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Providence Journal
Friday October 2, 2009
The New Yorker 3/20/1995 by Mort Gerberg
Figure 28-1 Page 567
Bacteria
Archaea
Eukarya
3 Domains
A common ancestor
Characteristics
plasma membrane
cell walls
DNA/RNA molecules
ribosomes
endosymbiosis
Common ancestor of all
species living today
Figure 28-11 Page 577
According to morphological
similarities, prokaryotes should
be closely related
Bacteria
Archaea
This view is incorrect!
Eukarya
Figure 28-13 Page 578
Small
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.
Large
Compare relative sizes
Biology:
life study of
What is Life?
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
CO2
Photoheterotroph
Light
Organic chem
Chemoheterotroph
Organic chem
Organic chem
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
light
CO2 + H2S  S2 + CH2O
chlorophyll
Cyanobacterial Vegetative Cell
cell wall
mesosome
cell membrane
cyanophycean starch
photosynthesis product
cyanophycin
vacuole
lipid droplet
polyphosphate granule
thylakoids
light
reactions
nucleoid
cytosol
Calvin cycle and
starch synthesis
http://www.botany.hawaii.edu/faculty/webb/BOT311/Cyanobacteria/CBDivideTEM.jpg
polyhedral body
RubisCO crystals!
Prokaryotes do not have chloroplasts…
they became chloroplasts!
Artificial coloration of TEM image
But thylakoids shown as green would be natural!
For the light reactions…
http://www.bio.utexas.edu/re
searchutex/photogallery/Ana
baena_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.
http://www.jgi.doe.gov/JGI_microbial/images/microbes2003/anava.jpg
The location of bacteriochlorophyll!
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 -
http://microbewiki.kenyon.edu/images/thumb/8/89/Zdrs0232.jpg/350px-Zdrs0232.jpg
internal membranes use NH4+ electrons in an ETS to produce ATP
ATP and protons used to reduce CO2 to CH2O
N N
O=O
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
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.”
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
– 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-  H3CCHOHCOONotice 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??
mesosome
electron
transport sytem
and oxidative
phosphorylation
vacuole
thylakoids
cell wall
cell membrane
cyanophycean starch
fuel for repiration
cyanophycin
lipid droplet
fuel for repiration
polyphosphate granule
If its metabolism is
facultative and the
organism is in
anaerobic conditions…
cytosol
nucleoid
polyhedral body
glycolysis and
http://www.botany.hawaii.edu/faculty/webb/BOT311/Cyanobacteria/CBDivideTEM.jpg
Krebs cycle
fermentation Prokaryotes do not have mitochondria…
steps
they became mitochondria!
Archaea have Homeostasis
Facultative (can do bo th, 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
CO2
Photoheterotroph
Light
Organic chem
Chemoheterotroph
Organic chem
Organic chem
Photoautotrophs use Calvin Cycle (Pyrococcus)
Chemoautotroph use reverse TCA to fix CO2
and sulfur transporters used drive ATP synthesis
Chemoheterotroph citric acid cycle, fermentation
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
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
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!
Periplasmic
space
Retinal
Cell
Membrane
lsu.epfl.ch/sh/bR_full.pdf
Cytoplasm
Bacteriorhodopsin
absorbs green from the
visible spectrum, so what
color is the pigment?
www.hawaii.edu/microbiology/ Alam/publications/PNAS96-ZHANG.pd
Hint: it reflects the other
colors of the spectrum
Which of these metabolic pathways
is Halobacterium demonstrating?
• Photoautotrophism
√
• Photoheterotrophism
• Chemoautotrophism
• Chemoheterotrophism
Hint:
• Light for energy
• Chemicals for carbon
Methanococcus jannischii
http://www.bact.wisc.edu/Bact303/
Methanococcus.jpeg
http://epr2004.sr.unh.edu/images/hires/hireswtsmoker.jpg
Isolated from “white smoker”
hydrothermal vent
2600m deep on the East Pacific Rise
http://upload.wikimedia.org/wikipedia/commons/thumb/a/ae/East_Pacific_Rise.jpg/300px-East_Pacific_Rise.jpg
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
http://www.bact.wisc.edu/Bact303/Methanococcus.jpeg
•H2 as energy source
•CO2 as carbon source
What does this electron
•CH4 as byproduct of metabolism
micrograph tell you?
•Temperature: 50-86°C
…about cell shape?
…about motility?
Other archaeon species found in
cow rumen (first stomach)
Cow belches 50 L of methane per day
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
http://dac.molbio.ku.dk/Sulfolobus.jpg
(same path we have, but in
a very different
environment)
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 2,3diphosphoglycerate.
• 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:
R
O
O
O
O
R
If C40, the membrane is a monolayer:
R
O
O
O
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!
Not all thermophiles are archaeons!
Thermus aquaticus
Gram negative eubacterium
http://www.molgen.mpg.de/~ag_ribo/
ag_franceschi/franceschi-projects-30S.html
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)
http://sci.agr.ca/crda/images/BACTERI1.JPG
Lives near cyanobacteria which
produce CH2O to feed Thermus
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
cyanobacteria and
eubacteria
form a natural
community
of producers
and
consumers.
Yellowstone National Park “Paint Pot”
Thermophilic cyanobacteria and eubacteria form a natural
http://lh5.ggpht.com/_6Im64WjoHS4/Sp8ESQjkwTI/AAAAA
community of producers and consumers.
AAAAHM/b3hXvyjQA6o/IMG_0663.JPG
According to morphological
similarities, prokaryotes should
be closely related
Bacteria
Archaea
Eukarya
Bacteria
Archaea
Gram-positive cells retain Gram stain more
than Gram-negative cells do.
Cell walls in Gram-positive bacteria have extensive
peptidoglycan.
Gram-positive
cell wall
Polysaccharides
Gram-positive
cells
Gram-negative
cells
Cell walls in Gram-negative bacteria have some
peptidoglycan and an outer membrane.
Cell
wall
Gram-negative
cell wall
Polysaccharides
Cell
wall
Outer
membrane
Peptidoglycan
Peptidoglycan
Plasma
membrane
Protein
Plasma
membrane
Protein
Gram-positive cells retain Gram stain more
than Gram-negative cells do.