1. Chapter 20
Metabolic Diversity: Phototrophy, Autotrophy, Chemolithotrophy, and Nitrogen Fixation

2. I. The Phototrophic Way of Life
Photosynthesis
Chlorophylls and Bacteriochlorophylls
Carotenoids and Phycobilins
Anoxygenic Photosynthesis
Oxygenic Photosynthesis

3. 20.1 Photosynthesis
Photosynthesis is the most important biological process on Earth
Phototrophs are organisms that carry out photosynthesis
Most phototrophs are also autotrophs
Photosynthesis requires light-sensitive pigments called chlorophyll
Photoautotrophy requires ATP production and CO2 reduction
Oxidation of H2O produces O2 (oxygenic photosynthesis)
Oxygen not produced (anoxygenic photosynsthesis)

4. Classification of Phototrophic Organisms
Figure 20.1

5. Patterns of Photosynthesis
Figure 20.2

6. Patterns of Photosynthesis
Figure 20.2

7. 20.2 Chlorophylls and Bacteriochlorophylls
Organisms must produce some form of chlorophyll (or bacteriochlorophyll) to be photosynthetic
Chlorophyll is a porphyrin
Number of different types of chlorophyll exist
Different chlorophylls have different absorption spectra
Chlorophyll pigments are located within special membranes
In eukaryotes, called thylakoids
In prokaryotes, pigments are integrated into cytoplasmic membrane

8. Structure and Spectra of Chloro- and Bacteriochlorophyll
Figure 20.3a

9. Structure and Spectra of Chloro- and Bacteriochlorophyll
Absorption Spectrum
Figure 20.3b

10. Structure of All Known Bacteriochlorophylls
Figure 20.4

11. Structure of All Known Bacteriochlorophylls
Figure 20.4

12. Structure of All Known Bacteriochlorophylls
Figure 20.4

13. Photomicrograph of Algal Cell Showing Chloroplasts
Figure 20.5a

14. Chloroplast Structure
Figure 20.5b

15. 20.2 Chlorophylls and Bacteriochlorophylls
Reaction centers participate directly in the conversion of light energy to ATP
Antenna pigments funnel light energy to reaction centers
Chlorosomes function as massive antenna complexes
Found in green sulfur and nonsulfur bacteria

16. Arrangement of Light-Harvesting Chlorophylls
Figure 20.6

17. The Chlorosome of Green Sulfur and Nonsulfur Bacteria
Electron Micrograph of Cell of Green Sulfur Bacterium
Figure 20.7

18. The Chlorosome of Green Sulfur and Nonsulfur Bacteria
Model of Chromosome Structure
Figure 20.7

19. 20.3 Carotenoids and Phycobilins
Phototrophic organisms have accessory pigments in addition to chlorophyll, including carotenoids and phycobiliproteins
Carotenoids
Always found in phototrophic organisms
Typically yellow, red, brown, or green
Energy absorbed by carotenoids can be transferred to a reaction center
Prevent photo-oxidative damage to cells

20. Structure of -carotene, a Typical Carotenoid
Figure 20.8

21. Structures of Some Common Carotenoids
Figure 20.9

22. Structures of Some Common Carotenoids
Figure 20.9

23. 20.3 Carotenoids and Phycobilins
Phycobiliproteins are main antenna pigments of cyanobacteria and red algae
Form into aggregates within the cell called phycobilisomes
Allow cell to capture more light energy than chlorophyll alone

24. Phycobiliproteins and Phycobilisomes
Figure 20.10

25. Absorption Spectrum with an Accessory Pigment
Figure 20.11

26. 20.4 Anoxygenic Photosynthesis
Anoxygenic photosynthesis is found in at least four phyla of Bacteria
Electron transport reactions occur in the reaction center of anoxygenic phototrophs
Reducing power for CO2 fixation comes from reductants present in the environment (i.e., H2S, Fe2+, or NO2-)
Requires reverse electron transport for NADH production in purple phototrophs

27. Membranes in Anoxygenic Phototrophs
Chromatophores
Lamellar Membranes in the Purple Bacterium
Ectothiorhodospira
Figure 20.12

28. Structure of Reaction Center in Purple Bacteria
Arrangement of Pigment Molecules
in Reaction Center
Figure 20.13

29. Structure of Reaction Center in Purple Bacteria
Molecular Model of the Protein Structure
of the Reaction Center
Figure 20.13

30. Example of Electron Flow in Anoxygenic Photosynthesis
Purple bacterium
Figure 20.14

31. Arrangement of Protein Complexes in Reaction Center
Figure 20.15

32. Map of Photosynthetic Gene Cluster in Purple Phototroph
Bacteriochlorophyll synthesis
Carotenoid synthesis
Figure 20.16

33. Phototrophic Purple and Green Sulfur Bacteria
Purple Bacterium, Chromatium okenii
Green Bacterium, Chlorobium limicola
Figure 20.17

34. Electron Flow in Purple, Green, Sulfur and Heliobacteria
Bacteriochlorophyll a
Bacteriochlorophyll g
Figure 20.18

35. 20.5 Oxygenic Photosynthesis
Oxygenic phototrophs use light to generate ATP and NADPH
The two light reactions are called photosystem I and photosystem II
“Z scheme” of photosynthesis
Photosystem II transfers energy to photosystem I
ATP can also be produced by cyclic photophosphorylation

36. The “Z scheme” in Oxygenic Photosynthesis
Figure 20.19

37. II. Autotrophy 20.6 The Calvin Cycle
20.7 Other Autotrophic Pathways in Phototrophs

38. 20.6 The Calvin Cycle The Calvin Cycle
Named for its discoverer Melvin Calvin
Fixes CO2 into cellular material for autotrophic growth
Requires NADPH, ATP, ribulose 1,5-bisphophate carboxylase (RubisCO), and phosphoribulokinase
6 molecules of CO2 are required to make 1 molecule of glucose

39. Key Reactions of the Calvin Cycle
Figure 20.21a

40. Key Reactions of the Calvin Cycle
Figure 20.21b

41. Key Reactions of the Calvin Cycle
Figure 20.21c

42. The Calvin Cycle
Figure 20.22

43. 20.7 Other Autotrophic Pathways in Phototrophs
Green sulfur bacteria use the reverse citric acid cycle to fix CO2
Green nonsulfur bacteria use the hydroxyproprionate pathway to fix CO2

44. Autotrophic Pathways in Phototrophic Green Sulfur Bacteria
Figure 20.24a

45. Autotrophic Pathways in Phototrophic Green Nonsulfur Bacteria
(Malonyl-CoA)
Figure 20.24b

46. Iginicoccus hospitalis, an archaeum, uses a new CO2 fixation pathway?

47. III. Chemolithotrophy 20.8 The Energetics of Chemolithotrophy
Hydrogen Oxidation
Oxidation of Reduced Sulfur Compounds
Iron Oxidation
Nitrification
Anammox

48. 20.8 The Energetics of Chemolithotrophy
Chemolithotrophs are organisms that obtain energy from the oxidation of inorganic compounds
Mixotrophs are chemolithotrophs that require organic carbon as a carbon source
Many sources of reduced molecules exist in the environment
The oxidation of different reduced compounds yields varying amounts of energy

49. Energy Yields from Oxidation of Inorganic Electron Donors

50. 20.9 Hydrogen Oxidation
Anaerobic H2 oxidizing Bacteria and Archaea are known
Catalyzed by hydrogenase
In the presence of organic compounds such as glucose, synthesis of Calvin cycle and hydrogenase enzymes is repressed

51. Two Hydrogenases of Aerobic H2 Bacteria
Figure 20.25

52. 20.10 Oxidation of Reduced Sulfur Compounds
Many reduced sulfur compounds are used as electron donors
Discovered by Sergei Winogradsky
H2S, S0, S2O3- are commonly used
One product of sulfur oxidation is H+, which results in a lowering of the pH of its surroundings
Sox system oxidizes reduced sulfur compounds directly to sulfate (e.g. Paracoccus pantotrophus, etc., 15 genes)
Usually aerobic, but some organisms can use nitrate as an electron acceptor

53. Sulfur Bacteria
Figure 20.26

54. Oxidation of Reduced Sulfur Compounds
Steps in the Oxidation of Different Compounds
Figure 20.27a

55. Oxidation of Reduced Sulfur Compounds
Figure 20.27b

56. 20.11 Iron Oxidation
Ferrous iron (Fe2+) oxidized to ferric iron (Fe3+)
Ferric hydroxide precipitates in water
Many Fe oxidizers can grow at pH <1
Often associated with acidic pollution from coal mining activities
Some anoxygenic phototrophs can oxidize Fe2+ anaerobically using Fe2+ as an electron donor for CO2 reduction

57. Iron-Oxidizing Bacteria
Acid Mine Drainage
Figure 20.28

58. Iron-Oxidizing Bacteria
Cultures of Acidithiobacillus ferrooxidans shown
in dillution series
Figure 20.28

59. Iron Bacteria Growing at Neutral pH: Sphaerotilus
Figure 20.29

60. Electron Flow During Fe2+ Oxidation
(Cu-containing protein)
Figure 20.30

61. Ferrous Iron Oxidation by Anoxygenic Phototrophs
Growing culture
Inoculated
Sterile
Fe2+ Oxidation in Anoxic Tube Cultures
Figure 20.31

62. Ferrous Iron Oxidation by Anoxygenic Phototrophs
Gas vesicles
Iron precipiatates
Phase-contrast Photomicrograph
Of an Iron-Oxidizing Purple Bacterium
Figure 20.31

63. 20.12 Nitrification
NH3 and NO2- are oxidized by nitrifying bacteria during the process of nitrification
Two groups of bacteria work in concert to fully oxidize ammonia to nitrate
Key enzymes are ammonia monooxygenase, hydroxylamine oxidoreductase, and nitrite oxidoreductase
Only small energy yields from this reaction
Growth of nitrifying bacteria is very slow

64. Oxidation of Ammonia by Ammonia-Oxidizing Bacteria
Figure 20.32

65. Oxidation of Nitrite to Nitrate by Nitrifying Bacteria
Figure 20.33

66. 20.13 Anammox Anammox: anoxic ammonia oxidation
- NH4+ + NO2- → N2 + 2 H2O
Performed by unusual group of obligate anaerobes
Anammoxosome is a membrane-enclosed compartment where anammox reactions occur
Lipids that make up the anammoxsome are not the typical lipids of Bacteria
Protects cell from reactions occuring during anammox
Hydrazine (H2N=NH2), a very strong reductant, is an intermediate of anammox
Anammox is very beneficial in the treatment of sewage and wastewater

67. Anammox Phase-contrast Photomicrograph of
Brocadia Anammoxidans cells
Transmission Electronic Micrograph of a Cell
Figure 20.34a-b

68. Anammoxosome
Reactions in the anammoxosome
Figure 20.34c

69. Autotrophy in Anammox Bacteria
- NO2-, actually hydrazine (N2H4), is an electron donor for the reduction of CO2
Lack Calvin cycle enzyme
Use an acetyl-CoA pathway

70. Reactions of the Acetyl-CoA Pathway
Figure 21.18

71. IV. Nitrogen Fixation 20.14 Nitrogenase and Nitrogen Fixation
Genetics and Regulation of Nitrogen Fixation

72. 20.14 Nitrogenase and Nitrogen Fixation
Only certain prokaryotes can fix nitrogen
Some nitrogen fixers are free living and others are symbiotic
Reaction is catalyzed by nitrogenase
Sensitive to the presence of oxygen
A wide variety of nitrogenases use different metal cofactors
Nitrogenase activity can be assayed using the acetylene reduction assay (C2H2 → C2H4)

73. FeMo-co, the Iron-Molybdenum Cofactor from Nitrogenase
Dinitrogenase
Alternative nitrogenase
- vanadium
- no Mo and Va
Figure 20.35

74. Nitrogenase Function Klebsiella pneumoniae
Pyruvate ferredoxin oxidoreductase - contains Iron-sulfur center
Pyruvate flavodoxin oxidoreductase - contains FMN
Klebsiella pneumoniae
Figure 20.36

75. Induction of Slime Formation by O2 in Nitrogen-Fixing Cells
Extensive slime
Very little slime
Under micro-oxic conditions
Under air
Figure 20.37

76. Reaction of Nitrogen Fixation in S. thermoautotrophicus
Requires less ATP
Does not reduce acetylene
Figure 20.38

77. The Acetylene Reduction Assay for Nitrogenase Activity
Figure 20.39

78. 20.15 Genetics and Regulation of Nitrogen Fixation
Highly regulated process because it is such an energy- demanding process
nif regulon coordinates regulation of genes essential to nitrogen fixation
Oxygen and ammonia are the two main regulatory effectors

79. The nif regulon in K. pneumoniae
Dinitrogenase: α2β2
Dinitrogenase reductase: α2
NtrC: active in the presence of limited amount of fixed nitrogen compounds and promotes transcription of regulate the expression of nifAL
NifA: a positive regulator
NifL: a negative regulator containing FAD, a redox coenzyme
Figure 20.40