BIOL-111 – Lab Exam 2 Review: PCR, DNA, and Gel Electrophoresis

You can tell which DNA band on a gel is the largest fragment by:

• Identifying the band closest to the top of the gel.

• Identifying the band closest to the bottom of the gel.

• Looking for the brightest band on the gel.

• Counting the number of bands in each lane.

Explain how you will prepare an agarose gel if the final concentration needs to be 2%. Show how you calculate the agarose needed.

• To prepare a 2% agarose gel, dissolve 2g of agarose in 100mL of buffer.

• To prepare a 2% agarose gel, dissolve 1g of agarose in 100mL of buffer.

• To prepare a 2% agarose gel, dissolve 0.5g of agarose in 100mL of buffer.

• To prepare a 2% agarose gel, dissolve 4g of agarose in 100mL of buffer.

What type of dye is commonly mixed with DNA or the gel to make the fragments visible under UV light? Describe how it works.

• Ethidium bromide is commonly mixed with DNA or the gel to make the fragments visible under UV light. It works by intercalating between DNA bases and fluorescing when exposed to UV light.

• Crystal violet is commonly mixed with DNA or the gel to make the fragments visible under UV light. It works by binding to DNA and emitting visible light.

• Methylene blue is commonly mixed with DNA or the gel to make the fragments visible under UV light. It works by staining DNA and making it visible under normal light.

• Coomassie Brilliant Blue is commonly mixed with DNA or the gel to make the fragments visible under UV light. It works by binding to proteins and fluorescing under UV light.

PCR is considered a powerful tool in molecular biology because:

• It can amplify specific DNA sequences rapidly and accurately.

• It can only be used to study proteins.

• It destroys DNA samples during analysis.

• It is only useful for observing cell structure.

5. Describe what physically happens to the DNA during denaturation step of PCR.

• The two strands of DNA separate as hydrogen bonds break.

• DNA is synthesized from nucleotides.

• DNA coils into a tighter helix.

• DNA fragments are ligated together.

Summarize the denaturation phase of PCR and include its approximate temperature.

• The denaturation phase of PCR involves heating the DNA to around 94-96°C to separate the strands.

• The denaturation phase of PCR involves cooling the DNA to around 50°C to separate the strands.

• The denaturation phase of PCR involves heating the DNA to around 70°C to separate the strands.

• The denaturation phase of PCR involves adding enzymes at room temperature to separate the strands.

The annealing phase of PCR involves binding of primers to the DNA template. What is the approximate temperature for this phase?

• 50-65°C

• 90-95°C

• 20-30°C

• 70-80°C

The extension phase of PCR occurs at which approximate temperature and what happens during this phase?

• It occurs at about 72°C, where DNA polymerase synthesizes new DNA strands.

• It occurs at about 95°C, where DNA strands separate.

• It occurs at about 55°C, where primers bind to DNA.

• It occurs at about 37°C, where enzymes are activated.

In the PCR cycle, what occurs during the annealing phase, and how does the change in temperature make this step possible?

• Primers bind to the single-stranded DNA as the temperature is lowered, allowing specific hybridization.

• DNA polymerase synthesizes new DNA strands as the temperature is raised.

• The double-stranded DNA is denatured into single strands by increasing the temperature.

• Nucleotides are added randomly to the DNA template as the temperature fluctuates.

10. Why is Taq polymerase specifically used in PCR instead of a typical human or bacterial polymerase?

• Because Taq polymerase is heat-stable and can withstand the high temperatures used in PCR.

• Because Taq polymerase is more accurate than all other polymerases.

• Because Taq polymerase is derived from humans and works best in PCR.

• Because Taq polymerase requires no primers for DNA synthesis.