chapter 20 metabolic diversity: phototrophy, autotrophy, chemolithotrophy, and nitrogen fixation

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)

Figure 20.1

Classification of Phototrophic Organisms

Figure 20.2

Patterns of Photosynthesis

Figure 20.2

Patterns of Photosynthesis

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

Figure 20.3a

Structure and Spectra of Chloro- and Bacteriochlorophyll

Figure 20.3b

Structure and Spectra of Chloro- and Bacteriochlorophyll

Absorption Spectrum

Figure 20.4

Structure of All Known Bacteriochlorophylls

Figure 20.4

Structure of All Known Bacteriochlorophylls

Figure 20.4

Structure of All Known Bacteriochlorophylls

Figure 20.5a

Photomicrograph of Algal Cell Showing Chloroplasts

Figure 20.5b

Chloroplast Structure

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

Figure 20.6

Arrangement of Light-Harvesting Chlorophylls

Figure 20.7

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

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

Figure 20.8

Structure of -carotene, a Typical Carotenoid

Figure 20.9

Structures of Some Common Carotenoids

Figure 20.9

Structures of Some Common Carotenoids

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

Figure 20.10

Phycobiliproteins and Phycobilisomes

Figure 20.11

Absorption Spectrum with an Accessory Pigment

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

Figure 20.12

Membranes in Anoxygenic Phototrophs

Chromatophores Lamellar Membranes in the Purple BacteriumEctothiorhodospira

Figure 20.13

Structure of Reaction Center in Purple Bacteria

Arrangement of Pigment Moleculesin Reaction Center

Figure 20.13

Structure of Reaction Center in Purple Bacteria

Molecular Model of the Protein Structure of the Reaction Center

Figure 20.14

Example of Electron Flow in Anoxygenic Photosynthesis

Purple bacterium

Figure 20.15

Arrangement of Protein Complexes in Reaction Center

Figure 20.16

Map of Photosynthetic Gene Cluster in Purple Phototroph

Bacteriochlorophyll synthesis

Carotenoid synthesis

Figure 20.17

Phototrophic Purple and Green Sulfur Bacteria

Purple Bacterium, Chromatium okenii Green Bacterium, Chlorobium limicola

Figure 20.18

Electron Flow in Purple, Green, Sulfur and Heliobacteria

Bacteriochlorophyll a Bacteriochlorophyll g

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

Figure 20.19

The “Z scheme” in Oxygenic Photosynthesis

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

Figure 20.21a

Key Reactions of the Calvin Cycle

Figure 20.21b

Key Reactions of the Calvin Cycle

Figure 20.21c

Key Reactions of the Calvin Cycle

Figure 20.22

The Calvin Cycle

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

Figure 20.24a

Autotrophic Pathways in Phototrophic Green Sulfur Bacteria

Figure 20.24b

Autotrophic Pathways in Phototrophic Green Nonsulfur Bacteria

(Malonyl-CoA)

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

Figure 20.25

Two Hydrogenases of Aerobic H2 Bacteria

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

Figure 20.26

Sulfur Bacteria

Figure 20.27a

Oxidation of Reduced Sulfur Compounds

Steps in the Oxidation of Different Compounds

Figure 20.27b

Oxidation of Reduced Sulfur Compounds

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

Figure 20.28

Iron-Oxidizing Bacteria

Acid Mine Drainage

Figure 20.28

Iron-Oxidizing Bacteria

Cultures of Acidithiobacillus ferrooxidans shown in dillution series

Figure 20.29

Iron Bacteria Growing at Neutral pH: Sphaerotilus

Figure 20.30

Electron Flow During Fe2+ Oxidation

(Cu-containing protein)

Fe2+ Oxidation in Anoxic Tube CulturesFigure 20.31

Ferrous Iron Oxidation by Anoxygenic Phototrophs

Sterile

Inoculated

Growing culture

Figure 20.31

Ferrous Iron Oxidation by Anoxygenic Phototrophs

Phase-contrast Photomicrograph Of an Iron-Oxidizing Purple Bacterium

Gas vesicles

Iron precipiatates

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

Figure 20.32

Oxidation of Ammonia by Ammonia-Oxidizing Bacteria

Figure 20.33

Oxidation of Nitrite to Nitrate by Nitrifying Bacteria

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

Figure 20.34a-b

Anammox

Phase-contrast Photomicrograph of Brocadia Anammoxidans cells

Transmission Electronic Micrograph of a Cell

Figure 20.34c

Anammoxosome

Reactions in the anammoxosome

Autotrophy in Anammox Bacteria

Autotrophy

- 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)

Figure 20.35

FeMo-co, the Iron-Molybdenum Cofactor from Nitrogenase

Dinitrogenase

Alternative nitrogenase

- vanadium

- no Mo and Va

Figure 20.36

Nitrogenase Function

Pyruvate ferredoxin oxidoreductase - contains Iron-sulfur center

Pyruvate flavodoxin oxidoreductase - contains FMN

Klebsiella pneumoniae

Figure 20.37

Induction of Slime Formation by O2 in Nitrogen-Fixing Cells

Under micro-oxic conditions

Under air

Very little slime

Extensive slime

Figure 20.38

Reaction of Nitrogen Fixation in S. thermoautotrophicus

Requires less ATPDoes not reduce acetylene

Figure 20.39

The Acetylene Reduction Assay for Nitrogenase Activity

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

Figure 20.40

The nif regulon in K. pneumoniae

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

Dinitrogenase: α2β2

Dinitrogenase reductase: α2