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Fermentation: Catabolism of carbon in the absence of a terminal electron acceptor (like O 2 ) for electron transport chain.

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Presentation on theme: "Fermentation: Catabolism of carbon in the absence of a terminal electron acceptor (like O 2 ) for electron transport chain."— Presentation transcript:

1 Fermentation: Catabolism of carbon in the absence of a terminal electron acceptor (like O 2 ) for electron transport chain

2 Compare the  E h for putting electrons onto O 2 vs. lactate

3 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?

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 A.General Aspects B.Types of Autotrophic Pathways


7 PHOTOSYNTHESIS (Photoautotrophy) X CO 2 CH 2 O NADP + NADPH e- photon Excited state Ground state

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

9 Phototrophic Prokaryotes: the metabolic menu GroupReducing powerOxidized product Purple nonsulfur bacteriaH 2, reduced organicOxidized organics Purple sulfur bacteriaH 2 SSO 4 -2 Green sulfur bacteriaH 2 SSO 4 -2 Green non sulfur bacteria*H 2 SSO 4 -2 Heliobacteria**Lactate, organicsOxidized organics CyanobacteriaH 2 OO 2 Prochlorophytes***H 2 OO 2 *Most ancient? **Gram positive, heterotrophs ***Related to cyanobacteria

10 Three types of photochemical energy capturing systems in microorganisms: 1.Carotenoid-based light-capturing system that is structurally similar to rhodopsin in eyes. In halophilic Archaea. 2.Anoxygenic (uses chlorophyll, no O 2 made) 3.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. 2005. 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 H 2 O; must use H 2 S instead Eventually, chlorophyll evolved. Utilizes a short enough wavelength (680 nm) to split H 2 O and generate O 2.

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) -O 2 is a reactive molecule: ·O 2 - H 2 O 2 OH · -At first, protected by Fe +2 (ferrous iron): Fe +2 + O 2  FeOH 3 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 O 2 in atmosphere -O 2 + sun (UV radiation) → O 3 (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 Compared to freshwater, nutrients (N, P, Fe) are limiting. Fewer cells found than in freshwater (only 10 6 /mL prokaryotes and 10 4 eukaryotes) Because oceans are huge, collective O 2 production and CO 2 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) Photosynthesis in the open oceans

21 Phototrophic Primary Producers (red = chlorophyll)

22 Phototrophic Prokaryotes: 1.Purple nonsulfur bacteria 2.Green nonsulfur 3.Purple sulfur bacteria (sulfur inside cell) 4.Green sulfur bacteria (sulfur outside cell 5.Heliobacteria (G+ relatives of Clostridium, endospores, N 2 - fixation) 5.Cyanobacteria 6.Prochlorophytes 7.Halobacterium-type 1 group of “photocapable” prokaryotes in the Domain Archaea (the halobacteria = extreme halophiles [salt-loving]) Domain Bacteria


24 Photosynthetic Prokaryotes GroupReducing powerOxidized product Purple nonsulfur bacteriaH 2, reduced organicOxidized organics Purple sulfur bacteriaH 2 SSO 4 -2 Green sulfur bacteriaH 2 SSO 4 -2 Green non sulfur bacteriaH 2 SSO 4 -2 Heliobacteria*Lactate, organicsOxidized organics CyanobacteriaH 2 OO 2 Prochlorophytes**H 2 OO 2 *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. 17.14, 17.15, and 17.18 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. 12.5 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: H 2 S, Fe 2+, S 0, etc.

37 Anoxygenic Photosynthesis Purple bacteria strong e - donor

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

39 Elemental sulfur globules outside filamentous cyanobacterium Oscillatoria limnetica Many cyanobacteria can use H 2 S as an electron donor for anoxygenic photosynthesis.

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

41 Variation on the Theme ATP onlyATP & NAD(P)H * * * Off to supply reducing power for CO 2 fixation via reverse citric acid cycle ATP only

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; CO 2 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. 17.19 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, N 2 fixing (heterocysts)

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


50 Electron donor: H 2 O


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 Halobacteria 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 Oops, wrong, outdated hypothesis

56 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. Light + H + = cis Loss of H + = trans Correct; see next slide Chloride ions flow across membrane in reverse direction for halorhodopsin

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 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.

59 Autotrophy General Aspects Heterotrophs: organisms requiring organic compounds as a carbon source Autotrophs: organism capable of biosynthesizing all cellular material from CO 2 ; CO 2 as a sole carbon source

60 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

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)

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