week 5 - microbes metabolism

Question 1

Heterotrophs

Answer 1

animal and fungi are commonly called heterotrophs

chemical reaction as energy source

organic matter as electron source

organic matter as carbon source

we tend to think that heterotrophic means a combination of all the above (this is too simple for microbes)

Question 2

phototrophs

Answer 2

plants are commonly called phototrophs

light as energy source

inorganic water as electron source

inorganic CO2 as carbon source

tend to think phototrophic means a combination of all the above (not true for phototrophic bacteria)

Question 3

energy source:
chemo-

Answer 3

energy derived from chemical reactions

e.g. oxidation of inorganic or organic compounds

Question 4

energy source:
photo-

Answer 4

energy from light

Question 5

electron source:
organo-

Answer 5

e- from organic matter

e.g. sugars, amino acids, fatty acids, ptetroleum

Question 6

electron source:
Litho-

Answer 6

e- from inorganic matter

e.g. H2, H2S, NH3, Fe2+

Question 7

carbon source:
hetero-

Answer 7

C from organic matter

e.g. sugars, amino acids, fatty acids, petroleum

Question 8

carbon source:
auto-

Answer 8

C from CO2

Question 9

making a distinction between energy source, electron source and a carbon source

Answer 9

For each one of these sources there are two alternative options
* Energy source can be light or chemical reactions
* Electron source can be inorganic (e.g. water, ammonia) or organic
* Carbon source can be CO2 or organic carbon

This makes 6 elements in the classification scheme

Question 10

humans are:

Answer 10

chemo-organo-hetero-trophs

Question 11

plants are:

Answer 11

photo-litho-auto-trophs

Question 12

bacteria are:

Answer 12

chemo-litho-auto-trophs

o 2H2 + O2 –> 2 H2O
o H2 is electron donor, O2 is electron acceptor, this respiration generates ATP

Question 13

metabolism consists of 2 parts

Answer 13

catabolism (breakdown) + anabolism (building up)

o Catabolism supplies anabolism with
 ATP
 NADPH but only if needed (if carbon source more oxidised than biomass so has to be reduced to the oxidation state of biomass)

Question 14

respiration

Answer 14

Have a substrate, released e-, and becomes oxidised
* Can often make ATP by substrate level phosphorylation
o Not always the case: depends on the substrate
* E.g. can with glucose, cant with hydrogen
Need to do something with the e-
* Can leave it in the cell as it is
* Use an external electronic acceptor (Xox)
o Xox will be reduced
o Always coupled to electron transport phosphorylation to make ATP
Oxidative and reduction branches are coupled by electrons

Question 15

fermentation

Answer 15

Almost the same as respiration but do not have external e- acceptor
Uses substate as e- acceptor and e- donor
* Scheme changes due to the absence of Xox
* Therefore substrate has two functions
Electrons again cannot be left
* So e- used to reduce another part of the same substrate
o This is redox disproportionation

Question 16

substrate level phosphorylation

Answer 16

example from glycolysis
- Oxidation of aldehyde to acid coupled phosphorylation of acid
- Transfer of Phospho group to ADP
- Exactly 1 ATP formed
- Stoichiometric coupling
- If not enough changeG in a reaction, then no ATP can be made, if too much changeG, surplus is wasted
- No membrane needed
- No Fe needed

Limit no. of reactions where this coupling is possible
* Only like a dozen
* Big limitation of substrate phosphorylation
* Mechanically feasible in only a few circumstances

Question 17

electron transport phosphorlyation

Answer 17

• Part of the respiration chain of Paracoccus denitrificans
• Same as in the mitochondrion, a close relative (both are alpha-Proteobacteria)

Different protein complexes that when e– are passing through (pump H+ through membrane) and end up reducing (1/2 O2) to water
Complexes step wise to a more positive redox potential
* This energy (from negative to positive) can potentially be used to translocate H+ ions across the membrane
* This can form a chemiosmotic gradient
* Which are then utilised in the ATP synthase reaction (as they move down their chemiosmotic gradient)
o To generate ATP
This is a coupling
* Can couple any reaction that pumps protons across membrane to the generate of ATP (via ATP synthase)
* Delta G can vary
* More flexible than substrate level

Protons can be produced outside or moved outside
* Doesn’t matter
* Just need chemiosmotic gradient

Question 18

ETP

Answer 18

Electron transport chain from electron donor (e.g. NADH) to electron acceptor (e.g. O2)  doesn’t have to be O2
- Requires membrane to separate change and H+
- Protons are pumped out through membrane
- Or n Protons are consumed inside and produced outside
o Outside: usually higher H+ conc. Meaning more +ve charge
- Proton motive force (pmf) has two components:
o pH difference
o membrane potential (in Volt)
o (gives flexibility: e.g. pH difference is smaller can compensate with larger difference in membrane potential  what matters if the sum hence proton motive force)
- sodium motive force in some bacteria and archea (mechanistically different -> much bigger ion)
- ETP requires Fe
- 10H+ enters cytoplasm through ATP synthase per 3 ATP formed – but can depend on ATP synthase accumulating protons (one turn of ATP synthase)
o This stoichiometry differs in some groups of bacteria and archaea
o So can use reactions that can only export 1 H+ to form ATP as you can accumulate protons outside the cell (or reactions that can export > 1 H+)
 Smaller energy quantum of 1 H+ = 0.3 ATP

Question 19

fermentation

Answer 19

• Does not need oxygen (no external electron acceptor)
  o But may take place in the presence of oxygen
• Fermentation is energy metabolism without using any external electron acceptors, such as oxygen, nitrate, sulphate, Fe^3+…
  o So only part of the substarte can be oxidised, another part of the substrate has to be reduced
   No net gain/loss of electrons, electron use has to be balanced
• Most fermentations form ATP via SLP, but not all
• Many fermentations also from ATP by ETP, but not all
• Common misconceptions
  o Fermentation does not use any electron transport chains: wrong
  o Fermentation is life without oxygen: wrong

Question 20

ethanol fermentation

Answer 20

• Budding yeast: Saccharomyces cerevisiae
  o Ethanol fermentation of sugars
  o Yeast ferments under aerobic conditions if glucose in excess
  o Number one fermentation in industry

On average the same because haven’t lost any e-
(no external e- acceptor needed)

Part of the substrate oxidised the other part reduced
Two ATP in this process
* Not great
o Glucose respiration between 30-38 ATP

Question 21

other fermentations

Answer 21

• Yeast’s ethanol fermentation yields 2 ATP per glucose
  o Alternative fermentations yield more ATP or less
   1-4 ATP per glucose (the range)
   Solvent and biofuel production (acetone-butanol-ethanol fermentation by Clostridium is number 2 in industry)
   More ATP is you can get rid of electrons as H2
• These are more complicated
• This gets it up to 4 ATP molecules
• Many fermentations have branched pathways
  o High ATP branch
  o Low ATP branch
   ATP yields variable
• Many fermentations use ETP

Question 22

respiration

Answer 22

• Oxidation of substrate = electron donor is coupled to reduction of external electron acceptor
  o Aerobic: oxygen as electron acceptor
   Generally the best in terms of thermodynamics (highest redox potential)
  o Anaerobic: various other electron acceptors
   NO3-. Fe^3+, SO4^2-, CO2
• Involves ETP and SLP
• More ATP than fermentation
  o Up to 38 ATP per glucose (big advantage)
• Needs external electron acceptor
• Needs Fe for cytochromes, FeS
  o In the complexes in the ETC

Question 23

Aerobic and anaerobic respiration in Paracoccus

Answer 23

• Paracoccus denitrificans
  o Relative of the mitochondrion (alpha-proteobacteria)
• Branched respiratory chain: aerobic and anaerobic respiration
  o 3 branches leading to oxygen as terminal e- acceptor (aerobic respiration)
  o 2 branches to nitrate (NO3-) as terminal e- acceptor (anaerobic respiration)
  o Further branches to nitrite (NO2-), nitric oxide (NO), nitrous oxide (N2O)
  o Denitrification: reducing nitrate to N2
• All electron donors but NADH omitted, so this scheme is very simplified
• Different pathways gives organisms opportunity to be flexible to different circumstances

Question 24

phototrophic bacteria

Answer 24

Phototrophs
- Have light friven electron transport chain to generate
o Proton motive force, which dirves ATP synthesis
o NADPH, which can be used to reduce CO2 in dark reaction
- Photons of visible light contain 100-200kJ/mol energy
- One single photon shifts the redox potential of (bacterio) Chlorophyll by 1-2 V more negative
- Reversing respiration with light energy
6CO2 + 6H2O –> C6H12O6 + 6O2
change in G’ = +2872 kJ/mol
o Without light energy, this reaction would be endergonic (a reaction that requires energy to be driven )and not occur
o Oxidizing the reduced end products of respiration: H2O, H2S, Fe^2+
o Oxidizing the reduced end products of fermentation: acetate, lactate. Ethanol, butyrate, hydrogen
o It’s a cycle:
 Phototrophs use the waste of respires and fermenters, the waste of phototrophs feeds respires, fermenters feed on the dead

Question 25

phototrophs
oxygenic

Answer 25

(generates oxygen)
o H2O as electron donor  O2
o Cyanobacteria (chloroplasts in plants are cyanobacteria)

Question 26

phototrophs
anoxygenic

Answer 26

o H2S as electron donor  SO4^2-
o Or H2, ethanol, butyrate…
o All other phototrophic bacteria apart from Cyanobacteria
o Purple bacteria
 Purple non-sulfur bacteria
* Use organic electron donors and carbon sources
* Photo-organo-hetero-trophs
 Purple sulfur bacteria
* Use H2S and S as electron donor and CO2 or aceteate as carbon source
* Photo-litho-auto-trophs
o Green sulfur bacteria