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Providence Journal Friday October 2, 2009

The New Yorker 3/20/1995 by Mort Gerberg

Bacteria Eukarya Archaea 3 Domains A common ancestor Characteristics Figure 28-1 Page 567 Bacteria Eukarya Archaea 3 Domains A common ancestor Characteristics plasma membrane cell walls DNA/RNA molecules ribosomes endosymbiosis Common ancestor of all species living today

This view is incorrect! According to morphological Figure 28-11 Page 577 According to morphological similarities, prokaryotes should be closely related Bacteria Archaea Eukarya This view is incorrect!

Size varies Shape varies Mobility varies Figure 28-13 Page 578 Small Large Compare relative sizes Size varies The sizes of bacteria and archaea vary. Mycoplasma cells (left) are about 0.5 µm in diameter, while Thiomargarita namibiensis cells (right) are about 150 µm in diameter. Shape varies The shapes of bacteria and archaea vary from rods such as Bacillus anthracis (left) and spheres to filaments or spirals such as Rhodospirillum. In some species, such as Streptococcus faecalis (right), cells attach to one another and form chains. Mobility varies A wide variety of bacteria and archaea use flagella (left) to power swimming movements. These cyanobacterial cells (right) move by gliding across a substrate.

Biology: What is Life? life study of Properties of Life Cellular Structure: the unit of life, one or many Metabolism: photosynthesis, respiration, fermentation, digestion, gas exchange, secretion, excretion, circulation –processing materials and energy Growth: cell enlargement, cell number Movement: intracellular, movement, locomotion Reproduction: avoid extinction at death Behavior: short term response to stimuli Evolution: long term adaptation

Homeostasis - metabolism Nutrition Mode Energy Source Carbon Source Photoautotroph Light CO2 Chemoautotroph Inorganic chem Photoheterotroph Organic chem Chemoheterotroph All of these nutritional modes are found among prokaryotes! Eukaryotes are not as diverse in their nutritional modes.

Photoautotrophs - photosynthesis Ancient pathway, but not universal Cyanobacteria, Algae, Plants light CO2 + H2O  O2 + CH2O chlorophyll Purple-sulfur bacteria CO2 + H2S  S2 + CH2O

Cyanobacterial Vegetative Cell cell wall mesosome cell membrane cyanophycean starch photosynthesis product cyanophycin vacuole lipid droplet polyphosphate granule thylakoids light reactions nucleoid cytosol polyhedral body Calvin cycle and starch synthesis http://www.botany.hawaii.edu/faculty/webb/BOT311/Cyanobacteria/CBDivideTEM.jpg RubisCO crystals! Prokaryotes do not have chloroplasts… they became chloroplasts!

Artificial coloration of TEM image But thylakoids shown as green would be natural! The location of bacteriochlorophyll! For the light reactions… http://www.jgi.doe.gov/JGI_microbial/images/microbes2003/anava.jpg http://www.bio.utexas.edu/researchutex/photogallery/Anabaena_cylindrica_629.htm In a light microscope image: Thylakoids would not be visible, so green color would appear throughout cytosol with the nucleoid region lighter in color.

Figure 28.5 Page 572

Chemoautotrophs - N metabolism Cyanobacteria, Rhizobium - N2 fixation H+ + ATP + N2  NH4+ Nitrosomonas - nitrification (forms nitrite) 2 CO2 + NH4+  NO2- + 2 CH2O Pseudomonas - denitrification 2 CH2O + 2 NO2-  N2 + 2 CO2 + 2 H2O √ Which of these processes is demonstrating chemoautotrophism?

Nitrosomonas - internal membranes use NH4+ electrons in an ETS to produce ATP ATP and protons used to reduce CO2 to CH2O http://microbewiki.kenyon.edu/images/thumb/8/89/Zdrs0232.jpg/350px-Zdrs0232.jpg

N O=O Rhizobium needs anaerobic conditions to convert N2 into NH4+ Legumes produce heme based molecules and rapid respiration to eliminate oxygen from root nodules that house the bacterium “symbiosis.” O=O N Chemical similarity between these two molecules results in competitive inhibition of nitrogen fixation by oxygen. http://www.interet-general.info/IMG/rhizobium-nodule-1.jpg

Photoheterotrophs - strange Bacteria: Rhodospirillum, Rhodomicrobium Light C2H4O2-  2 CH2O spirilloxanthin http://www.acadweb.wwu.edu/courses/envr429-rm/Robin/images/envr429/1_rhodospirillum_600x.jpg

Chemoheterotrophs - common! Escherichia coli and most eukaryotes…even plants! CH2O + O2  CO2 + H2O + ATP Carbohydrate, etc. provides both the energy source and the carbon source What is another chemoheterotrophic organism? Give the complete Latin binomial!

Chemoheterotrophy Aerobic Respiration CH2O + O2  CO2 + H2O Glycolysis carbohydrate to pyruvate (in cytosol!) Citric Acid Cycle pyruvate to carbon dioxide (in cytosol or matrix) Electron Transport and Oxidative Phosphorylation (in mesosomes or cristae) CH2O + O2  CO2 + H2O Anaerobic Fermentation Glycolysis to pyruvate (in cytosol) Fermentive step(s) to return NAD+ to glycolysis (in cytosol) C6H12O6  C3H3O3-  C2H5OH + CO2 C6H12O6  C3H3O3-  H3CCHOHCOO- Notice how fermentation can produce gas or acids… These are just a few of the fermentive possibilities!

Cyanobacterial Vegetative Cell I thought these were only photosynthetic?? cell wall mesosome electron transport sytem and oxidative phosphorylation cell membrane cyanophycean starch fuel for repiration cyanophycin vacuole lipid droplet fuel for repiration polyphosphate granule thylakoids If its metabolism is facultative and the organism is in anaerobic conditions… nucleoid cytosol polyhedral body glycolysis and Krebs cycle http://www.botany.hawaii.edu/faculty/webb/BOT311/Cyanobacteria/CBDivideTEM.jpg fermentation steps Prokaryotes do not have mitochondria… they became mitochondria!

Archaea have Homeostasis Facultative (can do both, but one better than another) and Obligate (strictly just one or the other) Anaerobes and Aerobes Nutrition Mode Energy Source Carbon Source Photoautotroph Light CO2 Chemoautotroph Inorganic chem Photoheterotroph Organic chem Chemoheterotroph Photoautotrophs use Calvin Cycle (Pyrococcus) Chemoautotroph use reverse TCA to fix CO2 and sulfur transporters used drive ATP synthesis Chemoheterotroph citric acid cycle, fermentation

Halobacterium NRC-1 Salt ponds where seawater is evaporating Figure 28.27 Page 590 Halobacterium NRC-1 Salt ponds where seawater is evaporating This red color is high population densities of Halobacterium salinarium!

Halobacterium salinarium 3 chromosomes: Main chromosome 2,015 kb 191 kb replicon 366 kb replicon Replicons have critical genes for: DNA polymerase Transcription factors Mineral uptake (K, PO4) Cell division The genome has many insertion sites for foreign genes How do the 3 chromosomes migrate properly in binary fission? Bacteriorhodopsin: Protein + retinal Amax 280 UV, 570 green nm energy for proton transport and phosphorylation without photosynthesis! Halobacterium salinarium http://biology.kenyon.edu/Microbial_Biorealm/archaea/halobacterium/halobacteria_1.jpg Aerobic Respiration Up to 5 M (25% NaCl)! Great Salt Lake, Utah Red Sea, Asia Minor

Hint: it reflects the other colors of the spectrum Periplasmic space Cell Membrane Retinal lsu.epfl.ch/sh/bR_full.pdf Cytoplasm Bacteriorhodopsin absorbs green from the visible spectrum, so what color is the pigment? Hint: it reflects the other colors of the spectrum www.hawaii.edu/microbiology/ Alam/publications/PNAS96-ZHANG.pd

√ Which of these metabolic pathways is Halobacterium demonstrating? Photoautotrophism Photoheterotrophism Chemoautotrophism Chemoheterotrophism √ Hint: Light for energy Chemicals for carbon

Methanococcus jannischii Isolated from “white smoker” hydrothermal vent 2600m deep on the East Pacific Rise http://www.bact.wisc.edu/Bact303/ Methanococcus.jpeg http://epr2004.sr.unh.edu/images/hires/hireswtsmoker.jpg

http://upload. wikimedia http://upload.wikimedia.org/wikipedia/commons/thumb/a/ae/East_Pacific_Rise.jpg/300px-East_Pacific_Rise.jpg

http://www. oceanexplorer. noaa http://www.oceanexplorer.noaa.gov/explorations/05galapagos/background/mid_ocean_ridge/media/EPR_relief_image_600.jpg

Methanococcus jannischii Isolated from “white smoker” hydrothermal vent 2600m deep on the East Pacific Rise Methanogen Obligate anaerobe H2 as energy source CO2 as carbon source CH4 as byproduct of metabolism Temperature: 50-86°C Other archaeon species found in cow rumen (first stomach) Cow belches 50 L of methane per day http://www.bact.wisc.edu/Bact303/Methanococcus.jpeg What does this electron micrograph tell you? …about cell shape? …about motility?

√ Which of these metabolic pathways is Methanococcus demonstrating? Photoautotrophism Photoheterotrophism Chemoautotrophism Chemoheterotrophism √ Hint: H2 for energy CO2 for carbon

Figure 28.25 Page 589 Sulfolobus species

Sulfolobus acidocaldarius 75°C Optimum Obligate aerobe pH 1 to 6 Oxidize Sulfur or can use Fe2+ or MnO42- as electron acceptors…uses glycolysis and TCA cycle (same path we have, but in a very different environment) http://dac.molbio.ku.dk/Sulfolobus.jpg

√ Which of these metabolic pathways is Sulfolobus demonstrating? Photoautotrophism Photoheterotrophism Chemoautotrophism Chemoheterotrophism √ Hint: Organic chemicals for energy Organic chemicals for carbon

How do Archaea tolerate the heat? Proteins stabilized by more ionic bridges between amino acid r-groups and more-hydrophobic core amino acids Heat shock protein (chaperonins) refold denatured proteins…Pyrococcus 121°C for 1 hour! DNA depurination reduced by presence of 2,3-diphosphoglycerate. DNA supercoiling by reverse gyrase reduces denaturation Sac7d in Sulfolobus is a minor groove protein increases the DNA melting temperature by 40°C Histone-like proteins help stabilize DNA as well Heat-resistant di-bi-phytanyl diether lipid membranes (monolayer) prevent delamination of membrane

Cell Membrane Structure Composed of diglycerides R group may be phosphate, sulfate, or sugar Long chain branched hydrocarbon (not fatty acid) Hydrocarbons may be C20 or C40 If C20, the membrane is a bilayer: O R If C40, the membrane is a monolayer: O R In some species, the membrane is a mixture of both C20 and C40 diglycerides forming a mixed mono-/bi-layer. The C40 diglycerides prevent the bi-layer from de-laminating!

Thermus aquaticus Gram negative eubacterium Thermophile isolated from Not all thermophiles are archaeons! Thermus aquaticus Gram negative eubacterium Thermophile isolated from Yellowstone Hot Spring Optimum temperature 85°C Stability of macromolecules excellent Enzymes for research or commercial use Taq polymerase is the enzyme of PCR (Polymerase Chain Reaction) Lives near cyanobacteria which produce CH2O to feed Thermus http://www.molgen.mpg.de/~ag_ribo/ ag_franceschi/franceschi-projects-30S.html http://sci.agr.ca/crda/images/BACTERI1.JPG

√ Which of these metabolic pathways is Thermus demonstrating? Photoautotrophism Photoheterotrophism Chemoautotrophism Chemoheterotrophism √ Hint: Organic chemicals for energy Organic chemicals for carbon

Yellowstone National Park “Paint Pot” http://www.usitrip.com/temp/image/1Yellowstone%20National%20Park4.jpg Thermophilic cyano-bacteria and eubacteria form a natural community of producers and consumers.

Yellowstone National Park “Paint Pot” Thermophilic cyanobacteria and eubacteria form a natural community of producers and consumers. http://lh5.ggpht.com/_6Im64WjoHS4/Sp8ESQjkwTI/AAAAAAAAAHM/b3hXvyjQA6o/IMG_0663.JPG

According to morphological similarities, prokaryotes should be closely related Bacteria Archaea Eukarya

Bacteria Archaea Firmicutes Spirochaeles Actinobacteria Chlamydiales Cyanobacteria -Proteobacteria -Proteobacteria -Proteobacteria -Proteobacteria -Proteobacteria Sulfolobus Aeropyrum Thermoplasma Archaeoglobus Methanococcus Pyrococcus

Gram-positive cells retain Gram stain more than Gram-negative cells do. Cell walls in Gram-positive bacteria have extensive peptidoglycan. Cell walls in Gram-negative bacteria have some peptidoglycan and an outer membrane. Gram-positive cell wall Gram-negative cell wall Gram-positive cells Polysaccharides Polysaccharides Gram-negative cells Cell wall Cell wall Outer membrane Peptidoglycan Peptidoglycan Plasma membrane Plasma membrane Protein Protein

Gram-positive cells retain Gram stain more than Gram-negative cells do.