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

I. The Phototrophic Way of Life 20.1 Photosynthesis 20.2 Chlorophylls and Bacteriochlorophylls 20.3 Carotenoids and Phycobilins 20.4 Anoxygenic Photosynthesis 20.5 Oxygenic Photosynthesis

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)

Classification of Phototrophic Organisms Figure 20.1

Patterns of Photosynthesis Figure 20.2

Patterns of Photosynthesis Figure 20.2

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

Structure and Spectra of Chloro- and Bacteriochlorophyll Figure 20.3a

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

Structure of All Known Bacteriochlorophylls Figure 20.4

Structure of All Known Bacteriochlorophylls Figure 20.4

Structure of All Known Bacteriochlorophylls Figure 20.4

Photomicrograph of Algal Cell Showing Chloroplasts Figure 20.5a

Chloroplast Structure Figure 20.5b

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

Arrangement of Light-Harvesting Chlorophylls Figure 20.6

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

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

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

Structure of -carotene, a Typical Carotenoid Figure 20.8

Structures of Some Common Carotenoids Figure 20.9

Structures of Some Common Carotenoids Figure 20.9

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

Phycobiliproteins and Phycobilisomes Figure 20.10

Absorption Spectrum with an Accessory Pigment Figure 20.11

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

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

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

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

Example of Electron Flow in Anoxygenic Photosynthesis Purple bacterium Figure 20.14

Arrangement of Protein Complexes in Reaction Center Figure 20.15

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

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

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

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

The “Z scheme” in Oxygenic Photosynthesis Figure 20.19

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

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

Key Reactions of the Calvin Cycle Figure 20.21a

Key Reactions of the Calvin Cycle Figure 20.21b

Key Reactions of the Calvin Cycle Figure 20.21c

The Calvin Cycle Figure 20.22

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

Autotrophic Pathways in Phototrophic Green Sulfur Bacteria Figure 20.24a

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

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

III. Chemolithotrophy 20.8 The Energetics of Chemolithotrophy 20.9 Hydrogen Oxidation 20.10 Oxidation of Reduced Sulfur Compounds 20.11 Iron Oxidation 20.12 Nitrification 20.13 Anammox

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

Energy Yields from Oxidation of Inorganic Electron Donors

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

Two Hydrogenases of Aerobic H2 Bacteria Figure 20.25

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

Sulfur Bacteria Figure 20.26

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

Oxidation of Reduced Sulfur Compounds Figure 20.27b

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

Iron-Oxidizing Bacteria Acid Mine Drainage Figure 20.28

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

Iron Bacteria Growing at Neutral pH: Sphaerotilus Figure 20.29

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

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

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

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

Oxidation of Ammonia by Ammonia-Oxidizing Bacteria Figure 20.32

Oxidation of Nitrite to Nitrate by Nitrifying Bacteria Figure 20.33

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

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

Anammoxosome Reactions in the anammoxosome Figure 20.34c

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

Reactions of the Acetyl-CoA Pathway Figure 21.18

IV. Nitrogen Fixation 20.14 Nitrogenase and Nitrogen Fixation 20.15 Genetics and Regulation of Nitrogen Fixation

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)

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

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

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

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

The Acetylene Reduction Assay for Nitrogenase Activity Figure 20.39

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

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