1. Metabolic Diversity
Overall, the chemical reactions that take place within microbial cells are highly diverse
There are 2 key “ingredients” in this diverse collection of recipes
Energy-to make things work
Carbon-for precursors and building blocks

2. Part Two-Carbon
An emphasis on the flow of carbon and other elements in fundamental metabolic pathways
3.8, 3.9 Glycolysis and Fermentative Diversity
3.12 Respiration: Citric Acid and Glyoxylate Cycle
13.5 ( ) Autotrophic Pathways

3. Broad Overview of Metabolism
Energy to run metabolism comes from ATP generated by
catabolism
Microbes have different ways to acquire or make precursor
molecules

5. 3.8 Glycolysis
(Stage I and II of Figure 3.14) Glycolysis (Embden–Meyerhof-Parnas or EMP pathway): a common and central pathway for catabolism of glucose
End product of glycolysis is pyruvate (pyruvic acid)
Stage III shows one type of fermentation

6. Diagram of reactions of Glycolysis
Start =
Glucose
End = Pyruvate

7. 3.9 Fermentative Diversity
Pentose Phosphate Pathway (Shunt)
“Alternate” pathway
Runs “parallel” to glycolysis
Different reactions thus different intermediates
Generates different precursor metabolites
Generates reducing power but no ATP
Allows metabolism of “unusual” or “weird” sugars

9. 3.9 Fermentative Diversity
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 basic and important process in which there is breakdown of carbon compounds (eg glucose) to smaller compounds with no oxygen required
Final steps different in different species
But…microbiologists use the term in different ways

10. 3.9 Fermentative Diversity
Fermentations may be classified by products formed (See Sec.13.12) in final stages
Ethanol
Lactic acid (homolactic vs heterolactic)
Propionic acid
“Mixed acids”
Butyric acid (extra ATP generated)
Butanol

11. 3.9 Fermentative Diversity
Some authors consider glycolysis to be a part of fermentation (Fig. 3.14) while others do not
Fermentations may be classified by substrate fermented (See Sec.13.12)
Amino acids
Purines and pyrimidines
Aromatic compounds
Usually glucose NOT specifically named

12. Figure 3.14 Reactions of Fermentation (lactic acid produced)
Figure 3.14 Embden–Meyerhof–Parnas pathway (glycolysis).
Figure 3.14

13. 3.9 Fermentative Diversity
Fermentation
Helps detoxify and eliminate waste products
Generates 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.

14. 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)
Follows after glycolysis
Pyruvate oxidized
Subsequently 6 CO2 molecules released and NADH and FADH generated
Plays a key role in both catabolism AND anabolism

15. 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 in gluconeogenesis
Succinyl-CoA: required for synthesis of cytochromes, chlorophyll, and other tetrapyrrole compounds
Acetyl-CoA: necessary for fatty acid biosynthesis

16. Figure 3.22a The citric acid cycle.

17. 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

18. 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
Anabolic-allows Ac-CoA from fatty acids to be used for carbohydrate synthesis-not energy harvest
Ac-CoA converted directly to succinate with glyoxylate as key intermediate
Also allows utilization of C2-C3 organic acids if larger molecules not available (Figure 3.23)

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

20. 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

21. 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)

22. Figure 13.17 The Calvin cycle.

23. 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

24. Reductive Ac-CoA Pathway for Carbon Fixation
Found in some Bacteria and Archaea
Electrons from hydrogen reduce CO2 to Ac-CoA
“acetogens”
Non-cyclic
Most ancient form of carbon fixation?

26. 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

27. 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

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

29. 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

30. Figure 13.23 Iron-oxidizing bacteria.

32. 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

33. 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

34. 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