3.3 DNA Structure
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Topic 3: Chemistry of Life
3.3 DNA Structure
Orange book: pg. 54-59
Green book: pg. 35
3.3.1 Outline DNA nucleotide structure in terms of sugar (deoxyribose), base
and phosphate (pg. 54).
3.3.2 State the names of the four bases in DNA (pg. 57)
3.3.3 Outline how DNA nucleotides are linked together by covalent bonds into a
single strand (pg. 57).
3.3.4 Explain how a DNA double helix is formed using complementary base
pairing and hydrogen bonding (pg. 57).
3.3.5 Draw and label a simple diagram of the molecular structure of DNA.
3.3.1 Nucleotides
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3.3.1 Outline DNA nucleotide structure in terms of sugar (deoxyribose), base
and phosphate.
Orange book: pg. 54-59
Green book: pg. 35
To do:
Visit the following website
 http://www.pbs.org/wgbh/nova/genome/dna.html#
Journey into DNA Animation - This is a simple introduction which takes you
from the cell right down to the structural level of DNA.
Draw the basic structure of a nucleotide in your green exercise book.
DNA and its close relative RNA are perhaps the most important molecules in
biology. They contain the instructions that make every single living organism on
the planet, and yet it is only in the past 50 years that we have begun to
understand them. DNA stands for deoxyribonucleic acid and RNA for
ribonucleic acid, and they are called nucleic acids because they are weak acids,
first found in the nuclei of cells. They are polymers, composed of monomers
called nucleotides.
Nucleotides
Nucleotides have three parts to them:
a phosphate group (PO42- ), which is negatively charged, and gives nucleic acids
their acidic properties.
a pentose sugar, which has 5 carbon atoms in it. By convention the carbon
atoms are numbered as shown (1', 2', etc, read as "one prime", "two prime", etc),
to distinguish them from the carbon atoms in the base. If carbon 2' has a
hydroxyl group attached (as shown), then the sugar is ribose, found in RNA. If
the carbon 2' just has a hydrogen atom attached instead, then the sugar is
deoxyribose, found in DNA.
a nitrogenous base. There are five different bases (and you don't need to know
their structures), but they all contain the elements carbon, hydrogen, oxygen
and nitrogen.
3.3.2 Bases
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3.3.2 State the names of the four bases in DNA
Orange book: pg. 57
Green book: pg. 35
To do:
List the names of the four bases found in DNA in your green books.
Since there are five bases, there are five different nucleotides:
Base:
Adenine (A)
Cytosine (C)
Guanine (G)
Thymine (T)
Uracil (U)
The bases are usually represented by the first letter in their name. The base
thymine is found in DNA only and the base uracil is found in RNA only, so there
are four different bases present at a time in one nucleic acid molecule.
Pyrimidines: Thymine and cytosine are pyrimidines. Note that all three words
contain a 'y' (note that uracil does not fit this pattern).
Purines: Adenine and guanine are purines (notice the word 'nine' in both adenine
and guanine!).
3.3.3 Polymerisation
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3.3.3 Outline how DNA nucleotides are linked together by covalent bonds into a
single strand.
Orange book: pg. 57
Green book: pg. 35
To do:
View the animation “Journey into DNA”
This is a simple introduction which takes you from the cell right down to the
structural level of DNA.
http://www.pbs.org/wgbh/nova/genome/dna.html#
View the animation “Summary of DNA”
A complete overview of the structure of DNA.
http://207.207.4.198/pub/flash/24/menu.swf
Draw and label a single strand of DNA to show how a nucleotide is attached to
the 3’ end of the growing strand.
Nucleotide Polymerisation
Nucleotides polymerise by forming phosphodiester (covalent) bonds between
carbon 3' of the sugar and an oxygen atom of the phosphate.
This is a condensation polymerisation reaction.
The bases do not take part in the polymerisation, so there is a sugar-phosphate
backbone with the bases extending off it. This means that the nucleotides can
join together in any order along the chain. Two nucleotides form a dinucleotide,
three form a trinucleotide, a few form an oligonucleotide, and many form a
polynucleotide.
A polynucleotide has a free phosphate group at one end, called the 5' end
because the phosphate is attached to carbon 5' of the sugar, and a free OH
group at the other end, called the 3' end because it's on carbon 3' of the sugar.
The terms 3' and 5' are often used to denote the different ends of a DNA
molecule.
3.3.4 DNA Structure
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3.3.4 Explain how a DNA double helix is formed using complementary base pairing and hydrogen
bonding.
Orange book: pg. 57
Green book: pg. 35
To do:
Draw a double stranded diagram of DNA to show complementary base pairing with the correct
number of hydrogen bonds.
Annotate the diagram using the points below.
Structure of DNA
The three-dimensional structure of DNA was discovered in 1953 by Watson and Crick in
Cambridge, using experimental data of Wilkins and Franklin in London, for which work they won a
Nobel prize. The main features of the structure are:

DNA is double-stranded, so there are two polynucleotide stands alongside each other. The
strands are antiparallel, i.e. they run in opposite directions.

The two strands are wound round each other to form a double helix.

The two strands are joined together by hydrogen bonds between the bases. The bases
therefore form base pairs, which are like rungs of a ladder.

The base pairs are specific. A only binds to T (remember ‘At’), and C only binds to G (and G
with C). These are called complementary base pairs. This means that whatever the sequence
of bases along one strand, the sequence of bases on the other stand must be complementary
to it.
3.3.5 Drawing DNA
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3.3.5 Draw and label a simple diagram of the molecular structure of DNA.
Orange book: pg. 57
Green book: pg. 35
To do
You have already done this in previous objectives so by now you should be able to draw and label
the structure of DNA to show:

complementary base pairing

hydrogen bonding

double strand (anti-parallel)

covalent bonds

nucleotides

phosphate

sugar

bases

phosphate-sugar backbone
* Extra
Your syllabus does not ask you to distinguish between RNA and DNA, however the following
table will help you as we go onto the HL section related to this topic.
Comparison of DNA and RNA
Characteristic
DNA
RNA
sugar present
Deoxyribose
Ribose
Structure
Double helix
Single Strand
Adenine (A) present
✔
✔
Thymine (T) present
✔
X
Uracil (U) present
X
✔
Cytosine (C) present
✔
✔
Guanine (G) present
✔
✔
HW3: DNA Questions (26 Marks)
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1. Complete the table to show three differences between the structure of DNA and RNA. (3)
Structure of DNA
Structure of RNA
1.
1.
2.
2.
3.
3.
2. Read through the following account of the structure of deoxyribonucleic acid (DNA), then
write on the dotted lines the most appropriate word or words to complete the account. (5)
DNA is a molecule consisting of a long chain of nucleotides, which are joined together by
................................... reactions. Each nucleotide in DNA consists of a nitrogenous
base, a phosphate group and ................................... .The nitrogenous base may be
adenine, guanine, cytosine or .................................... . A molecule of DNA is made up
of two polynucleotide chains coiled into a ................................... . The two chains are
held together by ................................... bonds between the nitrogenous bases
3. The diagram shows part of a molecule of DNA
(a) Complete the diagram with the first letters of the appropriate complementary base. (1)
(b) What is represented by:
(i) the part of the molecule in box B; (1)
(ii) the dotted lines between the complementary base pairs? (1)
4. The table shows the percentage of different bases in DNA from different organisms.
Source of
DNA
Adenine %
Guanine %
Thymine %
Cytosine %
Human
30
20
30
20
Rat
28
22
28
22
Yeast
31
19
31
19
Turtle
28
22
28
22
E.coli
24
Salmon
29
21
29
21
Sea urchin
33
17
33
17
(a) What information about the ratios of different bases in DNA can you work out from the
table? (2)
(b) Give the results that you would expect for DNA from the E.coli bacterium. Explain how you
arrived at your answer. (3)
(c) Turtles have the same percentages of the four different bases as rats. Explain why they
can still be very different animals. (1)
5. The table below shows the percentage of different bases in the DNA from a virus.
Adenine %
Guanine %
Thymine %
Cytosine %
25
24
33
18
(a) Describe how the ratios of the different bases in this virus differ from those in the first
table. (1)
(b) The structure of the DNA in this virus is not the same as DNA in other organisms. Suggest
what this difference in DNA structure might be. (1)
(c) The diagram shows the structure of a DNA nucleotide.
Name the parts of the nucleotide labelled A and Y. (2)
6. The table shows the percentage composition of bases in the DNA of cattle and octopus.
Organism
Adenine
Cattle
29
Cytosine
Guanine
21
Thymine
Octopus
33
33
(a) Use your knowledge of the structure of DNA to calculate the missing values and complete
the table above. (1)
(b) Explain your answer. (2)
(c) Describe two differences between the structure of DNA and RNA. (2)