124

Nucleic acids
Chapter 8
Polynucleotides
It is amazing to realise that until the middle
of the 20th century we did not even know that
DNA is the genetic material. Our DNA carries
the genetic code a set of instructions telling the
cell the sequence in which to link together amino
acids when proteins are being synthesised. Slight
diferences in the structure of these proteins
may result in slight diferences in our metabolic
reactions. Partly for this reason, we are all slightly
diferent from one another.
You probably know that DNA is a double
helix. A DNA molecule is made of two long
chains of nucleotide molecules, linked together
to form a twisted ladder. Each chain is called a
polynucleotide.
Figure 8.1 The components of a nucleotide in DNA.
deoxyribose organic bases
purine bases
pyrimidine bases
phosphate
adenine
thymine
adenine guanine
thymine cytosine
The structure of DNA
DNA stands for deoxyribonucleic acid. When it
was discovered, it was given the name nucleic acid
because it was mostly found in the nuclei of cells
and is slightly acidic.
Each nucleotide in a DNA molecule contains:

a phosphate group

the ve-carbon sugar, deoxyribose

an organic base.
Figure 8.1 shows the components of a nucleotide
in DNA. The base can be any one of four. These
are adenine, guanine, thymine and cytosine.
They are usually abbreviated to A, G, T and C.
Adenine and guanine each contain two rings in
their structure. They are known as purine bases.
Thymine and cytosine have only one ring. They are
known as pyrimidine bases.
Objectives
Background
e-Learning
Chapter 8: Nucleic acids
125
Figure 8.2 shows how these components are
linked in nucleotides and how the nucleotides
link together to form long chains called
polynucleotides.
You can see that the base in each nucleotide
sticks out sideways from the chain. In DNA, two
chains of nucleotides lie side by side, one chain
Figure 8.2 How nucleotides join to form a polynucleotide.
running one way and the other in the opposite
direction (Figure 8.3 and Figure 8.4). They are said
to be anti-parallel. The bases of one chain link up
with the bases of the other by means of hydrogen
bonds. The whole molecule twists to produce the
double helix shape.
The carbon atoms of
the ve-carbon sugar
are numbered. The top
phosphate is attached
to carbon 5, so is at
the 5 end. The bottom
phosphate is attached
to carbon 3, so is at the
3 end.
The direction of a polynucleotide
condensation
reaction
phosphate
nucleotide
ve-carbon
sugar
base
polynucleotide
5
3 2
4
1
5 end
3 end
Chapter 8: Nucleic acids
126
Figure 8.4 Hydrogen bonding joining the bases in DNA.
The key to the ability of DNA to hold and pass
on the code for making proteins in the cell is the
way in which these bases link up. There is just the
right amount of space for one large base a purine
to link with one smaller base a pyrimidine. And
the linking is even more particular than that. A can
only link with T, and C can only link with G. This
is called complementary base pairing.
The polynucleotide strands are held together
by hydrogen bonding between the bases.
hydrogen bonds between a TA
complementary base pair
3 end
3 end
5 end
5 end
G
T
C
A
Complementary base pairing ensures that the
code carried on a molecule of DNA can be copied
perfectly over and over again, so that it can be
passed down from cell to cell and from generation
to generation. It is also what enables the code on
the DNA to be used to instruct the protein-making
machinery in a cell to construct exactly the right
proteins. You will nd out much more about this if
you continue studying biology to A2 level.
Figure 8.3 The structure of DNA.
The two polynucleotide strands are twisted round forming a double helix.
antiparallel polynucleotide strands of DNA
3 end
3 end 5 end
5 end
Chapter 8: Nucleic acids
127
SAQ
1 One end of a DNA strand is called the 5
(ve prime) end, and the other is the 3 end.
Why are they given these
names?
Figure 8.6 Enzymes are involved in DNA replication.
Figure 8.5 DNA replication.
3 end
1 Hydrogen bonds
between the
bases are broken.
2 Free nucleotides
are present in
the nucleus.
3 Free nucleotides
pair up with
complementary
exposed bases.
5 There are now two
DNA molecules. Each
one contains one old strand
and one new one.
4 The new strand
is linked together.
DNA replication
We have seen that, before a cell divides by mitosis,
its DNA replicates to produce two copies. One
copy is passed on to each daughter cell. DNA
replication takes place during interphase of the cell
cycle (Chapter 3).
Figure 8.5 and Figure 8.6 show how DNA
replication takes place. This method is called semi-
conservative replication, because each of the new
DNA molecules is made of one old strand and one
new strand of DNA.
3 end
5 end
DNA helicase unwinds and
unzips the DNA by breaking the
hydrogen bonds between bases.
DNA polymerase links the
newly arrived nucleotides by
forming covalent bonds between
phosphates and sugars. It only
does this if the nucleotides are
correctly paired.
Answer
Extension
Chapter 8: Nucleic acids
128
The structure of RNA
DNA is not the only polynucleotide in a cell.
There are also polynucleotides which contain
the sugar ribose rather than deoxyribose. They
are therefore called ribonucleic acids, or RNA for
short. Figure 8.9 shows the structure of RNA.
RNA is generally single stranded, while DNA is
generally double stranded. Another diference
between them is that RNA always contains the
base uracil (U) instead of thymine.
While DNA stores the genetic information
in the nucleus of a cell, RNA is involved with
using that information to make proteins.
Figure 8.9 The structure of RNA.
Figure 8.7 The Human Genome Project has
worked out the base sequence in each human
chromosome.
RNA resembles
one polynucleotide
strand in DNA,
except that the
base uracil replaces
thymine and the
sugar is ribose.
U
G
C
A
ribose uracil
The role of DNA
DNA carries a code that is used by the cell when
making proteins. The sequence of bases in the
DNA molecules determines the sequence of amino
acids that are strung together when a protein
molecule is made on the ribosomes.
A length of DNA that codes for making one
polypeptide is called a gene. It is thought that there
are around 30 000 genes in our cells (Figure 8.7).
The code is read in groups of three letters
that is, triplets of bases. As we have seen, there are
four bases in a DNA molecule, A, T, C and G. A
sequence of three bases in a DNA molecule codes
for one amino acid (Figure 8.8).
Figure 8.8 How DNA codes for amino acid sequences in proteins.
These three bases
represent the amino
acid valine.
These three bases
represent the amino
acid glutamate.
If this part of the DNA is being used, a polypeptide chain
is made with the amino acid glutamate joined to valine.
Chapter 8: Nucleic acids
129
SAQ
2 Use a table, or a list of bullet points, to
summarise the diferences
between DNA and RNA.
Summary

DNA is deoxyribonucleic acid. It is a double-stranded molecule made up of two strands of
nucleotides.

A DNA nucleotide is made up of a phosphate group, a ve-carbon sugar called deoxyribose, and
a base. There are four bases in DNA adenine, guanine, cytosine and thymine. They are usually
abbreviated to A, G, C and T.

Adenine and guanine are purine bases. Cytosine and thymine are pyrimidine bases.

The nucleotides in a strand of DNA are linked to each other by strong covalent bonds between the
phosphate groups and deoxyribose. The phosphate groups bond to carbon 5 and to carbon 3 of the
deoxyribose ring. The end of the molecule where the phosphate is bonded to carbon 5 is called the 5
end, while the other is the 3 end.

The two strands of a DNA molecule are linked to each other by weak hydrogen bonds between the
bases. A always bonds with T, and C always bonds with G. A and T are linked by two hydrogen
bonds. C and G are linked by three hydrogen bonds.

The two strands of a DNA molecule run in opposite directions. They are said to be anti-parallel.
They twist around each other to form a double helix.

The DNA molecules in a cell nucleus are replicated before cell division takes place. First, the two
strands of the molecule are untwisted and unzipped. Free DNA nucleotides pair up with the exposed
bases on both strands. They are then linked together by the formation of bonds between their
deoxyribose and phosphate groups. This is catalsyed by the enzyme DNA polymerase. Two new
molecules are therefore formed, each identical to the original one. Each new molecule contains one
old strand and one new strand, so the process is called semi-conservative replication.

The sequence of bases in a DNA molecule codes for the sequence of amino acids in a protein to be
made on the ribosomes. Three bases code for one amino acid. A sequence of DNA nucleotides that
codes for one polypeptide is known as a gene.

RNA is ribonucleic acid. There are several kinds of RNA. Most are single stranded. They contain
the pentose sugar ribose, rather than deoxyribose. They contain the base uracil instead of thymine.

During protein synthesis, an RNA molecule is built up against one of the DNA strands in a gene.
The RNA then travels out of the nucleus to a ribosome, where its sequence of bases is used to
determine the sequence of amino acids in the polypeptide that is being constructed on the ribosome.
The sequence of bases on part of a DNA
molecule a gene is used to build an RNA
molecule with the complementary base sequence.
This RNA molecule then travels out into the
cytoplasm and attaches to a ribosome. Working
with other RNA molecules, the base sequence
is used to determine the sequence of amino
acids that are strung together to make a protein
molecule. The base sequence on the DNA therefore
determines the primary structure of the protein
that is made.
Answer
Extension
Glossary
Chapter 8: Nucleic acids
130
Questions
1 Figure 1 represents a nucleotide which forms part of a DNA
molecule.
a i Name A to C. [3]
ii State which part of the nucleotide contains nitrogen. [1]

During research into the mechanism of DNA replication,
bacteria were grown for many generations in a medium
containing only the heavy isotope of nitrogen,
15
N. This
resulted in all the DNA molecules containing only
15
N.
This is illustrated in Figure 2.



These bacteria were then grown in a medium containing only
light nitrogen,
14
N. After the time taken for the DNA to
replicate once, the DNA was analysed. The results are shown
in Figure 3.
b Explain how these data support the semi-conservative
hypothesis of DNA replication. [3]

The bacteria continued to grow in the light nitrogen,
14
N,
medium until the DNA had replicated once more. The DNA
molecules were analysed. The results are shown in Figure 4.
Figure 5 shows simple diagrams of DNA molecules,
indicating the nitrogen content of each.
Figure 1
A
B C
Figure 2
Figure 3
c With reference to Figure 5, select the letter or letters which
best represent the bacterial DNA in Figure 2, Figure 3
and Figure 4. [3]
The bacteria continued to grow in the light nitrogen,
14
N,
medium until the DNA had replicated once more. The DNA
molecules were analysed.
d Copy and complete the bar chart to the right to indicate
%

D
N
A

m
o
l
e
c
u
l
e
s
DNA
containing
14
N only
0
25
50
75
100
DNA
containing
15
N only
DNA
containing
14
N /
15
N
%

D
N
A

m
o
l
e
c
u
l
e
s
DNA
containing
14
N only
0
25
50
75
100
DNA
containing
15
N only
DNA
containing
14
N /
15
N
%

D
N
A

m
o
l
e
c
u
l
e
s
DNA
containing
14
N only
0
25
50
75
100
DNA
containing
15
N only
DNA
containing
14
N /
15
N
represents
DNA with
15
N
Key
represents
DNA with
1
N
the expected results of the composition of these DNA
molecules. [3]
OCR Biology AS (2801) January 2002 [Total 13]
%

D
N
A

m
o
l
e
c
u
l
e
s
DNA
containing
14
N only
0
25
50
75
100
DNA
containing
15
N only
DNA
containing
14
N /
15
N
Figure 4
Figure 5
A B C D E F
4
Answer