Glossary of Microbiology Lab Midterm Kent 2006
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- Bacterial transformation?
- process by which competent bacterial cells pick up DNA from the environment & make use of the genes it carries?
- How is E. Coli made "competent"?
- made artificially via CaCl2 transforming solution and heat shock
- What are plasmids?
- when a bacteria naturally contain one or more small circular pieces of DNA
- What causes bacterial resistance?
- the transmission of plasmids
- what is an operon?
- structural and functional genetic units of prokaryotes
- What is the basic structure of an operon?
- operon minimally induces a promoter site (for binding RNA polymerase) and two or more structural genes coding for enzymes in the same metabolic pathway
- What operon did we use in class?
- the arabinose operon
- What are the four components of the arabinose operon?
- the promoter PBAD and three structural genes (araB, araA, and araD) that code for enzymes used in arabinose digestion
- What part of the arabinose operon functions during lack of arabinose and how does it act?
- araC (a DNA binding protein) prevents RNA polymerase from binding to the promoter, so transcription cannot occur – the switch is “off.”
- How does araC act in arabinose presence?
- - When arabinose is present, it binds to araC and changes its shape so RNA polymerase can bind to the promoter and transcribe the genes – the switch is “on.”
- What is pGLO's use in our experiment?
- replaces the structural genes (araB, araA, and araD) with the GFP gene
- What antibiotic gene does pGLO contain?
- What is bla and what does it produce? What does that enzyme do/
- It is an gene coding for ß-lactamase, which hydrolyzes certain antibiotics, including penicillin and ampicillin
- A dish contains E. coli crossed with P. aeruginosa. It is a ...
- mixed culture.
- A dish contains only one species...
- pure culture
- What does the streak plate tenchinuque accomplish?
- to identify species from a mixed culture (see Fig 1-24 a-d)
- The zigzag technique is used when a sample does not have a high cell denisty and is with pure cultures. Why is this techinque used?
- The zigzag technique is one that is meant to harbor individual colonies. These colonies can then be isolated for growth in a new medium.
- What are the major components of Fluid Thioglycollate Medium.
- Sodium theioglycollate, L-cystine, pancreatic digest of casein, resazurin
- What is the main purpose of Fluid Thioglycollate Medium?
- To provide an anarobic environment with nutrients for growth.
- In Fluid Thioglycollate Medium, which components provide "food"?
- the yeast extract and casein (from pancreatic digest)
- In the fluid Fluid Thioglycollate Medium, which keeps the medium anaerobic?
- the thioglycollate and L-cystine
- What is resazurin? There are two colors it takes. Name the colors and which state is associated with it.
- Resazurin is an indicator.
pink when oxizidized
colorless when reduced
- What two layers exist in the Fluid Thioglycollate Medium.
- The top layer is aerobic. The bottom layer is anaerobic. It is a gradient between them.
- How does the top layer of Fluid Thioglycollate Medium form?
- Initially, the whole medium lack O2 from autoclaving. Afterwards at room temperature, O2 diffuses into the top layer without fully penetrating the bottom layer.
- What is autoclaving?
- Subjecting items to conditions of high pressure and high temperature sterilization.
- This needs oxygen to grow.
- An organism that grows in the absence of free oxygen
- I (bacteria) grow better with oxygen.
- faculative anaerobe
- Some O2 is OK is me (2 - 10%), but too much kills
- What are the unites of microbial cell denisty?
- How do we indirectly measure microbial cell density?
- By use of a standard plate count.
- What is serial about serial dillutions?
- It invovles multiple dilutions, each dillution from the PREVIOUS dillution, thus compounding the result to even as small as a millionth of original density.
- Process of counting number of colonies a portion of sample produces when spread onto an agar plate.
- standard plate count
- Why is it important to reduce cell density using serial dillutions?
- 1. yields countable plates
2. math can be used to find OCD (original cell denisty)
- What is the formula for DF?
- Dilution factor: volume of broth aded to diluent/
(total volume after the broth was added)
- What is OCD formula?
- colunies counted/
- Phenol red is a ...
- Phenol red is red in pH of ...
- 8 or higher
- Why would phenol red turn yellow?
- fermentation of carbohydrate (glucose, lactose, sucrose) creates acidic conditions. At pH below 6.6 the solution turns yellow.
- What does deamination do?
- Breaks down amino acids (duh). Main point: creates NH3, raising pH making solution red in phenol red presence.
- In PR test, how do we know if gas production occured?
- A bubble is found in the tube.
- If fermentation occurs in the PR test, there is a gas bubble in the ...
- ...Durham tube.
- Which tests analyses pH change from mixed acid fermentation?
- Methyl Red Test
- What colors occurs in the Methyl red test and at what pH?
- pH lower than 4.4 - red
pH higher than 6.2 - yellow
pH between - orange
- An organism in the methyl red test produces no acid. The color of the test is ___ and the organism does not use _____
- 1. yellow (orange maybe, inconclusive
2. mixed acid fermentation
- What is the main purpose of Voges-Proskauer Test?
- It tests for glucose use with the end product of acetoin
- What is acetoin? (IUPAC name)
Is it neutral, acidic or basic?
- (2,3 - butanediol fermentation )
- A student got a clear solution for the Voges-Proskauer test. What does he conclude?
- The bacteria may use glucose but without the endproduct of acetoin.
- Name 2 oxides toxic to organisms?
- hydrogen peroxide, superoxide radical
- What protein produces toxic oxides in bacteria?
- The flavoprotein is a part of the ...?
- electron transport chain
- What does catalase do?
- It breaks down hydrogen peroxide to water and O2
- What breaks down superoxide radical?
- superoxide dismutase
- What is superoxide radical converted?
- hydrogen peroxide
- A positive catalase result means one sees...
- gas due to hydrogen peroxide being added
- Cytochrome c oxidase transfers what to what
- It transfers electrons to oxygen in some ETC
- Tetramethyl-p-phenylenediamine transfers what to what
- electrons to cytrochrome c oxidase
- What is the purple from the Oxidase test due to?
- It is from the tetramethyl-p-phenylenediamine transfering electrons to cytocrome c oxidase, thus confirming its presense.
- If citrate is the only source of carbon for the bacteria, the medium turns ____ instead of _____
- blue instead of green
- What is the dye in the citrate test? What pH makes it blue.
- Bromthymol blue is blue at a pH of 7.6
- What is citrate converted to create a blue 7.6 pH environment?
- ammonia and ammomium hydroxide
- Nitrate reductase is found in many gram ______ bacteria. It converts what to what? (nitrate reduction question)
- negative .... Nitrate (NO3-) to nitrite (NO2-) (NH3, NO, N2O also acceptable, as long as nitrate is inital reactant)
- What is denitrification?
- When Nitrate is converted to N2 (molecular nitrogen)
- Why should the fermentation (PR tests) test done before the Nitrate reduction test?
- Both fermentation and denitrification create air in the Durham tube. To conclude denitrification, one must eliminate fermentation as the product.
- There is no gas bubble after initial nitrate reduction test. You conclude...
- denitrifcation is not present. Nitrate reduction can still exist.
- There was no bubble for Nitrate reduction test. You add ____ and ____ to test for ______. A red solution meant your test was _____.
- nitrate reagent a;
nitrate reagent B;
- There was no bubble for initial nitrate test. You add two reagents. The solution remains clear. You then add ____. You notice a clear solution. You conclude what?
- Zinc. You conclude that nitrate was reduced to either NH3, NO, Or N2O or other nongaseous nitrogenous compound.
- There was no bubble for initial nitrate test. You add two reagents. The solution remains clear. You then add ____. You notice a red solution. You conclude what?
- zinc; Nitrate is not reduced by organism
- Decarboyxlation broth contains what indicator?
- Bromcresol purple
- What part of the decarboxylation broth promotes fermentation?
- The mineral oil seals the broth from external oxygen, thus creating conditions for fermentation.
- The decarboxylation test is performed, the student gets a purple solution. This happened because the organism produced _____ the enzyme causing a build up of ______ ___ ______.
alkanline end products
- Decarboxylation occurs toa specific ____ _____.
- amino acids (different organisms will decarboxyalize different a. a's)
- The blue result from decarboxylation occurs when the pH is above ___.
- pH 6.8
- A student notices a yellow solution in the Decarboxylation test. He can conclude two things. What are they?
- 1. The test is still in progress and will later be positive when the organism makes decarboxylase
2. The organism does not produce the approiamte decarboxylase.
- Decarboxylases break down what functional group of a specific amino acid?
- the COOH
- The phenylalanine deaminase tests for an organisms to catalyze the ____ functional group of a specific ____ ____.
- A student notices a ____ color change for a positive phenylalanine deaminase test.
- What familiar indicator is used in the urease test?
- phenol red
- The substance urease will break down _____. Urease creates a basic environment by producing NH3/NH4/OH
- A student performing the urease tests notices a _____ slant. He assumes the pH is above 8.4 and the enzyme _____ is present.
- If the urease test is negative, it will be pink/yellow/red/orange.
- Yellow. Pink or organge is considered positive, weak positive respectively
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