Download DNA Replication Simulation WKST

DNA Replication Simulation
Name ________________________
Objective: To understand the process of DNA replication
Materials: yarn of various lengths, tape, paper, writing utensil, scissors
Yarn lengths:
One color – two 3 foot strands, two 1 ½ foot strands, ten 4 inch strands, and ten 2 cm strands
The other color – ten 2 cm strands
Introduction:
Cells must undergo the process of DNA replication to make new cells, whether making identical
daughter cells though the process of mitosis, or making genetically unique cells through the process of
meiosis. DNA must be replicated before cells can split, or the DNA in each cell would not be identical
(for one organism). Throughout this simulation you must use the materials to model the process of DNA
replication while answering the questions presented at each step. Do not move forward in the
simulation unless you are certain your answers are correct. You may use any resource to find the
answers, but make sure they are credible.
*Note: This is a model of DNA replication. Models are not perfect. Keep in mind that the strands
represent long strands of bound nucleotides. However, Nucleotides are never added in strands, but
rather, one at a time.
1. Draw out a diagram of the life cycle of the cell. In which stage does DNA replication occur?
2. Describe how DNA is organized within the nucleus.
3. During DNA replication, would you expect the chromatin to be condensed or extended? Why?
Imagine two strands of yarn represents two complementary strands of DNA. Take the two 3 foot
strands of yarn and lay them next to each other on your desk. Spin the yarn around each other to
represent the double helix. Answer the following questions below to review the structure of DNA.
4. What are the nitrogenous bases that make-up DNA? Which bases bind to each other?
5. Draw the complementary bases to the strand below:
5’ A T T G G T C C C C G A A A G T A C G G A T C G C 3’
6. What do the 5’ and 3’ mean? Draw a nucleotide below and explain using that drawing.
Now that you have reviewed the base pairing rules, we are ready to start the simulation. First, you need
to give the strands directionality. Make 2 paper tabs that say 5’ and two that say 3’. On one piece of
yarn, put the 3’ paper tab on one side and the 5’ paper tab on the other. Put the tabs on the other
strand opposite of the way you did the first (you may need to unwind them to make sure you have this
correct, just make sure to wind it back up). Next, pull apart the DNA strands from one point on the yarn,
called the origin of replication. This is completed by proteins that initiate replication and will occur on
many places on a DNA strand. See the figure below.
As you pulled the strands apart, you may have noticed the ends were still wound around each other. If
there was nothing to release this tension, it would continue to tangle up the DNA. To demonstrate this,
pull on two origins of replication on your string and notice what happens between the replication
bubbles. To fix this problem, your cells use an enzyme to break, swivel and rejoin the DNA strands.
7. What is the enzyme called that breaks, swivels and rejoins the DNA strands?
8. Look at table 16.1 in your book to define Helicase and single strand binding protein.
Model the above enzymes (topoisomerase, helicase, and single strand binding protein) using your yarn,
scissors, tape, and paper cutouts or clay. Be sure to label your enzymes so you can keep track of them.
Now you are ready to start adding new DNA nucleotides using the old strands. Before DNA replication
can start, a primer must be added so DNA polymerase can bind. A primer is a short stretch of RNA that
initiates DNA replication by allowing polymerase to bind and add nucleotides to the end of it. Primase is
an enzyme that adds the RNA primer to the DNA.
Now, to act this out using your model, cut out or use clay to make a primase enzyme. The primers are
the 2cm pieces of yarn of a different color (you only need two primase pieces right now but will need 10
all together). Use the primase enzyme to add one of the primers to each of the original strands right
next to the origin of replication. Next, make a paper or clay model of the enzyme DNA polymerase III
and DNA polymerase I.
Find the direction of each strand. It is okay to unwind your DNA strands now. DNA can be added only in
the 3’ to 5’ direction on the template strand and can only be added to the end of the primer. Use your
DNA polymerase III to add the new strand, the 1 ½ foot long yarn, to each of the template strands.
Notice, only one side of the point of replication on each strand can be replicated continuously (using the
3’-5’ direction and primer rule). These are called the leading strands.
9. Label the leading strands in the diagram below:
What do you think happens to the DNA on the other half of the strand? Remember, DNA can only be
added after the primer and can only be added moving along the template strand in the 3’ to 5’ direction.
Also, helicase is unwinding the DNA strands at the replication fork as Polymerase is adding nucleotides.
10. Estimate how you think new DNA strands are made given these rules.
If you estimated that they would be made in short stretches, you would be correct. Use primase to add
primers toward the 3’ end about 4 inches away from the first primer. Do this on both sides. Now, DNA
Polymerase III can add complementary DNA nucleotides starting from the primer. Do this using your
model and add the 4 inch strands of yarn. Add another primer 4 inches away from the previous primer
and add DNA to that segment. If you are having trouble understanding this, go to page 316 in your book
and study the diagram.
11. Use your book to describe the role of DNA polymerase I. Why do you need to replace the primers?
Hint: think about what they are made of.
When you add the DNA to replace the primers, DNA Polymerase I uses the newly made DNA fragment
(on the 5’ side) to adhere the new DNA. To represent this, use tape to paste together the newly made
DNA strand (the one on the 5’ side) to the DNA that replaced the primers. However, there are still gaps
between DNA fragments, due to the fact that polymerase cannot join together DNA strands that are
already bound to the template strand.
12. What is the name of the enzyme that seals a bond between the DNA fragments?
Pretend the tape dispenser is ligase and use the tape to seal up all your strands.
Continue to make your lagging strand using the correct method. When you get to the ends of your
string, you should encounter a problem.
13. Why is it that you cannot make a new DNA strand as long as the template strand?
This problem occurs in most cells, except those that do not replicate or gametes, and it turns out that
your cells have a solution to ensure that your genes don’t get cut out with more replication (that is until
you get older).
14. What are telomeres and how do they help solve this problem?
15. Read http://learn.genetics.utah.edu/content/begin/traits/telomeres/ or go to
http://abcnews.go.com/Health/Alzheimers/aging-reversed-mice/story?id=12269125 and watch the
news video. Discuss this with a classmate. What is your reaction? Write a short paragraph of your
reaction below.