Learning Cycle:
Bio 30 Genetics – DNA
Replication
Anthony G. Pacholko
John MacDonald
ESCI 300
December 11th, 2013
Format:
Engagement
86
Extension Cord Demonstration
Exploration
Strawberry DNA extraction
Replication model (students model the process of DNA replication)
Extend
Lego DNA
Evaluation
Buccal cell DNA extraction
DNA replication modelling and problem solving
Anthony G. Pacholko
200291841
Unit: Bio 30 - Genetics: DNA structure and replication
Introduction:
Objectives:
- Practice basic laboratory procedure.
- Examine the significance of the structure of DNA (i.e. why are nitrogenous bases oriented in a
consistent manner).
- Examine why events unfold the way they do during DNA replication (the aim is not to cover
DNA replication, but to explore the significance of certain events/elements).
Suitable topic:
- While finding suitable experiments/activities is more difficult for genetics than many other
disciplines, I feel the learning cycle format provides an opportunity to go beyond rote
memorization and to develop a true understanding of why replication works the way it does, and
why DNA structure is what it is.
Curriculum fit:
Genetics unit:
Discuss the relationships among chromosomes, genes, and DNA:
- 2.1 Describe how the genetic code is carried on the DNA.
- 2.2 Outline the process of replication.
Biological Chemistry unit:
Describe the structure of nucleic acids:
- 3.1 Describe the similarities and differences in the structure of DNA and RNA.
Judgement of success:
- Students progress will be assessed in both a formative and summative manner. Formative
assessment will take place in the form of monitoring the students response to the questions
associated with the engagement, exploration and extension activities. Summative assessment will
occur during the evaluation activities. A class average mark of 70% or greater would indicate a
satisfactory to good level of success. A class average below 60% would likely mean I failed to
teach the material properly, the activities/experiments were poorly designed, or I failed to
provide adequate instruction during the lectures prior to this series of activities.
Ideal time:
- 225 minutes – 285 minutes. 4
Engagement Activity: 14.5
Materials:
- 4 extension cords:
Two 2 prong cords and 2 three prong cords
Safety:
- Safety concerns are minimal. Ensure that the wires are intact, and that the power outlets in the
room are functioning properly. 1.5
What happens:
- This activity uses a demonstration + question format. The teacher is to provide some basic info,
but is not to provide any answers. Questions will be asked, and students will answer, but no input
from the instructor will be given at this time. For the purpose of this assignment, (D) will mark a
demonstration, and (Q) will mark the associated question.
Brief description (basic info to be given prior to beginning the demonstration):
- The extension cords represent nitrogenous bases (the ends, to be precise).
- The prongs represent hydrogen bonds.
D: Take one of the two pronged extension cords, and plug the inlet into the outlet of the same
cord.
Q: Why did this connection work so easily? Do the inlet and outlet match?
D: Try to plug a three pronged extension cord into the outlet of a two pronged extension cord.
Q: What is wrong with this connection? What is missing?
D: Using one of the three slot outlets, try to insert the three pronged inlet while it is upside down.
Q: Why isn’t this working? Does the inlet have to be in a specific orientation to plug into the
outlet? What does this tell us about bonding between nitrogenous bases?
D: Using the same three pronged extension cord, plug the inlet into the outlet of the same cord.
Q: Is the three slot outlet a better match for the two prong or three prong inlet? What does this
tell us about bonding between nitrogenous bases?
D: Hold up the outlets of all four extension cords. Ensure that they are in a neat row, with each
outlet oriented in the same direction.
Q: Tell me the sequence of inlets (two prong or three prong) needed to match these outlets. What
part or feature of DNA does this remind you of? 3.5
Why it happens:
- Adenine and Thymine form base pairs with two hydrogen bonds, while Cytosine and Guanine
form base pairs with three hydrogen bonds. For this demonstration, the two prong inlets and two
slot outlets represent Adenine and Thymine, while the three prong inlets and three slot outlets
represent Cytosine and Guanine. The activities performed highlight the need for not only
appropriate base-pairing, but for the correct orientation (3’ to 5’ orientation) of base pairs. 3
Questions:
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Why did this connection work so easily? Do the inlet and outlet match?
- The connection works because the inlet and outlet both match (two prong inlet
and two slot outlet).
What is wrong with this connection? What is missing?
- The outlet lacks the 3rd slot needed to properly accommodate a three prong inlet.
Why isn’t this working? Does the inlet have to be in a specific orientation to plug into the
outlet? What does this tell us about bonding between nitrogenous bases?
- The inlet is not aligned with the outlet. To connect, the prongs have to match up
with the slots. This tells us that nitrogenous bases must be properly aligned in a 3’
to 5’ direction.
Is the three slot outlet a better match for the two prong or three prong inlet? What does
this tell us about bonding between nitrogenous bases?
- Three prong inlet. This tells us that base pairs must be complementary to
bond properly.
Tell me the sequence of inlets (two prong or three prong) needed to match these outlets.
What part or feature of DNA does this remind you of?
- Depends on the sequence you decide to use (ex. Two, three, three, two, etc.).
This sequence is similar to that of the base pairs present in “junk” DNA or coding
DNA.
Why do Adenine and Thymine form base pairs?
- They are complementary, and from two hydrogen bonds.
Why do Cytosine and Guanine form base pairs?
- They are complementary, and form three hydrogen bonds.
What type of bond connects the bases within the same strand?
- Phosphodiester bonds
What type of bond connects the base pairs?
- Hydrogen bonds
Is the orientation of base pairs important? Why?
- Base pairs must be oriented in a 3’ to 5’ direction, as the formation of
phosphodiester and hydrogen bonds depends upon the interaction between
specific functional groups. 3.5
Goals and Objectives:
- To get students thinking about the structure of DNA, and the fidelity of replication. The idea is
to use analogous demonstrations to illustrate complementary base-pairing, hydrogen bonding,
and phosphodiester bonding. Also, an appreciation for the accuracy required during DNA
replication will hopefully be instilled. 2
Source:1
Activity/demonstration: - There is no source for the activities.
Background info:
- http://www.ncbi.nlm.nih.gov/books/NBK26821/
Exploration Activities:
Activity One: Strawberry DNA extraction (DNA structure exploration activity) 16.5
Materials: (per student/ group of students)
- 1 ripe strawberry
- ½ cup of tap water
- 2 small, clear plastic cups
- 2 measuring cups
- Paper towels (use for drying your other materials, number may very)
- 2 teaspoons of dish detergent
- 2 teaspoons of salt
- 1 Coffee Filter
- 1/3 cup of Rubbing Alcohol
- Wooden Popsicle Stick
- 1 Plastic Bag
Safety:
- Students will be required to wear latex gloves.
- Students will be required to wear laboratory-goggles (if possible).
- Students will be prohibited from ingesting the detergent or rubbing alcohol. Ensure that the
poison control number is known in case of emergency.
- Students will be prohibited from drinking the contents of their test-tubes.
- All materials are to be disposed of properly. 0.5
What happens:
- Students will extract DNA from strawberries through the following procedure:
Prepare the extraction solution:
- Add 2 teaspoons of detergent to one of the clear plastic cups
- Add 1 teaspoon of salt to the cup and mix
- Add ½ cup of tap water to the cup and mix
Extract the DNA:
- Insert your strawberry into the plastic bag
- Using your hand, mash up the strawberry (until it is a paste)
- Add 2 tablespoons of the DNA extraction liquid to the bag
- Gently swirl the mixture for 1 minute
- Allow the mixture to sit
Separate the fluids and solids:
- Take a coffee filter and place it over the unused plastic cup
- Pour the DNA mixture onto the filter and let it run for either 30 seconds or until the fluid
has stopped dripping
Isolate the DNA:
- Add a roughly equivalent amount of chilled rubbing alcohol to the cup. Pour the alcohol
down the side of the cup. Do not mix or stir
- After ten seconds have elapsed, observe the liquid. Identify whether or not a cloudy white
substance (DNA) is forming in the liquid layer above the strawberry solution.
- Remove the DNA from the cup using a wooden Popsicle stick
- Place the DNA into one of the measuring cups provided
- In summation, students will extract and isolate DNA, allowing them to visualize true DNA
structure. When paired with online images, students can establish a link between macro and
micro structure. The hope is that through the extraction of DNA, students will gain an
understanding of how it is packaged, and through the observation of DNA solubility, students
will gain an understanding of its structure. 3.5
Why it happens:
Detergent:
- The detergent breaks apart lipid membranes, allowing access to the DNA.
Salt:
- Salt serves to reduce the net negative charge of DNA through the removal of histone
and non-histone chromosomal proteins. This allows the DNA to “shake loose” and
form independent strands.
Water:
- DNA is highly soluble in water.
Mechanical break-up:
- Because the fruit is ripe, and hormonal signals have weakened much of the cell,
mechanical disruption is enough to expose genetic material to the extraction fluid.
Alcohol:
- DNA is highly insoluble in alcohol, but soluble in water. The alcohol causes the DNA
to precipitate out of the solution. Proteins; however, are soluble in alcohol, and will thus
not precipitate out of the solution. 3
- In summation, the step-wise treatment of the crushed strawberry with the above agents allows
the students to isolate DNA.
Questions:
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What happens when you add alcohol to the strawberry + extraction fluid solution?
- DNA precipitates.
What part of the extraction fluid allows access to the DNA? Why? How many “barriers”
needed to be removed? What does this tell us about the location of DNA in the cell?
- Detergent. Detergents break apart lipid bi-layers. There are two bi-layers that must be
removed. If detergents are necessary to gain access to DNA, then DNA must exist within
the nucleus.
What part of the extraction fluid allows the DNA to float in the solution? What does this
say about the net charge of DNA? What group(s) are responsible for this charge?
- Salt allows the DNA to float in the solution. DNA has a negative net charge. The
phosphate group is responsible for the negative charge.
What happens when alcohol is added to the strawberry solution? Why does this happen?
- The DNA precipitates. This happens because DNA is insoluble in alcohol, while
proteins are not.4.5
Goals and objectives:
- Students develop an understanding of how DNA is extracted from cells, and how the process of
extraction relates to DNA structure and where in the cell it is stored.
- Students develop an appreciation for DNA as a tangible, physical thing as opposed to some
microscopic goo alluded to in lecture.
- Students develop some basic laboratory skills. 3.5
Sources:1
Experimental procedure:
- http://www.education.com/science-fair/article/extract-dna-strawberries/
Activity Two: DNA replication model (DNA replication exploration activity) 14.5
Materials (groups of 4-5)
- DNA template print-out
- dNTP print-out
- RNA primer bases print-out
- Coloured paper for making replication enzymes
Safety:
- Safety concerns are minimal. 1
What happens:
- Students will create a model of DNA replication. The intent of this activity is to instill an
understanding not of the process of DNA replication, but of the significance of each part of
the process. They will create the model through completion of the following:
Prepare the DNA template:
- Using the DNA templates provided, each group will prepare DNA strands
Prepare the dNTP’s:
- Using the dNTP cards provided, students will prepare the dNTP’s for DNA strand
synthesis. Students will be required to model for the instructor the cleaving off of the
diphosphate by DNA polymerase so that they can develop an understanding for the reactions that
occur during replication.
Prepare the enzymes:
- Students will be required to “make” the necessary enzymes. If needed, the instructor can
offer some guidance, but the hope is that students will be able to perform this activity on their
own and gain a good understanding of the process of replication through visual representation.
Begin modelling synthesis:
- Here, students will use the materials they have prepared, and some RNA primer bases
provided by the instructor, to model DNA replication. Using the template, students will need to
correctly place the enzymes, dNTP’s and RNA primer bases to illustrate the full process of DNA
replication. 3
Why it happens:
- DNA replication is a highly regulated process. This activity mimics the steps involved in DNA
replication, allowing students to see for themselves the importance of primers, 3’ hydroxyl
groups, complementary base pairing, etc.
Required knowledge:
- This activity does require some prior knowledge, which should have been introduced both in
previous lessons and the strawberry DNA extraction experiment. The intent was to explore the
significance of the various parts of the process, not to explore the process itself. They are not
discovering DNA replication, but rather the significance of it. The students will need to know
some basic terms, such as Adenine, Guanine, Cytosine, Thymine, dNTP’s. RNA, DNA, primase,
DNA polymerase I and III, helicase, ligase, single-stranded DNA binding proteins, leading and
lagging strand, Okazaki fragment, 3’ and 5’, 3’ hydroxyl group and exonuclease.
- Students will also need to know the basic sequence of replication. For example (note, I am not
looking for the name of each step, but rather depictions of each relative time frame):
- Helicase activity
- Single-stranded DNA binding protein activity
- Primase and DNA polymerase I activity
- Exonuclease activity
- DNA polymerase III activity
- Ligase activity 2.5
Questions:
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Is the orientation of the DNA template important? Is it reversible?
- No, it is not reversible. The 3’ – 5’ orientation is crucial for replication, and
cannot
be reversed, as the phosphodiester bonds require 3’ hydroxyl groups in
order to form.
When you are constructing the lagging strand, which enzyme is of particular interest in
that it is unique to said strand (creates an RNA primer)?
- Primase.
When constructing the leading and lagging strands, what difference did you notice? Why
is this difference significant?
- The lagging strands is synthesized in chunks (Okazaki fragments), while the leading
strand is synthesized continuously. This is significant because DNA replication occurs in
a 5’ to 3’ direction. The problem that arises as a result is how to synthesize the lagging
strand, since DNA polymerase requires a free 3’ hydroxyl group to form phosphodiester
bonds between bases.
What purpose does primase serve? (be specific)
- Primase forms a RNA template from which DNA polymerase can work. DNA
polymerase needs a free 3’ hydroxyl group to establish phosphodiester bonds, while
primase does not.
When creating the base pairs, which pairs formed complementary bases?
-Adenine pairs with Thymine, and Cytosine pairs with Guanine.
Using both the information in front of you and the information gathered from the
engagement activity, what about base-pairing serves to prevent the insertion of the
incorrect base?
- Base pairing is complementary.
While making the complementary base pairs, you insert an incorrect base. What sort of
impact will this have on DNA replication in the future? What are you analogous to (think
of a certain type of light we receive that you need sun screen to protect yourself from)?
- DNA replication will occur as usual, but the code will have been changed. It is likely
that any proteins formed according to this code will be either useless or harmful, if they
even form at all.
- The student is analogous to something like UV light, or a carcinogen.4
Goals and objectives:
- Students gain an understanding of the significance of the various steps in DNA replication. It is
important for students to truly understand why steps occur, why certain enzymes are needed,
why replication occurs in a specific direction, etc. Anyone can regurgitate information.
- Students gain an appreciation for the accuracy required during DNA replication, and the
problems that can arise if replication lacks fidelity. 3
Sources: 1
Activity resource sheets (DNA templates, dNTP sheets, etc.):
- http://www.explorebiology.com/apbiology/labs/
Explanation: 10.5
Observation questions:
Engagement:
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What happens when I try to plug the 3 prong inlet into the 3 slot outlet upside down?
- The inlet will not connect with the outlet.
What happens when I try to plug the 3 prong inlet into the 2 slot outlet? What is wrong?
-The connection works, but one of the prongs is left unconnected.
Is the 3 prong inlet a more appropriate match for the 3 slot or 2 slot outlet?
- The 3 slot outlet.
Exploration:
Activity One:
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What happens when you add the extractions solution to the strawberry mixture?
- No immediate visible change occurs. After some time, the strawberry mixture begins to
somewhat dissolve.
What happens when you add alcohol to the extraction fluid + strawberry mixture
solution?
- A cloudy white precipitate forms.
Activity Two:
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If you try to insert one of your dNTP’s in such a way as to have an orientation counter to
that of the other dNTP’s, what happens?
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- While the piece may seem to “fit,” the new dNTP does not match up correctly with the
other dNTP’s, meaning the phosphodiester bond is not present. In a real scenario, no
bond would form.
When constructing the leading and lagging strands, what difference did you notice?
- The lagging strand is synthesized in chunks (Okazaki fragments), while the leading
strand is synthesized continuously.
When you are constructing the leading and lagging strands, there will be an enzyme that
is unique to one of the strands. It creates an RNA primer. What is the name of this
enzyme, and which strand is it found on?
- Primase. It will be found on or near the lagging strand.
Explanation based on observations questions:
Engagement:

Given that the 3 prong inlets/outlets represent Cytosine/Guanine, and the 2 prong
inlets/outlets represent Adenine/Thymine, what does the interaction between the 3 prong
inlet/3 slot outlet, and the 3 prong inlet/2 slot outlet tell us about base-pairing?
- Base-pairing is complementary. Guanine and Cytosine form 3 bonds while Adenine and
Thymine form 2 bonds. They have to match.
Exploration:
Activity One:
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A few minutes after adding the extraction fluid to the strawberry mixture, the strawberry
begins to break up. Why is this?
- The detergent is breaking apart the lipid membranes of the cells.
Why is the breaking apart of membranes important in DNA extraction? What does this
tell us about the location of DNA within the cell?
- Breaking apart the lipid membranes allows access to the DNA, indication that DNA is
held within membrane clad structures. Given our knowledge of the cell, we can
tentatively conclude that DNA is contained both within the cell membrane and nuclear
envelope.
What role does salt play in DNA extraction?
- Salt serves to negate the net negative charge of DNA, allowing the DNA to aggregate in
the solution.
What sort of bond/group is responsible for the negative charge?
- Phosphates of the phosphodiester bond, when taken in aggregate, create a net negative
charge on DNA.
DNA precipitates once alcohol is added to the mixture. What does this tell us about the
solubility of DNA in alcohol as opposed to water?
- DNA is soluble in water but insoluble in alcohol.
Activity Two:
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
Using both the information in front of you and the information gathered from the
engagement activity, what about base-pairing serves to prevent the insertion of the
incorrect base?
- Base pairing is complementary.
When constructing the leading and lagging strands, you will notice a difference between
how to two are synthesize. Why is this difference significant? What problem does this
difference create?
- The lagging strands is synthesized in chunks (Okazaki fragments), while the leading
strand is synthesized continuously. This is significant because DNA replication occurs in
a 5’ to 3’ direction. The problem that arises as a result is how to synthesize the lagging
strand, since DNA polymerase requires a free 3’ hydroxyl group to form phosphodiester
bonds between bases.
List three enzymes involved in the synthesis of the lagging strand that are not involved in
the synthesis of the leading strand.
- Primase, DNA polymerase I, and Ligase.
Why is it necessary for the synthesis of the lagging strand to occur in chunks (Okazaki
fragments)? Why is primase needed?
- DNA replication occurs in a 5’ to 3’ direction.
- DNA polymerase requires a free 3’ hydroxyl group to form phosphodiester bonds, while
primase and its RNA bases do not.
Questions to link activities to other scientific concepts:
Biology 30:
Biological Chemistry unit: appreciate the basic principles of chemistry which are involved in life
processes.
1.2 Realize the relationship between the electron structure of atoms and the type of bond which
forms.

When Adenine and Thymine form a base-pair, what sort of bond is being formed? Are
any electrons being shared (the second part of this question is dependent upon whether
students have already taken chemistry 20/30 or not).
- A hydrogen bond is being formed.
- No electrons are being shared.
2.1 - Explain how carbon-based molecules interact with each other through hydrogen bonding.
Chemistry 30:
Molecules and Compounds unit: Investigate the factors which influence solubility.
Recognize the importance of water as a solvent; compare the solubilities of several solute/solvent
combinations.

Why is water important in DNA extraction? (*hint* think about what water does to
sugar).
- DNA is soluble in water.

What role does alcohol serve in DNA extraction? How does this role compare to the role
of water?
- DNA is insoluble in alcohol. As a result, DNA precipitates out of the solution when
alcohol is added.
- DNA is soluble in water, allowing it to be “freed” from the cell, and insoluble in alcohol,
allowing it to precipitate out of the solution once the extraction is complete. 7
Definitions and principles students must arrive at:
- Complementary base-pairing: during replication, Adenine only pairs with Thymine, while
Guanine only pairs with Cytosine.
- How the orientation of nitrogenous bases and phosphodiester bonds are related:
phosphodiester bonds can only form when a 3’ hydroxyl group is aligned with the oxygen of the
5’ group in the presence of phosphate.
- Why Okazaki fragments are necessary: DNA replication occurs in a 5’ to 3’ direction.
- Why primase, DNA polymerase III and Ligase are needed: DNA polymerase requires a free
3’ hydroxyl to function, while primase does not. Primase creates an RNA primer from which
DNA polymerase I can work. Exonuclease then removes the primer; polymerase fills in the hole,
and ligase “glues” the two ends together.
- Why DNA has a negative charge and what it means for extraction: phosphate from the
phosphodiester bonds, when taken in aggregate, create a net negative charge. As a result,
independent DNA stands are unstable. For the purposes of extraction, DNA must be able to exist
outside of the cell. Salt is used to negate the net negative charge of DNA, which allows it to exist
outside of the cell.
- What direction the new DNA strand is synthesized in: the new strand is synthesized in a 3’
to 5’ direction, and will be anti-parallel to the template strand.
- DNA’s solubility in alcohol vs. water, and what it means for extraction: DNA is soluble in
water and insoluble in alcohol, allowing alcohol to serve as a means to precipitate DNA from a
solution.
- Why DNA replication is so accurate: Complementary base-pairing of nitrogenous bases and
internal repair mechanisms (proof-reading) of DNA polymerase ensure that the rate of error
occurrence is minimal. 3.5
Extend Activity: Lego block DNA 13.5
Materials: (Groups of 3-4)
- Lego blocks
Safety:
- Advise the students to not swallow the Lego blocks (I sincerely hope this would be
unnecessary). 1
What happens:
- The students will be asked to use Legos (directions and colour code will be provided on the
board) to create an accurate model of DNA replication. They will need to do three things. First,
they will have to create the templates. Second, they will need to place the following enzymes
appropriately: helicase, DNA binding proteins, primase, and DNA polymerase III. Finally, they
will be required to construct the new DNA strands (must be accurate, and must include correctly
oriented phosphodiester bonds and nitrogenous bases), correctly placing both the nitrogenous
bases and the following enzymes: exonuclease, DNA polymerase I, and ligase.3
Background Information:
- As this is not an experiment, there is no “science behind the scenes” to discuss in this section.
However, some background knowledge will be required by the students. Such knowledge should
have been covered in both previous lectures and the previous activities. This is a non-graded
problem solving activity.
Prerequisite knowledge:
Steps involved in DNA replication, such as:
- Helicase activity
- Single-stranded DNA binding protein activity
- Primase and DNA polymerase I activity
- Endonuclease activity
- DNA polymerase III activity
- Ligase activity
Components involved, including:
- Adenine, Guanine, Cytosine, Thymine
- Primase, DNA polymerase I and III, helicase, ligase, exonuclease, single-stranded
DNA binding proteins
- Leading and lagging strand, Okazaki fragment, 3’ and 5’, 3’ hydroxyl group 3
Questions:
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
When you prepare the DNA template, what orientation do you want each strand to have?
Are they parallel or anti-parallel?
- They should be anti-parallel.
When you are placing the enzymes on the leading and lagging stands, which of the
enzymes you place are unique to the lagging strand?
- Primase, DNA polymerase III, and ligase.
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When you pair a piece representing guanine with a piece representing cytosine, how
many theoretical bonds will be formed? What kind of bonds are they?
- Three bonds will be formed.
- They are hydrogen bonds.
When you “connect” a new dNTP to one of the nitrogenous bases on the newly
synthesized DNA strand, what sort of bond is being formed? Is the enzyme responsible
always the same?
- A phosphodiester bond is being formed. The DNA polymerase responsible will differ
depending on both the strand in question and the specific time point of replication.
Each time you place a new dNTP on the synthesized strand, DNA polymerase is reading
the DNA in specific direction. In what direction does DNA polymerase read the DNA
template? In what orientation is the new strand synthesized?
- The template strand is read in a 3’ to 5’ direction.
- The new DNA strand is synthesized in a 5’ to 3’ direction.
DNA polymerase requires a primer to synthesize the lagging strand. Why is the primer
needed, and what is the name of the DNA “chunks” that are synthesized?
- The primer is required since DNA polymerase requires a free 3’ hydroxyl group to
create phosphodiester bonds, while primase does not. The DNA “chunks” synthesized are
called Okazaki fragments. 3
Goals and objectives:
- This activity serves three purposes: allow the students to create a physical model of DNA
replication; provide a formative assessment opportunity to prepare the students for the evaluation
activities; encourage students to consider why things happen as opposed to simply knowing that
they happen. 2.5
Source: 1
Activity:
- Not applicable. I came up with the concept.
Background Information:
- http://www.ncbi.nlm.nih.gov/books/NBK26821/
- http://www.elmhurst.edu/~chm/vchembook/582dnarep.html
- http://www.dnareplication.info/stepsofdnareplication.php
Evaluation:
Assessment One: Buccal Cell DNA extraction 6.5
Aims of the assessment:
- Students will be asked to demonstrate their ability to successfully extract DNA. Some simple
directions will be given, and the materials will be listed and provided, but the students will not
receive instruction on how to extract the DNA. This is something they will have already
performed in the strawberry DNA extraction activity. The reason this activity was chosen for
assessment is to develop and assess laboratory skills and problem solving. Students will need to
draw from their knowledge of proper laboratory practices, DNA structure, and the role of each
agent. 1.5
Activity:
Procedure:
- Students are to receive minimal directions. The only direction they will receive is that they are
to use the Gatorade, and the Gatorade only, to “harvest” their cheek cells (this direction is needed
for safety reasons). Students will also be provided with an explanation of the role of the meat
tenderizer, as this was not needed for the strawberry DNA extraction exercise. All of the
remaining steps will be left for the students to discover.
Each student will receive the following materials (materials will be labelled):
- Meat tenderizer
- 1 small cup of Gatorade
- Test tube rack with two test tubes
- 1 chilled vial of alcohol (keep in ice or refrigerator until the start of the activity
- 1 pipette
- Detergent
- 1 micro-centrifuge tube
- Latex glove (safety precaution)
Expected results:
Students will be assessed in two ways: relative success of their DNA extraction; answers given
for associated questions.
Students will be required to answer the following questions before and during the activity (a
sheet will be provided).
Before:
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

Where in the cell is DNA contained?
- The nucleus
What is the cell membrane and nuclear envelope primarily composed of?
- They are primarily made of lipids
What is the net charge of DNA?
- The net charge is negative

What functional group is responsible for the net charge of DNA? What bond is this group
involved in?
- Phosphate is the group responsible. The phosphates in question are involved in
phosphodiester bonds.
During:


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What does the detergent do in regards to DNA extraction?
- The detergent serves to break apart the lipids of the cell membrane and nuclear envelop,
freeing the DNA.
What does the salt in the Gatorade/Powerade do in regards to DNA extraction?
- The salt serves to negate the net negative charge of DNA, allowing the strands to exist
as independent structures.
Is DNA soluble in alcohol?
- No, DNA is insoluble in alcohol.
What role does alcohol play in DNA extraction?
- Alcohol allows DNA to precipitate out of the solution.
What is the cloudy white mixture that forms at the end of the experiment?
- DNA 3
Rubric:2
Mark (experiment)
10
Requirement
7.5
- Some product was
gathered.
- Procedure was not
strictly adhered to.
- Technique was
sloppy (i.e they made
a mess).
5
2.5
- No product (DNA)
was gathered.
- The student was able
to explain why they
failed to extract the
DNA.
- Failure is shown to
be the result of a
minor error.
- No product (DNA)
was gathered.
Mark (questions)
9
8
7
Requirement
9 correct answers
8 correct answers
7 correct answers
6
5
4
6 correct answers
5 correct answers
4 correct answers
3
2
1
3 correct answers
2 correct answers
1 correct answer
- The student was not
able to adequately
explain why their
experiment failed.
- Failure is shown to
be the result of a lack
of attention and effort.
Total:
/19
Assessment Two: DNA replication modelling and problem solving 7
Aims of the assessment:
- Students will be given sheets depicting DNA strands. For each of these strands, there will be a
problem (i.e. something will be missing, something will be wrong/out of place). Students will be
required to identify and solve the problem.
- This activity was chosen to evaluate the student’s grasp of DNA replication. Each diagram is
designed to contain a problem that requires the students to draw upon their understanding of the
significance of each step/component of DNA replication, as opposed to simply their knowledge
of what it should look like. 1.5
Activity:
Students will be assessed in two ways: their ability to not only correctly identify what is wrong
with each DNA diagram, but to explain why the error is an error; their ability to accurately draw
a diagram of DNA replication.
It is important to note that each diagram will originate from the same template. Where the
diagrams will differ is in the missing step, missing component, incorrect step, incorrect base
insertion, etc. 2.5
Diagram 1:
- This diagram will contain two problems: an incorrectly inserted Guanine; a nitrogenous base
with the wrong orientation, and thus no phosphodiester bond.
Diagram 2:
- This diagram will contain two problems: the template strands are parallel; a nitrogenous base
lacks a 3’ hydroxyl group.
Diagram 3:
- This diagram will contain three problems: the template strands are split, and replication is
occurring, but there is no helicase on the diagram; DNA polymerase is synthesizing the new
strands in a 3’ to 5’ direction; DNA polymerase is synthesizing an RNA primer.
Diagram 4:
- This diagram will contain three problems: the DNA polymerase for the lagging strand is
synthesizing the new strand without a primer; the lagging strand is being synthesized
continuously; the leading strand is being synthesized as Okazaki fragments.
Drawing activity:
- Students will be given DNA template. They will be required to draw a model of DNA
replication.
Expected results:
Diagram 1:
- Guanine has been incorrectly substituted for Adenine/Thymine.
- One of the nitrogenous bases is oriented counter to the others in the strand. As a result, there is
no phosphodiester bond.
Diagram 2:
- The strands are parallel. For hydrogen bonds to form, the strands must be anti-parallel.
- One of the nitrogenous bases lacks a free 3’ hydroxyl group. As a result, DNA polymerase
cannot create a phosphodiester bond. Replication will halt.
Diagram 3:
- The diagram is incorrect, because the replication fork cannot form without helicase.
- DNA polymerase reads the template in a 3’ to 5’, but synthesizes in a 5’ to 3’ direction.
- Primers are composed of RNA. DNA polymerase cannot synthesize a primer. DNA polymerase
must be replaced with primase on the diagram.
Diagram 4:
- The lagging strand is synthesized in chunks called Okazaki fragments. DNA polymerase
requires a free 3’ hydroxyl group to begin synthesis, while primase does not. The diagram is
incorrect because DNA polymerase cannot synthesize the lagging strand without a primer.
Primase and a RNA primer must be added to the diagram.
- Since DNA polymerase can only synthesize DNA in a 5’ to 3’ direction, the lagging strand
must be synthesized in short “chunks” called Okazaki fragment. The diagram is incorrect
because continuous replication is not possible for the lagging strand.
- The diagram is incorrect because DNA polymerase, while synthesizing the leading strand, has
free 3’ hydroxyl groups to work from. As a result, synthesis is continuous. There is no need for
the synthesis of Okazaki fragment on the leading strand.
Drawing activity:
Students’ drawings must contain the following important features:
- Templates must be anti-parallel.
- Nitrogenous bases must maintain a consistent 5’ to 3’ orientation.
- Leading strands must be synthesized continuously; lagging strands must be synthesized
as Okazaki fragments.
- Base-pairing must be correct (Adenine and Thymine; Cytosine and Guanine); correct
number of bonds between base pairs must be shown (2 between Adenine and Thymine; 3
between Cytosine and Guanine).
- Phoshpodiester bonds and hydrogen bonds must be labelled as such.
Students’ drawings must contain the following important components (correctly positioned):
- Leading and lagging strand.
- Nitrogenous bases.
- Helicase.
- Primase.
- Single-stranded DNA binding proteins.
- DNA polymerase I and III.
- RNA primer.
- Exonuclease.
- Ligase.
- Okazaki fragment(s)
- Template strands (parent strands); sister strands.
Rubric: 3
Assessment Two:
Mark (Drawing activity)
20
17.5
15
12.5
10
7.5
5
0-2.5 (your discretion)
Assessment One:
Mark (Diagrams activity)
Diagrams 1 and 2 (x2) (each will be marked
separately out of 2. Cumulative total is 4):
2
1.5
1
0.5
0
Diagram 3 and 4 (x2) (each will be marked
separately out of 3. Cumulative total is 6):
3
2.5
2
1.5
1
0.5
Requirements
All necessary components and features are
accurately listed and placed.
Most of the necessary components and features
are accurately listed, but minor errors in the
placement/orientation are present
3-4 (your discretion) components and features
are missing, but those present are correctly
placed and oriented.
3-4 (your discretion) components and features
are missing, and some minor errors in the
placement/orientation are present.
5-6 (your discretion) components and features
are missing, but those present are correctly
placed and oriented.
5-6 (your discretion) components and features
are missing, and some minor errors in
placement/orientation are present.
Two qualifiers (only one needs to be met):
7 or more components and features are
missing.
Major errors in the placement/orientation are
presents (5 or more major errors).
The student’s work demonstrates a lack of
knowledge, understanding and/or effort.
Requirements (errors noted pertains to the
identification of answers in this case, not
student errors).
All errors are noted and described.
All errors are noted. Lacks description.
One error is noted and described.
One error is noted. Lacks description.
The student failed to identify any errors.
All errors are noted and described.
All errors are noted. Lacks description.
Two errors are noted and described.
Two errors are noted. Lacks description.
One error is noted and described.
One error is noted. Lacks description.
0
The student failed to identify any errors.
Comments: 3
I found this assignment to be quite useful. In my opinion, this format could be used in
one of two ways: as either a stand-alone sequence of activities or as a complement to lecture
material. I also thoroughly enjoyed the flexibility afforded by this template. The ability to blend
activities and experiments together was one I found very useful. The progression of the activities
is logical and facilitates learning.
The largest challenge I faced was finding/creating activities and experiments that related
to genetics. Given the nature of genetics, most of the applicable experiments I found required
extremely expensive equipment that is unlikely to be found in high school labs. That being said, I
do feel as though I was able to find and create some demonstrations, experiments and activities
that adequately introduced, explored, and expanded upon the material I hoped to cover.
As for criticisms, I do not have many. I suppose we could have used a little more practice
with evaluations prior to this assignment. That is really my only complaint, and it is one I really
had to stretch for.