Energy Metabolism V Autotrophy and Lithotrophy

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Fermentation Catabolism of carbon in the absence
of a terminal electron acceptor (like O2) for
electron transport chain
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Compare the DEh for putting electrons onto O2 vs.
lactate
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The unusual fermentation of oxalate by
Oxalobacter formigenes
Thank goodness for this hard-working anaerobe in
your gut it degrades oxalate from amino acid
catabolism, coffee, tea, fruits, veggies and
helps prevent kidney stones!! You can lose it
by taking doxycycline and other antibiotics, but
can regain it by guess how?
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And now for something completely different!
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Photosynthesis and Autotrophy

• I. Photosynthesis
• A. General Aspects
• B. Classes of Photosynthetic Bacteria
• C. Mechanism of Photosynthesis
• 1. Anoxygenic Photosynthesis
• 2. Oxygenic Photosynthesis
• D. Halobacterium (light-driven H pump)
• II. Autotrophy
• A. General Aspects
• B. Types of Autotrophic Pathways

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PHOTOSYNTHESIS (Photoautotrophy)
Excited state
X
CO2
NADP
photon
e-
CH2O
NADPH
Ground state
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PHOTOAUTOTROPHY 2 reactions
1. LIGHT ? CHEMICAL ENERGY
(ATP) 2. CO2 reduction ? Organic compounds
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Phototrophic Prokaryotes the metabolic menu

• Group Reducing power Oxidized product
• Purple nonsulfur bacteria H2, reduced
  organic Oxidized organics
• Purple sulfur bacteria H2S SO4-2
• Green sulfur bacteria H2S SO4-2
• Green non sulfur bacteria H2S SO4-2
• Heliobacteria Lactate, organics Oxidized
  organics
• Cyanobacteria H2O O2
• Prochlorophytes H2O O2

Most ancient? Gram positive,
heterotrophs Related to cyanobacteria
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• Three types of photochemical energy capturing
  systems in microorganisms
• Carotenoid-based light-capturing system that is
  structurally similar to rhodopsin in eyes. In
  halophilic Archaea.
• Anoxygenic (uses chlorophyll, no O2 made)
• Oxygenic (uses chlorophyll, splits water,
  generates oxygen)

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Carotenoid-based (bacteriorhodopsin) -no
chlorophyll, no metals protein with G-protein
coupled receptor-like structure plus chromophore
(retinal) -chromophore is a long-chain
hydrocarbon with extensive conjugation -ancient
protection for oxygenic phototrophs against toxic
O2 -light-powered ion transfer
Nagel et al. 2005. Mechanics of Biolenergetic
Membrane Proteins 33 863
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Photosystems do not absorb at short enough
wavelengths to split water, so must get e-s
somewhere else. Cyclic electrons run in closed
circuit
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Photosystems can take light energy strong enough
to split water. Non-cyclic (although cyclic can
occur)
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Chlorophyll Light Harvesting Molecule

• Porphyrin (like heme in cytochromes, but Mg
  instead of Fe)

Bacteriochlorophyll Absorbs at 700 nm allows
light harvesting at depths where light is low and
environment is anoxic Not enough energy to
extract e- from H2O must use H2S
instead Eventually, chlorophyll evolved.
Utilizes a short enough wavelength (680 nm) to
split H2O and generate O2.
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• Consequence of oxyenic photosynthesis in
  evolution
• DNA absorbs UV at 260 nm mutations occur
• Some exant organisms are resistant to damaging
  radiation
• (e.g. Deinococcus radiodurans survives 100 rad
  while 10 rads kills us D. radiodurans is
  resistant to chromosome shattering and mutation)
• O2 is a reactive molecule O2- H2O2 OH
  
• At first, protected by Fe2 (ferrous iron) Fe2
  O2 ? FeOH3

Banded iron formations from Wittenoom Gorge in
Australia
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• Consequence of oxyenic photosynthesis in
  evolution
• Bacteria began evolving carotenoids protection
  against singlet oxygen convert to less toxic
  state
• Eventually (at least 2 billion years ago), used
  up ferrous iron
• Accumulation of O2 in atmosphere
• O2 sun (UV radiation) ? O3 (ozone)
• Ozone screened out wavelengths below 290 nm
• - Life could evolve on land, because water no
  longer necessary to screen out damaging/mutagenic
  UV radiation

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Production of Reactive Oxygen Species (ROS)

• During normal cellular respiration, oxygen is
  reduced to water and highly reactive superoxide (
  O2- ).
• Reactive oxygen species react with nucleic acids,
  sugars, proteins and lipids - eventually leading
  to molecular degradation.

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Cellular Defense Mechanisms Prevent ROS Buildup.

• Due to the oxygen rich environment in which
  proteins exist, reactions with ROS are
  unavoidable.
• - Superoxide dismutase, catalase, and glutathione
  peroxidase are natural antioxidants present in
  organisms which eliminate some ROS. Other
  molecules are antioxidants too (e.g. ascorbic
  acid, or Ignose/Godnose!)
• - Glutathione peroxidase catalyzes the reduction
  of peroxide by oxidizing glutathione (GSH) to
  GSSG.

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Detection of algal blooms from satellites via
remote sensing relies on reflected spectral
properties of chlorophylls.
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Photosynthesis in the open oceans

• Compared to freshwater, nutrients (N, P, Fe) are
  limiting. Fewer cells found than in freshwater
  (only 106/mL prokaryotes and 104 eukaryotes)
• Because oceans are huge, collective O2 production
  and CO2 fixation there is a major contributor to
  Earths carbon balance.
• Influence food chain, global climate
• Many marine microbes use light to drive ATP
  synthesis.
• Photic zone upper 300 meters
• Oxygenic and anoxygenic photosynthesis
• Chlorophylls a and b (cyanobacteria and
  relatives algae)
• Proteorhodopsin (very similar to
  bacteriorhodopsin but Bacteria, not Archaea)

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Phototrophic Primary Producers (red
chlorophyll)
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Phototrophic Prokaryotes

• Purple nonsulfur bacteria
• Green nonsulfur
• Purple sulfur bacteria
• (sulfur inside cell)
• Green sulfur bacteria
• (sulfur outside cell
• Heliobacteria
• (G relatives of Clostridium, endospores,
  N2-fixation)
• 5. Cyanobacteria
• Prochlorophytes
• Halobacterium-type

Domain Bacteria
1 group of photocapable prokaryotes in the
Domain Archaea (the halobacteria extreme
halophiles salt-loving)
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Photosynthetic Prokaryotes

• Group Reducing power Oxidized product
• Purple nonsulfur bacteria H2, reduced
  organic Oxidized organics
• Purple sulfur bacteria H2S SO4-2
• Green sulfur bacteria H2S SO4-2
• Green non sulfur bacteria H2S SO4-2
• Heliobacteria Lactate, organics Oxidized
  organics
• Cyanobacteria H2O O2
• Prochlorophytes H2O O2

• Gram positive, heterotrophs
• Related to cyanobacteria

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Chlorophyll Diversity
Different absorbance maxima different niches
e.g. lower or higher in water column. Chlorophyll
(cyanobacteria) 680 nm Bchl a (purple
bacteria) 805, 870
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Structure of bacteriochlorophylls
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Accessory pigmentsCarotenoids
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Accessory pigmentsPhycobilins
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Photosynthetic Membranes
Reaction center chlorophyll -few -convert light
energy to ATP Light harvesting chlorophyll
-many - antenna -captures faint signal of
low light environments
Accessory pigments Carotenoids Phycobilins
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light harvesting complex in cyanobacteria,
plants
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Mechanism of Photosynthesis1) Anoxygenic
Photosynthesis

• Cyclic
• Your text Fig. 17.14 , 17.15, and 17.18
• Purple Bacteria
• Green Bacteria
• Heliobacteria

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Purple Bacteria (within phylum Proteobacteria)

• photosynthetic membranes are lamellae or tubes
  with the plasma membrane
• bacteriochlorophyll a or b
• accessory pigments are purple colored carotenoid
  pigments
• (see Fig. 12.5 in your text)
• may live as photoheterotrophs
• two types 1. sulfur
• 2. nonsulfur

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Green Bacteria

• photosynthetic membranes are vesicles attached to
  but not continuous with the plasma membrane
• bacteriochlorophyll c, b, or e (small amount of
  a in LH and RC)
• accessory pigments are yellow to brown-colored
  carotenoids
• two types 1. sulfur (green sulfur bacteria
  phylum)
• 2. nonsulfur (green nonsulfur bacteria phylum)

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Heliobacteria

• plasma membrane only (no specialized
  photosynthetic membranes)
• bacteriochlorophyll g
• Photoheterotrophs require organic carbon
• These are the only Gram-positive photosynthetic
  bacteria

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Electron donors H2S, Fe2, S0, etc.
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Anoxygenic Photosynthesis
strong e- donor
Purple bacteria
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Purple bacteria
Cyclic NAD(P)H and ATP can be generated by PMF
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Many cyanobacteria can use H2S as an electron
donor for anoxygenic photosynthesis.
Elemental sulfur globules outside filamentous
cyanobacterium Oscillatoria limnetica
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Purple bacterium (Chromatium) internal sulfur
deposits
Green bacterium (Chlorobium) external sulfur
deposits
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Variation on the Theme
ATP only
ATP NAD(P)H
ATP only


Off to supply reducing power for CO2 fixation
via reverse citric acid cycle
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Green Sulfur Bacteria

• (Chorobium, Chlorobaculum, Prosthecochloris)
• Aquatic, anoxic environments
• Most are facultative heterotrophs strict
  autotrophy requires reverse TCA cycle
• Have chlorosomes very efficient at light
  harvesting so live at great depths
• May form consortia aggregates of cells that
  have differing metabolic duties chemotrophic and
  phototrophic (epibiont) components. Example
  Chlorochromatium aggregatum (not a formal
  taxonomic name because not a single species)

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Green Non Sulfur Bacteria

• (Choroflexus)
• Filamentous, form microbial mats with
  cyanobacteria in neutral to alkaline hot springs
• Like Green Sulfur Bacteria has chlorosomes
• But reaction center of in cell membrane is like
  purple bacteria
• Earliest known photosynthetic bacterium perhaps
  reaction center first, chlorosome later by HGT
• Most are facultative heterotrophs CO2 fixation
  requires hydroxypropionate pathway (unique to
  very ancient organisms)

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Light harvesting complex in green photosynthetic
bacteria (both sulfur and non-sulfur)
Chlorosome is a giant antenna Bchl c, d, or
e BP baseplate (proteins) LH light
harvesting complex (Bchl a) RC reaction center
(Bchl a)
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Chlorosomes (EM, stained dark)-in green sulfur
bacteria-lie along the inside of cytoplasmic
membrane-proteinaceous (nonlipid) membrane-each
vesicle contains 10,000 bacteriochlorophyll c
molecules in tubes/rods-chlorosomes transmit
energy via subantenna of bacteriochlorophyll a.
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Mechanism of PhotosynthesisOxygenic
Photosynthesis

• Photosystems I II
• Noncyclic
• Your text, Fig. 17.19
• Cyanobacteria
• Algae (protists)
• Plants

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Cyanobacteria (phylum contains cyanobacteria and
prochlorophytes)

• Synechococcus, Oscillatoria, Nostoc, Anabaena
• photosynthetic mebranes are multilayered lamellae
• formerly called blue-green algae but now known
  to be prokaryotic and possess peptidoglycan
• chlorophyll a only
• accessory pigments are carotenoids and phycobilin
  proteins
• Photosystem I and II are present (oxygenic
  photosynthesis)
• Autotrophs
• Gas vesicles frequent
• Some are filamentous, N2 fixing (heterocysts)

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Lake Mendota up close eutrophic
(nutrient-rich) lake algal blooms July through
September (ag runoff)
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Electron donor H2O
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Halobacterium-type

• Use light-driven proton pump consisting of
  patches of the pigment bacteriorhodopsin in
  cytoplasmic membrane
• bacteriorhodopsin resembles rhodopsin, the visual
  pigment
• Absorbs light near 570 nm (green region of
  spectrum)
• Extreme halophile (2-4M NaCl 12-23) balances
  Na outside with K inside to maintain osmotic
  equilibrium
• Heterotrophs (use amino acids and organic acids
  for growth)
• Most are obligate aerobes some can do anaerobic
  respiration or fermentation

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Solar Salt Evaporation Ponds (salterns) in
CA Red coloration due to carotenoids
of halobacteria
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Colonies of halobacteria isolated from Portsmouth
salt piles. Plates contain 25 NaCl !
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Halobacteria
Oops, wrong, outdated hypothesis

• Domain Archaea

• Not autotrophs - grow as chemoheterotrophs but
  can function as phototrophs

• Bacteriorhodopsin, proteorhodopsin
  cytoplasmic membrane-associated photopigment
  similar to rhodopsin
• of mammalian eye.

• Bacteriorhodopsin is a light driven ion (proton)
  pump...
• Homologous protein in Halobacteria is called
  halorhodopsin a chloride pump

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Light at 570 nm excites the retinal chromophore
of bacteriorhodopsin, converting it from its
normal all-trans conformation to a cis form.
Conversion instigates the movement of a proton
across the membrane. Proton loss returns retinal
to its all-trans form.
Correct see next slide
Chloride ions flow across membrane in reverse
direction for halorhodopsin
Light H cis Loss of H trans
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Arrangement of bacteriorhodopsin in the
cytoplasmic membrane Purple structures are
proteins (opsin) that hold the chromophore
(retinal)
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Current model for how bacteriorhodopsin and
halorhodopsin work Biochemical studies show
that rather than transporting H out,
bacteriorhodopsin (BR) may actually transport OH-
in and halorhodopsin (HR) may transport in a Cl-
(from all that NaCl in its environment)
Bacteriorhodopsin and its retinal chromophore.
Yellow arrow indicates direction of ion transfer.
Bacteriorhodopsin in the cell membrane. CP
cytoplasm, EC extracellular space. Arrows
indicate direction of ion transfer.
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Autotrophy General Aspects

• Heterotrophs organisms requiring organic
  compounds as a carbon source
• Autotrophs organism capable of biosynthesizing
  all cellular material from CO2 CO2 as a sole
  carbon source

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Autotrophy Types of Autotrophic Pathways

• 1. Calvin Cycle Fig. 17.21 17.22
• 2. Acetyl-CoA Pathway Fig. 17.41
• 3. Reverse TCA Cycle Fig.17.24a
• 4. Hydroxypropionate Pathway Fig. 17.24b

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Calvin-Benson Cycle

• Fig. 17.21 17.22
• Key enzymes
• A. Ribulose biphosphate carboxylase (RuBisCo)
• carboxyosomes Inclusion bodies
• B. Phosphoribulokinase

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Calvin-Benson Cycle
Cyanobacteria Key enzymes ribulose biphosphate
carboxylase (RuBisCo) first enzyme,
phosphoribulokinase final enzyme in cycle
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Requires ATP and reducing power
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Reverse TCA Cycle
some methanogens Green Sulfur bacteria
(Chlorobium)
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Hydroxypropionate Pathway
Green Non-Sulfur Bacteria (Chloroflexus)