DNA Replication, SPR12
A POGIL exercise developed by Dr. A. Schivell
Nemhauser
MODEL 1: This model shows one entire chromosome from the eukaryotic cells in
Model 1. The original parent chromosome is shown before replication. The same chromosome
is shown about 30 minutes after the process of DNA synthesis has begun in each of the
granddaughter cells (no enzymes are shown). The chromosomes are aligned by sequence and
gray = new DNA.
parent
*
*
*
*
chromosome
granddaughter #
1
2
3
4
4. Based on the model, decide if each statement is most likely True or False.
FALSE DNA synthesis can start anywhere on a chromosome.
FALSE DNA synthesis starts only at one place on a chromosome.
TRUE DNA synthesis starts at specific locations on a chromosome.
FALSE DNA synthesis starts at every location at exactly the same time.
5. Using asterisks, indicate the specific locations where synthesis can start on the parental
chromosome. These are called "Origins of Replication"
"Replication
Bubble"
MODEL 2:
In this model, RNA is gray and DNA is black.
Each shape represents an enzyme.
"replication fork"
T
I
M
Leading strand
5’
Lagging strand
E
2
3’
8. a. Label the 5' and 3' ends of the new strands in the middle panel of Model 3.
b. On what end of a DNA strand are new nucleotides added? 3’
9. a. Match each enzyme's shape with its function and fill in the column on the left.
Shape:
Job:
Name:
Enzyme that synthesizes the largest part of the
new DNA strands
Enzyme that forms a phosphodiester bond
without adding a new nucleotide
DNA polymerase III
Enzyme that synthesizes a short RNA primer
Primase
Enzyme that replaces RNA nucleotides with
DNA
Enzyme that breaks H-bonds between strands
of the parent DNA helix
DNA polymerase I
Ligase
Helicase
b. Using logic, fill in the Name column in the table with one of the following enzymes. One
name will be used twice. Hint: "to ligate" means "to put together".
- DNA polymerase - Primase - Ligase
- Helicase
c. Go back and label the shapes on Model 3 with their enzyme names.
d. The enzyme that does the majority of DNA synthesis is called DNA polymerase III. The
enzyme that replaces RNA nucleotides with DNA is called DNA polymerase I. Add I and III
in the table above and in Model 3 names. (Unfortunately, there is no relationship between the
numbers and enzyme activity... they simply reflect the "order of discovery" by scientists.)
10. New DNA strands always begin with a short RNA primer. RNA eventually has to be
replaced with DNA, which seems to be a waste of energy. What can RNA polymerases do that
apparently DNA polymerases cannot?
RNA polymerases can start polymerizing onto a single strand. They do not need a hanging
3’ OH group on which to attach the first nucleotide.
11. a. One new DNA strand at each replication fork is made in pieces, while the other one is
made continuously. Explain in 1-2 sentences why this has to be the case.
Because of the antiparallel nature of the template (parental) strands, when helicase
separates them, one new strand will be synthesized "toward" the fork, whereas the other
will be made in a direction "away" from where the strands are separating. Therefore the
latter new strand will need to be made in sequential pieces.
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Exercises to Practice with On Your Own:
1. Watch the videos marked "Replication_.mov" on our website under the "Movies" link. You
may need to watch them several times to get a sense of how the replication enzymes work
together at a replication fork.
a. Which part of the DNA is phosphodiester backbone, red or yellow? red
b. Which part of the DNA represents the nitrogenous bases, red or yellow? yellow
c. Determine which strand is the leading strand and which is the lagging strand.
d. Try to identify as many enzymes as possible in the animation.
2. A cartoon of one replication bubble is shown below. On one template strand on one fork,
the newly made strands are shown. Draw in the rest for the rest of the bubble and label the 3'
and 5' ends as well as the leading and lagging strands. (Arrow indicates 3' end)
3. Drawn in detail below is a region of parental DNA with two replication forks
approaching from either direction. Explain what enzymes will be needed and diagram
how the replication will be completed when the two forks meet.
You will need DNA pol III to finish the main DNA synthesis, DNA pol I to replace the
RNA, and ligase to seal the last phosphodiester bond. But you will NOT need primase.
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