Gram-negative bacteria - Castle High School

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Nov 12, 2013 (3 years and 8 months ago)

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All organisms have:


Plasma membranes and ribosomes


Metabolic pathways (e.g., glycolysis)


Conservative DNA replication


DNA that encodes proteins


Shared features indicate that all life is related, but
major differences have also evolved.

Genetic studies show that the three domains had a
single common ancestor.


Some eukaryote genes are most closely related to
those of archaea, while others are most closely
related to those of bacteria.


Mitochondria and chloroplasts of eukaryotes
originated through endosymbiosis with a
bacterium.

Prokaryotes differ from eukaryotes.


All are unicellular


Divide by binary fission, not mitosis


DNA is often circular, not in a nucleus


No membrane
-
enclosed organelles


Study of prokaryotes was not possible until
microscopes were developed.


Before DNA sequencing, classification was
based on phenotypic characters such as
shape, color, motility, nutrition, and cell wall
structure.


Most bacteria cell walls contain peptidoglycan, which
is unique to bacteria.


Antibiotics target peptidoglycan because eukaryote
cells don’t have it, thus there is no harm to human
cells.


Bacteria can be grouped by the
Gram stain

response,
which is based on differences in cell wall structure:


Gram
-
positive bacteria

appear blue to purple.


Gram
-
negative bacteria

appear pink to red.

Common bacteria cell shapes:


Sphere

coccus

(plural
cocci
), occur singly or in plates,
blocks, or clusters


Rod

bacillus

(plural
bacilli
)


Spiral or helical

helix

(plural
helices
)


Rods and helical shapes may form chains or
clusters.


Other bacterial shapes form filaments and branched
filaments.

Sequencing of ribosomal RNA (rRNA) genes is useful
for phylogenetic studies because:


rRNA was present in the common ancestor of all
life.

• All free
-
living organisms have rRNA.

• Lateral transfer of rRNA genes among distantly
related species is unlikely.

• rRNA has evolved slowly.

Whole genome sequencing has revealed that
even distantly related prokaryotes
sometimes exchange genetic material.


Transformation, conjugation, and
transduction allow exchange of genetic
information between prokaryotes.




Genes that result in new adaptations that confer
higher fitness are most likely to be transferred.


Genes for antibiotic resistance are often transferred
among bacterial species.


Prokaryotes are the most successful
organisms on Earth in terms of number of
individuals.


The number of prokaryotes in the ocean is
perhaps 100 million times as great as the
number of stars in the visible universe.


They are found in every type of habitat on
Earth.


Eight main bacterial groups.

Low
-
GC Gram
-
positives

(
Firmicutes
)


Low ratio of G
-
C to A
-
T base pairs in DNA.


Some are gram
-
negative, and some have no cell
wall.


Some produce heat
-
resistant
endospores

that can
survive unfavorable conditions. Some can survive
for 1,000 years.


Includes
Clostridium
and
Bacillus
.


Bacillus anthracis
produces an exotoxin that causes
anthrax. The endospores have been used as a
bioterrorism agent.


Staphylococcus

(
staphylococci)
are abundant on
skin and cause boils and other skin problems.
S.
aureus
can also cause respiratory, intestinal, and
wound infections.


Mycoplasmas

have no cell wall, are extremely
small, and have a very small genome.



They have less than half as much DNA as
other prokaryotes, which may represent the
minimum amount of DNA needed for a
living cell.

High
-
GC Gram
-
positives

(
Actinobacteria
)


Higher ratio of G
-
C to A
-
T base pairs.


Branched filaments; some form reproductive spores
at filament tips.


Most antibiotics are from this group.


Mycobacterium tuberculosis
causes tuberculosis;
oldest know human pathogen.


Hyperthermophilic bacteria



Live at extreme high temperatures
(
extremophiles
)

hot springs, volcanic vents,
underground oil reservoirs.


High temperatures may have been the ancestral
condition on Earth when prokaryotes evolved.


Monophyly of this group is not well established.

Hadobacteria


Also extreme thermophiles.


Deinococcus
survive cold as well as hot
temperatures and are resistant to radiation. They
can consume nuclear waste.




Thermus aquaticus
was isolated from a hot spring;
source of the thermally stable DNA polymerase
used in PCR.

Cyanobacteria


Photosynthetic; have blue
-
green pigments.


Many species fix nitrogen.


Chloroplasts of eukaryotes are derived from
an endosymbiotic cyanobacterium.


Some colonies differentiate into
vegetative
cells
,
spores
, and
heterocysts

specialized for
N
-
fixation.

Spirochetes


Gram
-
negative; motile


Unique axial filaments (modified flagella)
that rotate


Many are human parasites, some are
pathogens (syphilis, Lyme disease), others
are free living
.

Chlamydias


Can live only as parasites in cells of other
organisms.


Gram
-
negative; extremely small


Can take up ATP from host cell with
translocase


Complex life cycle with two forms

elementary bodies

and
reticulate bodies


Proteobacteria
: largest group of bacteria


Mitochondria of eukaryotes were derived
from a proteobacterium by endosymbiosis.


Some are photoautotrophs that use light
energy to metabolize sulfur; some are N
-
fixers (
Rhizobium
).


Escherichia coli

is one of the most studied
organisms on Earth.



Agrobacterium tumefaciens

causes crown gall
disease of plants and has a plasmid used in
recombinant DNA studies.


The proteobacteria include many pathogens


cholera, bubonic plague, salmonella.

Separation of the Archaea domain from bacteria and
eukaryotes is based on genome sequencing.


Many archaea live in extreme habitats

high
temperatures, low oxygen, high salinity, extreme
pH.


Many others are common in soil and in the oceans.



Archaea are divided into two main groups,
Euryarcheota

and
Crenarcheota




Two recently discovered groups:


Korarchaeota

(known only from DNA in hot springs)


Nanoarchaeota
, a parasite on cells of a
crenarchaeote in deep sea hydrothermal vents


All lack peptidoglycan in the cell walls and have
unique lipids in the cell membranes.

Nutritional categories:


Photoautotrophs

perform photosynthesis; use CO
2

as carbon source.


Cyanobacteria use chlorophyll
a

and produce O
2
.


Others use
bacteriochlorophyll
and produce sulfur;
H
2
S is the electron donor.


Bacteriochlorophyll absorbs longer wavelengths
than chlorophyll.


Bacteria using this pigment can grow in deeper
water under dense layers of algae, using light that is
not absorbed by the algae.

Photoheterotrophs

use light as an energy source, but
get carbon from organic compounds made by other
organisms.


Chemolithotrophs

(
chemoautotrophs
) get energy by
oxidizing inorganic substances and use it to fix
carbon.

Chemoheterotrophs

get both energy and carbon from
organic compounds that have been synthesized by
other organisms.


Most known bacteria and archaea are
chemoheterotrophs

as are all animals, fungi, and
many protists.

Prokaryotes play a major role in the cycling of
elements.


Many are
decomposers
: they metabolize organic
compounds in dead organic material. The inorganic
products, such as CO
2
, are returned to the
environment.


Other prokaryotes oxidize inorganic compounds and
also play key roles in element cycling.


Denitrifiers
:


Bacteria that use nitrate (NO
3

) as an electron
acceptor in place of O
2

in anaerobic conditions.


They release N
2

to the atmosphere.


They play a key role in nitrogen cycling.


Nitrogen fixers
:


Convert N
2

to ammonia. Ammonia is a form of
nitrogen that is useable by organisms.


Nitrogen fixation is vital to life and is done only by
certain prokaryote species.


Nitrifiers
:


Chemolithotrophic bacteria that oxidize ammonia
to nitrate.


Nitrate is the form of nitrogen most easily used by
many plants.


Many prokaryotes live on or in eukaryotic organisms
(e.g., nitrogen fixers that live in plant root nodules).


Animals have many prokaryotes in their digestive
tracts.


Bacteria in the rumen of cattle produce the enzyme
needed to digest cellulose.



Humans have thousands of bacterial species on
their skin and in their guts. Gut bacteria help digest
and absorb nutrients and produce vitamins.


Only a small percentage of bacteria are


pathogens.


Consequences of bacterial infections depend on
invasiveness

of the pathogen (ability to multiply in
host’s body) and its
toxigenicity

(ability to produce
toxins).


Endotoxins

are released when certain Gram
-
negative bacteria
lyse

(burst); rarely fatal; they
cause fever, vomiting, and diarrhea.



Examples:
Salmonella
and
Escherichia


Exotoxins

are released by living bacteria; highly
toxic, often fatal.



Examples: tetanus (
Clostridium
tetani
), cholera
(
Vibrio

cholerae
), bubonic plague (
Yersinia

pestis
),
anthrax (
Bacillus
anthracis
),
botulism (
Clostridium
botulinum
).

Although viruses are not cellular, they have many
characteristics of living organisms.


Virus phylogeny is difficult to resolve: small
genomes restrict phylogenetic analyses; rapid
mutation and evolution rates cloud evolutionary
relationships; there are no fossils.


Instead, viruses are grouped based on genome
structure.



Viruses are obligate cellular parasites, but many
may have once been cellular components.


They may be “escaped” components cells that now
evolve independently of their hosts.

Negative
-
sense single
-
stranded RNA viruses
:


Negative
-
sense
RNA

the complement of mRNA.


They can make mRNA from their negative
-
sense
RNA genome.


These viruses probably arose by cellular escape
many times independently across the tree of life.


Includes viruses that cause measles, mumps, rabies,
and influenza.

Type IV

Positive
-
sense single
-
stranded RNA viruses
:


The most abundant and diverse group; includes
mosaic viruses of crop plants, polio, hepatitis C, and
the common cold.


They also appear to have evolved multiple times
across the tree of life from different groups of
cellular ancestors.

Type V

RNA retroviruses
:


Single
-
stranded RNA; probably evolved as escaped
cellular components.


Regenerate themselves by reverse transcription. DNA is
produced and integrated into the host genome, where
it is replicated along with host’s DNA.


Only infect vertebrates


includes HIV


some are associated with various


cancers.

Type VI

Double
-
stranded RNA viruses
:


May have evolved repeatedly from single
-
stranded
RNA ancestors.


Cause many plant diseases and infant diarrhea in
humans.

Type III

Double
-
stranded DNA viruses
:


May represent highly reduced parasitic organisms
that have lost their cellular structure and ability to
survive as free
-
living species.


Some have genomes as large as parasitic bacteria.


Includes bacteriophage, smallpox, and herpes
viruses.

Type I