  2. Anaerobic respiration
  3. fermentation
26
Q

Describe anaerobic respiration

A
  1. An e- transport chain delivers e- to a non-O2 e- acceptor

2. Electron transport phosphorylation generated ATP

27
Q

Describe fermentation

A
  1. In environments where no e- acceptor for e- transport chain
  2. Used instead of respiration
  3. Some bacteria have fermentation only (obligate fermenters)
  4. Limited to chemoorganotrophs
  5. Fermentation of inorganic compounds not possible- so little energy from inorganic electron donors and so little from fermentations so not enough energy
28
Q

Describe the redox processes in fermentation

A
  1. Oxidation of a substrate- Substrate only partially oxidised
  2. Reduction of e- carriers (NAD(P)+ or FAD)
  3. NAD(P)H or FADH is then oxidised (recycled)
  4. Reduction of a derivative of the starting substrate (typically) or an independent substrate (amino acid fermentation, electron is given to different amino acid than is taken from)
  5. Typically the e- acceptor is organic and “internally” supplied
  6. Reduced product has to be excreted as a fermentation product
29
Q

What is the delta G for fermentation

A
  1. An exergonic reaction
  2. A large substrate turns into two or more simpler molecules
  3. Therefore, entropy increase so ΔG goes down
30
Q

How is ATP produced in fermentation

A
  1. ATP produced mainly by substrate-level phosphorylation
  2. Typically during the 1st oxidation step(s)
  3. Direct transfer of P group from an organic P to ADP
  4. Significantly less ATP produced than in phototrophy or e- transport based respiration
  5. Some instances of ATP production by alternative methods
31
Q

Compare amount of ATP produced from lactate fermentation and respiration

A
  1. Far less energy from fermentation

2. e.g., 2 ATP from lactate fermentation vs. 38 ATP from respiration of lactate

32
Q

Describe different features of coenzymes

A
  1. NAD, NADP, FAD and FMN
    a) Water-soluble coenzymes (cofactors)
    b) Carry e- from oxidation reactions and donate them to wide variety of reduction reactions
  2. NAD and NADP
    a) Free moving from one enzyme to another
  3. FAD and FMN
    a) Tightly bound to enzymes (flavoproteins)
33
Q

What are coenzymes

A
  1. Small organic molecules

2. Interact with apoenzyme to form active holoenzyme

34
Q

What are the different types of fermentation pathway

A
  1. Linear- glycolysis etc

2. Branched/split- Multiple products but Everything needs to be redox balanced

35
Q

Describe basics of glycolysis

A
  1. Glycolysis is fermentation
  2. Pyruvate is reduced to fermentation products
  3. Balances redox
  4. Regenerates NAD+
  5. Substrate level phosphorylation
36
Q

How is it ensured

A
  1. Some fermentation pathways are endergonic- ΔG is positive
  2. But when concentration of reaction products are kept low, the reactions become exergonic
  3. Concentrations can be kept low if products either diffuse away or are consumed by another organism
  4. Syntrophy- a way to keep concentrations low
37
Q

What is syntrophy

A
  1. One species lives off the products of another species

2. Dependent organism is a syntrophic organism

38
Q

Give an example of syntrophy

A
  1. Interspecies hydrogen transfer
  2. Methanogens
  3. Hydrogen gas is eaten by methanogen so syntrophic organism can ferment ethanol and produce acetate
39
Q

Describe the range of substrates that can be fermented

A
  1. Relatively large no. of substrates can be fermented
  2. Therefore, large no. of fermentation products
  3. One organism may use/produce more than one substrate/product using the Same or different pathways
  4. Sugars (hexoses, pentoses, tetroses), polyalcohols, organic acids, amino acids, purines and pyrimidines
  5. Acetylene, citrate, glyoxylate, succinate, oxalate and malonate
  6. Some bacteria can ferment xenobiotic compounds- man made compounds - Anthropogenic compounds unknown in natural ecosystems
  7. e.g., polychlorinated biphenyls (PCBs)- bi product of many industrial processes
40
Q

What is the name if there is one fermentation product and give example

A
  1. One fermentation product
  2. Homofermentative
  3. e.g., lactate produced by Lactobacillus spp.
41
Q

What is the name if there are two fermentation products and give example

A
  1. Heterofermentative

2. e.g., lactate, acetate and ethanol produced by Bifidobacterium spp.

42
Q

How are pathways named and give examples

A
  1. Pathways are named by main product
  2. E.g. yeast fermentation to produce ethanol is ethanol fermentation
  3. Lactococus fermentation produces only lactate- homolactic acid fermentation
  4. Leuconostoc fermentation produced lactate + ethanol + CO2- heterolactic acid fermentation
43
Q

What is the difference between primary and secondary fermenters

A
  1. Sequential fermentation pathways
  2. Primary- ferment normal molecules
  3. Secondary – ferment the products of the primary
44
Q

How can Fermentation produce energy without substrate-level phosphorylation

A
  1. Use ion pumps to produce a potential difference
    E.g.
  2. Decarboxylation driven ion transport
  3. Ion-coupled end-product efflux via a symport
45
Q

Describe how energy can be produced by Ion-coupled end-product efflux via a symport

A
  1. Use sodium motive force- atpase runs of sodium gradients
  2. Or some Generate potential difference with sodium to flow back down the concentration gradient to pump out hydrogen ions to generate second ion gradient and use this to produce ATP
46
Q

Describe how energy can be produced by Decarboxylation driven ion transport

A
  1. Single molecule can decarboxylate to produce 2 molecules- exergonic
  2. Dicarboxylic acids- remove one carboxylate group
47
Q

How can a proton motive force be generated if not used to produce ATP

A
  1. Fermentation can produce ATP without creating a proton motive force
  2. Some processes require a proton motive force
  3. e.g., flagella rotation
  4. Some strict fermentative bacteria use ATP to run the ATPase in reverse!
48
Q

What is the basics of photosynthesis

A
  1. A process converting light E into biological E which in turn is consumed to fix CO2 into organic compounds
49
Q

What are the basics of fermentation

A
  1. A process converting chemical E into biological E without the use of an external e- acceptor
50
Q

What are the basics of respiration

A
  1. A process converting chemical E into biological E by oxidising organic or inorganic e- donors coupled with the reduction of externally supplied e- acceptors

BB10004 (14 decks)

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