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352 Cards in this Set

  • Front
  • Back
what are normal flora?
more or less permanent residents of your body
what are transient flora?
present only for days or weeks in/on the body
who was ignaz semmelweis?
introduced handwashing in chlorinated lime solutions at vienna general in 1846. committed to an asylum
who was joseph lister?
1. "father of antisepsis"
2. cleaned hands and instruments in carbolic acid solution
3.invented stitches
what is soap?
1. an anionic sufactant. has both a hydrophilic and a hydrophobic end. hydrophilic end dissolves in water and is capable of dissolving nonpolar grease molecules. hydrophobic portion dissolves dirt and oils. it allows water to remove normally insoluble matter by emulsification
what is antibacterial soap?
1. commonly triclosan which is concentration dependent. high concentration: capable of killing live microorganisms. low concentration: inhibits bacterial growth.
what are hand sanitizers?
a non water based hand hygiene agent. active ingredient is isopropanol or ethanol. needs to contain atleast 60% of alcohol to be effective.

HAND SANITIZERS ARE NOT MORE EFFECTIVE THAN SOAP AND WATER BASED CLEANING!
what is a sign?
objective evidence of disease as noted by an observer (coming from caregiver like doctor)

-fever, septicemia, chest sounds, rash, leukocytosis, antibodies
what is a symptom?
subjective evidence of disease as sensed by the patient

-chills, pain, ache, nausea, itching, headache, fatigue
asymptomatic infection:
although infected, the host doesn't show any signs of disease. unapparent infection so person doesn't seek medical attention.
what is latency?
after the initial symptoms in certain chronic diseases, the microbe can periodically become active and produce a recurrent disease; person may or may not shed it during the latent stage (ex= herpes)
what is a chronic carrier?
a person with a latent infection who sheds the infectious agent (constantly shedding)
what is a sequelae?
long term or permanent damage to tissues or organs

ex= leprocy (permanent damage to skin)
what are incubation carriers?
spread the infectious agent during the incubation period
what are convalescent carriers?
recuperating without symptoms
what is a passive carrier?
contaminated healthcare provider picks up pathogens and transfers them to other patients. (common with doctors and nurses)
what is a vector?
a live animal (other than human) that transmits an infectious agent from one host to another

ex= arthropods
what is a biological vector?
actively participate in a pathogens life cycle
what is a mechanical vector?
not necessary to the life cycle of an infectious agent and merely transports it without being infected
which of the following is NOT true regarding streaking for isolation on solid plate media?
1. it is easy to tell if contaminated
2. it will dry out quickly unless refrigerated
3. it is not good for separating mixed cultures
4. it is favorable to use for short term experiments
3. it is not good for separating mixed cultures
which of the following characteristics about agar is false?
1.solidifies at temperatures under 40 degrees celsius
2.degradable by most organisms
3.liquefies at 100 degrees celsius
4. once solidified, can be incubated at temperatures up to 100 degrees celsius
2. degradable by most organisms
who described "animalcules" that he observed in teeth scrapings and rain water?
leeuwenhoek
Antiseptic and disinfecting activity is affected by:
1.concentration of compound
2.type of organism
3.time of exposure
4.all the above
all the above
During the gram staining procedure, 95% ethyl alcohol is used as the:
decolorizing agent
Spirit blue agar tests for the presence of ____ which is an exoenzyme that breaks down lipids.
Lipase
True or false:
A methylene blue stain uses cationic (positive) chromagen to dye bacteria
True
____ must be capable of killing 99.999% of a specific bacteria in 30 seconds
Sanitizers
What does a durham tube test for in a carbohydrate fermentation tube?
Gas production
In a MRVP broth tube, if a ____ product is formed, the tube color will change from methyl red to yellow, and is an indication of a negative MR test.
Neutral
___'s experiment dealing with a swan necked flask effectively disproved spontaneous generation
Pasteur
In a Simmons Citrate agar slant, organisms break down ___ into ___ which can be used in fermentation
Citric acid, pyruvate
A SIM agar deep tests for what?
Sulfur, indole, motility
True or false:
Cold kills bacteria, heat promotes growth
False
Exoenzymes are capable of breaking down large compounds into smaller compounds by what process?
Hydrolysis
What does the introduction of H2O2 do to cells?
causes DNA damage
What phase of bacterial growth is known as the "gearing up" phase?
lag phase
Which of the following is not an observational result from a TSI slant?
1.Black ppt
2.red color
3.yellow color
4.motility
Motility
What exoenzyme breaks down hydrogen peroxide into water and oxygen?
Catalase
____ is a concept that states that individual isolated colonies are millions of microbial cells that arose from a single cell.
Clonality
____ is a property of a chemotherapeutic drug that kills harmful microbes without damaging the host.
Selective toxicity
A ____ is a propeller-like extracytoplasmic appendage in motile bacteria.
Flagella
24. If you grow two types of gram positive bacteria and two types of gram negative bacteria on a plate, and chemicals in the agar only allow the gram positive bacteria to grow, the media is said to be ___. On the same plate, if only one of the two types of gram positive bacteria have a color associated with their growth, the media is also said to be ____
Selective; differential
A ____ anaerobe grows best when oxygen is present, but can grow without it.
Facultative
26. If the concentration of solute is higher on the outside the cell membrane than inside the cell, the solution is __. As a result, water will flow ___the cell.
hypertonic; out of
____ is considered at its best when two points are distinct.
Resolution
____ is the theory that hypothesizes microorganisms are the cause of many different diseases.
Germ theory of disease
A _____ forms when bacteria lack essential nutrients or water. They are very hardy and long lasting.
Spore
30. The main difference in cell wall structure between gram positive and gram negative bacteria is the thickness of ____.
Peptidoglycan
Mannitol salt agar selects for ____ bacteria and differentiates bacteria through the presence of _____.
gram + ; mannitol
A ____ test is used to determine if cytochromes are present in aerobic bacteria.
Oxidase
A ____ is used to measure the absorbance of a sample by shining a beam of light through the sample.
Spectrophotometer
A _____ is used to kill microbes on living tissue but a ____ is used to kill bacteria on inanimate objects
Antiseptic; disinfectant
An ____ is a chemical produced by a microorganism that kills or inhibits the growth of another microorganism.
Antibiotic
The _____ is the minimum amount of antibiotic that it takes to kill bacteria.
minimum inhibitory concentration (MIC)
_____ is the exoenzyme that is tested for in a starch hydrolysis test. This enzyme breaks down starch molecules.
Amylase
38. Thioglycalate broth tubes are used to test for the ___ of bacteria by creating oxygen gradients within the tubes.
Aerotolerance
____ anaerobes cannot grow with oxygen present. Oxygen is toxic to them.
Obligate
The nitrate reduction test tests the ability of an organism to reduce ____ to ____.
Nitrate to nitrite
41. Draw the structure of an amino acid and give the by-product which is formed when an amino group of one amino acid forms a peptide bond with the carboxyl group of another amino acid.
1. Draw a picture
2. H2O
If a microscope has an ocular magnification of 7X and the objective has a magnification of 5X, what is the total magnification?
35X
What is the difference between a simple and negative stain? Be sure to include the reason why these stains are different.
Simple: stains organism because stain is positively charged and bacterial cell wall is negatively charged. Stain sticks to cell membrane

Negative: stains background because stain is negatively charged and bacterial cell wall is negatively charged so stain is repelled.
You just pulled your gelatin hydrolysis tubes from the cold room. Your cell phone rings and you leave your tubes on your lab bench for 20 minutes. After you come back, you read the results and your tube is liquefied. Is this a true positive test? Why or why not?
False positive because gelatin melts at room temperature whether gelatinase is present or not.
Explain the results that you would get if bacteria is able to perform starch hydrolysis (don’t forget to discuss the iodine addition).
Clear halo would form around the bacteria because amylase is the exoenzyme that the cells excreted to hydrolyze starch. Iodine stains starch so if the starch was broken down due to amylase presence, the iodine would have no starch to bind to, resulting in a clear halo.
Describe the relationship between zone of inhibition and minimum inhibitory concentration.
The larger the zone, the smaller the MIC and vice versa
What is the benefit of using oil in when looking at bacteria under the microscope?
Oil helps to increase resolution because it has a similar refractive index to glass so the light will not bend.
Would you expect a urinary tract pathogen to be urease positive or negative? Why or why not?
You would expect this bacteria to be urease positive because it could break down the urea present in urine as a source of energy.
What will happen to a red blood cell, which has an internal ion concentration of about 0.9 percent, if it is placed into a beaker of pure water?
It would swell with water and possibly burst.
During the performance of a simple staining procedure, you failed to heat fix your E. coli smear. How would you expect the slide to look after staining and why?
You probably would not get a very good smear because most of the bacteria was probably washed away with rinsing. Heat fixing increases adherence of the bacteria to the slide.
A) Describe the cell wall structure of both gram positive and gram negative bacteria.
B) List the four steps of a Gram Stain. Be sure to include the reagent used in each step as well as the function of that reagent.
C) Describe why gram negative bacteria stain differently than gram positive bacteria.
D) Identify which color gram positive and gram negative bacteria stain.
A) G+: thick layer of peptidoglycan, no LPS layer
G-: thin layer of peptidoglycan, LPS layer

B) Crystal violet: primary stain
Iodine: mordant
Alcohol: decolorizing agent
Safranin: counterstain

C) The LPS layer is washed away leaving the thin peptidoglycan layer. Because the peptidoglycan layer was not shrunk much by the decolorizing agent, the crystal violet-iodine molecules can escape and the safranin can enter to make the cells look pink.

D) G+: purple
G-: pink
List five things you should do every lab period to ensure you and everyone around you is safe.
Find this answer in slides
Who constructed a microscope that could magnify up to 30-100X?
Leeuwenhoek
Who reported that living things were composed of little boxes or cells after looking at a piece of tree bark?
Hooke
What is the germ theory of disease?
The theory that proposes that microorganisms are the cause of many diseases
Who disproved the theory of spontaneous generation?
Louis Pasteur
Who developed postulates that validated the germ theory of disease?
Robert Koch
Who was considered the father of microbiology?
Robert Koch
Who was Spallanzani?
1st to prove microorganisms were the cause of diseases but didn't get credit for it.His experiment effectively disproved spontaneous generation. Critics argued that "air" was required for spontaneous generation which paved the way for pasteur
Who believed that meat turned into flies and maggots?
Louis Pasteur
Who developed techniques for culturing microorganisms?
Robert Koch (Koch's Postulates)
What are the techniques for culturing microorganisms that Koch developed?
1. pure cultures (use of aseptic technique)
2. agar
3. petri dishes
Describe agar.
1. not degradable by most microorganisms
2. liquefies at 100 degrees C
3. solidifies at temps under 40 degrees C
4. Once solidified, can be incubated at temps up to 100 degrees C
What is a colony?
A cell, group of cells, or organism that is descended from and genetically identical to a single common ancestor, such as a bacterial colony whose members arose from a single original cell
What is clonality?
A concept that states that individual isolated colonies are millions of microbial cells that arose from one single cell
What can we tell from an agar streak plate?
1. types of colonies (overall shape)
2. morphology (colony edges and elevations)
What does a streak plate determine?
Determines "WHAT" is in the culture
What does serial dilution and plating determine?
Determines "HOW MUCH" is in a culture
Standard dilutions are often referred to as:
10-fold dilutions. Means 1 ul of your sample into 9 ul of your dilution medium; sample decreases in number by a factor of 10
What amount can be pipetted using a P1000?
100 ul- 1000 ul
What amount can be pipetted using a P200?
20 ul - 200 ul
What amount can be pipetted using a P20?
2 ul - 20 ul
What values do we see when reading a P20?
tens
ones
tenths
What values do we see when reading a P200?
hundreds
tens
ones
What values do we see when reading a P1000?
thousands
hundreds
tens
Dilutions ____ cell number and dilution factor ____ cell number
decrease; increase
What is the spot plating method?
Instead of using the entire plate and spreading 1 mL of a single dilution, can actually plate 4 separate dilutions on a single plate.

-spot 25 ul aliquots of each dilution tube onto an appropriately labeled quadrant
-count the number of colonies within each spot
-adjust the number to a per mL basis
What is TNTC for spot plating?
more than 30 colonies per spot
What is TFTC for spot plating?
less than 5 colonies per spot
For spot plating, most clinicians and researchers choose plates between ___ and ___ colonies per plate for cfu/mL calculations because it is the most accurate
10 to 20
What is TNTC for spread plating?
more than 250 colonies
What is TFTC for spread plating?
less than 25 colonies
For spread plating, most clinicians and researchers choose plates between __ and ___ colonies per plate for cfu/mL calculations
25 to 50
UTI's are only considered active in ___ cfu/mL or greater amounts
10 ^ 5
The ___ the lens, the ___ the magnification
Longer; greater
The ___ the magnification, the ___ the resolution
Greater ; poorer
What is resolution?
The ability of lenses to reveal fine detail or two points distinctly seperated
What does resolution depend on?
1. Light wavelength. (shorter wavelengths = better resolution)
2. Numerical aperture of the lens
What is numerical aperture?
-dependent upon max angle of light entering lens
-refractive index (the amount light bends) between the objective lens and the slide
What does oil increase?
Resolution (more light makes it to the objective)

-use of oil immersion increases magnification approximately 2.5-fold
What is a direct stain?
Stains the organism
Burgundy
Label Term: Commune
wines from a single commune (village) allowed own AC
What gives color to a stain?
Chromophores (charged ions). Can be acidic (-) or basic (+)
Why do we "fix" an organism?
1. to prevent autolysis (bursting)
2. to increase adherence
3. to kill the bacteria (depends)
Always begin focusing on the ___ possible power
Lowest
As you switch from low to high power, the field of view becomes ___.
Darker (to deal with this the iris diaphragm needs to be opened to allow in more light)
As you switch from low to high power the field of view becomes ___
Smaller
What is parfocal?
In focus with one lens= in focus with all
What are the three parts that differential staining is divided into?
1. primary stain
2. decolorizing agent
3. counterstain
What is a primary stain?
Imparts color to all cells
What is a decolorizing agent?
may or may not remove the primary stain from the entire cell or certain cell structures
What is a counterstain?
Provides color contrast to primary stain
In a ____ organism, 90% of cell wall is made of peptidoglycan
Gram +
In a ___ organism, 10% of cell wall is made of peptidoglycan
Gram -
Which type of organism has an outer lipopolysaccharide (LPS) layer?
Gram -
What is the primary stain used in gram staining?
Crystal Violet which dissociates into CV+ and CV-
What is the mordant used in gram staining?
Iodine which makes CV-I complexes

(mordant is what "locks" molecules together)
What is the decolorizing agent used in gram staining?
Alcohol which washes away outer layer of Gram - along with CVI. CVI in gram + cells stays in layer of peptidoglycan so stays PURPLE.
What is the counterstain used in gram staining?
Safranin which gives gram - its pink color
What gives gram - organisms a pink color?
Safranin (the counterstain used in gram staining)
What is the cell wall lipid content of Gram +? Gram -?
Gram + = low lipid
Gram - = high lipid (because of 2nd layer)
How susceptible to penicillin are Gram + organisms? Gram -?
Gram + = quite susceptible
Gram - = Less susceptible
What are common sources of error with gram staining?
1. loop too hot during culture transfer (this kills microbes)
2. excessive heat during heat fixing (can cause slide to break or microbes to boil)
3. alcohol (decolorizing agent) left on too long (causes variable results)
What is acid fast staining used for?
Used for bacteria that won't gram stain
Describe acid fast bacteria:
- resist decolorization with acid alcohol
- carbol fuschin contains phenol which solubilizes traditional cell walls
- methylene blue serves as a counter stain
What do acid fast bacteria contain?
Contain mycolic acids in their membranes which make them impermeable to traditional staining procedures
What color are acid fast cells?
Red
What do capsule stains look like?
Appear as a clear halo surrounding the stain bacterium and slide background
What does "PEA" in PEA agar stand for?
Phenyl Ethyl Alcohol Agar
What is PEA agar selective for?
Selective for gram + bacteria, inhibits the growth of gram - bacteria
What inhibits gram - organisms in PEA agar?
Phenyl ethyl alcohol inhibits DNA synthesis of gram - organisms, which is why they fail to grow
What type of bacteria is commonly grown using PEA agar?
Staphylococcal species
What does "MSA" in MSA agar stand for?
Mannitol Salt Agar
What does MSA agar contain ?
contains a high concentration of salt which inhibits the growth of gram - bacteria and most gram + bacteria
What does MSA agar select for?
Staphylococcal species. These bacteria are halophilic which means "salt loving". They prefer to grow in elevated salt environments
What makes MSA agar differentiable?
Contains mannitol. This can be used to differentiate between Staphylococcus aureus and Staphylococcus epidermidis.
Does S.aureus or S.epidermidis ferment mannitol in MSA agar?
S.aureus ferments mannitol, and the resulting acid produced changes the color of the media from red to yellow. S.epidermidis doesn't ferment mannitol so colonies appear white
What color do colonies appear in MSA agar with S.epidermidis bacteria?
White
What color is the media of MSA agar when S.aureus ferments mannitol?
Changes from red to yellow
What is the indication of a positive reaction on Pseudomonas P agar?
agar color will change from a dull beige color to anywhere from a light green to a dark blue
What is pseudomonas P agar selective for?
Pseudomonas species. Other gram - and gram + bacteria won't grow on this agar.
What does Pseudomonas P agar contain that promote the production of pigments?
MgCl2 and K2SO4
What antibiotic is Pseudomonas resistant to?
Irgasan is a broad spectrum antibiotic that inhibits the growth of other bacteria. Pseudomonas is resistant to this antibiotic so it will still grow.
Is MacConkey agar selective, differential or both?
Both selective and differential
What is Mac agar selective for?
Selective for gram - bacteria because the crystal violet dye and bile salts inhibit the growth of gram + bacteria
What is Mac agar differential for?
Differential in that it contains the carbohydrate(sugar) lactose and a pH indicator. If lactose is fermented, colonies will appear pink (+ reaction), if they dont ferment lactose the colonies will be white (- reaction)
What does the starch hydrolysis test test for?
Tests for the presence of the exoenzyme amylase
What does amylase do?
Amylase breaks down starch into smaller compounds that the bacteria can use
Starch media has ___ included in the agar.
Starch
In the starch hydrolysis test, when we pour iodine on the plate after the bacteria have grown, the iodine reacts with ___ in the agar turning it ___.
Iodine reacts with the starch in the agar turning it black
What indicates a positive result for the starch hydrolysis test?
If the bacteria is amylase + and can break down starch, a CLEAR AREA will appear around the region where the bacteria grew
What does spirit blue agar test for?
Tests for the presence of lipase, an exoenzyme that breaks down lipids
What indicates a positive result for the spirit blue agar test?
+ test indicated by a zone of clearing around the bacterial growth
What does spirit blue dye in the medium tend to migrate towards?
Tends to migrate towards areas of lipid clearing; is considered an indicator of lipolysis
What is the purpose of the OF glucose medium?
Determines whether an organism is oxidative or fermentative, which means it determines if the sugar can be fermented in the presence or absence of oxygen
How many tubes were used per organism in the OF glucose medium?
Two tubes per organism. One tube was overlaid with mineral oil.
OF glucose medium: what is a negative test?
If both tubes were still green, the test is negative, no fermentation of glucose occurred.
What colors of the tubes in the OF glucose medium indicated that the organism was oxidative?
If the non mineral oil tube was yellow but the mineral oil tube remained green; meaning it could break down sugar in the presence of oxygen
What colors of the tubes in the OF glucose medium indicated that the organism was fermentative?
If the + mineral oil tube was yellow but the non mineral oil tube remained green; meaning it could only break down sugar in the absence of oxygen
How could we determine if the organism was oxidative and fermentative in the OF glucose medium?
If both tubes were yellow
What does OF glucose medium contain other than glucose?
Contains a small amount of peptone. BACTERIA THAT CAN'T FERMENT CAN BREAK DOWN THE PROTEINS IN THE PEPTONE AND THIS CAUSES THE MEDIUM TO TURN FROM A NORMAL GREEN TO A VERY DARK BLUE, this usually occurs at the top of the tube where oxygen levels are highest.
What does the Carbohydrate Fermentation tube contain?
A carbohydrate, a pH indicator and a durham tube
What color is sterile/uninoculated media in the carbohydrate fermentation tubes?
dark red
What color is indicated by fermentation in the carbohydrate fermentation tubes?
If fermentation occurs, it will result in change from red to yellow. Record this as "A" for acid production
What happens if gas is produced during fermentation of the carbohydrate fermentation tube?
A gas bubble will become trapped in the durham tube
Can bacteria that can't ferment still grow in the carbohydrate fermentation tube?
Yes! bacteria that can't ferment may grow in the media, but there will be NO COLOR CHANGE and is considered a negative reaction
What does the MR test measure?
MR test measures the end products of the fermentation reaction. if it stays red, acid end products were produced. if it turns yellow, neutral end products were produced.

+ test = red
- test = yellow
What does the VP test test for?
VP test tests the presence of a specific neutral end product.

After adding VP reading 1 and 2 we shook the tube and let it be exposed to oxygen for 15-30 minutes.

+ test= change from dark brown/copper to deep red/purple
What is the pH baseline for methyl red?
pH 4.4
What happens if the pH of the medium is below 4.4 for the MRVP test?
STAYS RED
What happens if the pH of the medium is above 4.4 for the MRVP test?
turns YELLOW
What is the MRVP test used to differentiate between?
Used to differentiate between E. Coli and Enterobacter species
What does the nitrate reduction test test for?
Tests the ability of the organism to reduce nitrate (NO3) to nitrite (NO2) or even further to ammonia (NH3)
What indicates a + test after adding nitrate A and B reagents in the nitrate reduction test?
RED (indicates nitrate was reduced to nitrite)
What are the two possibilities that exist if no color change occurred after the addition of nitrate a and b reagents in the nitrate reduction test?
- no reduction occurred
-nitrate was reduced even further past nitrite to ammmonia or nitric oxide
What must we add in the nitrate reduction test if no color change was observed after adding nitrate a and b reagents?
Zinc dust.

red= no reduction occurred since NO3 is still present in the test tube
no color change= organism reduced but was reduced past nitrite
What indicates nitrate + test in the nitrate reduction test?
-if nitrite (pink color) is detected in the inoculated medium after the addition of reagents A and B
-no color is detected in the medium after the addition of zinc dust
What indicates nitrate - test in the nitrate reduction test?
-nitrite is not detected (no color change) after the addition of reagents A and B
-pink color develops after the addition of zinc dust
What does the catalase test test for?
Tests for the presence of the enzyme catalase
What does catalase break down?
Catalase breaks down H2O2 (hydrogen peroxide) into oxygen and water
What will happen if a bacterium is catalase +?
When we add H2O2 to bacteria growing on a plate we will see BUBBLES (this is the oxygen escaping from the water)
What will happen if a bacterium is catalase -?
No bubbles will form
What type of bacteria are generally catalase +?
Aerobic bacteria that don't ferment and require oxygen to grow
What does H2O2 damage?
Damages DNA.
What does the oxidase test test for?
Tests for the presence of cytochrome c, a specific protein in the electron transport chain
What indicates a + test in the oxidase test?
formation of a BLUE color after the addition of the oxidase reagent to bacteria growing on a plate
What indicates a - test in the oxidase test?
NO COLOR CHANGE (the oxidase reagent is colorless without the presence of a cytochrome c protein to react with)
What does the gelatinase test test for?
Tests for the presence of the enzyme gelatinase
Indication of a gelatinase + organism:
will liquefy the gelatin in the tube
Indication of a gelatinase - organism:
gelatin will remain solid
At what temperature does gelatin liquefy?
Liquefies at temperatures above 28 degrees C
What does the urea hydrolysis test test for?
Tests for the presence of the enzyme urease
Indication of a urease + organism:
Indicated by a color change from a light orange to a HOT PINK color
Indication of a urease - organism:
Light orange color
Urease liberates ____ from urea
Ammonia (NH3) which is a waste product of protein digestion
What does urea medium contain?
Contains phenol red. The pH prepared urea medium is 6.8 so phenol red is yellowish-orange
What causes the pH to go up in the urea hydrolysis test?
As ammonia builds up in the medium, the pH goes up, and the phenol red indicator changes color from yellowish orange to hot pink
What does phenylalanine deamination test for?
Tests for the organisms ability to remove an amino (NH2) group from the amino acid phenylalanine - this process is called deamination.

The liberated amino group is converted to ammonia, and you are left with PHENYLPYRUVIC ACID
What is added to the tubes after incubation in the phenylalanine deamination test?
FeCl3 added to the tubes after incubation reacts with the phenylpyruvic acid and results in a color change from reddish orange to green
+ test for phenylalanine deamination:
GREEN
- test for phenylalanine deamination:
NO COLOR CHANGE AFTER ADDING FECL3
What does the ornithine decarboxylase broth contain?
-Contains glucose. Most all bacterial species can ferment the glucose, and the resulting acid that results from fermentation will activate the pH indicator and the broth will turn YELLOW.

-contains the amino acid ornithine. Some bacteria can decarboxylate, or remove the CO2 (carbon dioxide) from ornithine. Removal of CO2 from ornithine leaves an amine by product which raises the pH.
Indication of ornithine decarboxylase + organism:
Broth will change from purple to yellow then BACK TO LIGHT PURPLE COLOR
Describe the medium of SIM agar deep:
Semi-solid so we can evaluate motility by looking for "spreading growth" from the stab line
What does the SIM agar deep medium contain?
Contains tryptophan. When tryptophan is broken down by bacteria, INDOLE IS PRODUCED
What is produced in the SIM agar deep medium when tryptophan is broken down?
INDOLE
What do we add to the SIM agar deep medium after incubation of the tubes?
Add Kovac's reagent which will react with the indole and produce a cherry red color

indole + = cherry red ring at top of tube
indole - = no color change (remains yellow) after adding kovacs reagent
Indication of indole + organism:
red color in top of tube
Indication of indole - organism:
tube remains yellow
What causes a black precipitate to form in the SIM agar deep medium?
If an organism can reduce sulfur to hydrogen sulfide, the hydrogen sulfide will combine with the iron to form ferric sulfide.

Blackening of the medium indicates the reduction of sulfur and is a POSITIVE test
What does black precipitate indicate in SIM agar deep medium?
Indicates the reduction of sulfur and is a POSITIVE test
What is the sulfur reduction test in the SIM agar deep medium useful for?
Differentiating enteric organisms
What does TSI stand for?
Triple Sugar Iron Agar
What is TSI agar?
Differential medium that contains lactose, sucrose and a small amount of glucose (dextrose) , ferrous sulfate and the pH indicator phenol red
What does TSI agar contain?
lactose, sucrose, a small amount of glucose (dextrose), ferrous sulfate and the pH indicator phenol red
What does TSI agar differentiate between?
Used to differentiate enterics based on the ability to reduce sulfur and ferment carbohydrates
When will TSI agar turn yellow?
If an organism can ferment any of the three sugars present in the medium the medium will turn yellow
When will a black precipitate form in the TSI agar?
If an organism can reduce sulfur, the hydrogen sulfide gas which is produced will react with the iron to form iron sulfide which appears as a black ppt
What will indicate that the TSI agar fermentation produced gas?
fissures in the medium or entire butt blown out of tube
What is an anionic surfactant?
(soap) that contains a hydrophilic end which interacts with water and a hydrophobic end which interacts with dirt, grease and oil
What has NO effect on viruses?
antibacterial soap
what is NON water based?
hand sanitizers - need to contain at least 60% alcohol to be effective. Added benefit of viral inactivation
Microbial abundance:
microbial cells are everywhere in abundance and the types of species is very diverse.

-100 trillion microbial cells in the human gut which is 10 times the # of human cells in the adult body
Germ Theory of Disease:
Microorganisms are the cause of many diseases
Koch's postulates:
1. a microorganism must be found in all individuals suffering the disease, can't be in abundance in healthy animals
2. microorganism must be isolated from a diseased individual
3. the isolated microorganism must cause the disease in a healthy organism after being induced
4. the microorganism must then be reisolated from the now sick organism
Agar:
useful for growing microorganisms because it can't be degraded by most microorganisms

-liquefies at 100 degrees C
-solidifies at temps under 40 degrees C
incubation:
growing an organism in an incubator at an optimum temperature
inoculation:
introduction of a microorganism to an agar, media or living organism
isolation:
culturing an individual species (only one type of bacteria)
identification:
use of differential medias
pellicle:
solid bacteria surface growth in media
turbid:
uniform growth throughout media (cloudy)
sediment:
solid bacteria growth in the bottom of the media
media classification:
-solid (plate and slant)

-semisolid

-liquid
motility test:
testing a microorganism's ability to actively move
positive result:
bacteria growth has spread throughout semi-solid media
negative result:
bacteria growth stays in the area where it was first stabbed in
cfu/mL
colony forming units per mL (how many colonies formed on the plate)
serial dilution:
consecutive reduction of the concentration of bacteria by adding media with bacteria to media which has no bacteria
10-fold dilution:
add 1 mL of your sample to 9 mL of media without bacteria
magnification:
enlarging something's image
resolution:
ability of lenses to reveal fine detail or two points distinctly seperated
numerical aperture:
maximum angle of light that can enter the lens and refractive index between the lens and the slide
chromophore:
a charged ion that gives a different color when in an acidic (+) or basic (-) solution
direct stain:
stains the organism
negative stain:
stains field/background
why do we "fix" slides?
to prevent autolysis, to increase adherence, and to kill bacteria
primary stain:
imparts color to all cells (first stain used)
decolorizing agent:
may remove primary stain (removes first stain from SOME cells)
counterstain:
provides color contrast to primary stain (stains the cells that had the primary stain removed by the decolorizing agent)
capsule:
tight arrangement of secreted chemicals that adhere to a bacteria's surface
slime layer:
an irregular arrangement of secreted chemicals
endospore:
form when bacteria lack essential nutrients or water, very hardy, long hastin
gram staining:
tests a bacteria's cell wall peptidoglycan content
positive gram staining:
bacteria is dyed purple (indicates a large peptidoglycan content in the cell wall)
negative gram staining:
bacteria is dyed pink (indicates a small peptidoglycan content in the cell wall)
acid fast stain:
testing a bacteria's cell wall for mycolic acids
acid fast positive stain:
bacteria is dyed pink (indicates mycolic acid content in cell wall)
acid fast negative stain:
bacteria is dyed blue (indicates no mycolic acid content in cell wall)
capsule stain:
testing for the presence of a viscous coat surrounding bacteria (involves a negative stain)
positive capsule stain:
a clear halo forms around the bacteria (capsule present)
negative capsule stain:
no clear halo (no capsule present)
spore stain:
tests for the formation of spores
positive spore stain:
small green stain within the cells or in the surrounding matrix (spore present)
negative spore stain:
no small green stained spores (no spores present)
selective media:
prevents growth of unwanted bacteria without inhibiting the growth of the desired organism
enriched media:
contains factors which enhance the growth of desired organism
differential media:
contains factors some bacteria can change in a recognizable way that allow it to be distinguished from other bacteria
Phenylethyl Alcohol Agar (PEA)
selective: selects for staphylococcus and inhibits gram -

+ = growth
- = no growth
MacConkey Agar
tests for the presence of lactose fermenters

selective: bile salts and crystal violet inhibit gram + organisms

differential: pH indicator and lactose differentiate lactose fermenters

+= colonies grow (gram -) colonies turn PINK (lactose fermenters). most coliforms are lactose fermenters
Mannitol Salt Agar (MSA)
differential: tests for ability to ferment mannitol

selective: inhibits gram -

+= agar around colony will be yellow (gram + organism can ferment mannitol)
Pseudomonas P Agar
differential: tests for color creation

selective: inhibits all microorganisms except pseudomonas

+= growth with a blue, green, red or dark brown (organism is a pseudomonas species)

- = no growth
Blood Agar
enrichment media: has 5% sheep or bovine blood

differential: tests for hemolysis

3 tests (alpha, beta, gamma)

alpha hemolysis= partial hemolysis, green to brown halo around colony

beta hemolysis= complete hemolysis - a clear area forms around colony

gamma hemolysis= no hemolysis (agar stays RED)
enterobacteriacae:
gram -

non spore forming bacilli found in the intestinal tract
carbohydrates
organic compounds containing carbon, hydrogen, oxygen

(CH2O)n
exoenzyme
secreted enzymes that break down carbohydrates (work outside the cell)
endoenzyme
enzymes that are not secreted but work inside the bacteria (work inside the cell)
oxidative
organisms that require oxygen to catabolize nutrients
Fermentative
organisms that don't require oxygen to catabolize nutrients

by-products of fermentation are usually acidic organic end products or gas

some organisms can catabolize in the presence and absence of oxygen
starch hydrolysis plate
tests for the presence of exoenzyme amylase

+= after iodine is added to plate there is an area around the bacteria that doesn't turn blue black. clear zone indicates there was no starch for the iodine to bond to. (indicates the presence of amylase, bacteria produces amylase)

- = after iodine is added to plate the whole plate turns blue black. (amylase is not present, bacteria doesn't produce amylase)
spirit blue agar
testing for the presence of exoenzyme lipase

+ = clear area where bacteria is growing and a blue halo around the bacteria (indicates the presence of lipase, bacteria produces lipase)

- = dye has been pulled away from the bacteria (lipase is not present, bacteria doesn't produce lipase)
OF glucose
testing to see if the bacteria is able to catabolize glucose and if it is oxidative or fermentative

+ for oxidative = yellow layer formed in the upper part of the test tube (should show no yellow production in the tube that had mineral oil added)

+ for fermentative: yellow formed throughout the test tube (should show a yellow formed throughout the tube for those that had mineral oil added)

- = no yellow color formed (bacteria is not able to catabolize glucose)
Carbohydrate (sucrose, glucose, or lactose) fermentation tubes
testing to see if the bacteria is able to catabolize the carbohydrate that is in the media

+ = yellow color formed (carbohydrate catabolized acid end product produced) ; gas seen in durham tube (carbohydrate catabolized gas end product produced)

- = media stays red and no gas is seen in the durham tube
MRVP
test to distinguish between to bacteria found in fecal contaminated samples, (E.COLI AND ENTEROBACTER SPECIES)

MR test: tests for the presence of a pH around 4.5
+= after methyl red is added the tube stays red (high pH, E.coli present)
- = after methyl red is added the tube turns yellow (neutral pH, enterobacter species present)

VP test: tests for the end product acetoin
+ = after VP 1 and 2 reagents added a reddish pink color forms (acetoin present)
- = after VP 1 and 2 reagents added a brown/copper color forms (no acetoin present)
TSI slant agar
tests to see if bacteria can catabolize glucose, sucrose, lactose, produce end product gas or produces end product H2S

+ gas formation= agar breaks up due to gas formation (bacteria produces gas as an end product of fermentation)
+ glucose fermentation= bottom of tube turns yellow (bacteria ferments glucose)
+ for glucose, sucrose, and lactose fermentation= the entire agar in tube turns yellow (bacteria ferments glucose, sucrose and lactose)
+ for H2S production= bottom of agar turns black (bacteria produces H2S as an end product of fermentation)

BACTERIA CAN SHOW ANY OR NONE OF THESE + RESULTS
Simmins citrate agar
tests to see if organisms can break citric acid down to pyruvate

+ = agar changes from blue to green (bacteria can break down citric acid)

- = agar stays green (bacteria can't break citric acid down)
deamination
the removal of the amino group of an amino acid (NH2)

PH IS LOWERED
decarboxylation
removal of carbon dioxide (CO2) from the amino acid

PH IS RAISED
what is the by product of a peptide bond formation?
water
what is used to break a peptide bond?
enzyme uses a molecule of water
Gelatin hydrolysis test
tests for the presence of exoenzyme gelatinase

+= presence of a liquid after removal of the tube from incubator and recooling the gelatin tube (indicates the presence of gelatinase, bacteria produces gelatinase)

- = no liquid present, after removal of the tube from incubator and recooling the gelatin tube
Urea test tube
tests for the presence of exoenzyme urease

+ = tube turns hot pink (pH is now basic, indicates the presence of urease, bacteria produces urease)

- = tube stays yellow (pH is neutral)
Phenylalanine deaminase
tests if the bacteria is able to break down phenylalanine into phenylpyruvic acid

+ = after 1-% FeCl3 is added a GREEN COLOR forms on top of agar (indicates the presence of phenylpyruvic acid, bacteria can deaminate phenylalanine)

- = after 1-% FeCl3 is added COLOR REMAINS THE SAME
Motility Indole Ornithine Tube (MIO)
tests if bacteria has motility, produces an end product indole, can decarboxylate ornithine or ferments glucose

+ for motility= bacteria growth has spread throughout semisolid media
- for motility= bacteria stays in the area where it was first stabbed in
+ for indole production= after kovacs reagent is added to the tube, a red ring forms (indicates the presence of indole, the bacteria produces indole as an end product)
- for indole production= after kovacs reagent is added to the tube there is NO color change
+ for ornithine decarboxylation= a dark purple color forms in the agar (high pH , indicates ornithine is being decarboxylated, bacteria can break down ornithine)
+ for glucose fermentation= yellow color forms in the agar (low pH , indicates glucose is being fermented, bacteria ferments glucose)
- for glucose fermentation= tube color stays the same
Sulfur Indole Motility agar (SIM)
tests if the bacteria produces an end product H2S, produces an end product indole or has motility

+ for H2S production= part of tube turns black (bacteria produces H2S as an end product of fermentation)
+ for indole production= after kovacs reagent is added to the tube a red ring forms (indicates the presence of indole, the bacteria produces indole as an end product)
+ for motility= bacteria growth has spread throughout the agar
obligate aerobe
can't grow without oxygen present
obligate anaerobe
can't grow with oxygen present; oxygen is toxic, will kill bacteria
microaerophiles
grow best at suboptimal atmospheric oxygen levels (7-10%)
facultative anaerobes
grow best when oxygen present, but can grow without it
aerotolerant anaerobes
can't use oxygen for growth but aren't killed by it
Metabolism
-series of oxidation reduction reactions
-transfer of electrons to different molecules
-aerobic=metabolism occurs in the presence of oxygen
-anaerobic= metabolism occurs in the absence of oxygen
-facultative= metabolism occurs in both the presence and absence of oxygen
Thioglycollate tubes
have an oxygen gradient (lots of oxygen at top- no oxygen at bottom)

looking to see where bacteria grows in the tube

obligate aerobe- bacteria grows at the top only

obligate anaerobe- bacteria grows at the bottom only

microaerophile- bacteria will grow in a single band somewhere in the middle

facultative anaerobe- bacteria will grow best at top but there will be some growth throughout

aerotolerate anaerobe- bacteria will grow uniformly throughout the entire tube
Oxidase test
tests for the presence of cytochromes (tests if aerobic respiration is occurring)

+ = after placing 1 drop of oxidizing reagent on the bacteria you see a blue color form (aerobic respiration is occurring in the bacteria)

- = no color change takes place (aerobic respiration is not occurring at that moment)
Catalase test
tests for the presence of catalase enzyme (breaks down H2O2 a natural by product of aerobic respiration, H2O2 can damage DNA so must be removed)

+ = after placing a drop of H2O2 on the bacteria, bubbles start to form (indicates catalase is present)

- = after placing a drop of H2O2 on the bacteria, no bubbles form
Nitrate Reduction Test
tests ability of an organism to reduce nitrate (NO3) to nitrite (NO2) or even further to ammonia (NH3)

+ for nitrate reduction to nitrite= when nitrate reagents A and B are added, a red color forms (indicates nitrate has been reduced to nitrite , test stops here if red color forms -bacteria reduces nitrate to nitrite)

IF NO RED IS FORMED ZINC IS ADDED

+ for nitrate reduction to nitrite and then nitrite reduction to ammonia = no color change happens when zinc is added (zinc binds to nitrate to produce a red color. so , if there is no nitrate in the media then no red color will be produced, indicates bacteria reduced nitrate to nitrite and then nitrite to ammonia)

- = red color forms when zinc is added (indicates no reduction has happened at all and the nitrate is still there in full amount)
autoclave
a type of sterilization in which an object is heated (moist heat) in a pressurized chamber
thermal death time (TDT)
time required to kill a specific bacteria at a specific temperature
decimal reduction time (DRT)
time required to kill 90% of organisms present
heat sensitivity rule of thumb
cold inhibits growth; heat kills bacteria
Dry heat
less efficient at heat transfer than moist heat (need hotter temperatures or longer times)

end result = ash and different types of gas
moist heat
highly efficient way to transfer heat

mechanism: enzyme denaturation and protein coagulation (clumping)
autoclaving
uses pressure within a closed vessel to raise water's boiling temperature

KILLS SPORES
electromagnetic spectrum
shorter wavelength= higher energy

longer wavelength= lower energy
DNA structure
-double helix
-phosphate backbone: hydrogen bonds between backbone groups reason for double helix shape
ionizing radiation
enough energy to create free radical (free electrons)

(electrons have a negative charge)
types of DNA repair enzymes
light repair= photolyses are activated by light and repair damage

dark repair= not dependent on the presence of light for activation
semipermeable
some things can pass through but not all
diffusion
solute movement that results from kinetic energy

- this occurs in the cell when the solute that is moving is capable of traveling through the membrane
osmosis
specific type of diffusion involving water

-occurs when there is a difference in concentration of an impermeable solute between the environment outside the cell and the environment inside the cell. water moves so the concentration of solute to water is equal
hypotonic
there is a higher solute concentration inside the membrane (low outside concentration, high inside concentration)

- net flow water in
hypertonic
there is a higher solute concentration outside the membrane (high outside concentration, low inside concentration)

-net flow of water out
halophilic
salt loving
facultative halophilic bacteria
bacteria that can tolerate a 10% salt environment
extreme halophiles
bacteria that require 15%-20% salt environment to grow
psychrophiles
bacteria that grow at 0 degrees to 20 degrees celsius (VERY COLD)
psychrotrophs
bacteria that grow at 15-35 degrees C (CAN HANDLE COLD)
mesophiles
bacteria that grow at 20-40 degrees C (NORMAL)
thermophiles
bacteria that grow at 40-90 degrees C (HOT)
hyperthermophiles
bacteria that grow at 65-115 degrees C (VERY HOT)
know what molecules are likely to pass through membrane and which are not
hydrophobic molecules can easily pass through (non polar carbon molecules)

hydrophilic molecules don't pass easily through (ionic molecules, have a charge)
know about pH
more H+ = more acidic = lower pH

less H+ = more basic = higher pH
antimicrobial agent
something that inhibits bacterial growth or kills bacteria
disinfectants
chemical agents used on inanimate objects (to inhibit or kill bacteria)
antiseptics
chemical agents used on living tissue (to inhibit or kill bacteria)
sanitizers
must be capable of killing 99.999% of a specific bacterial population in 30 seconds
bacteriostatic
doesn't kill bacteria, temporarily inhibits bacterial growth
antibiotic
chemotherapeutic agent that can be used topically (on skin) or absorbed internally (taken as a pill) to inhibit bacterial growth (bacteriostatic) or kill the bacteria (bacteriodcidal)
minimum inhibitory concentration (MIC)
the minimum amount of a specific type of antibiotic that is needed to inhibit the growth of bacteria
Disinfectant test tube
tests to see if a certain bacteria can grow in a tube mixed with disinfectant (tested at different times)

+ = no bacteria growth seen in tube (disinfectant can stop the growth of that type of bacteria - given the time of interaction)

- = bacteria growth seen in tube (disinfectant cant stop the growth of that type of bacteria- given the time of interaction)