10
Modeling DNA Structure
modeling
• 2 class sessions
Overview
Students investigate the molecular structure of DNA. They
analyze historical base-pairing data and draw conclusions
from the data to construct DNA models. They also compare
their models to several images of DNA and discuss what each
conveys about the molecular structure of DNA.
Key Content
1. The genetic material of cells is deoxyribonucleic acid
(DNA).
2.DNA is a macromolecule composed of nucleotide
subunits.
3.DNA is composed of two complementary strands, each
made of a sequence of nucleotides.
4. Each strand of DNA has a sugar–phosphate backbone
and a sequence of nitrogenous bases. Two strands of
DNA together form a double helix.
For each pair of students
DNA model kit containing:
plastic bag*
36 black deoxyribose sugars*
36 white phosphate tubes*
orange, yellow, blue, and green nitrogenous base
tubes*
18 white hydrogen bond rods*
Note: This activity is written to use the SEPUP DNA modeling
kit. If you will be using a different kit, adjust the instructions as
appropriate.
The DNA model kits contain pieces for this activity, and additional pieces to model protein synthesis later in the unit. For
each kit separate the pieces needed for this activity, as noted
above, and place them into one of the plastic bags. Label the
bag DNA Subunit Models. Store the remaining parts for use in
Activity 12, “ DNA Replication.”
Teaching Summary
Key Process Skills
1. Students identify and describe trends in data.
2. Students interpret data.
Getting Started
• Students discuss their ideas about the structure of DNA.
Doing the Activity
Materials and Advance Preparation
For the teacher
Transparency 10.1, “DNA Structure”
Transparency 10.2, “DNA Nucleotides”
Transparency 10.3, “Antiparallel DNA”
Transparency 10.4, “DNA Images”
• Students build a DNA model.
Follow-up
•
✓ Students analyze the strengths of various DNA models.
For each group of students
set of colored pencils
Copyright 2011 The Regents of the University of California
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science and global issues/biology • Genetics
Background Information
DNA Structure
Deoxyribonucleic acid (DNA) is a large polymer, or macromolecule, made of numerous repeating monomers, or subunits. These subunits of nucleic acids are called nucleotides.
Each nucleotide in DNA consists of the five-carbon sugar
deoxyribose, a phosphate group, and one of four nitrogenous
bases. Because they all contain deoxyribose, the nucleotides in
DNA are more specifically called deoxy­ribonucleotides. However, most of the time they are simply referred to as nucleotides. Note that RNA and ribonucleotides will be discussed in
the Teacher’s Edition Background Information for Activity 16,
“Protein Synthesis: Transcription and Translation.”
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The complete atomic structure of a nucleotide containing
thymine is shown below. The phosphate group is attached
to carbon 5 of the deoxyribose sugar, and the bases are
attached to carbon 1.
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from this backbone. Each base hydrogen bonds to only one
other nitrogenous base to form a base pair. The purine adenine pairs only with the pyrimidine thymine via two
hydrogen bonds. Similarly, guanine pairs with cytosine via
three hydrogen bonds. These hydrogen bonds between complementary nucleotides link two DNA strands together,
making the resulting DNA molecule double-stranded. This
double-stranded molecule takes on a helical shape called a
double helix. It resembles a ladder, with the sides formed by
the sugar phosphate backbones and the rungs formed by successive base pairs.
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modeling dna structure • Activity 10
Because the phosphate groups are always on carbon 5 of the
deoxyribose sugar, a single strand of DNA has a polarity. The
end that terminates with a phosphate group is called the 5’
end, while the other end is the 3’ end. In a double-stranded
DNA molecule, the 5’ end of one strand is opposite the 3’ end
of the other strand. Thus, the two strands of DNA in a double
helix are said to be antiparallel.
The Work of Erwin Chargaff
In the late 1940s, Erwin Chargaff, an Austrian biochemist
working at Columbia University in New York, was spurred
into action after reading the scientific findings of Oswald
Avery. Avery was an American physician renowned for his
studies on disease-causing bacteria. Avery’s research supported the hypothesis that genes are made of DNA. At the
time many leading scientists believed cellular proteins served
as the genetic material because they couldn’t figure out how
such a simple molecule as DNA, with only four different
nucleotide subunits, could carry genetic information. Chargaff, in an effort to support Avery’s findings, changed the
work focus of his research team and began investigating the
biochemical composition of DNA.
Chargaff ’s team used two biochemical analysis techniques
that were new at the time: chromatography, to analyze the
nucleic acid content of a sample, and ultraviolet spectrophotometry, to measure the amount of each nitrogenous base in
a DNA sample. These techniques allowed the group to characterize the ratio of DNA nucleotides in various DNA samples. Chargaff published his first papers describing their
work in 1950.
The research group further refined its analysis methods to
determine the nitrogenous base composition of DNA from
several organisms, including plants, animals, and bacteria.
From the data generated, the team concluded that the
amounts of adenine and thymine in a DNA sample were
approximately equal and that the amounts of cytosine and
guanine were also approximately equal. In addition, the data
disproved a widely held idea that DNA is the same in all
organisms. The data supported the idea that the DNA of different organisms is composed of unique ratios of nitrogenous bases.
The work of Chargaff and his team provided critical evidence for the discovery of the double-helical structure of
DNA. James Watson and Francis Crick realized that the data
Chargaff collected could be the result of pairing between A
and T and between G and C in complementary strands of
DNA. Thus, what later became known as Chargaff ’s rules,
that A bonds with T and C bonds with G, were an essential
piece of evidence in Watson and Crick’s discovery of the
double-helical structure of DNA.
References
Chargaff, E. & Davidson J., eds. (1955). The nucleic acids.
New York: Academic Press.
Chargaff, E., Zamenhof, S., & Green, C. (1950).
Human ­desoxypentose nucleic acid: Composition
of human desoxypentose nucleic acid. Nature 165,
756–757.
Chargaff, E., Lipshitz, R., & Green. C. (1952). Composition
of the desoxypentose nucleic acids of four genera of
­sea-urchin. Journal of Biological Chemistry 195(1):155–60.
Chargaff, E., Lipshitz, R., Green, C., & Hodes, M. E. (1951).
The composition of the desoxyribonucleic acid of
salmon sperm. Journal of Biological Chemistry
192, 223–230.
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science and global issues/biology • Genetics
Getting Started
1
Write the word genes on the
board, and ask students to describe
what they know about them. List
students’ ideas on the board. If necessary, encourage them to add information about what genes are made
of and where they are located. Students’ answers will likely indicate
that genes, in conjunction with environmental factors, determine traits
in an organism’s phenotype. They
also will likely point out that all
organisms have DNA, and, therefore,
all organisms have genes. If they
completed the “Cell Biology: World
Health” unit of Science and Global
Issues, they may remember that the
genetic material is in the cell
nucleus. They will explore the relationship between genes and DNA,
as well as chromosomes, in this and
future activities. This is an opportunity to find out their ideas so that
you may address any misconceptions or gaps in basic knowledge of
genes throughout the remainder of
the unit.
10
1
2
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Modeling DNA Structure
genetic material of all living organisms. Like proteins, carbohydrates, and lipids, DNA is a polymer—a large molecule made of many
repeating subunits, called monomers. The subunits of DNA are nucleotides.
NA IS THE
DNA contains information that codes for life’s processes. Understanding the
chemical structure of DNA allows scientists to understand how DNA codes for
proteins. Scientists also need to understand the structure of DNA to determine
how to isolate a specific desirable or undesirable gene from an organism.
In this activity, you will model the structure of DNA and explore how it provides
information that directs the processes in a cell.
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Doing the Activity
328
2 Project Transparency 10.1, “DNA
Structure.” Explain that DNA has
the shape of a double helix, and that despite its size, it is
relatively simple in structure. It is made of only four subunits and always takes on a double-helical shape. Refer to
the diagram in the Student Book to show students additional detail, but do not explain base pairing rules at this
point. If students completed the “Cell Biology” unit of
­Science and Global Issues, remind them about proteins,
which are polymers made of long chains built from 20
amino acid monomers and take on a wide variety of
shapes. For a long time, scientists assumed that only proteins were complex enough to carry the genetic material.
It was after they gained a more detailed understanding
of the structure of DNA that scientists figured out how it
could carry genetic information.
508
modeling dna structure • Activity 10
3DNA is a polymer that is made
of repeating monomers (nucleotide
subunits) that vary in one distinct
way—the nitrogen bases that the
nucleotides carry. Connect this back
to what students learned in the “Cell
Biology” unit about polymers and
subunits in cells. Show students the
deoxyribose sugar, the phosphate
group, and the nitrogenous-base
pieces from the DNA model kit.
Explain that each kit piece represents a nucleotide structure but
does not show its detailed atomic
structure.
4 With Transparency 10.2, “DNA
Nucleotides,” show the class four
nucleotides—adenine, cytosine,
guanine, and thymine—and their
corresponding kit pieces. Point out
that each nucleotide has the same
deoxyribose sugar and phosphate
group, but the nitrogenous (nitrogen-containing) base attached to
the sugar–phosphate backbone can
vary. Depending on your instructional goals, you may wish to
explain that each of the four nitrogenous bases has its own molecular
structure, but all are based on cyclic
molecules made of carbon and
nitrogen rings, as shown on the
bottom half of Transparency 10.2.
MODELING DNA STRUCTURE • ACTIVITY 10
Challenge
� What is the molecular structure of DNA?
MATERIALS
FOR EACH GROUP OF FOUR STUDENTS
set of colored pencils
p
FOR EACH PAIR OF STUDENTS
bagg containingg DNA model kit pieces
p
36 black deoxyribose
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sugars
g pentagons
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36 white p
phosphate
p
tubes
various orange,
g , yellow,
y
, blue,, and green
g
nitrogenous
g
base tubes
18 white hydrogen
y g bond rods
Procedure
3
1. DNA is made of repeating subunits called nucleotides. A nucleotide is made
of a sugar, a phosphate group, and a nitrogen-containing base. Identify each of
these in the figure below.
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The nucleotide shown is
composed of a deoxyribose
sugar, a phosphate group,
and a nitrogenous base.
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2. There are four different nucleotides in DNA. These four vary only by which
of the four bases they contain. The four bases are adenine, cytosine, guanine,
and thymine. With your partner, use the DNA model kit to construct a DNA
nucleotide as shown in the figure above.
Key for DNA
Model Nitrogenous Bases
NITROGENOUS BASES
COLORED TUBE
Adenine (A)
• Orange
Cytosine (C)
• Blue
Guanine (G)
• Yellow
Thymine (T)
• Green
329
509
science and global issues/biology • Genetics
5Discuss the role of hydrogen
bonds in DNA. Explain that
hydrogen bonds form between two
nitrogenous bases on two strands of
DNA. This is shown on Transparency 10.1, “DNA Structure.” The
diagram shows the two hydrogen
bonds that connect A and T and the
three that connect C and G. In their
models, students make one connection to represent these bonds. When
hydrogen bonds link two nitrogenous bases, the result is a base pair.
6 Use this opportunity to discuss
the historical discovery of the structure of DNA. For additional information, see the links on the science
and Global Issues page of the SEPUP
website (sepuplhs.org/sgi).
7 Students should conclude that
SCIENCE & GLOBAL ISSUES/BIOLOGY • GENETICS
3. Continue to build and connect a single chain of eight nucleotides, using any
sequence of bases.
5
4. DNA occurs in its natural state as two strands linked down the middle by
hydrogen bonds. Identify the two strands and the location of the hydrogen
bonds in the figure below.
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A base pairr is two nucleotides in
double-stranded DNA connected
by hydrogen bonds.
6
BACKGROUND INFORMATION
Discovering the Structure of DNA
I N T H E 1950 S ,
discovering the structure of DNA became a subject of
intense scientific investigation and
rivalry. Several research groups
competed to be the first to find the
answer. These groups included
the laboratory of Linus Pauling
(who had earlier determined the
structure of proteins) at the California Institute of Technology;
scientists at Cambridge University
in England; and another group of
scientists at Kings’ College of the
University of London.
paper that proposed that DNA is
made of two strands spiraling to
form a double helix. This structure
not only accounts for the chemical
makeup of DNA, but also allowed
Watson and Crick to predict how
DNA replicates when a cell divides.
Their discovery opened up the field
of molecular biology, which provides insights into the molecular
basis of genetics, development, evolution, and other biological processes. Watson, Crick, and Wilkins
were awarded the Nobel Prize in
1962, for their breakthrough. Unfortunately, Rosalind Franklin did not
share in the prize because she had
died in 1958, and the Nobel Prize
is not awarded to someone who has
died. The story of these scientists
and their work is the subject of
a number of books and articles.
since the amount of adenine (A) and
thymine (T) are practically equal in
each organism, adenosine pairs with
James Watson and Francis Crick of
Cambridge University won the race.
thymine. They should draw the same
In 1953, after careful analysis of
structural and chemical data—
conclusion for cytosine (C), which
much of which was provided by
pairs with guanine (G). If students
Maurice Wilkins and Rosalind
Franklin at Kings’ College—Watson
need assistance processing the data
and Crick published a scientific
you might ask, What patterns do you
notice? What does this data set show
330
about the percentages of bases in different organisms? What does it tell
you about the relative ratio of A, T,
9Develop the concept of antiparallel strands of DNA.
G, and C in DNA? Help students see that the percentages of
Project Transparency 10.3, “Antiparallel DNA.” Explain
adenine (A) are close to those of thymine (T) and the perthat the 5' end of a DNA strand terminates with a phoscentages of guanine (G) are close to those of cytosine (C)
phate group. The 3' end terminates with a deoxyribose
for each organism on the table. Explain that the reason the
sugar. Both of the complementary DNA strands in doublepercentages in Chargaff’s data are not exactly equal is most
stranded DNA have a 5' and 3' end, but in opposite orientalikely a matter of experimental errors resulting from the
tions. Therefore, the two complementary strands of DNA
very new procedures that Chargaff and his laboratory develare said to be antiparallel. This aspect of DNA structure
oped. This is a good time to introduce students to the
becomes more important to students as they learn about
common convention of noting the nitrogenous base adeDNA replication in Activity 12, “DNA Replication.”
nine as A, guanine as G, thymine as T, and cytosine as C.
8 As students build their models, check them to see that
students have paired adenine with thymine and cytosine
with guanine. Listen for and discuss as necessary students’
correct usage of the key terms: sugar–phosphate backbone,
base pair, nucleotide, and hydrogen bond.
510
10 Students’ drawings should identify the key components
of DNA listed in the Student Book, as shown in the sample
image on the next page.
modeling dna structure • Activity 10
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MODELING DNA STRUCTURE • ACTIVITY 10
7
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5. In the mid-1940s, Erwin Chargaff, an Austrian scientist, analyzed the percentages of each of the four nitrogenous bases in DNA. A summary of his
findings is shown in the table below. With your group, review the data, and
search for patterns. Discuss what these patterns might suggest about the
nucleotides in DNA.
Percentages of DNA Nucleotides in Selected Organisms
SOURCE OF DNA
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end-to-end. Twist this longer model
to demonstrate the double-helix
structure of DNA. Explain that this
represents a minute portion of the
3.3 billion DNA base pairs contained in an average human cell. Tell
students that it is the sequence of
nitrogenous bases in an organism’s
DNA that provides the genetic
information that determines an
organism’s phenotype, in conjunction with environmental factors.
8
9
10
ADENINE (A)
CYTOSINE (C)
GUANINE (G)
THYMINE (T)
Human
30.2%
18.8%
18.8%
32.2%
Rat
28.6%
21.6%
21.4%
28.4%
Sea Urchin
31.2%
19.1%
19.2%
30.5%
Salmon
29.2%
20.8%
21.9%
28.1%
6. Based on your conclusions from the data in Step 5, construct a second strand
of DNA that pairs with the strand you built in Step 3.
7. Connect the two strands down the middle with hydrogen bonds.
8. With colored pencils sketch the resulting double-stranded DNA model in
your notebook. On your sketch, label the following:
• Phosphate group
• Deoxyribose sugar
• DNA nucleotide
• Nitrogen base
• Hydrogen bond
• Base pair
• Sugar–phosphate backbone
11
9. At this point, your piece of DNA should resemble a ladder. Watch as your
teacher connects several DNA models and demonstrates the shape of a DNA
molecule.
12
10. With your group, look at the series of DNA models shown in the figures on
the next page. Compare your DNA Model with the DNA in each image. Discuss what each model demonstrates about the structure of DNA. Record your
ideas in your science notebook.
Emphasize again that a gene is a
segment of DNA with a unique base
sequence that encodes for a specific
protein that influences an organism’s phenotype. Genes for different
proteins vary tremendously in
length, both within an organism
and from one organism to another. Human genes have
from 1,000 to hundreds of thousands or even millions of
base pairs, with the average human gene being 10,000–
15,000 base pairs in length. Genes in prokaryotes tend to
be shorter than the comparable genes in eukaryotes.
Connect this to the DNA students observed in Activity 9,
“DNA Isolation.” Explain that although the physical characteristics of the DNA they observed from different types
of organisms are the same, the DNA from each organism
contains a unique sequence of nucleotides characteristic of
that species.
Note: At the end of the activity, store the complete longer
model to use again in Activity 12.
331
12 Encourage students to identify the DNA characteristics
shown by the physical model and each of the figures in
the Student Book. Prompt them to discuss the similarities
and the differences they observe between the images and
their model. All five models show the overall double-helix
structure of DNA, and the structure of the sugar–phosphate
backbone. The individual components emphasized in each
vary from image to image. The figures at the top of the page
clearly show nucleotides in the center of the helix. The figure
at the top left shows the nucleotides in a base pair bonded
by hydrogen bonds. Discuss which images are computergenerated models and which are scientific drawings. (The
figures at the bottom of the page are computer generated.
The figures at the top are schematic drawings of DNA.)
511
science and global issues/biology • Genetics
SCIENCE & GLOBAL ISSUES/BIOLOGY • GENETICS
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332
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modeling dna structure • Activity 10
✓
13 Procedure Step 11 serves as a
Quick Check to assess students’
grasp of the structure of DNA and
to make sure they can describe the
shape and key structural components of DNA. Showing Transparency 10.4, “DNA Images,” will help
in this assessment.
MODELING DNA STRUCTURE • ACTIVITY 10
13
11. With your partner, identify the following in the images of DNA shown on the
previous page:
• Phosphate group
• Deoxyribose sugar
• DNA nucleotide
• Nitrogen base
• Hydrogen bond
• Base pair
• Sugar–phosphate backbone
14 To provide students with a sense
of the amount of DNA contained
in an average human cell, explain
that the model they built was eight
base pairs (bp) in length. The combined length of all of the DNA in
the 23 human chromosome pairs
(46 chromosomes) is approximately 3 billion base pairs.
Analysis
1. How would you describe the structure of DNA to a 10-year-old?
2. What nucleotide sequence would bond with the following strand?
5' ATCGCC 3'
3. Arrange the following cell structures from the smallest to the largest, left to right:
DNA
chromosomes
gene
cell
14
Sample Responses
1. Students’ answers should explain
the double-helical structure of
DNA and that it is composed of
repeating subunits that contain
one of four bases. One possible
response is:
DNA is shaped like a ladder that is
twisted. It has rungs that are the
same shape that repeat over and
over. Each rung is made when two
molecules called bases bond
together. There are four possible
bases, and they carry the genetic information.
4. The table below shows the number of base pairs in the DNA of selected organisms. From the data in the table, what can you say about the amount of DNA
contained in the cells of these three organisms?
Amount of DNA in an Average Cell
of Selected Organisms
ORGANISM
NUMBER OF BASE PAIRS
E. Coli
4.7 million
Corn (Zea Mays)
2.5 billion
Human (Homo sapiens)
3.3 billion
KEY VOCABULARY
base pair
hydrogen bond
double helix
nucleotide
deoxyribonucleic
acid (DNA)
sugar–phosphate backbone
2. 3' TAGCGG 5'
3. gene DNA chromosome cell
4. The amount of DNA in an average human cell is more
than 1,000 times the amount of DNA in an E. coli cell.
333
Revisit the Challenge
Students should be able to explain the overall molecular
structure of DNA as a repetition of subunits called nucleotides. They should understand that there are four possible
nucleotides, and that pairing of A with T and G with C links
two strands of nucleotide subunits. They should be able to
explain that DNA has sugar–phosphate sides that run along
the outer edge of the DNA molecule like a ladder, with the
nitrogenous bases forming the rungs that connect the two
helical sides.
513