BFRI II Review

Lab 1: PCR and Gel Electrophoresis IRAT

1. PCR is used to
a. Make more copies of DNA
b. Separate DNA
c. Detect a certain type of protein
d. Determine the order of the nucleotides in a DNA segment
2. Which of the following is not one of the steps in PCR?
a. Electrophoresis
b. Denaturing
c. Annealing
d. Extension
3. PCR is performed in a...
a. Thermocycler
b. Incubator
c. Centrifuge
d. Gel-Electrophoresis system
4. Which of the following components is not needed for PCR?
a. Deoxynucleotide triphosphates (dNTPs)
b. DNA polymerase (Taq Polymerase)
c. Promoters
d. DNA template
5. During the denaturing step of PCR, __________ are broken
a. Bonds between bases on the same DNA strand
b. Bonds between bases of different DNA strand
6. Which of the following PCR components will be obtained from isolating
DNA from cells?
a. Primer
b. DNA template
c. Bacteria cells
d. Deoxyribonucleotides
7. In gel electrophoresis, molecules are separated by
a. Color
b. Size
 c. Fluorescence
d. charge
8. DNA fragments are ___ charged and will migrate to the ____ end of the gel
electrophoresis apparatus.
a. Positive, positive
b. Negative, negative
c. Positive, negative
d. Negative, positive
9. What is used to bind to a DNA fragment and allow it to be visualized under
UV?
a. DNAzole
b. Loading dye
c. Ethanol
d. Ethidium bromide
10.The gel for DNA gel electrophoresis is made out of what?
a. Agarose
b. Chitosan
c. Glucose
d. Ethidium bromide
Lab 1a Pre-Lab Questionnaire

1. After centrifuging your cells that have been lysed with DNAzol, you will be
keeping the supernatant and discarding the pellet obtained.
a. TRUE

2. The DNA template that you use for PCR is single stranded.
a. FALSE

3. What is added to precipitate the DNA (form a solid from a solution)?

a. 100% ethanol

4. In PCR,___ is amplified and this is done based on the ___used in the

reaction.
a. A specific DNA fragment, primer

5. How much of a 5 μM of primer stock solution do you need to make a 50 μL

PCR solution with a primer concentration of 0.4 μM?
a. 4μL

6. If you have a DNA concentration of 0.5 ng/μL and you need 10 ng for your
PCR reaction, what is the volume of DNA template that you will need?
a. 20μL
Lab 1b Pre-Lab Questionnaire

1. Why is a loading dye used in gel electrophoresis

I. to visualize the DNA under UV

II. to make the sample sink into the wells
III.to track the sample as it runs through the gel
a. II and III
1.

2. How much agarose do you need to make 200 mL of a 1% wt./vol gel?

a. 2g

3. Ethidium bromide will be added

a. Into the agarose/TAE buffer solution after microwaving the
solution.

4. The gel wells should be placed nearer to the ________end so that the
samples will be allowed to run towards the_________end.
a. Negative, positive

5. DNA in your agarose gel can be visualized with your naked eye.
a. FALSE

6. DNA fragments that are large will be able to migrate further down the gel.
a. FALSE
LAB 2 IRAT
1. What is used to clean the biosafety cabinet/hood surfaces and anything else
that is brought into the hood?
a. Media
b. trypsin-EDTA
c. 70% ethanol
d. antibiotics
2. What is added to the cell culture media to avoid contamination with
microbiological organisms?
a. Propidium iodide
b. trypsin-EDTA
c. 70% ethanol
d. antibiotics
3. What is added to the cell culture media to provide nutrient and growth
factors to promote cell growth?
a. trypsin-EDTA
b. Trypan blue
c. Antibiotics
d. Fetal bovine serum
4. A biosafety cabinet/ tissue culture hood protects the _____
i. user/ researcher
ii. experiment
a. i only
b. ii only
c. i and ii
d. NONE
5. ______ cells will be stained blue with tyrpan blue
a. Dead
b. Alive
c. Clean and live
6. What is used to lift adherent cells by cleaving the proteins that bind the cells to
the plastic petri dish?
a. trypsin-EDTA
b. Trypan blue
c. Antibiotics
d. Fetal bovine serum
7. You can count cells manually with a ____ and automatically with a ___
a. Cellometer, hemocytometer
b. Hemocytometer, cellometer
c. Incubator, hemocytometer
d. Hemocytometer, incubator
8. Cells are cultured at physiological temperature (37 C) in a/an
a. Biosafety cabinet
b. Centrifuge
c. Incubator
d. thermocycler
9. What should not be done to avoid contamination when doing cell culture?
a. Spraying things with 70% alcohol
b. Using biosafety cabinet
c. Reusing pipettes
d. Using antibiotics
10. DMSO is used as a cryoprotectant when freezing down cells and it is not toxic
to cells
a. FALSE
LAB 2A PRE-LAB QUESTIONNAIRE
1. When thawing cells, make sure to work slowly because DMSO is good for
the cells.
a. FALSE
2. We will wash the frozen cells with media before plating them in the culture
dish.
a. TRUE
3. What must be added to cell culture media before using it?
i. Fetal bovine serum
ii. DMSO
iii. 70% ethanol
iv. Antibiotics
a. i and ii
b. i and iv
c. ii and iii
d. iii and iv
4. The first things you will be doing this week in lab is
a. Prepare media with supplements
b. Thaw cells
c. Wash cells
d. Count cells
5. Why do we make sure we mix the frozen cells with media before centrifuging to
collect the cells?
a. To wash the cells
b. To dilute the DMSO with the media
c. To provide nutrients to the cells
d. To provide antibiotics to the cells
6. After observing the cells under the microscope, we will place the cells in a ___
to allow them to expand and divide.
a. Cell culture hood
b. Incubator
c. Centrifuge
d. Freezer
LAB 3 IRAT
1. Immunoblotting is performed to
a. Detect total protein
b. Detect total mRNA
c. Detect a specific protein
d. Detect a specific mRNA
2. Bradford assay is used to
a. Quantify total protein concentration
b. Evaluate if the protein was successfully transferred
c. Evaluate if the mRNA was successfully transferred
d. Quantify total mRNA concentration
3. What is Ponceau Stain used for?
a. Quantify total protein concentration
b. Quantify total mRNA concentration
c. Evaluate if the mRNA was successfully transferred
d. Evaluate if the protein was successfully transferred
4. Order the following steps of Immunoblotting
i. Detect the protein
ii. Lyse the cells
iii. Transfer the protein
iv. Run the protein in the gel
a. iii, ii, i, iv
b. ii, iv, iii, i
c. ii, iii, iv, i
d. i, ii, iii, iv
5. The lower molecular weight proteins will be towards the bottom of the gel
a. TRUE
6. Unlike DNA gel electrophoresis in immunoblotting the samples do not have to
be negatively charged to be run in the gel
a. FALSE
7. For immunoblotting, a molecular weight ladder is not needed.
a. FALSE
8. As in DNA gel electrophoresis in immunoblotting, the gel is placed and run
horizontally.
a. FALSE
9. For detection of the protein bands of interest, the primary antibody is added first
and then the second antibody is added to bind the primary antibody.
a. TRUE
10. Blocking is performed to
a. Wash the antibodies off the membrane
b. Place the proteins on the membrane
c. Avoid non-specific binding of the antibodies
d. Block the proteins in sections
LAB 3A QUESTIONNAIRE
1. What is used to measure the total protein concentration of your samples?
a. Immunoblotting
b. Bradford assay
c. Ponceau S stain
d. BSA
2. What protein is usually used to make the standards of known concentrations
for your standard curve?
a. Bradford dye
b. BSA
c. Milk
d. Your sample
3. What is the reaction for measuring the concentration of your samples?
a. To make sure we denature the samples
b. To make sure we make a standard curve
c. To make sure we load different amounts of samples in each well
d. To make sure we load the same amount of sample in each well
4. The microplate reader will provide us with the ___ of your sample
a. Fluorescence
b. Absorbance
c. Concentration
d. volume
5. The standard curve is used to determine the ___ of your samples
a. Fluorescence
b. Absorbance
c. Concentration
d. volume
6. What will you dilute your samples with to make sure they have the same
concentration?
a. ddH20
b. PBS
c. Lysis buffer
d. Bradford dye
LAB 3B QUESTIONNAIRE

1. When making a gel, how do you make sure the gel is flat?
a. Add water on top of the gel solution
b. Insert a comb
c. Make sure the plates are flat
d. Make sure there is a sponge in the casting system
2. Arrange the following transfer components.
i. Membrane and gel
ii. Sponge
iii. Filter paper
a. iii,ii,i,ii,iii
b. ii,iii,i,iii,ii
c. ii,iii,i
d. iii,i,ii
3. How much 10x transfer buffer do you need to make 3 L of 1X buffer?
a. 300L
b. 0.3L
c. .333L
d. 0.333L
4. How far should the resolving gel solution be filled to?
a. Just below the comb
b. Half of the tall plate
c. 1 cm below the comb
d. To the top of the short plate
5. When preparing the transfer apparatus, the gel should be by the positive end and
membrane should e the negative end
a. TRUE
b. FALSE
6. The short plate should be in front and the tall plate should be in the back in the
casting frame?
a. TRUE
b. FALSE
LAB 3C QUESTIONNAIRE
1. Blocking is done to add the proteins in milk to areas on the membrane that
are already covered by protein
a. True
b. False
2. How much milk do you need to make 20 mL of 10% (w/v) blocking
solution?
a. 2 g
b. 200g
c. 0.5g
d. 50g
3. You should expect to see the same GAPDH protein for all the samples in
your group.
a. TRUE
b. FALSE
4. When you stain your membranes with Ponceau S Stain, you should only see
1 band in each well which correspond to your protein of interest
a. TRUE
b. FALSE
5. What needs to be added to react with the enzyme horseradish peroxidase
(HRP) to allow visualization of the protein bands?
a. Blocking Solution
b. BSA
c. Substrate
d. Primary Antibody
6. Arrange the following immunoblotting components, starting with the
component that is closest to the membrane
i. Primarily antibody
ii. Enzyme horseradish peroxidase (HRP)
iii. Protein of interest
iv. Secondary antibody
a. i,ii,iii,iv
b. iii,i,iv,ii
c. iii,iv,i,ii
d. i,iii,iv,ii