Class 02 – 01-15-10 – Chapter 1

What is microbiology (MB) = Study of small living things = looking at

organisms that you need a microscope
(MS) to see
What types of organisms are studied in MB 1. Viruses (need electron MS (EMS)
b/c they are too small for light MS
(LMS)
2. Bacteria
3. Protozoan
4. Fungi = yeast and mold (hyphae +
spore which is for reproduction)
5. parasites (parasitology)
How does the vet know your dog has Vet looks at the eggs (ovum) of the worms
worms (parasites)? under a MS
What else (besides organisms) does 1. ecology
someone in MB study? 2. immunology (antibodies and
antigens)
3. Genetics
What are the 5 kingdoms studied in MB? 1. Monera = bacteria and
cyanobacteria
2. Animalia = animals
3. Plantae = plants
4. Fungi = yeast and molds
5. Protista = algae and protozoan
MB revolves around 2 themes: 1. understanding basic life processes
2. Application of that understanding to
benefit of humans.
When you want to isolate a bacteria, you Grow it in a culture.
have to______. How is this done? This is done by a quadra-streak.
How many bacteria does it take to make 1 1 bacteria that replicates itself through
colony? binary fission. This produces a pure
culture.
Bacteria replicate by ______. binary fission
How old is the Earth? around 4 billion years old.
What is the oldest form of life and how old Microorganisms (ie: bacteria) which are
are they? about 3.5 BILLION years old
______ constitute the largest mass of living Microorganisms
material on Earth.
______ causes the biogeochemical cycles enzymes (NOTE: these come from
to occur. bacteria)

Bacteria come in ______ basic shapes. three

What are they? 1. bacillus = rod
2. cocci = circle
3. spirilla = spiral

1
The cytoplasmic membrane (or cell 1. Phospholipid bilayer
membrane) is made of a ______. This is 2. fluid mosaic
also known as a ______.
Do all cells have cell membranes? Yes. Located inside of the cell wall (for
those that do have cell walls).
Do all cells have cell walls? No. (ie: Animalia cells do not have cell
walls.
Do bacteria have a cell membrane and a Yes.
cell wall?
What does the cell wall do for the cell? Provides shape (ref. above), protects (ie:
protects from osmotic pressure)
What is unique to the cell walls of: 1. Peptidoglycan
1. bacteria 2. Chitin
2. fungi 3. Cellulose (we don’t have enzyme to
3. plants break this down)
NOTE: these are all sugars (derived from
glucose)
Describe bacteria: 1. prokaryotic = no nucleus or nuclear
membrane (but it does have a
“chromosome” in cytoplasm which
is circular, composed of DNA, and
carries genes to code for mRNA to
code for protein synthesis)
2. ribosomes present (free floating)
3. Cell wall with PG + cell wall
4. supercoil (enzymes that coil
bacteria) allows chromosome to
stay inside cell
List the characteristics of living systems. 1. Compartmentalization and
Metabolism
2. Regeneration
3. Reproduction
4. Differentiation
5. Communication
6. Movement
7. Evolution
Bacteria use ______ to move flagella
NOTE: bacteria DO NOT have cilia.
Replication in bacteria is copying the 1. DNA (chromosome)
______ and then copying the ______. This 2. cell
process is called ______. 3. binary fission (ie: 1 to 2, 2 to 4, etc)
Chromosomes are circular, therefore Bi-directional which makes replication
replication in bacteria is ______. very fast (ie: E-Coli which lives in colon
replicates or doubles every 20 minutes).
In nature, microorganisms exist in nature in Microbial communities
assemblages called ______.

2
A microorganism is going to live until it 1. food
runs out of ______ or it is ______. 2. killed
NOTE: they do not have a lifespan like we
do.
What kills bacteria? Heat (ie: fever to fight an infection)
Denaturing proteins is important in Microorganisms
controlling _____.
Microorganisms interact in microbial 1. cooperation
communities by _____ or _____. 2. competition
_____ produced O2 for the Earth’s 1. cyanobacteria
atmosphere. When did this happen? 2. around 2.5 BILLION years ago
What does it mean to say that a disease is The disease can be transmitted from one
an infectious disease? person to another (ie: HIV, Flu) (aka
contagious)
The number one killer in the early 1900’s Infectious disease
was _____.
The number one killer in the early 2000’s Lifestyle disease
was _____.
What were the main causes of the 1. Antibiotics (used against bacteria
difference b/w the number one killer in and fungi)
1900 and 2000? 2. health practices (ie: water supply)
NOTE: there are no antibiotics for viruses
The role of microbes in cleaning up Bioremediation (ie: pseudomonas converts
pollutants is known as _____. oil to CO2 and H2O)
What are biofuels? Fuels made from microbes (ie: corn to
make ethanol)
What are the 4 classes of macromolecules? 1. proteins (amino acids)
2. Nucleic acids (nucleotides)
3. Lipids (fatty acids + glycerol)
4. Polysaccharides (monosaccharides)
Why are each of the 4 classes above imp? 1. proteins = enzymes, structural
2. nucleic acids = DNA, RNA, protein
synthesis, genetic storage (codes for
everything)
3. cell membrane, energy source
4. ATP, structure, storage
mRNA codes for the ______. Amino acid sequence
tRNA carries the ______. Amino acid
rRNA binds to ______ to hold it to the 1. mRNA
______ at a location called the ______ for 2. ribosome (NOTE: only organelle
______ to occur. w/o a limiting membrane)
3. shindel yarda sequence (sp?)
4. translation
What is the function of the cytoplasmic 1. controls transport
membrane? 2. separates inside from outside
Nucleoid = DNA material in bacteria = “chromosome”

3
The ribosome is the site for ______. Translation
What does catalase do? Enzyme that breaks down H2O2 (get H20
+ O2 = bubbles).
Why would you have catalase in a cut? Catalase is natural in the blood and the
bacteria staphylococci live on the skin and
the staph is catalase +.

NOTE: test in lab to figure out whether a

bacteria is staph or strep = pour peroxide
on it. If it bubbles = staph. If it does not
bubble, likely to be strep (b/c strep is
catalase -.
What does strep do? Causes strep throat.
Do microorganisms typically live in a pure No.
culture?
What factors influence the types of Food, pH, temperature, H20
microorganisms present?
What do microorganisms do to the When they grow, they produce acid and
environment they live in? lower environment pH. They also use up
the nutrients.
Where are most of the microorganisms In the ocean and in the soil.
found?
What are food safety techniques? 1. clean
2. separate
3. cook
4. chill

Class 03 – 01-20-10 – Chapter 1 and Chapter 2

What did Koch’s postulates do? Proved that a disease is caused by a

microbe (he worked with anthrax and
tuberculosis).
Bacteria on a plate appear ______. Spotted all over plate (NOTE: none around
disk containing disinfectant if applicable)
Fungi on a plate appear ______. Fuzzy
A chemical produced by one living An antibiotic
organism against another is _____.
Penicillum works against _____. Gram + cocci
Endospores are unique to _____. Bacteria (found in bacillus and clostridium
in the soil – NOTE:found only in Gram+ )
Robert Hooke 1st to see cells (“little boxes”)
Anton van Leeuwenhoek invented microscopes
Ferdinand Cohn Endospores (TIP: ‘COHN’dospores)
What do endospores do? Makes bacteria harder to kill. They are for
survival. (NOTE: endospores appear clear)
What are fungal spores for? reproduction

4
Fungi are composed of _____ and _____. Fungal spores and hyphae.
Are bacteria bigger or smaller than fungi? Smaller. Therefore need higher
magnification to view bacteria.
Louis Pasteur 1. developed Pasteurization
2. disproved spontaneous generation
What does turbidity indicate? (aka cloudiness) It is a sign that something
grew.
What does sterile mean? No living organism
Can something be partially sterile? No.
How can you sterilize a solution? Heat (denatures proteins = enzymes),
autoclave, boil
Robert Koch Developed Koch’s postulates (refer above)
NOTE: will NOT for viruses.
What is a pure culture? One type of organism
How can you isolate bacterial colonies? Quadrant streak
What are the dishes that the media is in Petri dish
called?
What makes the media solid? Agar = seaweed (melts @ 100C and solid
@ 42C)
Why are pure cultures important? Must have pure culture to identify the
culture
Transfer an _____ _____ with a sterile loop 1. isolated colony
into fresh media to form a _____ _____. 2. pure culture
Advantage of agar over gelatin is: Bacteria have enzymes that break down
gelatin (gelatin liquefies and doesn’t work)
What is the proper way to incubate a plate? Upside down
Martinus Beijerinck Enrichment Culture Technique
Sergei Winogradsky Discovered chemoautotrophy
Robert Lister Used phenols to develop antimicrobial
chemical
Eli Metchnikoff Phagocytosis (cell eating)
Karl Landsteiner Blood typing
Paul Ehrlich Developed salvarsan (treatment against
syphilis)
Frederick Griffith Transformations
Alexander Fleming Penicillin
Barbara McClintock Jumping genes (won Nobel)
Watson and Crick DNA double helix structure
Francois Jacob
Thomas Brock Found bacteria in hot springs
Fred Sanger DNA sequencing
Stanley Prusiner Discovered prions (infectious self
reproducing pathogens)
Luc Montagnier Discovered HIV
A microscope is required to see _____. Microorganisms

5
Compound Light Microscope is compound Uses two lenses
b/c _____. (lens at top = ocular = 10x)
(lens at botton = objective lens =
1. 4x = scanning power
2. 10x = low power
3. 40x = high power
4. 100x = oil immersion
Working distance = _____. Distance b/w objective lens and slide
Limit of resolution for light microscopes = .2 micrometers (microns) = 200 nm
To increase resolution we can: 1. use blue filter (shorter wavelength)
2. use oil immersion (decreases
scattering of light)
Total magnification = Ocular x objective
What does the condenser do? Focuses the light(condenses the light)
What is stain used for? Increase contrast
How does a stain work? Cells have a negative charge. Stains are
basically salts with color. The color is
called chromophore. There are basic stains
(which have + charged chromophore) and
acidic stains (which have – charged
chromophore).
A basic stain stains the _____. Cell because it has + chromophore.
An acidic stain stains the _____. Background (cell is colorless).

Class 04 – 01-22-10 - Chapter 2

Oil immersion is used to view _____. Bacteria

Shortest wavelength of visible light = 390nm
Simple stains are used to determine 1. size
2. shape
3. arrangement
NOTE: simple = “one”
List 3 types of basic dyes 1. crystal violet
2. methylene blue (blue)
3. safranin (red or pink)
Before staining, one must do a _____. Smear
What does heat fixing do: 1. stick cells to slide
2. kills cell
What is used to measure the size of cells? Occular micrometer
What is the most commonly used stain in Differential Stains (use more than 1 dye)
MB?
What are differential stains useful for? Useful to differentiate b/c diff. structures.
List the types of differential stains. 1. Gram stain
2. Acid Fast stain
3. Endospore stain
The primary stain in the Gram stain is: Crystal violet (basic stain=all stains purple)

6
The second step of the Gram stain is the: Mordent = iodine (Gram’s iodine) which
enters cell and binds to iodine (creating
CV-I complex). Everything is still purple.
The third step of the Gram stain is the: Decolorizer = 70% ethanol = colorless
Describe Gram – cells 1. thin peptidoglycan cell wall
2. outer cell wall with
lipopolysaccharides (lipids)
NOTE: the LPS is what allows the CV-
I complex to leave the cell making
them colorless before safranin stain
Describe Gram + cells 1. thick peptidoglycan cell wall
2. no outer LPS membrane therefore
Gram + cells remain purple when
decolorizer is applied.
TIP: Positive = Phat = Purple
What step of the gram stain process is the The 3rd step = the decolorizer = 70%
most important? ethanol
The fourth step of the Gram stain is the: Counterstain = safranin = red
Describe [Link] Gram –
rod
1x3 microns
NOTE: Gram – cells just kinda do what
they want to do = no specific arrangement
(ie: chains, clusters, etc)
Describe Staph Gram +
cocci
1 micron in diameter
In clusters
Describe strep Gram +
cocci
1 micron in diameter
In chains
What does “strepto” mean? “chains”
What does Streptococcus Pyogenes cause? Strep throat
Describe Bacillus Cerus Gram +
Rod
1x5 microns
In chains
Cocci = Circle
Bacillus = Rod
Staphylococcus Aureus =
Acid-Fast stains are used for _____. Mycobacterium b/c they are acid-fast
meaning they will keep the primary stain.
TIP: like color-fast=keep the color
What do mycobacterium cause: Tuberculosis (rods)
Leprosy

7
Why are mycobacterium acid-fast? Because they have a waxy material called
mycoic acids in their cell walls.
What are the steps for the Acid-Fast stain? 1. Carbal Fuschin = red
2. Acid/Alcohol = 3%HCL in ethanol
3. counterstain = methylene blue
An acid fast bacteria after being stained is Red
A bacteria that is not acid-fast after staining Blue
is _____.
What could you do to test for tuberculosis? 1. cough up and send to lab
2. Acid-Fast stain bacteria
3. Red = mycobacteria = T.B. (not
likely to be anything other than
mycobacterium)
What could you do to test for meningitis? 1. pull cerebral spinal fluid with
lumbar puncture
2. see Gram – diplococci = meningitis

NOTE: there shouldn’t be any bacteria in

cerebral spinal fluid b/c this is a sterile
body site as is the respiratory tract.
What color is an endospore stain? The spore stains green (malachite green)
and the cell stains red (safranin)
If a spore stain comes up positive for 1. bacillus = aerobic = Gram + rod
spores, what two bacteria should you 2. clostridium = anaerobic = Gram +
consider? rod
What does bacillus cause? 1. food poisoning
2. anthrax
What does clostridium cause? 1. food poisoning (aka botulism)
2. gangrene
If an organism that stains for spores is bacillus (would not be clostridium b/c it is
growing in an incubator, what would it anaerobic and an incubator is an aerobic
likely be? environment)
Flagellar stains are used to _____. See flagella
NOTE: this is not a common stain and
seeing the flagella is hard to do and read. It
is more common to view flagella with an
electron microscope.
Why are capsules important to bacteria? A capsule increases virulence by allowing
the bacteria to avoid phagocytosis by
microphages or neutrophils.
What is a capsule? Made of polysaccharides and is located
outside the cell wall. (increases virulence)
Virulence = More deadly = can cause disease easier
What is a bacteria likely to be if it has a Pathogen
capsule?
Is a capsule stain + or -? Negative = acidic stain = stain background

8
What chromophores are used for a capsule 1. nigrosin (black) (or India ink)
stain? 2. congo red (red)
Many times, when using a capsule stain, The basic stain will stain the cell its color
they will first apply safranin or crystal (NOTE that the capsule does not take this
violet first, then do negative stain. What stain b/c it’s polysaccharide and
will this do? polysaccharide doesn’t stain) Then the
negative (aka acidic) stain is applied which
stains the background.
EXAMPLE: background = red or black
Capsule = clear
Cell = red or purple
What is fluorescence microscopy useful Technique to identify bacteria (a stain). It
for? fluorescently labels antibodies (a protein
produced by Beta cells in response to
antigens). Therefore, make an antibody
against a specific bacteria and put a
fluorescent stain on it and mix this
antibody with the bacteria (mixed culture).
(antibody will attach to the microbe it was
designed to attack). If the antibody is seen
in the microscope = bacteria is present.
Phase-contrast allows you to view Live samples (halo around sample)
What is different about dark-field MS Image light on dark background
What are yeasts? Fungi that reproduce by budding
What kind of light is used in fluorescent UV light
microscopy?
What kind of culture does syphilis grow in? None. Fluorescent microscopy is useful to
identify syphilis.
Scanning electron microscope views The surface
(stain and plate with gold)
NRG source = electrons = work in vacuum
Transmission election microscope views The inside
(stain and cut specimen)
NRG source = electrons = work in vacuum
Confocal Scanning Laser Microscope = 3-dimensional image

Class 05 – 01-25-10 - Chapter 2

Why are viruses not cells? b/c they can not reproduce on own b/c
don’t have DNA AND RNA (has only 1 or
other).NOTE: viruses are smaller than
bacteris. IE: smallest known = 10nm dia.
What is a plasmid? Small amount of extra-chromosomal DNA
found only in some prokaryotes that offer
antibiotic resistance (carry genes for
resistance)

9
Resolution = Being able to differentiate 2 points from
one another
What is the cell wall of bacteria of? PG
What is the cytoplasmic membrane of Phospholipid bilayer
bacteria made of?
What is cytoplasm made of? H2O with things in it.
What happens at ribosomes? Translation
What’s another name for nucleoid? Chromosome
Prokaryotic chromosomes are _____. Circular (only one and made of DNA)
What is a plasmid made of? DNA
Are plasmids self replicating? Yes.
What is phylogeny? Evolutionary relationship b/c organisms
Where do bacteria make energy? In the cytoplasm usually close to the
cytoplasmic membrane.
What is chloroplast? Site of photosynthesis (pigment that allows
to be photosynthetic = chlorophyll)
How are the ribosomes of eukaryotic and Eukaryotic = 80x ribosomes
prokaryotic cells different? Bacteria = 70x ribosomes
What is evolution? Process of change over time
What is a useful molecule for determining rRNA
phylogeny?
Which units are used for light Microns = 10 -6 meters
microscopes?
Which units are used for electron Nanometers = 10 -9 meters = nm
microscopes?
Viruses are surrounded by a protein coat = Capsid
HIV is an _____ virus. RNA
What cells do HIV infect? T cells (CD-4 cells)
What kind of a virus is HIV? A retrovirus.
What kind of enzyme does HIV have? Reverse Trancriptase (makes DNA from
RNA)
What kind of virus affects bacteria? Bacteriaphages
What are two important types of 1. Lamba
bacteriaphages? 2. T-4
What special kind of enzyme do Lysozyme
bacteriaphages carry?
What does lysozyme do? Breaks through bacterial cell walls.
Lyse = burst
How do viruses get into animal cells? Usually phagocytosis. Sometimes cell
(without cell walls) membranes will fuse. NOTE: bacteria has
to bring along with it the lysozyme.
How many copies of chromosomes are 1. eukaryotes = 2
found in eukaryotes? Prokaryotes? Why is 2. prokaryotes =1
this important? Important b/c 1. Prokaryotes reproduce
quicker but 2. Mutations show up faster

10
Are archaea and bacteria closely related? No. Archaea are more closely related to
eukarya.
Where is endosybiosis demonstrated? 1. mitochondria
2. chloroplast
This is believed to be true b/c DNA/RNA
in these are similar to prokaryotic cells.
Chemoorganotrophs = Use organic molecules for NRG
NOTE: we are chemoorganotrophs
“troph” = To eat
Chemolithotrophs = Use inorganic molecules for NRG
Where is the chemolithotroph process Only in prokaryotes. ONLY IN
found? BACTERIA.
Phototrophs = Use light for NRG.
Autotrophs = Make own food. (ie: cyanobacteria, plants)
(aka “primary producers”)
Heterotrophs = Obtain food from environment
What is an example of an extremophile? Archaea
Where are extremophiles found? Hot springs, glaciers, extremely salty
water, high pH environments.
All known pathogens are in the domain Bacteria
What makes up the largest division of Proteobacteria (aka “true bacteria”)
Bacteria? = Gram - = E. Coli, Pseudomonas, and
Salmonella
Is cyanobacteria related to Gram – or Gram Gram +
+ bacteria?
What is Chlamydia? Bacteria = #1 STD
Examples of Gram + bacteria include Staph, strep, bacillus, clostridium
Spirochetes may cause Syphilis, lyme disease
What are the spores in fungi used for? Reproduction
What is a heterocyst? Round structure found in cyanobacteria
that is important for nitrogen fixation
(allows free nitrogen to be taken from air to
be converted to NRG)
What type of bacteria are extremely Deinococcus
resistant to radiation?
Domain Archaea includes these 3 groups: 1. Methanogens – produce methane
2. Extreme halophile – req. high salt
(not in high salt = lyse = burst)
3. Thermoacidophiles – love high
temp, low pH environments
Where would you find a hyperthermophile? In REALLY hot environments (ie: ocean
vents, hot springs, etc)
Major groups of eukaryotic 1. algae
microorganisms include: 2. fungi
3. protozoa
4. slime molds

11
 Lichens are an example of a _____ b/w 2 Mutualistic (ie: fungia and cyanobacteria
groups of protists. OR fungi and algae)
Why are algae kind of like plants? They are protists but they have a green
pigment which allows them to undergo
photosynthesis
What are the two main parts of fungi and 1. spores – used for reproduction
what do they do? 2. hyphae – get nutrients, attach to
something
What are one of the first things to grow Lichens
back after a fire?

Class 06 – 01-27-10 - Chapter 4

Morpholgy = cell shape

measure bacteria in microns
cytoplasmic membranes are known as phospholipids bilayers
cytoplasmic membrane referred to as fluid mosaic
membrane proteins are used for transport
eukaryotic cells have sterols. Bacteria do Hopanoids (sterols found in eukaryotes)
not have sterols. They have _____. (planar structure gives it strength)
archaea are different from true bacteria b/c 1. they have ETHER linkages in their
PBL (whereas true bacteria have
ester linkages)
2. they do not have fatty acids
3. they have monolayers (not bilayers)
NOTE: this structure helps them to survive
in extreme environments.
Major functions of cytoplasmic membrane [Link] barrier
[Link] anchor
[Link] conservation
“ase” = enzyme = lower the NRG of activation
The protein responsible for exporting translocases
proteins through and inserting into
prokaryotic membranes are called _____.
Polar and charged molecules must be Transported
_____ across the cell membrane.
Peptidoglycan is unique to _____. What is 1. bacteria (cell wall)
it composed of? What connects the layers 2. N-acetylglucosamnie and N-
of PG together? acetylmuramic acid (derivatives of
glucose – basically polysaccharides
= sugars) (B-1,4 linkages)
3. amino acids in a short polypeptide
chain (polypeptides)
_____bacteria do not have cell walls. Mycoplasms (group of pathogenic bacteria,
ie: cause walking pneumonia)
What is the periplasm? This is found in Gram – bacteria. It is the

12
 space b/w CM, PG, and LPS. (not found in
Gram + bacteria b/c no LPS)
Where is a teichoic acid found? Unique to the structure of Gram + bacteria.
What is Lipid A? Endotoxin (= anything that poisons) found
in membrane of Gram – bacteria that is
released when cell lyses.
Archaea have _____ instead of PG. Pseudomurein
NOTE: pseudo = false, murein = cell wall
How in peptidoglycan linked? B 1,4
How is pseudomurein in archaea linked? B 1,3
The enzyme that destroys cell walls Lysozyme (the polypeptide bond b/w PG
causing cells to lyse or burst is _____. layers is sensitive to this enzyme)
The type of bacteria that does not have a Mycoplasm (these cause walking
cell wall is called a _____. pneumonia)
What is the endotoxin found in the Lipid A
membrane of Gram – bacteria that is
released when the cell lyses?
Is the B-1,3 linkage in archaea lysozyme No. B-1,4 linkages are affected. Not B-1,3.
sensitive? (B-1,4 in other bacteria.)
The most common cell wall type of archaea S-layers.
bacteria is called _____.
A _____ layer assists in the attachment to Slime. (almost always polysaccharide
surfaces. layers)
_____ increases virulence of bacteria. Capsules. (almost always polysaccharide
layers)
_____ is for movement. Flagella
_____ is for attachment. Fimbrae
_____ is the genetic exchange b/w cells. Conjugation (asexual reproduction), Pili
This process is assisted by _____.
Magnetic storage inclusions are ______. Magnetosomes
_____ are composed of elemental sulfur. Sulfur globules
Carbon storage polymers consist of: 1. PHB (poly-B-hydroxybutyric acid)
2. Gycogen
The accumulation of inorganic phosphate is Polyphosphates
The _____ assists bacteria in floating. Gas vesicles (like a fish bladder)
Endospores are found in ___ and ____. Bacillus, clostridium (find in soil) (ONLY
Gram +)
The ____ is found only in cyanobacteria Heterocyst (the rest of the cell with
and functions in nitrogen fixation. chlorophyll do photosynthesis) (heterocysts
are not found in ALL cyanobacteria)
Do endospores absorb a stain? No. (unless it’s a special stain that uses
heat and phenol)
What are endospores for? Survival
____ spores are located near the ends. Terminal
____ spores are located near the center. Central

13
When does a bacteria make endospores? 1. lack of nutrients
2. too dry
3. chemicals around
NOTE: makes endospore before it dies
(this is why anthrax is so deadly … very
hard to kill) (spore = can be aerosoled)
(spores can live for hundreds of years)
Peritrichous flagella = Radiating out from center (around)
Polar flagella = One at one end
Lophotrichous flagella = Multiple coming out of one end
What does taxis mean? Movement = go somewhere
Response to chemicals = Chemotaxis
Response to light = Phototaxis
Response to oxygen = Aerotaxis
Response to ionic strength = Osmotaxis
Response to water = hydrotaxis
_____ taxis is moving toward something. +
_____ taxis is moving away from - (ie: photosynthetic bacteria move away
something. from light to avoid getting dried out)
The flagella in bacteria moves in a _____ Corkscrew. (bacteria “run” in one direction
motion. then “tumble” when they hit an object and
continue to “run” in another direction)

Class 07 – 01-29-10 - Chapter 5

Culture = organisms that grow

What is metabolism conversion of food to energy
enzymes make this happen
metabolism = bio chemistry = pathways
macromolecules to monomers
(ie: proteins to A.A.
carbohydrates to monosaccharides
nucleic acids to nucleotides
lipids to glycerol + F.A.)
Glycolysis pathway = glucose to pyruvate
Kreb’s Cycle pathway =
Electron Transport Chain pathway = most ATP formed
Cell takes monomers and does what? puts them back together to grow
Catabolism = break down of macromolecules to
monomers = break bonds = release NRG =
NRG formation
Anabolism = bonds are reformed = monomers back into
polymers = require NRG
Bacteria gets NRG from media they live in, body, environment, etc
In bacteria, the E.T.C. happens in the cell membrane

14
In eukaryotes, the E.T.C. happens in the mitochondria
Macro = large
Micro = small
Monomers = A.A.
glucose
nucleotides
glycerol + fatty acids
All organisms need carbon
hydrogen
nitrogen
oxygen
phosphorus
sulfur
selenium
heterotroph live on organic molecules = glucose
autotroph make own food = use CO2 to make glucose
= photosynthetic
Nitrogen important for A.A.
Nucleic acids
proteins
next most important nutrient to glucose
Phosphorus important for phosphate bonds in A.A.
phospholipids bilayer
Sulfur important for A.A. like Methionine and Cysteine
Potassium deals with cofactors for enzyme activity
transport for anything in and out of the cell
All ions (ie: Mg, Ca, Na) important for enzymes
help with stabilization of organism
siderophores to obtain iron from insoluble mineral form
(bring out of environment to be used)
growth factors = usually vitamins or A.A.
2 broad classes of media = Defined media = know structure and
composition of all the ingredients =
glucose = water = NaCl = everything
controlled

Complex media = most common media =

beef extract (broth) = yeast extract (broth)
= peptones (hydrolyzed proteins = partially
broken down)
Solid media = agar (seaweed) = melt at 100C and solidify
at 42C (NOTE: most bacteria (human
pathogens) grow at 37C so agar won’t melt
at this temp)
Solid media can be put in a Petri dish
slant form or slant tube (media at 45 deg

15
 slant in tube and bacteria grown at top of
slant)
a deep (media straight in tube)
broth = liquid media
broth useful for growing bacteria grow a whole bunch of culture at one time
Petri dish useful for growing bacteria in isolated colonies
Slant useful for making a staph culture
Deep can be used depending on whether organism needs O2 or not
general purpose growth media = TSA (trypticase soy agar)
TSB (trypticase soy broth)
SaB dex = agar or broth = gen. purpose for
fungi
general purpose media is just for growing
selective media is for isolating bacteria from another bacteria
selective media = MSA (mannitol salt agar = 7.5% NaCl) =
selective for staph. NOTE: this is also a
differential media

EMB (eosin methylene blue agar =

selective for Gram – bacteria because it
contains eosin which is a dye and crystal
violet and b/c it contains bile salts
(produced by liver and found in gall
bladder) NOTE: this is also a differential
media
Differential media is either + or -
MSA is differential b/c the mannitol is a sugar = some bacteria can
ferment this to produce gas = produces
alcohol and an acid = acid lowers pH and
test for this with phenol red (pH indicator)
(yellow = acid) (red = not acid)

while others cannot ferment the sugar b/c

they lack the enzyme
what is fermentation incomplete breakdown of sugar (usually
into an alcohol and an acid)
How does phenol red react? in acid = turns yellow = fermented
mennitol = staph aureus = pathogen

in nonacidic = remains red = not fermented

mennitol = staph epidermis which lives on
skin = not pathogen
if an organism grows in the presence of it’s probably staph = organism can grow in
MSA, that tells us that a high salt concentration
EMB is selective for Gram – (like [Link]) because of the eosin
EMB is differential because it has lactose = sugar = broken down by organism

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 creates an acid = colonies turn red or dark
purplish color
[Link] in EMB turns green sheen b/c metabolism of [Link]
produces a whole lot of acid = causes eosin
to precipate (eosin is a metal based dye)
Green metallic sheen in a plate indicates [Link] growing in EMB media
Blood agar = TSA + 5% sheep blood = differential media
(aka enriched media b/c of blood)

strep (won’t grow in just TSA)

Fastidious = hard to grow (ie strep = use Blood agar)
hemolysins = enzymes that break (lyse) red blood cells
TIP: “HEMO” refers to red blood cells

alpha = partial hemoysis = green

beta = total hemolysis or total lysis = zone

is clear = pathogen (like organism that
causes strep throat) NOTE: beta
hemolysins in our blood will lyse our red
blood cells

gamma = don’t produce anything = no

hemolysis
alpha hemolysins found a lot in normal, healthy people

septis = disease
Aseptic technique = what you do to prevent contamination of
yourself and the environment = “without
disease”

aka univerasal precautions = prevent spread

of disease
Big part of aseptic technique is to 1. disinfect benchtop
2. use cool loop (inoculating loop) NOTE:
hot loop in a culture will kill them but will
also cause an aerosol (bacteria in air)
3. gloves
4. gowns
5. masks
6. proper dispose of sharps
enzymes lower the energy of activation = NRG required to
bring all molecules in a chemical reaction
into the reactive state = speeds up RXNs
enzymes = proteins
enzymes denatured by heat, pH, salt concentration, temperature

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active site = region of enzyme that binds substrate
substrate catalase (enzyme) products = H2O + O2 = bubbles
H2O2 ----------------------------
Are enzymes used up in a RXN? No, reused and recycled
Pure culture = culture containing only a single kind of
microbe
Contaminants = unwanted organisms in a culture
Macronutrients = nutrients required in large amounts
Micronutrients = nutrients required in trace amounts
Respiration = complete breakdown of glucose to CO2
and H2O

More efficient = more ATP (ETC)

anaerobic = final electron acceptor not O2 (could be
nitrate, nitrite, sulfate, etc)
aerobic = final electron acceptor = O2
Fermentation = incomplete breakdown of glucose which
forms organic molecules (ie: acid, gas
CO2, H2)
Glycolysis = glucose to pyruvate (aka pyruvic acid)

Class 08 – 02-01-10 - Chapters 5 and 6

Which sugar is used primarily by the cell? Glucose

How does glucose enter a bacterial cell? Facilitated diffusion (can’t enter through
simple diffusion b/c too big)
ETC in bacteria happens in the _____ and Cell membrane (in periplasmic space = b/c
is simply a series of _____ RXNS. CM and cell wall), oxidation/reduction
Respiration = Complete breakdown of glucose
Fermentation = Incomplete breakdown of glucose (CO2 +
acids)
What type of media can be used to test for Glucose Fermentation Media (+ or -) (able
fermentation? to ferment = acids formed = lower pH
A differential test will give you a ____ or + or -
____ answer.
Lithotrophy = Using inorganic molecules for food
What is a bacterial cell wall made of? N-acetylglucosamine and N-acetylmuramic
acid
Regulation of the amount of enzymes Gene (on or off)
happens at the _____ level.
_____ regulation regulates enzyme activity. Activity
Allosteric = Shape

18
T or F ; bacteria produce lysine all the time. False, it is made only when the cell needs
it. Lysine is used in feedback inhibition by
binding to that allosteric site on the 1st
enzyme which causes the active site shape
to change.
Where does lysine bind? Allosteric site (which changes active site’s
shape)
Different enzymes that catalyze the same Isoenzymes
reaction but are subject to different
regulatory controls are known as _____.
How is bacterial growth measured? # of cells
The time required for a population of Generation time
microbial cells to double is called the ____.
During binary fission, a _____ is formed Septum
by the bacteria just before it physically
divides.
The type of special protein involved in the Min Proteins (MinC, MinD, MinE)
division of bacterial cells is called _____.
The default shape of bacteria is _____. Cocci = round
What is the shape determining factor in MreB
prokaryotes?
Beginning at the FtsZ ring, small openings Autolysins (break down old cell wall and
in the PG wall are created by _____ during form new cell wall)
binary fission.
The lipid carrier molecule that plays a Bacteroprenol, transport (big deal b/c
major role in the insertion of PG precursors precursors are made inside and
is _____. This molecule is also important bacteroprenol allows building blocks to get
for _____. across membrane so they can be linked)
PG is repeating units of N-acetylglucosamine and N-acetylmuramic
acid
What links different layers of PG together? Short peptide chains (polypeptides)
The final step in cell wall synthesis is ___. Transpeptidation (forms peptide cross links
b/w muramic acid residues in adjacent
glycan chains)
NOTE: penicillin works this way to
prevent formation of complete PG wall
causing cell to lyse. This ONLY happens
when the cell is growing (dividing).
The microbial growth cycle consists of 1. Lag phase (before growth begins)
these phases. 2. Exponential phase (growth) (aka
logarithmic growth)
3. Stationary phase (growth rate = 0)
(uses up all food, waste builds up,
etc causing growth to stop)
4. Death phase(die exponentially also)
An open system microbial culture of fixed Continuous culture

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 volume is called a _____.
What is the most common type of this? Chemostat
A continuous culture is also known as a Batch culture
The growth rate of a batch culture is Dilution
controlled by the _____ rate.
Bacteria growth is counted by Plate counts (viable cell counts) b/c
bacteria are too small to count individually.
An accountable plate contains b/w __ and 30 < accountable plate < 300 colonies
___ colonies.
Each colony on a plate comes from ____ 1 (single) (before dividing by binary
bacteria. fission)
More dense spectrophotometer count = More bacteria

REVIEW VIABLE CELL COUNTING (section 6.10)

REMEMBER: the calculation is for 1 ml (total count must be multiplied by 100 for
example if given question with 100ml)

A plate count every 20 minutes is required Standard curve

to develop a _____.

Class 09 – 02-03-10 - Chapter 6

NRG from catabolic processes is used to Anabolic processes

drive _____.
Bacteria grow in 4 phases known as: 1. Lag = go from dormant to active
(number of new cells = dead cells)
(growth = 0)
2. Log (aka exponential) =
exponential growth through binary
fission (aka logarithmic growth)
3. Stationary = # new cells = # cells
dying (growth = 0)
4. Death = to survive must go back to
dormant state
A _____ is formed in the center of a Septum
bacteria cell as it divides through binary
fission.
MSA is a _____ and _____ media. Selective and Differential
What makes MSA selective? Salt (7.5% NaCl) = normal bacteria put in
MSA will crenate and die
What type of bacteria is MSA selective Staph (make compatible solutes that make
for? insides more concentrated than regular
bacteria so they don’t dehydrate in MSA)
What makes MSA differential (turn Mannitol (=sugar) b/c staph is able to
yellow)? ferment mannitol producing acids and

20
 gases = pH drops = turns yellow (originally
red = neutral = phenol red = red)
Phenol red in acid = Yellow
Phenol red in neutral = Red
Differential means that you will get _____ Yes or No
or _____ answers.
Blood agar = TSA that has 5% blood in it (= enriched
media)
Why is blood agar a differential media? Hemolysins (enzymes that do the
hemolysis)
1. beta = total lysis = clear zones =
pathogens
2. alpha = partial lysis = green zones =
non pathogens
3. gamma = no zones
Non pathogens produce _____ hemolysins. Alpha
Pathogens produce _____ hemolysins. Beta
What makes EMB selective? Eosine crystal bile salts
What makes EMB differential? Lactose
What is EMB selective for? Gram – (ie: [Link])
If lactose is fermented in EMB, it turns Red
_____.
If lactose is not fermented in EMB, it turns Colorless
_____.
The minimum and maximum temperatures proteins
that an organism could grow has to do with
the organism’s _____.
We use cold to _____ organism growth. Slow down (ex. Slows down spoilage)
Psychrophile = Like cold temps
(TIP: b/c they’re “psycho”)
Mesophile = Like mid-temp range. (ie: staph, strep,
[Link], etc – cause pathogens in humans)
Thermophile = Like high temp
Hyperthermophile = Like extremely high temp (ie: archaea)
What will a hyperthermophile do at rm. Will not grow (like being in fridge for it-
Temp? won’t die, though)
Psychrotolerant = Tolerant to cold (don’t like it but will
tolerate it)
The _____ is the key for a bacteria being Enzyme (ie: archaea bacteria have diff.
able to function either in very cold or very membranes that make it more suited for its
hot temps. environment)
Hyperthermophiles can be found in _____. Hot springs (thermophilic cyanobacteria
can be found here also)
Taq polymerase = DNA polymerase = copies DNA
Where does taq polymerase come from? Isolated from thermos aquaticus (a
thermophile) and therefore functions at

21
 high temps.
How is taq polymerase used? PCR = polymerase chain reaction = copies
DNA = need single strand of DNA to copy
so they heat DNA to separate the strands
and then the taq polymerase comes in and
copies it. (PCR is based upon the ability of
this enzyme to function at higher temps)
In what pH do most bacteria like to grow? Between 6 and 8 (around 7)
Acidophiles = Bacteria that grow in acidic env (below 6)
Alkaliphiles = Bacteria that grow in basic env (above 9)
Microbial culture media typically contain Buffers
_____ to maintain constant pH.
Halophile = Does better in high salt concentration
Extreme halophiles = Has to have the salt to grow
What salt concentration does staph like to 7.5%
grow in?
Halotolerant = Bacteria that can tolerate some salt conc.
Osmophiles = Bacteria that like high sugar content (ie:
yeast and molds)
Xerophiles = Bacteria able to grow in very dry env. (ie:
leather)
Compatible solutes = Compound used by cell to put up with high
conc in solution (ie: 7.5% NaCl in staph)
Aerobes = Require O2 to live
Anaerobes = Do not require O2 to live (and may die in
presence of O2) (ie: clostridium) (kills
some because O2 behaves as a receptor for
electrons = takes electrons)
Facultative organisms = Can live with or without O2 (ie: [Link])
Aerotolerant anaerobes = Can tolerate O2 and can grow but can’t use
it
Microaerophiles = Need only a little bit of O2
What media is used in a deep? Agar
Reducing agents = Chemicals added to culture media to reduce
O2
What bacteria bubbles in the presence of Staph because they are catalase + (enzyme
H2O2? that breaks down H2O2 to H2O + O2)
Do batch cultures enter stationary phase?
Which type of bacteria would you most Psychrotolerant
likely find growing in your refrigerator?
MreB protein gives _____ shape in cell. Rod (round is default shape and occurs w/o
this protein)
In _____ phase, # of dying cells is greater death
than new cells.
45 to 80 C is the optimum temp for a ___. Thermophile

22
Spectrophotometer = Used to measure turbidity
T or F – Doing Lag phase, bacteria are not False. They are not growing but they are
metabolically active. metabolically active producing enzymes,
etc.
____ is the type of the protein that directs Min proteins (MinC, MinD, MinE)
the placement of Fts Z in [Link]. (sp?)
An organism that grows in a pH of 9 is an Alkalophile
_____ is a lipid carrier that plays a major Bactoprenol (big deal b/c crosses cell
role in the insertion of PG precursors. membrane and is important for transport)

23