1. III. Fermentation and Respiration Overview
An emphasis on the flow of carbon and other elements in fermentation and respiration
3.8 Glycolysis
3.9 Fermentative Diversity and the Respiratory Option
3.10 Respiration: Electron Carriers
3.11 Respiration: The Proton Motive Force
3.12 Respiration: Citric Acid and Glyoxylate Cycle
3.13 Catabolic Diversity

2. III. Fermentation and Respiration Overview
Two key metabolic pathways
Complementary
Overlapping
Definition depends on context-industrial, medical, biochemical

3. Fermentation
In food science fermentation can refer to the production of foods such as yogurt
In chemical engineering it can refer to the production of ethanol as an additive for gasoline
In microbiology it refers to the breakdown of carbon compounds (eg glucose) to smaller compounds with a limited harvest of energy through substrate level phosphorylation and no oxygen used

4. Respiration
In medicine or exercise science respiration refers to breathing
In microbiology respiration refers to the removal of electrons from a substance and their transfer to a terminal acceptor with a significant harvest of energy through oxidative phosphorylation (redox reactions). Oxygen may be used as the terminal acceptor (aerobic respiration) or not (anaerobic respiration).

5. Fermentation: substrate-level phosphorylation; ATP is directly synthesized from an energy-rich intermediate
Respiration: oxidative phosphorylation; ATP is produced from proton motive force formed by transport of electrons

6. Fermentation A basic and important process for microorganisms
A sugar is the starting material and the end product depends on the species
Three Stages (I) Preparation, (II) Energy Harvesting, (III) Reboot
Reboot stage is very diverse!

7. 3.8 Glycolysis
Stage I and Stage II (Figure 3.14) called Glycolysis (Embden–Meyerhof-Parnas or EMP pathway): a common pathway for catabolism of glucose
End product of glycolysis is pyruvate (pyruvic acid)
In fermentation pyruvate is processed through Stage III
It accepts electrons so is reduced

8. Figure 3.14 Fermentation with lactic acid produced
Figure 3.14 Embden–Meyerhof–Parnas pathway (glycolysis).
Figure 3.14

9. 3.9 Fermentative Diversity and the Respiratory Option
Fermentations may be classified by products formed (See Sec.13.12) in Stage III
Ethanol
Lactic acid (homolactic vs heterolactic)
Propionic acid
“Mixed acids”
Butyric acid (extra ATP generated)
Butanol

10. 3.9 Fermentative Diversity and the Respiratory Option
Fermentations may be classified by substrate fermented (See Sec.13.12)
Usually NOT glucose
Amino acids
Purines and pyrimidines
Aromatic compounds

11. 3.9 Fermentative Diversity and the Respiratory Option
Fermentation
Helps detoxify and eliminate waste products
Provides metabolites for other microbes in the environment
May help to recover additional ATP
Maintains redox balance (page 87 and Fig. 3.14) of NAD and NADH.

12. 3.9 Fermentative Diversity and the Respiratory Option
Fermentation
Helps detoxify and eliminate waste products
Provides metabolites for other microbes in the environment
May help to recover additional ATP
Maintains redox balance (page 87 and Fig. 3.14)
AND…….
Helps to generate precursor metabolites for anabolism

13. Broad Overview of Metabolism
Prokaryotes will not make something if they can import it
There are only a few key precursor molecules (but lots of ways
to make them)
Energy sources vary

15. 3.9 Fermentative Diversity and the Respiratory Option
Pentose Phosphate Pathway (Shunt)
“Alternate” pathway
Runs “parallel” to glycolysis
Different reactions thus different intermediates
Generates different precursor metabolites
Generates reducing power

17. 3.12 Respiration: Citric Acid and Glyoxylate Cycle
Citric acid cycle (CAC): pathway through which pyruvate is completely oxidized to CO2 (Figure 3.22a) (aka Krebs or TCA cycle)
Initial steps (glucose to pyruvate) same as glycolysis
Subsequently 6 CO2 molecules released and NADH and FADH generated
Plays a key role in both catabolism AND anabolism…why?

18. Figure 3.22a The citric acid cycle.

19. 3.12 Respiration: Citric Acid and Glyoxylate Cycle
The citric acid cycle generates many compounds available for biosynthetic purposes
- α-Ketoglutarate and oxaloacetate (OAA): precursors of several amino acids; OAA also converted to phosphoenolpyruvate, a precursor of glucose
Succinyl-CoA: required for synthesis of cytochromes, chlorophyll, and other tetrapyrrole compounds
Acetyl-CoA: necessary for fatty acid biosynthesis

20. In other words-the citric acid cycle generates key precursor metabolites
As well as
harvesting energy

21. 3.12 Respiration: Citric Acid and Glyoxylate Cycle
The Citric Acid Cycle is also a key collection point and entry point for metabolites
C4-C6 citric acid cycle intermediates (e.g., citrate, malate, fumarate, and succinate) are common natural plant and fermentation products and can be readily catabolized through the citric acid cycle alone
Fatty acids metabolized via Acetyl-CoA

22. 3.12 Respiration: Citric Acid and Glyoxylate Cycle
A variation of the citric acid cycle with glyoxylate as a key intermediate
Shares enzymes with citric acid cycle
Allows utilization of C2-C3 organic acids if larger molecules not available (Figure 3.23)
Isocitrate to glyoxylate and succinate
For anabolism or catabolism

23. Figure 3.23 The glyoxylate cycle.

24. 3.10 Respiration: Electron Carriers
Important electron carriers embedded in membranes include:
NADH dehydrogenases
Flavoproteins
Cytochromes (heme)
Iron-sulfur proteins
Quinones

25. Respiration is much more productive than fermentation
Aerobic respiration is the most productive of all
Figure 3.22b

26. 13.5 Autotrophic Pathways (pp 390-391)
Carbon fixation is reduction of CO2 to carbohydrate-a key feature of autotrophy
At least 6 pathways exist in various Archaea and Bacteria
But the Calvin cycle (Figure 13.16, 13.17) is the most important

27. 13.5 Autotrophic Pathways (pp 390-391)
Named for its discoverer, Melvin Calvin
Fixes CO2 into cellular material for autotrophic growth
Requires NADPH, ATP, CO2 and special enzymes e.g. ribulose bisphophate carboxylase (RubisCO),
6 molecules of CO2 are required to make 1 molecule of glucose (Figure 13.17)

28. Figure 13.17 The Calvin cycle.

29. 13.5 Autotrophic Pathways: RUBISCO
Responsible for most carbon fixation on planet
Unusual enzyme-”weak”- when CO2 is low
easily inhibited by oxygen
Often found sequestered in carboxysomes to increase CO2 and lower O2

30. 3.13 Catabolic Diversity Chemolithotrophy
Uses inorganic chemicals as electron donors
Examples include hydrogen sulfide (H2S), hydrogen gas (H2), ferrous iron (Fe2+), ammonia (NH3)
Begins with oxidation of inorganic electron donor
Uses an electron transport chain and transmembrane ion gradient

31. Dissimilative Iron Oxidizers are chemolithotrophs (13.9 and 14.15)
Oxidize Fe2+ to Fe3+
Very widely distributed in many environments where Fe2+ is available
Autotrophic or heterotrophic
Aerobic or anaerobic
Archaea or Bacteria

32. Acidithiobacillus ferrooxidans is a representative iron oxidizer
Acidophile at pH 2-3
Acid environments with Fe2+
Fe2+ -> Fe3+ -> FeOH3

33. Figure 13.24 (pH 2) (pH 6) + ATP ATP e– e– Out Outer membrane cyt c
Electron transport generates proton motive force.
Rusticyanin e–
Periplasm
Reverse e– flow e–
NAD+ Q
cyt bc1
cyt c
cyt aa3
Figure Electron flow during Fe2+ oxidation by the acidophile Acidithiobacillus ferrooxidans. In
(pH 6) +
ATP
NADH
Cell material
ADP
ATP
Figure 13.24

34. Figure 13.23 Iron-oxidizing bacteria.

35. 3.17 Nitrogen Fixation (Sec 3.17 also pp 438-439)
Living systems require nitrogen in the form of NH3 or R-NH2
“Fixed” or “reduced” nitrogen, not N2
Only some prokaryotes can fix atmospheric nitrogen: diazotrophs

36. 3.17 Nitrogen Fixation
Some nitrogen fixers are free-living, and others are symbiotic
Cyanobacteria are free-living
nitrogen fixers
Soybean root nodules contain
endosymbiotic
Bradyrhizobium japonicum

37. 3.17 Nitrogen Fixation Energetically expensive (8 ATP per N atom)
Requires electron donor, often pyruvate
Reaction is catalyzed by nitrogenase
Sensitive to the presence of oxygen
Fe plus various metal cofactors
Can catalyze a variety of reactions