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 Test
1
Review
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Unformatted text preview: Microbiology
 Test
1
Review
 CHAPTER
1
 
 Terms:
 
 
 
 Scientists:
 • Bassi:
Showed
that
a
disease
affecting
silk
production
in
silkworms
was
 caused
by
a
fungal
infection
 • Cohn:
Demonstrates
the
existence
of
a
heat‐resistant
form
of
germs
 (endospores)
 • Hess:
suggested
to
Koch
to
use
agar
in
place
of
gelatin
 • Koch:

Germ
theory
of
disease.
Developed
solid
microbiological
medias
for
 obtaining
isolated
&
pure
cultures
of
bacteria.

 • Lister:
founded
aseptic
technique,
heat
sterilized
instruments
to
avoid
 infection
 • Pasteur:
swan‐neck
flask
experiment,
spontaneous
generation
was
solidly
 disproved
 • Redi:
Disproved
spontaneous
generation
of
maggots
from
rotting
meat
using
 3
experimental
containers
 • Spallazani:
—Sealed
glass
flasks
and
boiled
contents.
Concludes
air
either
 carries
germs
into
the
broth
or
air
is
required
for
the
growth
of
the
germs
 • Schwann:
Concludes
air
carries
germs
with
open
flask
experiment
 • Shroder:
Flasks
with
boiled
broths
are
stoppered
with
sterilized
 cotton/wool.
Ait
therefore
carries
germs
that
can
be
stopped.
 • Tyndall:
Hypothesizes
that
some
forms
of
germs
may
be
more
resistant
to
 heat
after
everyone
tried
to
repeat
Pasteurs
experiment
 • Van
Leeuwenhoek:
haberdasher
that
constructed
first
microscope.
 Discovered
“animalcules”
 
 1. Kingdoms
vs.
Domains
 • 5
kingdoms:

 o Animalia‐
duh
 o Plantae‐
duh

 o Fungi‐
unicellular
and
multi,
take
nutrients
from
enviornment
 o Protista‐
generally
large,
unicellular
(algae,
protozoa,
slime/water
 molds)
 o Monera‐
all
prokaryotes
 • 3
domains:

 o Eukarya‐
include
protist,
fungi,
and
plants/animals
 o Bacteria‐
usually
single
celled,
mostly
prokaryotic
 o Archaea‐
rRNA
sequences,
lack
peptidoglycan,
unique
lipid
 membranes
 • Viruses
are
not
included
because
they
are
acellular
 
 2. rRNA
model
 • Why
rRNA
a
suitable
marker?
—rRNA
is
universally
present
in
all
living
 organisms
 • RNA
is
capable
of
storing,
copying,
and
expressing
genetic
information
 • Comparing
rRNA:
sequences
of
nucleotides
in
the
genes
in
rRNA
are
 compared
between
2
organisms.
The
amount
of
difference
in
sequence
 tell
how
evolutionary
related
the
organism
are.
Doesn’t
tell
time
relation
 though
 
 3. Endosymbiotic
theory
 • Theory
holds
that
mitochondria,
chloroplasts
and
hydrogenosomes
were
 their
own
bacteria
that
incorporated
themselves
into
another
and
became
 internal
structures
 • Evidence:
 o 
They
have
their
own
DNA
and
ribosomes
(both
are
similar
to
 bacterial
DNA
and
ribosomes).


 o Bacterium
Rickettsia
prowazekii
genome
is
more
similar
to
 modern
mitochondrial
genome
than
bacterium
genome.

 o Cholorplasts
of
green
algae
have
high
homology
similarity
with
 cyanobacteria
genus
Prochloron
which
lives
within
marine
 invertebrates
 
 4. Spontaneous
Generation
 • Leeuwenhoeks
communications
on
microorganisms
renewed
 controversy.
Some
proposed
that
microorganisms
arose
form
 spontaneous
generation
even
though
larger
organisms
did
not.
 • Spallanzani
performed
improved
Needham
experiment
and
proposed
 that
air
carried
microorganisms
into
culture
medium.
Schwann
and
 Shroder
also
performed
similar
experiments
 • Pasteur
then
used
his
swan
neck
experiment
and
proved
that
dust
and
 germs
cause
growth
through
air
movement.
Germs
couldn’t
travel
 through
swan
neck.
 • Tyndall
and
Cohn
shut
the
door
more.
Tyndall
showed
dust
carried
 germs.
Cohn
discovered
heat
resistant
bacteria
 
 5. Germ
Theory
of
Disease

(Koch)
 • The
microbe
must
be
present
in
every
case
of
disease
but
absent
in
 healthy
organisms
 • The
suspected
microbe
must
be
isolated
and
grown
in
pure
culture
 • The
same
disease
must
result
when
the
isolated
organism
is
inoculated
 into
a
healthy
host
 • The
same
microbe
must
be
re‐isolated
from
the
diseased
host
 
 6. Pure
Cultures
and
Isolation
 • To
study
a
disease
and
its
effects
correctly,
you
need
that
disease
to
be
 isolated
in
a
culture,
If
the
disease
is
not
isolated,
your
culture
could
grow
 more
than
one
microbe,
thus
your
culture
would
be
impure
 
 7. Roles
of
Microbes
 • Produce
&
preserve
foods‐
yeast
in
bread
making,
yeast
to
make
ethanol,
 produce
cheese,
sour
cream,
buttermilk
 • Recycle
nutrients
and
fertilize
soils‐
N2
fixing
bacteria
for
soil
(replace
 nitrates
in
soil)
 • Industrialized
synthesis
of
natural
&
engineered
products‐
made
bacteria
 to
produce
products
(insulin,
vitamins,
insecticides,
etc)
 • Bioremediation‐
GEMs
used
to
clean
up
oil
spill,
degrade
toxic
 compounds
(PCBs)
 
 
 
 CHAPTER
2
 
 Terms:
 
 
 
 1. Microscopy
Comparison
 • Light
Microscopes:
use
light,
1000x
magnify
 o Bright
field‐
image
dark,
sometimes
specimen
requires
stain
(not
 good
for
live
specimen)
 o Dark
field‐
background
dark,
good
for
live
specimen
 o Phase
contrast:
image
bright,
background
dark.
Good
for
live
 specimen.
Denser
parts
are
darker
 o Fluorescence‐
use
dyes
or
natural
pigments
 • Electron
Microscope:
bean
of
electrons
to
produce
image,
more
 clear/magnified
than
light
 
 o Transmission:
penetrate
specimen
and
bounce
back,
1000x
better
 resolution
than
light.
Examine
intracellular
detail
 o Scanning:
bounce
of
surface
of
specimen.
Examine
surface
 structures.
100x
better
resolution
than
light
 
 2. Stained
vs.
Unstained
 • Basic
dyes:
Carry
a
positively
charged
chromophore
group
which
is
 attracted
to
the
negatively
charged
components
of
cells
 • Acidic
dyes:
Carry
a
negatively
charged
chromophore
group
which
is
 attracted
to
positively
charged
parts
of
the
cell
 • Positive
stain:
cell
is
stained
 • Negative
stain:
background
is
stained
 Acid
fast
stains:
type
of
differential
stain.
Based
on
presence
of
waxy
 mycolic
acids
in
these
species.
Diagnostic
for
pathogen
presence.

 • Gram
stain:
differential
stain,
most
widely
used,
Based
on
the
chemistry
 differences
of
bacterial
cell
walls
(peptidoglycan
content)
 • Capsule
stain:
Nigrosin
or
India
ink
is
used
to
visualize
the
capsule
 (capsule
important
part
for
cell
survival)
 • Endospore
stain:
dormant,
have
hard
outside
layer,
malachite
green
in
 steam
bath
used
to
soften
endospore
wall
so
green
can
enter.
Their
 presence/position
within
the
cell
can
be
used
to
identify
the
species
 • Flagella
stain:
flagellas
hard
to
see
in
light
microscope.
Presence,
number
 and
position
of
flagella
can
help
identify
unknown
bacterial
specimens
 o Memorize
flagella
types!
 
 3. Refraction
and
Resolution
 • Resolution:
ability
of
lens
to
distinguish/separate
small
object
close
 together
 • Refraction:
how
much
an
object
slows
the
velocity
of
light
and
splits
off
 light
waves
 • The
higher
the
refractive
index,
the
higher
the
resolution
 • Immersion
oil
helps
increase
the
refractive
index
(it
has
same
refractive
 index
as
glass).
Oil
causes
less
light
to
be
refracted
and
therefore
more
 light
goes
through
object,
creating
a
higher
resolution.
 
 4. Fixation
 • Kills
&
adheres
microbes
to
a
slide’s
surface
 • Preserves
the
structure
if
the
cells
and
inactivates
enzymes
within
the
 cells
that
may
alter
morphology
 • Heat
fixation:
specimen
passed
through
flame,
good
preservation
of
cell
 morphology
but
not
on
delicate
internal
cell
structures.
Lysing
threat
if
 not
fully
air‐dried
 • Chemical
fixation:
Penetrates
the
cells
to
internal
structures
and
toughens
 them
so
that
details
can
be
easily
observed.
Some
chemicals
toxic
to
us
 and
bacteria
 • 
 5. Types
of
Staining
 • Simple
vs.
Differential
 o Simple:
one
dye
used,
simple,
easy
to
use
 o Differential:
multiple
dyes,
divides
bacteria
into
2
distinct
groups,
 more
complex,
harder
to
do
 • Positive
vs.
Negative‐
(see
above
stain
section)
 
 6. Gram
Stain
 • Gram
(+)
–
cell
walls
have
lots
of
peptidoglycan
 • Gram
(‐)
–
cell
walls
have
little
peptidoglycan,
mostly
LPS
 • Primary
stain:
crystal
violet‐
all
cells
go
purple
 • Mordant:
grams
iodine‐
crystallizes
purple
in
cell
 • • 
 
 
 
 
 
 
 
 
 
 
 Decolorizer:
ethanol‐
dissolves
gram
(‐)
cell
walls
(lipopolysaccharide)
 sand
purple
runs
out
 Counterstain:
Safranin‐
stains
vacant
cells
pink/red
 
 7. Acid
Fast
Stain
 • Acid
fast
cells
(pathogens
for

ex.
TB)
have
mycolic
acid
in
their
cell
walls
 • Primary
stain:
Carbol
fuchsin
 • Heat
is
used
(steam
bath)
to
soften
the
mycolic
acids
and
allow
stain
to
 penetrate
 • Mordant:
Cooling‐
Slides
are
cooled,
allowing
the
mycolic
acids
to
solidify.
 Traps
stain
within
the
cells
 • Decolorization:

Acid
alcohol‐
Dissolve
the
walls
of
non‐acid
fast
bacteria
 (i.e
those
lacking
mycolic
acids)
 • Counterstain:
Methylene
blue‐
Stain
non
acid‐fast
cells
 8. Endospore
Stain
 • Distinguishes
between
endospores
and
vegetative
cells
 • Primary
stain:

Malachite
green

 • Used
over
steam
bath
to
soften
endospore
walls
allowing
penetration
 • Mordant
(physical):
Cooling‐
Slides
are
cooled
allowing
spore
walls
to
re‐ harden.
Traps
green
stain
inside
 • Decolorizer:

Water­
Removes
stain
from
vegetative
cells
 • Counterstain:

Safranin‐
Turns
vegetative
cells
pink/red

 9. Types
of
Dyes
 • Basic
dyes
 o Carry
a
positively
charged
chromophore
group
which
is
attracted
 to
the
negatively
charged
components
of
cells
(proteins,
surfaces
 of
cells)
 o Most
commonly
used
dyes
in
MIBO
labs!
 o Examples:
methylene
blue,
crystal
violet,
safranin,
malachite
green
 o Stain
best
in
high
pH
 • Acidic
Dyes
 o Carry
a
negatively
charged
chromophore
group
which
is
attracted
 to
positively
charged
parts
of
the
cell
 o Examples:
eosin
and
rose
Bengal,
acid
fuchsin
 o Stain
best
in
low
pH
 CHAPTER
3
 
 Terms:
 
 
 
 
 
 1. Morphology
&
Arrangements
 • Morphology
(shape):
 o Coccus:
spherical
 o Bacillus:
straight
rods
 o Vibrio:
gently
curved
rods,
comma‐shaped
 o Spirilla
or
Spirochete:
helical
rods
 o Pleomorphic:
multiple
shapes
 o Appendaged:
have
tubes
or
stalks
 • Arrangements:
 o Individual
cells
 o Diplo‐
pairs
 o Strepto‐
chains
 o Staphylo‐
clusters
 o Tetrads‐
“squares”
of
4
cells
 o Sarcina‐
cubical
packets
of
8
cells
 
 2. Prokaryotic
Cell
Organization
 • Internal
structure
 o Cytoplasm
 o Cytoskeleton‐
microtubules,
etc.
for
cell
support
 o Intercytoplasmic
membrane‐
invagination
of
plasma
membrane
 o Nucleoid‐
single
circular
chromosome
(DNA),
no
membrane,
only
 life‐essential
genes
 o Plasmid‐
storage
closet
for
extra
genes
not
regularly
used
 o Inclusions‐
gas
vacuoles
for
storage
 o Endospores‐
dormant
state,
for
surviving
extreme
conditions.
 Metabolically
inactive,
has
dipicolinic
acid
 • External
Shell
(Cell
Envelope)
 o Cytoplasmic
membrane‐
boundary
b/t
cell
and
environment.
Has
 peripheral
and
integral
membrane
proteins
 o Cell
Wall
(bacteria)‐
peptidogylcan‐containing
wall,
withstands
 osmotic
pressure.
**Look
at
differences
b/t
gram
–
and
gram
+
 walls
 o Glycocalyx‐
polysaccharides.
2
types:
capsules
and
slim
layers.
 Serves
as
energy
storage
or
to
hid
cell
form
immune
cells
 o S‐layers:
protect
against
ion
and
pH
fluctuations

 
 
 3. Chromosome
vs.
Plasmid
 • Chromosomes:
singular,
circular
chromosome
that
contain
genes
that
are
 only
essential
for
life
and
basic
metabolic
function
 • Plasmids:
contains
genes
that
aren’t
used
everyday,
but
enhance
 survivability.
It
stores
excess
genes
so
they
don’t
take
up
needed
space
in
 nucleoid.
 
 
 
 4. Endospores
vs.
Vegetative
Cells
 • Endospore
formation
begins
normally
when
growth
ceases
due
to
lack
of
 nutrients
(sporulation)
 • Vegetative
growth
stops
in
endospore
state
 • Endospores
are
extremely
resistant
to
environmental
stresses,
they
have
 low
water
concentration
 • When
nutrients
(sugars,
amino
acids,
etc)
are
detected
in
the
 environment
by
special
proteins,
activation
can
begin
 • Spores
can
activate
to
vegetative
state
in
3
stages:
 o Activation:
usually
by
heat
 o Germination:
swelling
and
the
coat
ruptures
 o Outgrowth:
pore
protoplasts
makes
new
components
and
returns
 to
vegetative
state
 • Spore
Formation
 o Axial
filament
of
DNA
forms

 o Cell
membrane
folds
inward
to
form
a
septum
between
forespore
 &
rest
of
cell
 o Forespore
engulfed
by
rest
of
former
cell
–
double
layer
 membrane
formed
(protection)
 o Cortex
forms
around
forespore
 o Spore
coat
synthesis
begins
 o Spore
coat
is
complete
–
true
endospore;
resistant!
 o Lysis
results
in
free
(released)
endospore
 
 5. Gram
(+)
vs.
Gram
(‐)
Cell
Walls
 • Gram
(+)
 o Thick
peptidoglycan
layer,
thin
periplasmic
space,
plasma
 membrane
 o Petidoglycan
has
5
glycines
connecting
NAM
and
NAG
strands

 (Alanine
to
5
lycines
to
L
Lysine)
 o Teichoic
acid
is
present
and
helps
stabilize
wall
 • Gram
(‐)
 o LPS
outer
membrane,
thick
periplasmic
space
with
THIN
 peptidoglycan
layer
in
the
middle,
plasma
membrane
 o Peptidoglycan
has
DIRECT
link
b/t
NAM
and
NAG
strands
(alanine
 to
DAP)
 o NO
teichoic
acid
present
 6. Cell
Walls
vs.
Lysis
 • Preventing
synthesis
of
peptidoglycan
is
an
effective
way
to
control
new
 microbial
growth
 • If
peptidoglycan
strength
is
compromised,
cells
cannot
prevent
osmotic
 pressure
from
bursting
(lysing)
 o Existing
cells
are
lysed,
preventing
microbial
growth
of
existing
 cells
 • Penicillin:
prevents
new
cell
wall
growth
 o Binds
to
transpeptidases
to
prevent
cross‐linking
of
glycan
chains
 o More
effective
on
Gram
(+)’s
than
Gram
(–)’s
 Lesser
peptidoglycan
in
Gram
(‐)
cell
walls
 Peptidoglycan
compromised
but
outer
membrane
layer
still
 provides
major
structural
support
 Porins
in
outer
membrane
of
Gram
–’s
act
to
selectively
 exclude
penicillin
and
other
chemicals
 • Lysozyme
–
weakens
existing
peptidoglycan
 o Breaks
the
glycosidic
bonds
between
NAM
&
NAG
 o Forms
protoplast
(Gram
+)
or
a
spheroplast
(Gram
‐)
 o More
effective
on
Gram
(+)’s
than
Gram
(–)’s
 Spheroplasts
still
have
outer
membrane
for
osmotic
 stability
 
 
 
 CHAPTER
6

 
 General
 • Food
sources
 o Autotrophs
–
make
own
food,
use
CO2
as
C
source
 o Heterotrophs
–
eat
stuff
 • Energy
Sources
 o Phototrophs
–
use
light
 o Chemotrophs
–
oxidize
organic
and
inorganic
compounds
 • Electron
Sources
 o Lithotrophs
–
reduced
inorganic
compounds
 o Organotrophs
–
organic
molecules
 Inorganic
electron
and
energy
sources
usually
go
together.
 Purple
nonsulfur
bacteria
can
change
based
on
O2
presence.
Normal
=
chemotroph,
 low
=
photoorganoheterotroph
 
 • Food
source
uses
 o Lipids:
C
H
O
P
 o Proteins:
C
H
O
N
S
 o Carbohydrates:
C
H
O
 o Nucleic
Acids:
C
H
O
N
P
 • Catalytic
activity
and
structure
stabilization:
K,
Ca,
Mg,
Fe
 • Trace
elements
(cofactors):
Mn,
Co,
Zn,
Mo,
Ni,
Cu
 • Growth
factors
cannot
be
synthesized
an
need
to
be
acquired
elsewhere
 o Vitamins
(usually
enzyme
co
factors)
 o Amino
acids
(proteins)
 o Purines/Pyrimidines
(Nucleic
Acids)
 
 
 TRANSPORT
 
 • Passive
Diffusion
 o [High]
to
[Low]
 o Used
for
small
molecules
like
CO2
and
O2
 o Go
straight
through
membrane
 • Facilitated
Diffusion
 o [high]
to
[low]
 o Uses
(integral)
carrier
proteins,
SATURABLE
 o Binding
substrate
to
protein
changes
shape,
usually
larger
 substrates
 o Maintain
concentration
gradient
by
altering
nutrient
 o can
go
backwards
to
expel
cellular
waste
 o NOT
prominent
transport
for
nutrients
into
prokaryotic
cell
 • Active
Transport
 o Can
use
ATP
or
Generated
concentration
gradients
 o [lower]
to
[higher]
 • • 
 MEDIA
 • • • • • • • o carrier
protein
used,
saturable
 SYMPORT,
ANTIPORT,
UNIPORT
 o ABC
Transporter
 Uses
peripheral
solute‐binding
protein
to
bind
and
change
 shape
of
carrier
protein.
(Gram
–
in
periplasmic
space,
 gram
+
in
outer
PL
bilayer)
 Two
domains:
one
binds
ATP
inside
cell
(nucleotide
 binding
domain),
other
is
transport
domain
(spans
 membrane)
 Group
Translocation
 o Alters
the
solute
in
some
form,
i.e.
Adds
a
phosphate
as
a
sugar
 molecule
comes
through
membrane
protein.
 o Usually
breaks
a
phosphate
bond
off
some
already
formed
 compound
and
forms
a
new
one
 o Uses
metabolic
energy
 o PEP
/
PTS
 Used
widely
in
prokaryotes,
PEP
becomes
pyruvate
 Coupled
Antiport/Symport
 o Antiport
–
Proton
motive
force
expels
Na+
from
cell
as
H+
enters
 o Symport
–
Na+
binds
to
protein
carrier
outside
cell
and
allows
 solute
to
enter
carrier
protein
and
bind
 Release
of
Na+
caused
by
protein
conformational
change
 Agars
used
for
solid
medias

 o Inert
to
most
bacteria,
not
nutrient
source
 o Melts
around
95
°
solidifies
around
45
°
 Complex
Media
 o Chemical
formula
unknown,
broth,
extract,
etc…
 Chemically
defined
(synthetic)
 o Exact
formulas
are
known
 Supportive
Media
 o Sustaining
growth
is
only
function,
enriched
w
nutrients
 o Used
mainly
for
stocks
and
maintenance
 Selective
Media
 o Allows
a
few
organisms
to
grow
while
inhibiting
others
 o Thayer­Martin
Agar
has
antibiotics
to
kill
off
non
target
bacteria.
 Used
in
STD
testing
 Differential
 o NO
INHIBITION,
just
differentiates
between
organisms
 o i.e.
blood
agar
and
hemolysis
(alpha
hemolyzeres
turn
blood
 green,
beta
turns
it
clear,
gamma
is
no
hemolysis)
 Selective
and
Differential
 o MacConkey
Agar
selects
against
growth
of
GRAM
+
bacteria
and
 differentiates
based
on
lactose
fermentation.
 o Fermenters
produce
acidic
environment,
TURN
PINK
due
to
pH
 indicators
 
 BACTERIA
COLONIES
 
 • Bacteria
colony
=
1
million
cells,
multiply
by
binary
fission,
progeny
 identical
 • Streak
Plate
 o Loopful
of
bacteria
diluted
over
series
of
flame
sterilized
brush
 strokes
 o Doesn’t
let
you
enumerate
bacteria,
just
isolate
them
kind
of
 o S
 o
 • Spread
Plate
 o Uses
a
diluted
mixture
of
the
bacteria
and
puts
them
straight
into
 the
culture
 • Pour
Plate
 o Like
spread
plate
but
bacteria
diluted
in
stepwise
fashion
in
liquid
 agar
 o Cells
show
up
in
culture
embedded
in
agar
in
stead
of
on
top
 o ALLOWS
YOU
TO
ENUMERATE
THE
NUMBER
OF
BACTERIA
by
 diluting
until
no
more
bacteria
are
left.
 
 CHAPTER
7
 
 Cardinal
Terms
(have
to
do
with
oxygen)
 • Obligate
(strict)
anaerobes
 o Undergo
aerobic
respiration
(O2
terminal
electron
acceptor)
 o Growth
in
a
broth
medium
only
near
top
of
liquid
(to
get
to
O2)
 • Facultative
anaerobes
 o Can
live
without
O2
if
needed
 o Undergo
aerobic
respiration
in
presence
of
O2,
anaerobic
 respiration
if
no
O2
 o More
ATP/growth
in
presence
of
O2
 o Broth
Medium:
dense
at
top
but
scattered
throughout
 • Obligate
(strict)
anaerobes
 o Anaerobic
respiration,
use
NO3
as
terminal
e‐
acceptors
 o O2
is
TOXIC,
causes
free
radicals.
No
enzyme
like
superoxide
 dismutase
and
catalase
to
turn
superoxides
to
peroxides.
 Catalase
breaks
down
H2O2
 o Broth
medium:
only
near
bottom
 • Aerotolerant
anaerobes
 o Like
obligate
anerobes
but
tolerant
of
O2
 o Have
superoxide
dismutase
 o Broth
medium:
even
throughout
 • Microaerophiles
 o Need
2‐10
%
O2,
lots
of
it
damaging.
Air
is
20%
O2
 o Respiratory
pathogens
are
an
example
 o Low
levels
SOD
and
catalase
 o Broth
medium:
close
to
the
top
 • NOTE:
peroxidases
convert
peroxides
to
water
and
NAD+
 
 Factors
Influencing
Growth
 • Solutes
and
Water
Activity
 o Moderate
halophile
(Marine
bacteria)
 .2M
to
3.4M
NaCl
 o Extreme
Halophile
 2.0
to
6.2
M
NaCl
(hypersaline
environments)
 o Osmotolerant
(skin
bacteria)
 Wide
range
of
water
activity
and
[solute]
 o Saccharophiles
(yeasts
and
molds)
 High
[sugar]
to
regulate
osmosis
 o EFFECTS
 Low
water
activity
=
high
osmotic
pressure/[solute]
 Low
water
activity
makes
cells
shrink/lose
water
 High
water
activity
lyses
cells
 Cell
walls
protect,
some
channels
also
 • pH
 o Acidophiles
–
1
–
5.5
 • • • • o Neutrophiles
(most)
–
5.5
–
8.5
 o Alkalophiles
–
8.5
–
11.5
 o Acido/alkalotolerant
can
persist
outside
normal
environment
but
 do
not
reproduce
 o pH
can
inhibit
enzymes
and
transport
proteins
 o To
protect:
 Antiport
exchange
of
K+
for
H+
for
neutrophiles
 Make
special
proteins:
acid
shock
proteins
 Export
wastes
to
environment
 Fermentation
makes
acids,
putrefaction
makes
 ammonias
 Temperature
 o Psychrophiles:
0
–
20
(cause
food
spoilage
in
refrigerador)
 o Mesophiles:
15‐45
(most
human
pathogens)
 o Thermophiles:
45‐70
(found
in
compost
heaps)
 o Hyperthermophiles:
70‐120
(hydrothermal
vents/hot
springs)
 Oxygen
Availability/Presence
 o See
above
 (Hydrostatic)
Pressure
 o Land
=
1
atm,
deep
sea
=
600
–
1100
atms
 o Membrane
lipids
change
with
increases
in
pressure
 o Barotolerant:
survive
in
varying
pressure
environments
 o Barophiles:
grow
best
where
pressure
>
atmospheric
pressure.
 High
temps
mostly
archaea,
low/moderate
are
bacteria
 Radiation
 o Damages
DNA,
indirectly
kills
cells
(thymine
dimer
mutations)
 o Can’t
replicate
chromosomes,
can’t
transcribe
mRNA
 o UV
light
DNA
damage
repair
 Photoreactivation
–
blue
light
energizes
photolyase
which
 breaks
dimers
 Alows
normal
base
pairing
 Dark
Reactivation
(base
excision)
 Endonuclease
removes
thymine
dimers
 Missing
bases
replaced
by
other
endonucleases
 o Ionizing
Radiation
 Causes
atoms
to
lose
electrons
(x­ray
and
gamma
 radiation)
 Low
levels
cause
mutations
and
indirectly
lead
to
cell
death
 High
levels
of
exposure
lethal,
breaks
H‐H
bonds/rings,
 oxidizes
double
bonds,
polymerize
some
molecules
 STERILIZING
TREATMENT
 
 Batch
Culture
Growth
 • Lag
Phase
 o Metabolically
active
cells
but
NO
REPRODUCTION
 o Make
enzymes,
organelles,
repair
components,
cell
may
grow
 (Log)
Exponential
Phase
 o population
doubles
each
generation,
average
is
20
min.
 o growth
asynchronous,
not
all
cells
divide
at
same
time
 o rate
limited
to
[cellular
enzyme]
 o balanced
growth:
all
cellular
constituents
made
at
constant
rates
 to
one
another
 may
change
if
nutrient
becomes
limiting
 • Stationary
Phase
 o Curve
goes
horizontal:
cells
die
at
same
rate
new
ones
made
 o Caused
by
nutrient/O2
limitation,
toxic
waste
buildup,
cell
density
 o Cell
may
change:
gene
expression,
extra
peptidoglycan
cross
 linking,
nucleoid
condensation,
endospores,
changes
to
make
them
 more
resistant
to
unfavorable
conditions
 • Death

 o Decrease
in
cell
numbers,
death
defined
by
inability
to
reproduce.
 o New
lag/log
phase
may
rise
after
some
of
culture
dies
off,
more
 nutrients
available
for
other
cells
 o Cells
don’t
really
lyse,
so
dead
or
dormant?
THEORIES:
 Just
die
and
some
survive
 VBNC
 Genetic
response
to
survive
starvation,
resuscitates
 when
in
new
environment
 Dormancy
occurs
without
morphology
change,
 unlike
endospore
formation
 Programmed
Cell
Death
 Genetic
response
for
certain
%
of
cells
that
 suicide/die
 Provides
nutrients
and
reduced
competition
for
O2
 and
space
for
other
cells
 
 Predicting
Cell
Number
 • Nt
=
N0
x
2n

 • Nt
=
#
at
time
t,
N0
=
initial
#,
n
=
number
generations
 
 Measuring
Microbial
Growth
 • BY
CELL
NUMBER
 o Viable
vs.
Total
 o Direct
Microscopic
Counts
 Petroff­Hauser
Counting
Chamber
counts
number
of
cells
 per
0.1
mL.

 Can’t
distinguish
live
from
dead
 o Cell
Counters/Flow
Cytometry
 Coulter
Counter
directs
suspension
through
a
small
hole,
 change
in
electrical
resistance
=
1
cell
 Can’t
distinguish
live
from
dead,
arifacts
can
get
counted
 too
 • Flow
Cytometry
uses
similar
devices,
just
uses
scattered
 light
instead
of
electrical
field
 o Viable
Plate
Counts
 Measures
colony
forming
units,
NOT
necessarily
all
living
 bacteria
present,
only
those
able
to
grow
under
conditions
 given
 Membrane
filters
can
sift
microbes
out
of
solution
and
 colonies
can
be
observed
on
medium
 BY
CELL
MASS
 o Calculations
and
converstions
 Total
cell
weight
 Weight
of
one
component
 Turbidity
 Measures
amount
of
light
scattered
by
cells
(more
 mass
=
more
scatter)
 Uses
spectrophotometer
to
measure
optical
 density,
must
be
performed
in
conjunction
with
 viable
counts
initially
to
establish
relationship
bt
OD
 and
cell
number
(comparison
factor)
 • ...
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