DNA Virtual Lab Flashcards

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Questions and Answers

What identifies sites where DNA can be cut by restriction enzymes?

A plasmid map

Where do restriction enzymes bind?

Specific DNA sequences

Once they bind, what do restriction enzymes do?

Cut the sugar-phosphate backbone of the DNA

What happens if the restriction enzyme cuts unevenly?

Leaves overhangs, or 'sticky ends' Signup and view all the answers

What is the enzyme called that can reattach sticky ends together?

Ligase Signup and view all the answers

What technique is used to separate DNA fragments?

Gel electrophoresis Signup and view all the answers

How does the gel electrophoresis process work?

Uses electricity to separate different-sized molecules of DNA in a porous, sponge-like matrix Signup and view all the answers

What is the matrix made of?

Agarose, purified from seaweed Signup and view all the answers

What is in the tank of the apparatus?

A salt solution that conducts electricity Signup and view all the answers

What is the purpose of adding blue 'tracking dye' to the DNA samples?

It makes it easier to load the samples and visually track the migration of DNA through the gel Signup and view all the answers

Explain why DNA has an overall negative charge.

Phosphate groups in the DNA backbone carry negatively-charged oxygen molecules Signup and view all the answers

Why is the fact that DNA has a negative charge so important in the gel electrophoresis process?

The negatively-charged DNA can be pulled toward the positive pole of the electrophoresis chamber Signup and view all the answers

Which moves faster and further through the agarose, large fragments or small fragments? Why?

Smaller fragments move faster and further than larger fragments Signup and view all the answers

What is the purpose of ethidium bromide in gel electrophoresis?

Ethidium bromide is a dye used to see where the DNA fragments are located in the gel. Signup and view all the answers

What is DNA transformation?

The process by which DNA can be transferred into bacteria Signup and view all the answers

Why can DNA not enter cells under the usual conditions?

The negative charge on the phosphate groups of DNA are repelled by the negative charges on the lipid membrane Signup and view all the answers

What, in theory, can interact with the negative charges and create a neutral situation?

The calcium ions (Ca2+) from a solution of calcium chloride (CaCl2) Signup and view all the answers

Why is the temperature lowered as one step in transformation?

To congeal the lipid membrane, making the negatively-charged phosphate groups easier to shield Signup and view all the answers

What does the 'heat shock' accomplish?

Creates a temperature imbalance on either side of the bacterial membrane and sets up a current Signup and view all the answers

Study Notes

DNA Virtual Lab Key Concepts

A plasmid map identifies sites where restriction enzymes can cut DNA.
Restriction enzymes bind to specific DNA sequences.
Upon binding, restriction enzymes cut the sugar-phosphate backbone of DNA.
If a restriction enzyme cuts unevenly, it results in overhangs known as "sticky ends."
The enzyme ligase is responsible for reattaching sticky ends together.

Gel Electrophoresis Techniques

Gel electrophoresis separates DNA fragments based on size.
The process employs electricity to move DNA through a porous matrix.
The matrix is composed of agarose, which is derived from seaweed.
A salt solution in the apparatus tank conducts electricity for the process.

DNA Sample Handling

Adding blue "tracking dye" to DNA samples facilitates loading and tracking their migration in the gel.
DNA possesses an overall negative charge due to negatively-charged phosphate groups in its backbone.
DNA's negative charge is crucial as it allows migration towards the positive pole during gel electrophoresis.

Fragment Movement in Gel

Smaller DNA fragments travel faster and farther through the agarose than larger fragments due to less hindrance in the gel matrix.

Visualization of DNA

Ethidium bromide serves as a visual marker in gel electrophoresis, binding to DNA and emitting fluorescence under UV light.

DNA Transformation Process

DNA transformation is the transfer of DNA into bacteria.
DNA typically cannot enter cells due to negative charges on its phosphate groups repelling against the similarly charged lipids in cell membranes.
Calcium ions (Ca2+) from calcium chloride (CaCl2) can neutralize charges, aiding in DNA entry.

Temperature and Transformation

Lowering the temperature during transformation stabilizes the lipid membrane, making it easier for DNA to penetrate.
Heat shock induces a temperature gradient that facilitates DNA uptake by creating a current across the bacterial membrane.

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Description

Test your knowledge with these flashcards on DNA and restriction enzymes from the DNA Virtual Lab. Each card covers essential concepts like plasmid maps, restriction enzyme binding, and cutting mechanisms. Perfect for students studying molecular biology.