CHAPTER 1

DNA: The
Hereditary
Molecule

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Cyt

Gu
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ne SECTION C
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Thy

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What is the
Ad

Structure of
DNA?

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The Puzzle of DNA Structure

and Replication
INTRODUCTION

THE FUNCTION OF DNA is based entirely on its structure. A single strand of DNA con-
sists of many individual building blocks called nucleotides that are connected, in a long
string, by chemical bonds. Each nucleotide contains one of four possible nitrogenous
bases: either adenine (A), cytosine (C), guanine (G), or thymine (T). In principle, it is
possible to construct a DNA strand that contains these four types of nucleotides in any
conceivable sequence. In nature, however, DNA exists as a double-stranded molecule in
which the two strands that lie side by side interact in a very specific way. The nature of the
interactions that occur between these two strands is such that the sequence of nitrogenous
bases on one strand always has a predictable relationship to the sequence of nitrogenous
bases on its partner strand. This relationship underlies the ability of DNA to serve as the
hereditary material and has sometimes been called “the fundamental secret of life.”

In this exercise, you will be provided with half of a file folder and a set of puzzle pieces of
different shapes and colors that represent the four kinds of nitrogenous bases that are found
in all DNA molecules. You will use these pieces to solve a simple puzzle, and from the fin-
ished puzzle, you should be able to figure out the nature of the relationship that exists
between opposite strands of a double-stranded DNA molecule, and why DNA is so easy to
replicate when a cell gets ready to divide.

MATERIALS

For each student or pair of students:

one half of a file folder
puzzle pieces

PROCEDURE, PART A
A
G
1. Draw a straight line near and parallel to the left
hand edge of your piece of file folder.

2. Select ten of your puzzle pieces at random, or in

any order that you wish. Place each of these
pieces on the paper so that it is letter-side-up and
so that its flat end touches the line you have
drawn (Fig. 1). This will be the left-hand strand
of your DNA puzzle.
Figure 1

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3. Now form the right-hand strand of the DNA by T

A
placing the remaining puzzle pieces on the paper
G
so that the non-flat end each of them fits snugly
against the non-flat end of one of the pieces in the
left-hand strand.

4. Draw a straight line next to the flat ends of the

pieces in the right hand strand (Fig. 2).

5. Use your finished puzzle to answer the first four

questions on the next page.

Figure 2
PROCEDURE, PART B

6. Pair up with another person in your class. A

T

7. One person in each pair should put all of his or

her puzzle pieces back in the bag (Fig. 3).

Figure 3

A
8. Carefully transfer the right-hand strand of the G
remaining DNA puzzle to the right hand side of
the other person’s piece of cardboard, leaving the
left-hand strand where it is (Fig. 4).

Figure 4

9. Use the puzzle pieces in the bag to build a second A

T
A
T

G G
DNA strand on each piece of cardboard (Fig. 5).

10. Answer questions 5 and 6 on the next page.

Figure 5

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ANALYSIS AND CONCLUSIONS

1. Do you see any consistent relationship between the DNA bases (puzzle pieces) in one
strand of your puzzle and the bases with which they are paired in the other strand? If
so, state the nature of the relationship(s) you see.

______________________________________________________________________

______________________________________________________________________

2. Half of the puzzle pieces that you were given (the A’s and G’s) were much larger than
the other pieces (the C’s and T’s). Did this size difference cause your DNA model to be
significantly wider in some parts than in others? If not, why not?

______________________________________________________________________

______________________________________________________________________

3. Is there any consistent difference in the way that the pieces in the right-hand strands
and the left-hand strands of your model are oriented? If so, what is the difference?

______________________________________________________________________

______________________________________________________________________

4. How can you account for the fact that no matter which bases were selected for the left-
hand strand of a DNA molecule, everyone had just the right pieces left over to assem-
ble a matching right-hand strand?

______________________________________________________________________

______________________________________________________________________

Do Part B of the puzzle before you answer the next two questions.
5. Are the two DNA puzzles you now have the same or different? How can you account
for this?
______________________________________________________________________

______________________________________________________________________

6. What do you suppose biologists call this process of making two identical double-
stranded DNA molecules from one when it occurs in cells?

______________________________________________________________________

______________________________________________________________________

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The Spiral Staircase

N 1944, A TEAM OF BIOLOGISTS LED BY OSWALD

IAVERY MADE A VERY IMPORTANT DISCOVERY: DNA
EXTRACTED FROM ONE KIND OF BACTERIUM COULD BE
USED TO TRANSFER HERITABLE TRAITS OF THAT BAC-
TERIUM TO A SECOND BACTERIUM! THIS WAS THE FIRST
CLEAR INDICATION THAT DNA WAS THE CARRIER OF
HEREDITARY INFORMATION. OTHER REPORTS DRAWING
THE SAME CONCLUSION SOON FOLLOWED.

BEFORE AVERY, SCIENTISTS HAD PAID LITTLE ATTEN-

TION TO DNA. THEY KNEW IT CONTAINED THE SUGAR
DEOXYRIBOSE, PLENTY OF PHOSPHATE AND FOUR
BASES.

Reprinted with permission from Gonick, L. and Whellis, M. (1991).

The Cartoon Guide to Genetics. New York: Harper Collins

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What is a Model?
And What is it Good For?
AS WE GREW UP, most of us
played with various models:
model cars, model planes, model
houses (doll houses), model peo-
ple (dolls), etc. Not all models are
designed for childhood play, how-
ever. Models serve important
functions in many areas of adult
life. Engineers, for example, eval-
uate various possible airplane
designs by building scale models
and examining how they behave
in a wind tunnel (which is itself a
model of the atmosphere).

Models are usually highly simpli-

fied relative to the objects that
they portray, and often several different models, simplified in different ways, are required
to study different aspects of the same object. For example, the engineer who is designing
the seats for a commercial airliner requires a very different kind of model than does the
engineer who is designing the wings. Neither of these models would necessarily be more
correct than the other; they would merely be simplified in different ways in order to serve
different purposes.

DNA MODELS

Scientists find models of various kinds of molecules very useful for visualizing how their
parts fit together and for predicting what their properties should be. Indeed, it was only
when two biologists by the names of Watson and Crick built the first fairly accurate scale
model of DNA that it became clear what the structure of real DNA molecules must be.

In the next exercise, you will build a much simpler DNA model than Watson and Crick did
in order to visualize certain very simple aspects of its structure. But as you progress in the
study of biology, you will probably encounter several other kinds of DNA models that are
constructed so as to reveal other, more detailed aspects of DNA structure and function.

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Building a Three-Dimensional
DNA Model
MATERIALS

For each student or pair of students: Use the following list to make sure that your model-
building kit contains the correct number of pieces of each type. Then use it to determine
what each of these pieces represents.

Short straws representing the nitrogenous bases:

3 blue straws = A (adenine)
3 red straws = T (thymine)
3 green straws = G (guanine)
3 gray straws = C (cytosine)

Pieces used to build the sugar-phosphate ladders:

12 black connectors = sugars (deoxyribose)
12 red connectors = phosphate groups
24 yellow straws = sugar-to-phosphate bonds
6 white connectors = hydrogen bonds

Pieces used to build the stand for the model:

1 long gray straw
3 medium-length green straws
1 four-prong black or silver connector

PROCEDURE Phosphate
(red)
1. Make 12 nucleotides as shown in
figure 1. Each nucleotide will Deoxyribose (sugar)
require one deoxyribose sugar, two (black)
yellow sugar-to-phosphate bonds,
one red phosphate group, and one Sugar-to-phosphate bonds
(yellow)
nitrogenous base (either red, green,
blue, or gray). Nitrogen base
(blue, red, gray or green)

Figure 1: Making a nucleotide

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2. After you have made all the

nucleotides you can, use the
white connectors (hydrogen Hydrogen bond
bonds) to join them in pairs (white)

according to the base-pair-

ing rules (A to T and G to
C), as in figure 2.

Figure 2: Making a nucleotide pair

3. After you have finished

forming the nucleotide
5’ end
pairs, use the sugar-phos-
phate bonds to join them 3’ end
(fig. 3), in any order you
want.
Deoxyribose sugar
(black)

Sugar-phosphate ladder
4. Note that the sugar-phos- Hydrogen bond
(white)
phate chain on the left side
has a red phosphate group Phosphate
(red)
at the bottom (its 5’ end)
but not at the top (its 3’
end) and that the sugar-
Nitrogen base
phosphate chain on the right (blue, red, gray or green)
side is just the opposite.
This is one of the ways that
enzymes that interact with
DNA molecules can tell the
two strands apart.
Sugar-to-phosphate bonds
(yellow)
3’ end

5’ end

Figure 3: Joining the nucleotide pairs

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5. Build the stand for your

model using the one long
gray straw, the three medi-
um-length green straws and
the four-pronged black con-
nector.

6. Slide the white hydrogen

bonds that run down the
middle of your model onto
the stand.

7. To get all of your model to

fit on the stand, you will
need to twist it counter-
clockwise at the top (fig. 4).
Now you have a representa-
tion of the famous double-
helix of DNA.

8. Answer the questions on the

next page.

Figure 4: The completed model on a stand

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ANALYSIS AND CONCLUSIONS

YOU HAVE NOW built two models of double-stranded DNA: the flat one in the puzzle at
the beginning of this exercise that you used to deduce the base-pairing rules and how DNA
is replicated (which we will call “model A”), and the one you have just built with straws
and connectors (which we will call “model B”). As mentioned earlier, often two models of
the same thing will be simplified in different ways to emphasize different features of the
object they are representing.

1. What feature or features of a double-stranded DNA molecule are represented better in

model A than in model B?

______________________________________________________________________

______________________________________________________________________

______________________________________________________________________

2. What feature or features of a double-stranded DNA molecule are represented better in

model B than in model A?

______________________________________________________________________

______________________________________________________________________

______________________________________________________________________

3. What feature or features of a double-stranded DNA molecule that you read about in the
excerpt from the Cartoon Guide to Genetics are not well represented in either model A
or model B?

______________________________________________________________________

______________________________________________________________________

______________________________________________________________________

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DNA Model Questions

THE DIAGRAM ON THE left represents an
untwisted, double-stranded DNA molecule.
O A 1. Label each sugar group on the diagram with
a letter S.
O
2. Label each phosphate group with a letter P.

O 3. One adenine (A) and one guanine (G) have

already been labeled. Label the rest of the
O nitrogenous bases.

4. Circle one nucleotide. What three things go

together to make a nucleotide?
O
G ___________________________________
O
___________________________________

___________________________________
O
5. The sides of the DNA ladder are made up
O
of alternating ________________________

and ________________________ groups.

O
6. The rungs of the DNA ladder are made
O
up of _______________________________

7. A is always paired with ________________

O
8. G is always paired with ________________
O
9. Paired bases are held together by weak

O bonds called __________________ bonds.

O 10. When the DNA ladder twists the way it

normally does, the shape of the molecule

is called a ___________________________

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DNA Word Search

FIND AND I J Y R L W X B V X M I U R W Y T Q W D
CIRCLE the U S P G P Y J W L S V Q E H B K D N I I
words that go B E L D K E Z P H O S P H A T E L C T U
with each of N S N P E E D Y W B L T T Q O U A S H K
the clues B A E I N Y E O X I F C H X N C Q Y J R
given below. E B D A S Z K M C R R Q L S I D D G A T
Then write O S D B R O H A K C P R M E P R N G D I
the answers C U A W M O T C J H I X L G O L U L E S
on the lines Z O L W N I V Y N B N C N G V S B F N L
next to the H N D V O O L D C U U K E N E W I S I Q
clues. T E E N R X O S C N Y N U N I S N N N L
Q G T A E B E L O F B Q I V E B O Q E I
T O S D O G E B J O E N I M Y H T B N X
X R I S A O I W N P A L B S P D Q Q N R
C T W B T R S D G U A H B J Z Z Y F O P
V I T I Y S S T G M T S R A U H S X A V
E N D X B A S E P A I R X Y Z O C Y N Y
D E O Y E Y O W X I L E H E L B U O D Q
I E J S E A I E Q V W Q X M L C B X P V
D A X F M N H G K N X I I A F R R G M Y

1. The nitrogenous base A ____________
2. The nitrogenous base C ____________
3. The nitrogenous base G ____________
4. The nitrogenous base T ____________
5. The genetic material inside all cells
__________ (abbreviation)
6. The full name for DNA ____________
_______________________________
7 The scientific name for the shape of
the DNA molecule ________________
_______________________________
(two words)
8. The arrangement of two bases in the
DNA molecule forms a ____________
_____________________ (two words)
9. The name of the bonds that hold the
two strands of DNA together (between
the bases) ____________ (two words)
10. Pairs of these molecules form the steps
or rungs in the DNA molecule ______
_______________________________
(two words)
11. This subunit of DNA has three parts: a
phosphate, a sugar and a nitrogenous
base __________________________
12. The long backbones of the DNA mole-
cule are made of alternating sugar and
__________________________ bonds.
13. This process occurs when DNA makes
a copy of itself ___________________

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