Deck 5: Resolution and Detection of Nucleic Acids

Question 1

Which of the following molecules polymerize to form a support medium through which nucleic acids move?

A) Ethidium bromide
B) Ethylenediaminetetraacetic acid
C) Sodium dodecyl sulfate
D) Polyacrylamide

Answer 1

Polyacrylamide

Question 2

What concentration of agarose should be used for optimal separation of DNA fragments of 100, 250, and 350 bp in length?

A) 0.5%
B) 0.7%
C) 2.0%
D) 12.0%

Answer 2

2.0%

Question 3

What is an advantage of agarose over polyacrylamide gels?

A) Agarose is more stable than polyacrylamide.
B) Agarose monomers are not toxic.
C) Acrylamide takes a long time to polymerize.
D) Polyacrylamide gels must be used immediately after polymerization.

Answer 3

Agarose monomers are not toxic.

Question 4

Which of the following molecules will migrate fastest in capillary electrophoresis?

A) Large and positively charged
B) Small and positively charged
C) Large and negatively charged
D) Small and negatively charged

Question 5

A very limited amount of nucleic acid, 500-1500 bp in size, is to be analyzed in a short time (same day) with the results available immediately. Which of the following electrophoresis procedures will satisfy those conditions?

A) Capillary electrophoresis
B) Pulse-field gel electrophoresis
C) Field inversion gel electrophoresis
D) Contour-clamped homogeneous electric field

Question 6

Which of the following molecules is added to an electrophoresis buffer for the purpose of denaturing DNA?

A) Ethylenediaminetetraacetic acid
B) Polyacrylamide
C) Formamide
D) Tris borate

Question 7

Nucleic acids migrate toward which pole in electrophoresis?

A) Cathode
B) Anode

Question 8

How does one prepare a 2% agarose gel?

A) Mix 0.01 g agarose/mL running buffer and heat.
B) Mix 0.02 g agarose/mL running buffer and heat.
C) Mix 2 g agarose/mL running buffer and heat.
D) Mix 1 g agarose/mL running buffer and heat.

Question 9

Which of the following is not an example of pulse-field gel electrophoresis?

A) Field inversion gel electrophoresis
B) Contour-clamped homogeneous electric field
C) Polyacrylamide gel electrophoresis
D) Transverse alternating field electrophoresis

Question 10

Nucleic acids are injected into the capillary in capillary electrophoresis by which of the following injection methods?

A) Hydrostatic
B) Electrokinetic
C) Pneumatic
D) Vacuum

Question 11

To increase the density of a sample relative to the density of the buffer prior to loading the sample into a gel, which of the following is added to the sample?

A) Glycerol
B) Ethidium bromide
C) Formaldehyde
D) Tris acetate EDTA

Question 12

The positive pole in electrophoresis is indicated by which color?

A) Red
B) Black
C) Green
D) White

Question 13

A molecular biologist is to separate and analyze a mixture of nucleic acids that are about 100,000 bp in size. Which of the following methods will yield the best results?

A) Capillary electrophoresis
B) Rotating gel electrophoresis
C) Polyacrylamide gel electrophoresis
D) Traditional agarose gel electrophoresis

Question 14

The matrix in capillary electrophoresis through which nucleic acids pass is:

A) Silica
B) Agarose
C) Agarobiose
D) Optimized polymer

Question 15

Polyacrylamide gel properties can be altered by adjusting T and C values. What are T and C in this context?

A) Temperature of polymerization and concentration of acrylamide
B) Time of polymerization and number of cytosines in the nucleic acid to be separated
C) Total concentration of acrylamide plus cross-linker and percent cross-linker
D) TEMED concentration and concentration of APS used for polymerization

Question 16

To separate a mixture of oligonucleotides with a resolution between bands of 1 bp, which of the following methods should be used?

A) Contour-clamped homogeneous electric field
B) Rotating gel electrophoresis
C) Polyacrylamide gel electrophoresis
D) Traditional agarose gel electrophoresis

Question 17

A molecular technologist has run a vertical gel. While analyzing the gel, the technologist notices that the bands in the outer lanes did not run as far as similar-sized bands in the inner lanes, so the bands look like a smile on the gel. What is the explanation for this?

A) Samples were loaded into the inner wells first and got a head start moving down the gel.
B) A larger volume of sample was loaded into the outer wells so that they ran slower.
C) The electrodes in the middle of the gel were working better than at the edges of the gel.
D) The temperature across the gel was not constant, so the inner wells were warmer.

Question 18

As compared with traditional slab gel electrophoresis, which of the following is not an advantage of capillary electrophoresis?

A) Analyzes smaller amounts of samples
B) Ability to run more than one sample together
C) Cost of instrumentation and labels
D) Real-time sample detection and analysis

Question 19

What is one reason that polyacrylamide gels have higher resolution than agarose gels for small fragments?

A) Agarose polymer spaces are bigger than those of polyacrylamide.
B) Agarose polymers are very fragile.
C) Agarose won't separate molecules over a certain size.
D) Agarose is a synthetic polymer in which sieving properties can be precisely controlled.

Question 20

Which of the following are used to make wells in a solidifying gel into which samples are loaded?

A) Brushes
B) Combs
C) Picks
D) Shovels

Question 21

Which is an important property of gel running buffers?

A) Solubility at low temperature
B) Ability to maintain constant pH
C) Capacity to heat up quickly
D) High ultraviolet light absorption

Question 22

The functions of which of the following include carrying the current and protecting the sample nucleic acids during electrophoresis?

A) Glycerol
B) Formaldehyde
C) Ammonium persulfate
D) Tris borate EDTA

Question 23

Which of the following can be used to detect the location of DNA bands in a gel after electrophoresis?

A) SYBR Green
B) Xylene cyanol green
C) Bromophenol blue
D) Hematoxylin

Question 24

To monitor the progress of electrophoresis, which of the following is added to a sample that does not associate with DNA and runs ahead of the smallest fragments in the sample?

A) Ethidium bromide
B) Acrylamide
C) Bromophenol blue
D) SYBR Green

Question 25

Which of the following properties is true for ethidium bromide?

A) Emits green light when excited at 200 nm
B) Level of detection is 5 pg of DNA
C) Intercalates between nitrogen bases
D) Has no background fluorescence in agarose