Activities for engaging students in Biology using animations

Justin Pruneski

Heidelberg University

jprunesk@heidelberg.edu

Introduction

The Polymerase Chain Reaction (PCR) is a technique developed in 1983 by Kerry Mullis.  It has since become a standard method employed in nearly all biological research for its ability to selectively amplify tiny amounts of DNA into millions of copies in just a few hours.  Computer animations are valuable learning tools that can help you visualize a fast multi-step process like PCR.  This assignment will allow you to explore multiple animations depicting the process of PCR to help you learn the technique before we use it in lab.

Instructions

View each of the three animations listed below and answer the following questions.  Be sure to turn the sound on your computer on so you can hear the narration.  I recommend opening each animation in a separate browser tab and leaving them open so you may easily go back and forth among them throughout the assignment.  You may need to watch them multiple times to answer the questions.  Complete this assignment by typing the answers into this document on your computer and printing it out to turn in before lab begins.

Animation #1:

http://www.youtube.com/watch?v=JRAA4C2OPwg&feature=plcp&context=C46b9611VDvjVQa1PpcFMp8m_wfy428g3AaifiStwJOsiR6fhHz00%3D

Animation #2:

http://www.youtube.com/watch?v=2KoLnIwoZKU&feature=relmfu

Animation #3:

http://www.youtube.com/watch?v=lcuvdG9n9nw&feature=related

Questions

Question 1:

Describe the purpose of adding each of the following to the PCR reaction:

Taq DNA Polymerase -

Nucleotides (deoxyribonucleotides) -

Primers –

Template DNA –

Question 2:

Do each of the animations explicitly show all four of the components listed above? Explain 

Questions 3:

Each cycle of PCR consists of three steps.  Describe each step and what it accomplishes: 

Step 1: Denaturation –

Step 2: Annealing –

Step 3: Extension –

Question 4:

Which animation best depicts the following features of PCR: Explain your reasoning

During the first few cycles, extra sequence outside the target sequence sometimes gets copied.

The target sequence gets amplified exponentially producing over a billion copies after 30 cycles.

 Question 5:

Animation #2 portrays the DNA and Polymerase very differently from the way the other two animations depict them.  Describe the differences.  Which do you think is more accurate to real life? Which is most helpful for your understanding of the process?