Head to www.savemyexams.

com for more awesome resources

CIE A Level Biology Your notes

6.1 Structure of Nucleic Acids & Replication of DNA

Contents
Nucleotides
The Structure of DNA
Semi-Conservative DNA Replication
The Structure of RNA

Page 1 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Nucleotides
Your notes
Nucleotide Structure
Nucleic acids such as DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are macromolecules
Like proteins (polypeptides) and carbohydrates (polysaccharides), these nucleic acids are polymers
This means they are made up of many similar, smaller molecules (known as subunits or monomers)
joined into a long chain
The subunits that make up DNA and RNA are known as nucleotides
Therefore DNA and RNA can also be known as polynucleotides

Nucleotides
Nucleotides are made up of three components:
A nitrogen-containing base (also known as a nitrogenous base)
A pentose sugar (containing 5 carbon atoms)
A phosphate group
Nucleotide Structure Diagram

The basic structure of a nucleotide

Nucleotide Structure Table

Properties DNA RNA

Page 2 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Pentose sugar Deoxyribose Ribose

Your notes

Adenine (A) Adenine (A)

Thymine (T) Uracil (U)
Bases
Cytosine (C) Cytosine (C)
Guanine (G) Guanine (G)

Double-stranded
Number of strands Single-stranded
(double helix)

Nucleotides in DNA & RNA Diagram

Page 3 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Your notes

There is much overlap of the nucleotides found in DNA and RNA, the only difference is that RNA contains
uracil (U) instead of thymine (T)
ATP
Adenosine triphosphate (ATP) is the energy-carrying molecule that provides the energy to drive many
processes inside living cells
ATP is another type of nucleic acid and hence it is structurally very similar to the nucleotides that make
up DNA and RNA
It is a phosphorylated nucleotide

Page 4 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Adenosine (a nucleoside) can be combined with one, two or three phosphate groups
One phosphate group = adenosine monophosphate (AMP)
Two phosphate groups = adenosine diphosphate (ADP) Your notes
Three phosphate groups = adenosine triphosphate (ATP)
ATP Structure Diagram

The structure of AMP, ADP and ATP

Page 5 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Exam Tip
Your notes
Don’t worry – you are not expected to know the structural formulae for the nucleotides that make up
DNA and RNA or AMP, ADP and ATP (as in the diagram above)! You just need to learn the different
groups that they are made up of (phosphate groups, pentose sugars and nitrogenous
bases).Remember that adenine is a nitrogenous base whereas adenosine is a nucleoside (a base –
adenine, attached to a pentose sugar).

Page 6 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Purines & Pyrimidines

The nitrogenous base molecules that are found in the nucleotides of DNA (A, T, C, G) and RNA (A, U, C, Your notes
G) occur in two structural forms: purines and pyrimidines
The bases adenine and guanine are purines
This means that they have a double-ring structure
The bases cytosine, thymine, and uracil are pyrimidines
These bases have a single-ring structure
Purines & Pyrimidines Diagram

Page 7 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Your notes

The molecular structures of purines and pyrimidines are slightly different

Exam Tip
You don’t need to know the structural formulae of these bases, just which are purines and which are
pyrimidines.

Page 8 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

The Structure of DNA

Your notes
DNA Structure
The nucleic acid DNA is a polynucleotide – it is made up of many nucleotides bonded together in a
long chain

A DNA nucleotide
DNA molecules are made up of two polynucleotide strands lying side by side, running in opposite
directions – the strands are said to be antiparallel
Each DNA polynucleotide strand is made up of alternating deoxyribose sugars and phosphate groups
bonded together to form the sugar-phosphate backbone. These bonds are covalent bonds known
as phosphodiester bonds
The phosphodiester bonds link the 5-carbon of one deoxyribose sugar molecule to the
phosphate group from the same nucleotide, which is itself linked by another phosphodiester bond
to the 3-carbon of the deoxyribose sugar molecule of the next nucleotide in the strand
Each DNA polynucleotide strand is said to have a 3’ end and a 5’ end (these numbers relate to
which carbon on the pentose sugar could be bonded with another nucleotide)
As the strands run in opposite directions (they are antiparallel), one is known as the 5’ to 3’ strand
and the other is known as the 3’ to 5’ strand

Page 9 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

The nitrogenous bases of each nucleotide project out from the backbone towards the interior of the
double-stranded DNA molecule
Your notes
DNA Polynucleotide Strand Diagram

A single DNA polynucleotide strand showing the positioning of the ester bonds
Hydrogen bonding

Page 10 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

The two antiparallel DNA polynucleotide strands that make up the DNA molecule are held together by
hydrogen bonds between the nitrogenous bases
These hydrogen bonds always occur between the same pairs of bases: Your notes
The purine adenine (A) always pairs with the pyrimidine thymine (T) – two hydrogen bonds are
formed between these bases
The purine guanine (G) always pairs with the pyrimidine cytosine (C) – three hydrogen bonds are
formed between these bases
This is known as complementary base pairing
These pairs are known as DNA base pairs
Hydrogen Bonding in DNA Diagram

A section of DNA – two antiparallel DNA polynucleotide strands held together by hydrogen bonds
Double helix
DNA is not two-dimensional as seen in the diagram above

Page 11 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

DNA is described as a double helix

This refers to the three-dimensional shape that DNA molecules form
Your notes
DNA Double Helix Diagram

DNA molecules form a three-dimensional structure known as a DNA double helix

Page 12 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Exam Tip
Your notes
Make sure you can name the different components of a DNA molecule (sugar-phosphate backbone,
nucleotide, complementary base pairs, phosphodiester bonds, hydrogen bonds) and make sure you
are able to locate these on a diagram.You must know how many hydrogen bonds occur between the
different base pairs.Remember that the bases are complementary so the number of A = T and C = G, as
you could be asked to determine how many bases are present in a DNA molecule if given the number
of one of the bases.

Page 13 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Semi-Conservative DNA Replication

Your notes
Semi-Conservative DNA Replication
DNA replication occurs in preparation for mitosis when a parent cell divides to produce two genetically
identical daughter cells
This is because each daughter cell contains the same number of chromosomes as the parent cell,
therefore the number of DNA molecules in the parent cell must be doubled before mitosis takes
place
DNA replication occurs during the S phase of the cell cycle
This occurs during interphase when a cell is not dividing
The hydrogen bonds between the base pairs on the two antiparallel polynucleotide DNA strands are
broken
This ‘unzips’ or unwinds the DNA double helix to form two single polynucleotide DNA strands
Each of these single polynucleotide DNA strands acts as a template for the formation of a new strand
– the original strand and the new strand then join together to form a new DNA molecule
This method of replicating DNA is known as semi-conservative replication because half of the original
DNA molecule is kept (conserved) in each of the two new DNA molecules
Semi-conservative replication was shown to be the method of replication by Meselson and Stahl in
1958.
They used E. coli (a bacteria) and two nitrogen isotopes, a heavy form 15N and the ‘normal’ form 14N,
to demonstrate how the density of DNA changes over generations as the 15N isotope was replaced
with the 14N isotope
Semi-conservative Replication of DNA Diagram

Page 14 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Your notes

Semi-conservative replication of DNA means that half of the original DNA molecule is conserved in each
new DNA molecule

Page 15 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

DNA Polymerase
In the nucleus, there are free nucleotides to which two extra phosphates have been added Your notes
These free nucleotides with three phosphate groups are known as nucleoside triphosphates or
‘activated nucleotides’
The extra phosphates activate the nucleotides, enabling them to take part in DNA replication
The bases of the free nucleoside triphosphates align with their complementary bases on each of the
template DNA strands
The enzyme DNA polymerase synthesises new DNA strands from the two template strands
It does this by catalysing condensation reactions between the deoxyribose sugar and phosphate
groups of adjacent nucleotides within the new strands
This creates the sugar-phosphate backbone of the new DNA strands
DNA polymerase cleaves (breaks off) the two extra phosphates and uses the energy released to
create the phosphodiester bonds (between adjacent nucleotides)
Hydrogen bonds then form between the complementary base pairs of the template and new DNA
strands
DNA Replication Diagram

Page 16 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Your notes

Page 17 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Your notes

Nucleotides are bonded together by DNA polymerase to create new complementary DNA strands
Leading & lagging strands
DNA polymerase can only add new DNA nucleotides in the 5’ to 3’ direction, so the new DNA strand is
built from its 5' end towards its 3' end
This is because DNA polymerase is an enzyme with a specific active site, so can only attach to the
3’ end of the original strand and move towards its 5' end
On one of the DNA template strands the DNA polymerase enzyme can move continuously towards the
replication fork as the DNA molecule is unzipped, so the new strand will be produced in one long piece
The strand that DNA polymerase synthesises continuously in this way is known as the leading
strand

Page 18 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

On the other strand, which is antiparallel to the strand described above, DNA polymerase moves away
from the replication fork, meaning that the new DNA is synthesised in short segments as the new
sections of the template strand are exposed Your notes
The strand in which DNA is synthesised in short segments is known as the lagging strand
The short segments are known as Okazaki fragments
A second enzyme, DNA ligase, is needed to join these short segments together to form a
continuous new DNA strand
Leading & lagging strands diagram

Page 19 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Your notes

The synthesis of the leading and lagging strands occurs slightly differently due to the fact that DNA
polymerase can only add nucleotides in a 5' to 3' direction

Page 20 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Exam Tip
Your notes
Take note that there are other enzymes that are also involved with DNA replication, but you only need
to know about the roles of DNA polymerase and DNA ligase for exam purposes.

Page 21 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

The Structure of RNA

Your notes
RNA Structure
Like DNA, the nucleic acid RNA (ribonucleic acid) is a polynucleotide – it is made up of many
nucleotides linked together in a long chain
Like DNA, RNA nucleotides contain the nitrogenous bases adenine (A), guanine (G) and cytosine (C)
Unlike DNA, RNA nucleotides never contain the nitrogenous base thymine (T) – in place of this they
contain the nitrogenous base uracil (U)
Unlike DNA, RNA nucleotides contain the pentose sugar ribose (instead of deoxyribose)

Page 22 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Your notes

An RNA nucleotide compared with a DNA nucleotide

Unlike DNA, RNA molecules are only made up of one polynucleotide strand (they are single-stranded)

Page 23 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Each RNA polynucleotide strand is made up of alternating ribose sugars and phosphate groups linked
together, with the nitrogenous bases of each nucleotide projecting out sideways from the single-
stranded RNA molecule Your notes
The sugar-phosphate bonds (between different nucleotides in the same strand) are covalent bonds
known as phosphodiester bonds
These bonds form what is known as the sugar-phosphate backbone of the RNA polynucleotide
strand
The phosphodiester bonds link the 5-carbon of one ribose sugar molecule to the phosphate
group from the same nucleotide, which is itself linked by another phosphodiester bond to the 3-
carbon of the ribose sugar molecule of the next nucleotide in the strand
An example of an RNA molecule is messenger RNA (mRNA), which is the transcript copy of a gene that
encodes a specific polypeptide. Two other examples are transfer RNA (tRNA) and ribosomal RNA
(rRNA)
mRNA Structure Diagram

Page 24 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
 Head to www.savemyexams.com for more awesome resources

Your notes

Messenger RNA (mRNA) provides a good example of the structure of RNA

Exam Tip
You need to know the difference between DNA and RNA molecules (bases, number of strands,
pentose sugar present).

Page 25 of 25

© 2015-2024 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers