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Bio 100 - Study Guide 15
The First Prokaryotes
• Prokaryotes were Earth’s sole inhabitants
•
From 3.5 to about 2 billion years ago
• As prokaryotes evolved, they exploited and changed
young Earth
• The oldest known fossils are stromatolites
•
Rocklike structures composed of many layers of
bacteria and sediment
•
Which date back ~3.0 billion years ago
Prokaryotes and the Origins of Metabolic Diversity
Energy and Stuff
How an organism gets carbon
How an organism gets energy
Prokaryotes exhibit much more nutritional
diversity than eukaryotes
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Prokaryotes and the Origins of Metabolic Diversity
I. Energy crises and Metabolism
II. Four steps in the evolution of metabolism
Glycolysis
Photosynthesis
Electron transport chain
Aerobic respiration
Anaerobic respiration
LE 9-8
Energy investment phase
Glucose
2 ATP used
2 ADP + 2 P
Glycolysis
Citric
acid
cycle
Oxidative
phosphorylation
Energy payoff phase
ATP
ATP
ATP
4 ADP + 4 P
2 NAD+ + 4 e– + 4 H+
4 ATP formed
2 NADH + 2 H+
2 Pyruvate + 2 H2O
Net
Glucose
4 ATP formed – 2 ATP used
2 NAD+ + 4 e– + 4 H+
2 Pyruvate + 2 H2O
2 ATP
2 NADH + 2 H+
Chemiosmosis: The Energy-Coupling Mechanism
• Electron transfer in the electron transport chain causes
proteins to pump H+ from the mitochondrial matrix to
the intermembrane space
• H+ then moves back across the membrane, passing
through channels in ATP synthase
• ATP synthase uses the exergonic flow of H+ to drive
phosphorylation of ATP
• This is an example of chemiosmosis, the use of energy
in a H+ gradient to drive cellular work
Chemiosmosis is the movement of ions across a
selectively-permeable membrane, down their
electrochemical gradient. More specifically, it relates to
the generation of ATP by the movement of hydrogen
ions across a membrane during cellular respiration.
LE 9-15
Inner
mitochondrial
membrane
Glycolysis
Citric
acid
cycle
ATP
ATP
Oxidative
phosphorylation:
electron transport
and chemiosmosis
ATP
H+
H+
H+
H+
Intermembrane
space
Cyt c
Protein complex
of electron
carriers
Q
IV
III
I
ATP
synthase
II
Inner
mitochondrial
membrane
FADH2
NADH + H+
2H+ + 1/2 O2
H2O
FAD
NAD+
Mitochondrial
matrix
ATP
ADP + P i
(carrying electrons
from food)
H+
Electron transport chain
Electron transport and pumping of protons (H+),
Which create an H+ gradient across the membrane
Oxidative phosphorylation
Chemiosmosis
ATP synthesis powered by the flow
of H+ back across the membrane
LE 9-14
INTERMEMBRANE SPACE
H+
H+
H+
H+
H+
H+
A rotor within the
membrane spins
as shown when
H+ flows past
it down the H+
gradient.
H+
A stator anchored
in the membrane
holds the knob
stationary.
A rod (or “stalk”)
extending into
the knob also
spins, activating
catalytic sites in
the knob.
H+
ADP
+
P
ATP
i
MITOCHONDRAL MATRIX
Three catalytic
sites in the
stationary knob
join inorganic
phosphate to
ADP to make
ATP.
Origin of Microbial Life and Photosynthesis
http://courses.cm.utexas.edu/emarcotte/ch339k/fall2005/Lecture-Ch19-3/Slide5.JPG
ATP synthesis in photosynthesis bears several
similarities to that in aerobic respiration. Both
involve a series of electron carriers arranged in a
membrane to generate a proton motive force.
http://cwx.prenhall.com/bookbind/pubbooks/brock/chapter13/objectives/deluxe-content.html
• Photosynthetic groups are scattered among
diverse branches of prokaryote phylogeny.
Fig. 27.12
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The presence of oxygen has a positive impact on
the growth of some prokaryotes and a negative
impact on the growth of others.
• Obligate aerobes require O2 for cellular respiration.
• Facultative anerobes will use O2 if present but can
also grow by fermentation in an anaerobic
environment.
• Obligate anaerobes are poisoned by O2 and use either
fermentation or anaerobic respiration.
• In anaerobic respiration, inorganic molecules
other than O2 accept electrons from electron
transport chains.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Corresponding
tube no. above
Oxygen
relationship
designation
1
2
3
4
STRICT
(OBLIGATE)
AEROBE
FACULTATIVE
ANAEROBE
AEROTOLER
ANT
ANAEROBE
STRICT
(OBLIGATE)
ANAEROBE
Molecular systematics has lead to a phylogenetic
classification of prokaryotes
• The limited fossil record and structural simplicity
of prokaryotes created great difficulties in
developing a classification of prokaryotes.
A breakthrough came
when Carl Woese and
his colleagues began to
cluster prokarotes into
taxonomic groups based
on comparisons of
nucleic acid sequences.
Especially useful was
the small-subunit
ribosomal RNA (SSUrRNA) because all
organisms have
ribosomes.
16S rRNA molecules make great chronometers for
determining the patterns of microbial evolution because:
 Conserved regions are useful for aligning sequences
determined from different organisms.
 Most bacteria contain rRNA and it carries out the
same function in each of them.
 They are big enough (1500 nt) to provide useful
information.
 They can be relatively easily isolated and sequences
using direct methods and/or PCR.
The Universal Tree of Life
• The tree of life
•
Is divided into three great clades called domains: Bacteria,
Archaea, and Eukarya
• The early history of these domains is not yet clear
0
Bacteria
Eukarya
Symbiosis of
chloroplast
ancestor with
ancestor of green
plants
3
Symbiosis of
mitochondrial
ancestor with
ancestor of
eukaryotes
2
Possible fusion
of bacterium and
archaean,
yielding ancestor
of eukaryotic
cells
1
Last common
ancestor of all
living things
Archaea
1
Billion years ago
4
4
2
3
2
3
1
Figure 25.18
4
Origin of life
• Carl Woese used signature sequences, regions of SSUrRNA that are unique, to establish a phylogeny of
prokarotes.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 27.13
Can link fluorescent molecules to short
complementary 16s rRNA sequences and generate
probes to look for microorganisms by microscopy!!
Photomicrographs of the
methanotrophic nonproteobacterial
strain Kam1. (A) Phase-contrast image
of Kam1 cells at 1,000×
magnification. (Scale bar, 5 μm.) (B
and C) Fluorescent in situ
hybridization images of Kam1 cells
visualized with DAPI staining and the
Cy3-labeled 16S rRNA gene probe
Kam1_964 (5′CTGTGCCGTTCGCCCTTGC-3′),
specifically designed for the
Verrucomicrobia thermoacidophilic
methanotroph (VTAM) cluster,
respectively. (Scale bar, 5 μm.) (D)
Transmission electron micrograph of a
thin section of a Kam1 cell. (Scale bar,
200 nm.) (E) Magnified part of the
Kam1 cell in D, highlighting the
polyhedral organelles. (Scale bar, 200
nm.)
Thermoacidophilic bacterium belonging to the Verrucomicrobia phylum
http://cvtree.cbi.pku.edu.cn/pics/gallery/72-k6.png
Indicators of Horizontal Gene Transfer
(HGT)
• BLAST shows greater similarity to sequence in an
organism that is distant on the 16 S r-RNA tree
• Difference in tree of these sequences relative to the
16 S rRNA tree
• GC Analysis different relative to rest of genome
• Location in the genome is different than in other
organisms
• Differences in codon usage from other genes in the
organism
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
http://www.bmb.psu.edu/courses/micro401/Handout_1.htm
Summary of Major Differentiating Features Among Bacteria, Archaea, and Eucarya
Characteristic
Bacteria
Archaea
Eucarya
Membrane-bound
nucleus
Absent
Absent
Present
Muramic Acid
Muramic Acid
Cell Wall
Muramic Acid present present
present
Membrane lipids
Ester-linked
Ether-linked
Ester-linked
Ribosomes
Initiator tRNA
Introns in tRNA genes
Operons
Capping and poly-A
tailing of mRNA
Plasmids
Protein synthesis
sensitive to diptheria
toxin
70S
Formyl-methionine
Rare
Yes
70S
Methionine
Yes
Yes
80S (70S organelles)
Methionine
Yes
No
No
Common
No
Yes
Yes
Rare
No
Yes
RNA polymerases
Sensitivity to
chloramphenicol,
streptomycin,
kanamycin
Methanogenesis
One-type (4 subunits)
Yes
Several (8-12
subunits)
Yes
No
No
Yes
No
No
Reduction of S 0 to H2S Yes
Nitrogen fixation
Yes
Chlorophyll-based
photosynthesis
Yes
Yes
Yes
No
No
No
Yes (chloroplasts)
3 (12-14 subunits)
3. Most known prokaryotes are
Eubacteria
• The name bacteria was once synonymous with
“prokaryotes,” but it now applies to just one of
the two distinct prokaryotic domains.
• However, most known prokaryotes are bacteria.
• Every nutritional and metabolic mode is
represented among the thousands of species of
bacteria.
• The major bacterial taxa are now accorded
kingdom status by most prokaryotic systematists.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Table 27.3, continued
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Prokaryotes are responsible for the key steps in
the cycling of nitrogen through ecosystems.
• Some chemoautotrophic bacteria convert ammonium
(NH4+) to nitrite (NO2-).
• Others “denitrify” nitrite or nitrate (NO3-) to N2,
returning N2 gas to the atmosphere.
• A diverse group of prokaryotes, including
cyanobacteria, can use atmospheric N2 directly.
• During nitrogen fixation, they convert N2 to NH4+,
making atmospheric nitrogen available to other
organisms for incorporation into organic molecules.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
http://www.bact.wisc.edu/Microtextbook/images/book_4/chapter_2/2-53.jpg
http://www.keweenawalgae.mtu.edu/ALGAL_IMAGES/cyanobacteria/Anabaena_jason_dbtow17_2016.jpg
http://biotech.szbk.u-szeged.hu/KK_Jegyzet/pic/heterocyst.gif
Anabaena filaments which have been genetically engineered so
that the heterocysts are expressing a fluorescent protein:
http://www.mun.ca/biochem/courses/3107/Topics/Site_specific_Recomb.html
2. Researchers are identifying a great
diversity of archaea in extreme
environments and in the oceans
• Early on prokaryotes diverged into two lineages,
the domains Archaea and Bacteria.
• A comparison of the three domains demonstrates
that Archaea have at least as much in common
with eukaryotes as with bacteria.
• The archaea also have many unique characteristics.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Archaea
Kingdom Crenarchaeota: mainly hyperthermophiles
Kingdom Euryarchaeota: methanogens, halophiles,
Thermoplasma & Archaeoglobus
Kingdom Korarchaeota: based on 16S rRNA sequences from
uncultured microbes from terrestrial hot springs
http://trishul.sci.gu.edu.au/~bharat/courses/ss13bmm/archaea.html
http://www.nature.com/nrg/journal/v6/n1/images/nrg1504-i1.gif
• Most species of archaea have been sorted into the
kingdom Euryarchaeota or the kingdom
Crenarchaeota.
• However, much of the research on archaea has
focused not on phylogeny, but on their ecology their ability to live where no other life can.
• Archaea are extremophiles, “lovers” of extreme
environments.
• Based on environmental criteria, archaea can be
classified into methanogens, extreme halophiles, and
extreme thermophilies.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Methanogens obtain energy by using CO2 to
oxidize H2 replacing methane as a waste.
• Methanogens are among the strictest anaerobes.
• They live in swamps and marshes where other
microbes have consumed all the oxygen.
• Methanogens are important decomposers in sewage
treatment.
• Other methanogens live in the anaerobic guts of
herbivorous animals, playing an important role in
their nutrition.
• They may contribute to the greenhouse effect, through
the production of methane.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Extreme halophiles live in such saline places as
the Great Salt Lake and the Dead Sea.
• Some species merely tolerate elevated salinity;
others require an extremely salty environment to
grow.
• Colonies of halophiles form
a purple-red scum from
bacteriorhodopsin, a
photosynthetic pigment very
similar to the visual pigment
in the human retina.
Fig. 27.14
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• Extreme thermophiles thrive in hot
environments.
• The optimum temperatures for most thermophiles are
60oC-80oC.
• Sulfolobus oxidizes sulfur in hot sulfur springs in
Yellowstone National Park.
• Another sulfur-metabolizing thermophile lives at
105oC water near deep-sea hydrothermal vents.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• If the earliest prokaryotes evolved in extremely
hot environments like deep-sea vents, then it
would be more accurate to consider most life as
“cold-adapted” rather than viewing thermophilic
archaea as “extreme”.
• Recently, scientists have discovered an abundance of
marine archaea among other life forms in more
moderate habitats.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• All the methanogens and halophiles fit into
Euryarchaeota.
• Most thermophilic species belong to the
Crenarchaeota.
• Each of these taxa also includes some of the
newly discovered marine archaea.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
The End