Topic: Modeling the Structure of DNA

Reference to Massachusetts State Frameworks

3.1: Describe the basic structure (double helix, sugar/phosphate backbone, linked by
complementary nucleotide pairs) of DNA, and describe its function in genetic
inheritance.

Reflective Introduction:
The main goal of this lesson is to get students to see DNA in a different way by asking
them to engineer a segment of DNA using specially designed model components.
Understanding the structure of DNA is a crucial step in ultimately understanding the
complexities of genetics and inheritance. In the previous lesson, the students will have
been given information about the basic structure of DNA. The strategy of this lesson is to
have students illustrate their understanding by creating a model of the DNA structure.
This will challenge students to think critically and recall past knowledge to work through
the design and creation of their own unique models. The goal of this modeling exercise is
to cement students conceptions as well as their ability to explain the different parts of
DNA and how they come together to create the blueprints for all living things.

Instructional objectives for students: (keep in mind these must be measureable by your stated
student assessments you enter below)
Students will demonstrate their knowledge of the structure of DNA by creating an
accurate 3D model.
Students will be able to describe how differences in base pairings of DNA relate
to how proteins are made, and how this relates to gene expression and genetic traits.

Brief description of lesson (include start, middle, and end)

Before:Prior to this class the information on the structure of DNA will be delivered
through short notes as well as a reading and pre-laboratory questions.

Start: The Do Now/Activator Question will ask students to recall information from the
previous lesson. This will be followed up by a short class discussion and going over the
instructions for building the DNA model.
Draw and label the basic structure of a nucleotide
What kind of bonds hold the nitrogen bases together?
How do the nitrogen bases pair up in DNA?

Middle: Students will work in pairs to construct an accurate model of DNA using a
KNex Kit. The teacher will check in with students to answer questions and correct
possible student errors.
 End: Debrief activity through a class discuss. The teacher will start with leading
questions and students will respond thoughtfully as well as propose their own questions.

Timing: 60 Minutes
Time Teacher activity Student activity

Before Complete pre-lab reading and

questions prior to class

0-5 min Project Do Now On the board. answer questions in notebooks.

Check in with students.
Draw and
label the basic structure of
a nucleotide
What kind
of bonds hold the nitrogen
bases together?
How do
the nitrogen bases pair up
in DNA?

6-10 min Prompt student responses to Do Now answer teacher prompted questions.
question. Engage in class discussion.
Review material from previous lesson. Ask clarifying questions.

Review pre-lab questions. Actively listen to instructions.

11-17 min Discuss instructions to building KNEX Ask clarifying questions.
model.

18-50 min Check in with students to ensure they Use lab procedures and guiding
are on track. questions to construct a unique model
Redirect when needed with guiding and of DNA.
leading questions. Answer questions in lab packet.
Answer student questions and Ask questions as needed.
concerns as needed.

51-60 min debrief lesson with students through engage in class debrief with thoughtful
prompting discussion questions. responses.

After class Finish lab questions and watch MITx

video The Structure of DNA for homework

Homework:
Finish Lab packet if needed
 Watch MITx video The Structure of DNA - https://www.youtube.com/watch?v=o_-
6JXLYS-k

Lesson evaluation
Success of the lesson will be evaluated using the following criteria:
Students demonstrated adequate recall during the Do Now
Checks for understanding during review portion elicited positive results, and
students actively participated with questions and responses
Students were able to follow instructions for the KNex components and
successfully create correct DNA double helix models
Students could use their models to explain the Central Dogma and identify
codons in their models and describe how those codons are used to make proteins
Student assessment (Knowledge, skills, and understanding) (keep in mind these must address all of
your stated instructional objectives above)
Students will be assessed in several ways. One way will be based on the accuracy of the
model DNA KNEX model that the students create. Full credit will be give to a
successful display of base pairs, hydrogen bonds, nucleotide structure, and the double
helix. Students will also be asked to identify codons represented by their model. Another
way will be through the short answer responses in the lab packet. The questions will be
thought provoking and seek to probe students to begin to think about how the differences
in the sequencing of DNA base pairs influences how proteins are made, and ultimately,
genetic traits.

Adjustments for special needs students: (list some common adjustments)

Pair activity - peer support
Targeted assistance
Extra time as needed

Materials, equipment and supplies:

Student notebooks
Elmo/smartboard
Lab packets
DNA KNEX Kits

Safety concerns:
General personal safety
Watch for small pieces of KNEX on the floor to avoid possible slipping hazards
Name:_____________________________________ Date: _____________

KNex Modeling of DNA Lab

Recall that the nucleus is a small spherical, dense body in a cell. It is often called the "control
center" because it controls all the activities of the cell including when a cell divides into two, and
heredity. Chromosomes are microscopic, threadlike strands composed of the chemical DNA
(short for deoxyribonucleic acid). In simple terms, DNA holds the instructions for making
proteins within a cell. In fact, the only things that DNA is capable of producing is proteins.
These proteins in turn, form the structural units of cells and control all chemical processes within
the cell. Think of proteins as the building blocks and work horses for an organism. How you
look is largely determined by the proteins that are made. The proteins that are made are
determined by the sequence of DNA in the nucleus. In short, DNA makes proteins, and proteins
run all the processes in your cells.
DNA is composed of genes, which are segments of DNA that codes for a particular protein
which in turn codes for a trait. Hence you hear it commonly referred to as the gene for baldness
or the gene for blue eyes. There are an estimated 20,000 to 25,000 genes in the human genome.
Thats only 20 to 250 more than our close relative the chimpanzee. Yet those 200 to 250 genes
make a big difference.
DNA is a polymer of a nucleic acid because it was first found in the nucleus. We now know that
DNA is also found in other organelles such as the mitochrondria and chloroplasts, though it is the
DNA in the nucleus that actually controls the cell's workings.
In 1953, James Watson and Francis Crick figured out the structure of DNA, with the help of
Rosalind Franklin, Maurice Wilkens and Erwin Chargraff. The shape of DNA is a double
stranded helix, which is like a twisted ladder. The two strands run antiparallel to one another, or
in opposite directions. The sides of the ladder are made of alternating deoxyribose sugar and
phosphate molecules.
The rungs of the ladder are pairs of 4 types of nitrogen bases. The bases are known by their
coded letters A, C, G, T. These bases always bond in a certain way. Adenine will only bond to
thymine. Guanine will only bond with
cytosine. This is known as the "Base-Pair
Rule". The bases can occur in any order
along a strand of DNA. In fact, the order
of these bases will determine the type of
protein that is made. For instance, the
gene ATGCACATA would code for a
different protein than the gene
AATTACGGA. Our example is
oversimplified. In reality, a strand of
DNA contains millions of bases.
Note: looking at the picture on the previous page you will see that the bases attach to the sugars
and not the phosphates.
DNA is actually made of smaller repeating monomers called nucleotides. Each nucleotide
consists of three molecules: a sugar (deoxyribose), a phosphate which links the sugars together,
and then one of the four bases. Two of the bases are classified as purines - adenine and guanine,
and the other two bases are classified as pyrimidines - thymine and cytosine. Note that the
pyrimidines are single ringed and the purines are double ringed.
The two sides of the DNA ladder are held together loosely by hydrogen bonds. The DNA can
actually "unzip" when it needs to replicate - or make a copy of itself. DNA needs to copy itself
when a cell divides, so that the new cells each contain a copy of the DNA. Without these
instructions, the new cells wouldn't have the correct information.
Every cell in your body has the same "blueprint", or the same DNA. Just as the blueprints of a
house tell the builders how to construct a house, the DNA "blueprint" tells the cell how to build
the organism. Yet, how can a heart be so different from a brain if all the cells contain the same
instructions? Although much work remains in genetics, it has become apparent that a cell has
the ability to turn off most genes and only work with the genes necessary to do a job. We also
know that a lot of DNA apparently is nonsense and codes for nothing. These regions of DNA
that do not code for proteins are called "introns", or sometimes "junk DNA". The sections of
DNA that do actually code from proteins are called "exons".

PRELAB QUESTIONS:

1. What is the function of DNA?

______________________________________________________________________________
______________________________________________________________________________
________________________

2. What does DNA code for in our cells?

________________________________________________________

3. What is a gene?
__________________________________________________________________________

4. Where in the cell are chromosomes located?

___________________________________________________

5. Besides the nucleus, name two other organelles that contain DNA? _______________ &
_______________.

6. What three scientists are credited for discovering the structure of DNA?
___________________, ________________ & ________________.

7. What shape is DNA compared to?

___________________________________________________________
8. How many sides does DNA have?
____________________________________________________________

9. What are the two sides of the DNA ladder made of?
______________________________________________________________________________
____________

10. What are the rungs of the DNA ladder made up of?
___________________________________________

11. The nitrogen base Adenine pairs with _______________ and Cytosine pairs with
_______________.

13. DNA is made up of repeating units called: _________________________________.

14. What are the three components of a nucleotide? __________________, ______________,

_____________.

15. Draw the basic structure of a nucleotide:

16. The coding segments of DNA are called ___________________________.

17. The non-coding segments or junk DNA are referred to as _______________________.

18. What does antiparallel mean?

____________________________________________________________
______________________________________________________________________________
____

19. Write the complementary sequence to the following DNA sequence: The first three have
been written for you.

T A T T G C A G A T AA C T G

20. How many rings does a purine have? ______________

21. What two nitrogen bases are considered purines? ______________________,

_______________________

22. How many rings does pyrimidine? _______________

23. What two nitrogen bases are considered pyrimidine purines? ________________,
___________________

24. What kind of bonds hold the two sides of DNA together?
________________________________________

25. How many of these bonds are found between Adenine & Thymine? ____________

26. How many of these bonds are found between Guanine & Cytosine? ____________

LAB PROCEDURE:

1. Using the instructions in the KNex manual build several nucleotides. (There is a
key on the back of the manual that shows you what each piece represents)
a. At this time make: 6 Adenine, 6 Guanine, 6 Cytosine, and 6
Thymine.
2. At RANDOM, attach the nucleotides to one another so that the end of the
phosphate group in one nucleotide connects to x/the deoxyribose sugar of the next one to
make one strand of nucleotides. Remember, make it using a RANDOM sequence of
nucleotides. DONT copy the manuals DNA sequence.
3. After youve made one random DNA sequence, follow the rules of DNA base-
pairing, and the instructions in the Manual (pages 3-5) in order to build the
complementary strand. MAKE SURE YOUR STRANDS RUN ANTIPARALLEL to one
another.
4. Before you twist your strand into a helix, read post-lab question 5 below.
5. Use the manual to hydrogen bond the DNA strands together, add red rods, create
the base, and twist the double-stranded DNA into a helix (as shown on pages 6-7 of
manual). FOUR BASES MUST BE USED PER RED ROD. YOU ONLY NEED
 THREE RED RODS IN THE CENTER.

*Once you have constructed your DNA model, write down the sequence of bases in one of the
strand.

*Compare your sequence to the other groups in the classroom. Are any of them the same? Why
or why not?

POST LAB QUESTIONS:

1. Which pieces represent the deoxyribose sugar? ________________________

2. Which pieces represent the phosphate group? _________________________

3. Which nitrogenous base does each of the following represent?

White: __________ Black: ___________ Silver: ___________ Green: ___________

4. Why are the adenine and thymine bases joined with an orange connector, while the
cytosine and guanine bases were joined together by a brown connector?

5. Compare the stability of the flat DNA model (before you twisted it) to the helical (spiral)
DNA model that you created. Which one is more stable? (Hint: if you cant figure it out, think
about if a sheet of paper is more stable than a sheet that is twisted into a cord).
6. Based on your answer to number 5, why do you think the DNA is shaped like a helix in our
cells (how is it helpful)?

7. Compare the sequence you made to the sequence of other groups DNA models in the room.
Are any of them the same? _________________ .

How does this relate to a comparison between your DNA, and others DNA in the room? Does
anyone in the room have the exact same DNA? Explain.

Grading Rubric:

1. DNA Model (10 pts)

A. Model contains 12 correctly paired complementary bases _____ / 2 pts

B. Deoxyribose and phosphate group connected correctly _____ /2 pts

C. Helix is shown accurately (four bases per red rod) _____ /2 pts
 D. DNA strands were assembled in ANTIPARALLEL fashion _____/2pts

E. Stand was created correctly, and DNA molecule sits properly ___ /2 pts

2. Pre-Lab (8 pts)

A. all questions answered accurately _________ /8 pts

3. Post Lab Questions ( 8 pts)

A. all questions answered accurately _________ / 8 pts

Lab worth A TOTAL of 26 points _________ /26 pts