1. Fermentation:
Catabolism of carbon in the absence of a terminal electron acceptor (like O2) for electron transport chain

2. Compare the DEh for putting electrons onto O2 vs. lactate
Figure: 05-09
Caption:
The electron tower. Redox couples are arranged from the strongest reductants (negative reduction potential) at the top to the strongest oxidants (positive reduction potentials) at the bottom. As electrons are donated from the top of the tower, they can be “caught” by acceptors at various levels. The farther the electrons fall before they are caught, the greater the difference in reduction potential between electron donor and electron acceptor and the more energy that is released. As an example of this, on the left is shown the differences in energy released when a single electron donor, H2, reacts with any of three different electron acceptors, fumarate, nitrate, and oxygen.

3. The unusual fermentation of oxalate by Oxalobacter formigenes
Figure: 17-52a
Caption:
The unique fermentations of succinate and oxalate. (a) Succinate fermentation by Propionigenium modestum. A sodium-translocating ATPase produces ATP; sodium export is linked to the energy released by succinate decarboxylation.
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?

4. And now for something completely different!

5. 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
B. Types of Autotrophic Pathways

7. PHOTOSYNTHESIS (Photoautotrophy)
Excited state X
photon
CO2
NADP+ e-
CH2O
NADPH
Ground state

8. PHOTOAUTOTROPHY: 2 reactions
1. LIGHT  CHEMICAL ENERGY
(ATP)
2. CO2 reduction → Organic compounds

9. 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

10. 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)

11. 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 Mechanics of Biolenergetic Membrane Proteins 33: 863

12. Photosystems do not absorb at short enough wavelengths to split water, so must get e-’s somewhere else.
Cyclic: electrons run in closed circuit

13. Photosystems can take light energy strong enough to split water.
Non-cyclic (although cyclic can occur)

14. 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.

15. 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- H2O OH ·
At first, protected by Fe+2 (ferrous iron): Fe+2 + O2  FeOH3
Banded iron formations from Wittenoom Gorge in Australia

16. 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

17. 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.

18. 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.

19. Detection of algal blooms from satellites via remote sensing: relies on reflected spectral properties of chlorophylls.
Nutrient upwelling (El Nino) = phytoplankton blooms

20. 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 Earth’s 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)

21. Phototrophic Primary Producers (red = chlorophyll)

22. 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])

24. 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

25. 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

26. Structure of bacteriochlorophylls

28. Accessory pigments: Carotenoids

29. Accessory pigments: Phycobilins

30. 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

31. … light harvesting complex in cyanobacteria, plants

32. Mechanism of Photosynthesis 1) Anoxygenic Photosynthesis
Cyclic
Your text: Fig , 17.15, and
Purple Bacteria
Green Bacteria
Heliobacteria

33. 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 in your text)
may live as photoheterotrophs
two types: 1. sulfur
2. nonsulfur

34. 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)

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

36. Electron donors: H2S, Fe2+, S0, etc.

37. Anoxygenic Photosynthesis
strong e- donor
Purple bacteria

38. Purple bacteria
Cyclic
NAD(P)H and ATP can be generated by PMF

39. Many cyanobacteria can use H2S as an electron donor for anoxygenic photosynthesis.
Elemental sulfur globules outside filamentous cyanobacterium Oscillatoria limnetica

40. Purple bacterium (Chromatium):
internal sulfur deposits
Green bacterium (Chlorobium):
external sulfur deposits

41. Variation on the Theme * * ATP & NAD(P)H ATP only ATP only
* Off to supply reducing power for CO2 fixation via reverse citric acid cycle

42. 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)

43. 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)

44. 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)

45. 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.

46. Mechanism of Photosynthesis Oxygenic Photosynthesis
Photosystems I & II
Noncyclic
Your text, Fig
Cyanobacteria
Algae (protists)
Plants

47. 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)

48. Lake Mendota up close: eutrophic (nutrient-rich) lake
algal blooms July through September (ag runoff)

50. Electron donor: H2O

52. 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

53. Solar Salt
Evaporation
Ponds (salterns) in CA
Red coloration
due to carotenoids of
halobacteria

54. Colonies of halobacteria isolated from Portsmouth salt piles.
Plates contain 25 % NaCl !

55. Oops, wrong, outdated hypothesis
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

56. Correct; see next slide
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

57. Arrangement of bacteriorhodopsin in the cytoplasmic membrane:
Purple structures are proteins (opsin) that hold the chromophore (retinal)

58. 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 in the cell membrane. CP = cytoplasm, EC = extracellular space. Arrows indicate direction of ion transfer.
Bacteriorhodopsin and its retinal chromophore. Yellow arrow indicates direction of ion transfer.

59. 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

60. Autotrophy Types of Autotrophic Pathways
1. Calvin Cycle Fig & 17.22
2. Acetyl-CoA Pathway Fig
3. Reverse TCA Cycle Fig.17.24a
4. Hydroxypropionate Pathway Fig b

61. Calvin-Benson Cycle Fig. 17.21 & 17.22 Key enzymes:
A. Ribulose biphosphate carboxylase (RuBisCo)
carboxyosomes : Inclusion bodies
B. Phosphoribulokinase

62. Calvin-Benson Cycle Cyanobacteria
Key enzymes: ribulose biphosphate carboxylase (RuBisCo) = first enzyme, phosphoribulokinase = final enzyme in cycle

63. Requires ATP and reducing power

64. Reverse TCA Cycle
some methanogens
Green Sulfur bacteria (Chlorobium)

65. Hydroxypropionate Pathway
Green Non-Sulfur Bacteria (Chloroflexus)