1. PCR & Gel Electrophoresis Webquest PDF

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Gel electrophoresis: sort and see the DNA Pre-class activity Directions:



1. Go to the DNAi website www.dnai.org > Manipulation > Techniques > amplifying. 2. View the PCR animation 3-D animation, and answer the following questions.

Questions: 1.

What is Polymerase Chain Reaction?

2.

In one cycle the PCR machine will change the temperature 3 times. Briefly describe what happens in each of the 3 steps.

3.

How many cycles does it take to start accumulating the targeted strand of DNA?

4.

How many copies of the targeted DNA section do you have after 30 cycles?

Directions:

 In the menu on the left click on Making many copies of DNA 2-D animation > Amplification and answer the following questions. Questions: 5.

Briefly describe what happens. Note what happens to DNA, how temperature is affected and which enzymes are involved. (a) Denature: (b) Annealing: (c) Extend:

6.

Notice how many targeted DNA sequences do you have at the end of the 3rd cycle?

Directions:

 7.

1. In another window watch this short video clip: Click here or bit.ly/37kFArk What are your thoughts about this process? Why do you think this is important?

Gel electrophoresis: sort and see the DNA Pre-class activity Directions:



1. Go to the DNAi website www.dnai.org > Manipulation > Techniques > sorting and sequencing. 2. View the Gel Electrophoresis 2-D animation, and answer the following questions.

Questions: 1.

How does the process of gel electrophoresis separate DNA fragments?

2.

What is the purpose of the agarose gel?

3.

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

4.

Explain why DNA has an overall negative charge.

5.

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

6.

Explain how an agarose gel can separate DNA fragments of different lengths.

7.

What is the purpose of ethidium bromide in gel electrophoresis?

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8.

Why is a marker used when running the fragments through the gel?

9.

What is a restriction map?

10.

On the gel picture below, (a) circle the smallest fragment produced by a restriction enzyme and label it “smallest.” (b) circle the largest fragment produced by a restriction enzyme and label it “largest.”

11. In one or two sentences, summarize the technique of gel electrophoresis.

OPTIONAL- This is NOT required but can help you understand this process better Restriction maps of the linear λ genome Lambda (λ) 0

10,000

20,000

30,000

40,000

48,502

l----------------------l-------------------------l-------------------------l--------------------------l-------------------------l

EcoRI Sites 21,226

26,104

31,747

39,168

44,972

----------------------------------------------------l------------l--------------l-------------------l------------------l--------

HindIII Sites

25,157 23,130

37,459

27,479

36,895

37,584

44,141

---------------------------------------------------------l-----------l----------------------l-ll---------------------l----------

BamHI Sites 5,505

22,346

27,972

34,499

41,732

-------------l-----------------------------------------l--------------l-----------------l------------------l--------------------

NcoI Sites 19,329

23,901 27,868

44,238

-----------------------------------------------l------------l---------l------------------------------------------l--------------

BmrI Sites 7,054

11,608

25,691

30,332

----------------l-----------l-----------------------------------l-----------l---------------------------------------------------

StuI Sites

32,997 12,434

31,478

40,596 39,992 40,614

------------------------------l------------------------------------------------l-----------------------l---l-l--------------------

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Gel electrophoresis: sort and see the DNA Making a DNA fingerprint In this activity, you will model the construction of DNA fingerprints for a viral genome using different restriction enzymes. You will also practice interpreting restriction maps and visualize how the process of gel electrophoresis separates DNA fragments.

DNA restriction fragment size chart Directions: List your DNA fragments in the following chart under the column of the appropriate restriction enzyme. List each fragment, from largest to smallest.

EcoRI

HindIII

BamHI

NcoI

BmrI

StuI

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DNA fingerprints Marker

EcoRI

HindIII

BamHI

NcoI

BmrI

StuI

(50,000) (30,000) (20,000)

(15,000)

(10,000)

(5,000)

(2,500)

(1,000)

5...