Blackline Master # 1

Guide to Creating Models- Teacher Handout

Something Old, Something New… page 1

Blackline Master # 2

Name_________________________________________Period__________Date___________________
Something Old, Something New…
You are a Molecular Biologist who is studying the process of DNA replication. Your task is to build a
model that represents this process. Next you will investigate where DNA replication took place in the
human body and explain why it occurred. This activity is divided up into three parts.

Part 1: Modeling DNA

Materials:
- 2 jumbo sticks
- Markers, sharpie
- 6 pipe cleaners
- 12 colored beads

1. Obtain a DNA sequence strip from your teacher.

2. Working in groups of two or four, create a model of DNA by following the steps below.
a. To make the backbone of DNA, take two jumbo craft sticks and color them with a blue
marker.
b. Next, with a sharpie marker, draw 7 alternating circles and 6 pentagons as seen in the picture
below. Repeat the same for the second craft stick.

c. What does the series of circles and pentagons on our craft sticks model? ________________
__________________________________________________________________________
What does the circle represent? _________________________________
What does the pentagon represent? ___________________________________

d. Determine what color beads you will need to complete your DNA model by reading the DNA
sequence on your DNA Sequence Card.
Adenine (A) = Red
Thymine (T) = Blue
Cytosine (C) = Yellow
Guanine (G) = Green

You should also determine the complementary strand sequence by matching the base pairs
following base pairing rules. When you are finished matching your base pairs, you should
have 12 beads total.

What part of the DNA strand do the colored beads model? _______________________

Something Old, Something New… page 2

e. Next, take a pipe cleaner and wrap it around your jumbo stick on each pentagon and twist the
two ends of the pipe cleaner together so the pipe cleaner is attached to the stick. Repeat five
more times.
What part of DNA do the pipe cleaners model? __________________________________

f. Following your DNA sequence on your paper, insert your beads in order onto each pipe
cleaner. See image below for an example.

g. Next, insert your matching base pairs onto the pipe cleaner.
h. Finally wrap the remaining amount of pipe cleaner around the second craft stick and twist to
attach it to the stick. Repeat five more times.
What does attaching the pipe cleaners to the other stick model? _______________________
__________________________________________________________________________
Describe the shape of your DNA model? What does it look like to you?
__________________________________________________________________________

i. You have now completed your DNA model. Your model should look similar to the image
below (colors of beads should be different).

 Why might it be IMPORTANT to model DNA?

__________________________________________________________________________
__________________________________________________________________________
 Why would it be NECESSARY to model DNA?
__________________________________________________________________________
__________________________________________________________________________
 What are the LIMITATIONS of your DNA model? In other words, what can real DNA show or
do that your model cannot show or do?
__________________________________________________________________________
__________________________________________________________________________

Something Old, Something New… page 3

Part 2: Modeling DNA Replication
Materials:
- DNA model
- Scissors
- 2 jumbo sticks
- 6 pipe cleaners
- 12 colored beads
- forceps
1. Now you are ready to model the process of DNA replication.
2. Working in your same groups, complete the steps below.
a. Take a pair of scissors and cut along the middle of the pipe cleaner in between your beads.
See image below.

What is happening in your DNA model? __________________________________________

__________________________________________________________________________

What are the scissors modeling? _______________________________________________

b. Next, take two craft sticks and color them using an orange marker.

What do you think the orange craft stick might be modeling? _________________________
__________________________________________________________________________

c. With a sharpie marker, draw an alternating series of 7circles and 6 pentagons as seen in the
picture below. Repeat the same for the second craft stick.

d. Next, wrap a pipe cleaner around your jumbo stick on each pentagon. Twist the pipe cleaner
together so that it is attached to the stick. Repeat five more times.
e. Repeat the above step with the second orange craft stick.
f. Then, align your original DNA strand (blue craft stick with half of the beads) with the new
orange craft stick.
g. Using base pairing rules, insert a matching bead along the pipe cleaner attached to the
orange craft stick.
h. Continue to insert your matching beads until you reach the end of the DNA Sequence.

Something Old, Something New… page 4

i. Finally, take the loose end of the pipe cleaner from the orange stick and twist it to the pipe
cleaner attached to the original DNA strand (blue stick) using the forceps. Your DNA model
should look similar to the image below (colored beads may be different).

 What enzyme was modeled by the forceps used to seal the pipe cleaners together?
_______________________________________________________________________

 Explain why the process of DNA replication is described as “semi-conservative?”

__________________________________________________________________________
__________________________________________________________________________
__________________________________________________________________________

 Why might it be IMPORTANT to model DNA replication?

__________________________________________________________________________
__________________________________________________________________________

 Why would it be NECESSARY to model DNA replication?

__________________________________________________________________________
__________________________________________________________________________

 What are the LIMITATIONS of your DNA replication model? In other words, what can real
DNA replication show or do that your model cannot show or do?
__________________________________________________________________________
__________________________________________________________________________

Something Old, Something New… page 5

Part 3: Investigating DNA Replication in the Human Body
Materials:
- Newly synthesized DNA model
- DNA replication cards

1. After completing your newly synthesized DNA through DNA replication, obtain the DNA replication
cards from your teacher and do the following:
a. Match the DNA Replication Card to your DNA sequence to find out where your model of DNA
replication occurred in the human body.
b. Next, answer the questions below.

Where did your process of DNA replication occur in the human body? How do you know?
____________________________________________________________________________________
____________________________________________________________________________________
____________________________________________________________________________________
____________________________________________________________________________________

Explain why it is important for that area of the body to undergo DNA replication?
____________________________________________________________________________________
____________________________________________________________________________________
____________________________________________________________________________________
____________________________________________________________________________________
____________________________________________________________________________________
____________________________________________________________________________________

Explain what structure(s) and action(s) DNA takes in order to prevent mismatches and mistakes from
occurring during the process of DNA replication?_____________________________________________
____________________________________________________________________________________
____________________________________________________________________________________
____________________________________________________________________________________

Predict what might happen (to genotype and phenotype) if there was a mismatch in base pairing during
the process of DNA replication? _________________________________________________________
____________________________________________________________________________________
____________________________________________________________________________________
____________________________________________________________________________________

Something Old, Something New… page 6

Blackline Master # 3
DNA Sequences
Choose ONE of the following samples to create your model.

DNA Sample 1: DNA Sample 2:

T– G–
A– A–
G– C–
C– T–
T– G–
A– A–

DNA Sample 3: DNA Sample 4:

C– G–
A– A–
T– C–
T– C–
C– G–
A– A–

DNA Sequences
Choose ONE of the following samples to create your model.

DNA Sample 1: DNA Sample 2:

T– G–
A– A–
G– C–
C– T–
T– G–
A– A–

DNA Sample 3: DNA Sample 4:

C– G–
A– A–
T– C–
T– C–
C– G–
A– A–

Something Old, Something New… page 7

Blackline Master # 4
DNA Replication Cards

Something Old, Something New… page 8

Blackline Master #5
DNA Mutation Simulation Activity
You will be using the given base pairs to model how each mutation affects the DNA sequence. Write the
new DNA sequence in the square boxes to show how the DNA is altered in each mutation.

Point Mutation: change in one base

Original Strand:

DNA Sequence after Point Mutation:

What are the possible consequences of a point mutation?

Insertion Mutation: add in one additional base

Original Strand:

DNA Sequence after Insertion Mutation:

What are the possible consequences of an insertion mutation?

Deletion Mutation: remove one base

Original Strand:

DNA Sequence after Deletion Mutation:

What are the possible consequences of a deletion mutation?

Something Old, Something New… page 9

Inversion Mutation: reverse one section of bases (a whole gene)
Original Strand:

DNA Sequence after Inversion Mutation:

What are the possible consequences of an inversion mutation?

1. You are visiting a local lake when you notice a sign that says, “WARNING: This area
contains chemicals known by the State of Florida to cause cancer and birth defects.”
How is it possible for the chemicals in the lake to have this sort of effect?
______________________________________________________________________
______________________________________________________________________
______________________________________________________________________

2. Make and defend a claim based on evidence from this activity that 1) mutations in the
DNA sequence may or may not result in phenotypic change, 2) mutations in gametes
may result in phenotypic changes in offspring, and 3) mutations may be the result of
environmental factors or inherited traits.
Claim: ________________________________________________________________
______________________________________________________________________
Evidence supporting #1: __________________________________________________
______________________________________________________________________
______________________________________________________________________
Evidence supporting #2: __________________________________________________
______________________________________________________________________
______________________________________________________________________
Evidence supporting #3: __________________________________________________
______________________________________________________________________
______________________________________________________________________

Something Old, Something New… page 10

Blackline Master #6
DNA Replication Assessment
1. Which of the following accurately reflects the correct order of DNA replication?
a. Primase creates an RNA primer, helicase unzips the DNA, DNA polymerase
adds nucleotides and creates new DNA, DNA polymerase fills in the gaps,
DNA ligase seals the fragments of DNA, exonuclease removes the primers.
b. Helicase unzips the DNA, primase creates an RNA primer, DNA polymerase
adds nucleotides and creates new DNA, exonuclease removes the primers,
DNA polymerase fills in the gaps, DNA ligase seals the fragments of DNA.
c. DNA polymerase adds nucleotides and creates new DNA, helicase unzips
the DNA, primase creates an RNA primer, exonuclease removes the primers,
DNA polymerase fills in the gaps, DNA ligase seals the fragments of DNA.
d. DNA ligase seals the fragments of DNA, DNA polymerase fills in the gaps,
DNA polymerase fills in the gaps, exonuclease removes the primers, DNA
polymerase adds nucleotides and creates new DNA, primase creates an
RNA primer, helicase unzips the DNA.

2. How is DNA polymerase related to the reduction of genetic mutations?

a. It seals up the DNA strands to ensure that mutations cannot occur.
b. It signals the helicase to unzip the DNA strand and fix mutations to the DNA
nucleotides.
c. It proofreads the DNA nucleotides, deletes errors, and replaces errors with
the correct nucleotides.
d. It creates primers that are able to proofread the DNA and delete, reverse,
and translocate mutations.

3. Why is DNA replication often referred to as the “semi-conservative” model?

a. Because one strand contains mutations and the other strand does not.
b. Because one strand has more base pairs and the other strand has less base
pairs.
c. Because one strand comes from the mother and the other strand comes from
the father.
d. Because one strand is the original strand and the other strand is the newly
synthesized one.

Something Old, Something New… page 11

4. Why is it important for DNA replication to continuously occur in integumentary
system (skin)?
a. To constrict the amount of blood flow to the skin
b. To decrease the amount of melanin or the pigmentation of one’s skin color
c. To regenerate the amount of keratinocytes and promote healing faster
d. To decrease the amount of sweat being released from the sudoriferous
glands.

5. According to base pairing rules, complete the complementary DNA sequence

below:
A-T-G-T-C-G
a. C – G – A – C – A – U
b. G – C – A – C – T – A
c. T – A – C – A – G – C
d. U – A – C – A – G – C

6. How could a DNA mutation lead to changes in the organism?

a. A mutation could occur in sex cells and result in a phenotypic change.
b. A mutation could occur in somatic cells and be passed on to offspring.
c. A mutation could occur in somatic cells and result in a phenotypic change.
d. A mutation could occur in sex cells that result in changes to the sex organs.

7. Why might it be important to model DNA and DNA replication?

a. DNA and DNA replication is a long process that would take too long to
observe.
b. DNA and DNA replication observation creates a dangerous situation for
scientists.
c. DNA and DNA replication is so small that it cannot be observed except with
an electron microscope.
d. DNA and DNA replication can only be simulated under very specific
conditions that are difficult to observe.

8. Which of the following would not be an appropriate way to model DNA and DNA
replication?
a. A 3-D video simulation
b. A mathematical model
c. A physical model
d. A sketch or drawing

Something Old, Something New… page 12

Blackline Master #7– Answer Keys
Something Old, Something New…
You are a Molecular Biologist who is studying the process of DNA replication. Your task is to build a
model that represents this process. Next you will investigate where DNA replication took place in the
human body and explain why it occurred. This activity is divided up into three parts.

Part 1: Modeling DNA

Materials:
- 2 jumbo sticks
- Markers, sharpie
- 6 pipe cleaners
- 12 colored beads

3. Obtain a DNA sequence strip from your teacher.

4. Working in groups of four, create a model of DNA by following the steps below.
a. To make the backbone of DNA, take two jumbo craft sticks and color them with a blue
marker.
b. Next, with a sharpie marker, draw 7 alternating circles and 6 pentagons as seen in the picture
below. Repeat the same for the second craft stick.

c. What does the series of circles and pentagons on our craft sticks model? The sugar
phosphate backbone of DNA
What does the circle represent? __________phosphate ___________________
What does the pentagon represent? ____________ sugar_________________

d. Determine what color beads you will need to complete your DNA model by reading the DNA
sequence on your DNA Sequence Card.
Adenine (A) = Red
Thymine (T) = Blue
Cytosine (C) = Yellow
Guanine (G) = Green

You should also determine the complementary strand sequence by matching the base pairs
following base pairing rules. When you are finished matching your base pairs, you should
have 12 beads total.

What part of the DNA strand do the colored beads model? _____the DNA bases_____

Something Old, Something New… page 13

e. Next, take a pipe cleaner and wrap it around your jumbo stick on each pentagon and twist the
two ends of the pipe cleaner together so the pipe cleaner is attached to the stick. Repeat five
more times.
What part of DNA do the pipe cleaners model? ______the bond between the sugar
phosphate molecule and the base______

f. Following your DNA sequence on your paper, insert your beads in order onto each pipe
cleaner. See image below for an example.

g. Next, insert your matching base pairs onto the pipe cleaner.
h. Finally wrap the remaining amount of pipe cleaner around the second craft stick and twist to
attach it to the stick. Repeat five more times.
What does attaching the pipe cleaners to the other stick model? ___DNA ligase sealing the
old strand to the new strand of DNA__
Describe the shape of your DNA model? What does it look like to you? Student responses
may vary but could include that the DNA model looks a lot like a ladder.

i. You have now completed your DNA model. Your model should look similar to the image
below (colors of beads should be different).

 Why might it be IMPORTANT to model DNA?

Student responses may vary but could include that it would be important to model DNA to
learn about its structure to better understand the different parts of the DNA double helix
structure.
 Why would it be NECESSARY to model DNA?
Student responses may vary but could include that DNA is too small to observe the parts and
features.
 What are the LIMITATIONS of your DNA model? In other words, what can real DNA show or
do that your model cannot show or do? Student responses may vary but could include the
model cannot direct the instructions to the cell and cannot make proteins.

Something Old, Something New… page 14

Part 2: Modeling DNA Replication
Materials:
- DNA model
- Scissors
- 2 jumbo sticks
- 6 pipe cleaners
- 12 colored beads
- forceps
3. Now you are ready to model the process of DNA replication.
4. Working in your same groups, complete the steps below.
a. Take a pair of scissors and cut along the middle of the pipe cleaner in between your beads.
See image below.

What is happening in your DNA model? The DNA is unzipping. Students may mention
helicase.

What are the scissors modeling? The scissors are modeling the helicase unzipping the
double helix into two separate strands of DNA.

b. Next, take two craft sticks and color them using an orange marker.

What do you think the orange craft stick might be modeling? The orange sticks will be
modeling the new strands of DNA.

c. With a sharpie marker, draw an alternating series of 7circles and 6 pentagons as seen in the
picture below. Repeat the same for the second craft stick.

d. Next, wrap a pipe cleaner around your jumbo stick on each pentagon. Twist the pipe cleaner
together so that it is attached to the stick. Repeat five more times.
e. Repeat the above step with the second orange craft stick.
f. Then, align your original DNA strand (blue craft stick with half of the beads) with the new
orange craft stick.
g. Using base pairing rules, insert a matching bead along the pipe cleaner attached to the
orange craft stick.

Something Old, Something New… page 15

h. Continue to insert your matching beads until you reach the end of the DNA Sequence.
i. Finally, take the loose end of the pipe cleaner from the orange stick and twist it to the pipe
cleaner attached to the original DNA strand (blue stick) using the forceps. Your DNA model
should look similar to the image below (colored beads may be different).

 What enzyme was modeled by the forceps used to seal the pipe cleaners together? The
forceps are modeling the DNA ligase that seals the old and new DNA strands together.
 Explain why the process of DNA replication is described as “semi-conservative?” DNA
replication is called “semi-conservative” because one strand is old DNA which is conserved
and one strand is new DNA.
 Why might it be IMPORTANT to model DNA replication?
Student responses may vary but could include that DNA replication is an important process to
understand and using a model would allow you to manipulate the process and understand
how it works.
 Why would it be NECESSARY to model DNA replication?
Student responses may vary but could include that DNA replication is too small and too fast
to observe.
 What are the LIMITATIONS of your DNA replication model? In other words, what can real
DNA replication show or do that your model cannot show or do? Student responses may vary
but could include that their model doesn’t generate new DNA like the real DNA does.

Something Old, Something New… page 16

Part 3: Investigating DNA Replication in the Human Body
Materials:
- Newly synthesized DNA model
- DNA replication cards

2. After completing your newly synthesized DNA through DNA replication, obtain the DNA replication
cards from your teacher and do the following:
a. Match the DNA Replication Card to your DNA sequence to find out where your model of DNA
replication occurred in the human body.
b. Next, answer the questions below.

Where did your process of DNA replication occur in the human body? How do you know? Student
responses may vary depending on what sequence they received. They will know because they were able
to successfully follow base pairing rules.
Explain why it is important for that area of the body to undergo DNA replication?
Student responses may vary but could include that each part of the body needs to replace dead cells,
repair injuries or disease, and grow.
Explain what structure(s) and action(s) DNA takes in order to prevent mismatches and mistakes from
occurring during the process of DNA replication? DNA polymerase proofreads the DNA sequence and
deletes and replaces mis-written DNA code.

Predict what might happen (to genotype and phenotype) if there was a mismatch in base pairing during
the process of DNA replication? If there was a mismatch in base pairing, this would code for a different
amino acid. This could result in a genotype change and thus, a phenotype change. This could also result
in no changes. If the changes occur in the sex cells, this could result in a new, mutated trait being passed
on to offspring.

Something Old, Something New… page 17

 DNA Mutation Simulation Activity
You will be using the given base pairs to model how each mutation affects the DNA sequence. Write the
new DNA sequence in the square boxes to show how the DNA is altered in each mutation.
***These are possible answers. Students may come up with other, also accurate responses.***
Point Mutation: change in one base
Original Strand:

DNA Sequence after Point Mutation:

A C T G T A A G A C T T
What are the possible consequences of a point mutation?
A point mutation could cause a change in the protein that is synthesized, it could get corrected by DNA
polymerase, or it could be in an inactive area and nothing could happen.

Insertion Mutation: add in one additional base

Original Strand:

DNA Sequence after Insertion Mutation:

A C T G C A T A G A C T T
What are the possible consequences of an insertion mutation?
An insertion mutation could cause a frameshift or “slippage” which would change the proteins that are
synthesized and alter the function of the gene, it could get corrected by DNA polymerase, or it could be in
an inactive area and nothing could happen.

Deletion Mutation: remove one base

Original Strand:

DNA Sequence after Deletion Mutation:

A C T G A A G A C T T
What are the possible consequences of a deletion mutation?
A deletion mutation could cause a change in the protein that is synthesized, it could get corrected by DNA
polymerase, or it could be in an inactive area and nothing could happen.

Something Old, Something New… page 18

Inversion Mutation: reverse one section of bases (a whole gene)
Original Strand:

DNA Sequence after Inversion Mutation:

A C A C G T A G A C T T
What are the possible consequences of an inversion mutation?
An inversion mutation could cause a change in the protein that is synthesized, it could have major effects
on the function of the gene, or it could be in an inactive area and nothing could happen.

1. You are visiting a local lake when you notice a sign that says, “WARNING: This area
contains chemicals known by the State of Florida to cause cancer and birth defects.”
How is it possible for the chemicals in the lake to have this sort of effect?
The chemicals in the lake are carcinogens and can damage the dhemicals that make up DNA (cytosine,
guanine, thymine and adenine). These chemicals can be swapped out or disguised for one another. This
would result in insertion, deletion or substitution mutation. When the DNA then duplicates, it writes the
code incorrectly. Proteins that were previously created from the original DNA sequence can potentially be
altered.

2. Make and defend a claim based on evidence from this activity that 1) mutations in the
DNA sequence may or may not result in phenotypic change, 2) mutations in gametes
may result in phenotypic changes in offspring, and 3) mutations may be the result of
environmental factors or inherited traits.
Claim: Example: DNA mutations may or may not result in phenotypic changes due to mutations in
somatic cells, mutations in offspring due to mutations in the parents’ sex cells, or mutations caused by
environmental factors.

Evidence supporting #1: A mutation could occur and then be corrected by the DNA polymerase. A
mutation could occur in an area of the DNA that does not code for anything that is visible.

Evidence supporting #2: A mutation in the sex cells could be passed on to the offspring and could
show phenotypic changes in the offspring. When DNA is replicated, it is replicated with the incorrect code.

Evidence supporting #3: Carcinogens and other stressful conditions in the environment can result in
weakening the DNA or miscoding of the DNA which would result in mutations. Mutations occurring in the
sex cells would be passed on to offspring.

Something Old, Something New… page 19

 DNA Replication Assessment
1. Which of the following accurately reflects the correct order of DNA replication?
a. Primase creates an RNA primer, helicase unzips the DNA, DNA polymerase
adds nucleotides and creates new DNA, DNA polymerase fills in the gaps,
DNA ligase seals the fragments of DNA, exonuclease removes the primers.
b. Helicase unzips the DNA, primase creates an RNA primer, DNA polymerase
adds nucleotides and creates new DNA, exonuclease removes the primers,
DNA polymerase fills in the gaps, DNA ligase seals the fragments of DNA.
c. DNA polymerase adds nucleotides and creates new DNA, helicase unzips
the DNA, primase creates an RNA primer, exonuclease removes the primers,
DNA polymerase fills in the gaps, DNA ligase seals the fragments of DNA.
d. DNA ligase seals the fragments of DNA, DNA polymerase fills in the gaps,
DNA polymerase fills in the gaps, exonuclease removes the primers, DNA
polymerase adds nucleotides and creates new DNA, primase creates an
RNA primer, helicase unzips the DNA.

2. How is DNA polymerase related to the reduction of genetic mutations?

a. It seals up the DNA strands to ensure that mutations cannot occur.
b. It signals the helicase to unzip the DNA strand and fix mutations to the DNA
nucleotides.
c. It proofreads the DNA nucleotides, deletes errors, and replaces errors with
the correct nucleotides.
d. It creates primers that are able to proofread the DNA and delete, reverse,
and translocate mutations.

3. Why is DNA replication often referred to as the “semi-conservative” model?

a. Because one strand contains mutations and the other strand does not.
b. Because one strand has more base pairs and the other strand has less base
pairs.
c. Because one strand comes from the mother and the other strand comes from
the father.
d. Because one strand is the original strand and the other strand is the newly
synthesized one.

Something Old, Something New… page 20

4. Why is it important for DNA replication to continuously occur in integumentary
system (skin)?
a. To constrict the amount of blood flow to the skin
b. To decrease the amount of melanin or the pigmentation of one’s skin color
c. To regenerate the amount of keratinocytes and promote healing faster
d. To decrease the amount of sweat being released from the sudoriferous
glands.

5. According to base pairing rules, complete the complementary DNA sequence

below:
A-T-G-T-C-G
a. C – G – A – C – A – U
b. G – C – A – C – T – A
c. T – A – C – A – G – C
d. U – A – C – A – G – C

6. How could a DNA mutation lead to changes in the organism?

a. A mutation could occur in sex cells and result in a phenotypic change.
b. A mutation could occur in somatic cells and be passed on to offspring.
c. A mutation could occur in somatic cells and result in a phenotypic change.
d. A mutation could occur in sex cells that result in changes to the sex organs.

7. Why might it be important to model DNA and DNA replication?

a. DNA and DNA replication is a long process that would take too long to
observe.
b. DNA and DNA replication observation creates a dangerous situation for
scientists.
c. DNA and DNA replication is so small that it cannot be observed except with
an electron microscope.
d. DNA and DNA replication can only be simulated under very specific
conditions that are difficult to observe.

8. Which of the following would not be an ideal way to model DNA and DNA
replication?
a. A 3-D video simulation
b. A mathematical model
c. A physical model
d. A sketch or drawing

Something Old, Something New… page 21