2.3 Biology

Head to savemyexams.
com for more awesome resources
YOUR NOTES
AS Biology OCR 
2.3 Nucleotides & Nucleic Acids
CONTENTS
2.3.1 Nucleotides & Phosphodiester Bonds
2.3.2 Phosphorylated Nucleotides
2.3.3 DNA: Structure
2.3.4 DNA Purification
2.3.5 DNA Replication
2.3.6 The Genetic Code
2.3.7 Transcription
2.3.8 Translation
Page 1 of 34
© 2015-2023 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
Head to savemyexams.com for more awesome resources
2.3.1 Nucleotides & Phosphodiester Bonds YOUR NOTES


Nucleotides
DNA and RNA are nucleic acids: polymers that are made up of many repeating units
(monomers) called nucleotides
Each nucleotide is formed from:
A pentose sugar (a sugar with 5 carbon atoms)
A nitrogen-containing organic base
A phosphate group
The basic structure of a nucleotide

DNA nucleotides
The components of a DNA nucleotide are:
A deoxyribose sugar with hydrogen at the 2' position
A phosphate group
One of four nitrogenous bases - adenine (A), cytosine(C), guanine(G) or thymine(T)
RNA nucleotides
The components of an RNA nucleotide are:
A ribose sugar with a hydroxyl (OH) group at the 2' position
A phosphate group
One of four nitrogenous bases - adenine (A), cytosine(C), guanine(G) or uracil (U)
The presence of the 2' hydroxyl group makes RNA more susceptible to hydrolysis
This is why DNA is the storage molecule and RNA is the transport molecule with a
shorter molecular lifespan
Page 2 of 34
YOUR NOTES

An RNA nucleotide (top) compared with a DNA nucleotide (bottom)

Purines & pyrimidines
The nitrogenous base molecules that are found in the nucleotides of DNA (A, T, C, G) and
RNA (A, U, C, G) occur in two structural forms: purines and pyrimidines
The bases adenine and guanine are purines – they have a double ring structure
The bases cytosine, thymine and uracil are pyrimidines – they have a single ring structure
Page 3 of 34
YOUR NOTES

Page 4 of 34
YOUR NOTES

Page 5 of 34
YOUR NOTES

The molecular structures of purines and pyrimidines are slightly different

Nucleotide Structure Table
 Exam Tip
Although DNA and RNA nucleotides are very similar, make sure you know the key
differences between them: unlike DNA, RNA nucleotides never contain the
nitrogenous base thymine (in place of this they contain the nitrogenous base
uracil) and unlike DNA, RNA nucleotides contain the pentose sugar ribose (instead
of deoxyribose).You don’t need to know the structural formulae of the bases, just
which are purines and which are pyrimidines.
Page 6 of 34
Phosphodiester Bond YOUR NOTES

DNA and RNA are polymers (polynucleotides), meaning that they are made up of many 
nucleotides joined together in long chains
Separate nucleotides are joined together via condensation reactions
These condensation reactions occur between the phosphate group of one
nucleotide and the pentose sugar of the next nucleotide
A condensation reaction between two nucleotides forms a phosphodiester bond
It is called a phosphodiester bond because it consists of a phosphate group and two
ester bonds
The chain of alternating phosphate groups and pentose sugars produced as a result of
many phosphodiester bonds is known as the sugar-phosphate backbone (of the DNA or
RNA molecule)
As the synthesis of polynucleotides requires the formation of phosphodiester bonds,
the same is true for the reverse process: the breakdown of polynucleotides requires the
breakage of phosphodiester bonds
A section of a single polynucleotide strand showing a phosphodiester bond (and the

positioning of the two ester bonds and the phosphate group that make up the
phosphodiester bond)
 Exam Tip
In condensation reactions, a molecule of water is released. In hydrolysis reactions, a
molecule of water is added.
Page 7 of 34
2.3.2 Phosphorylated Nucleotides YOUR NOTES


Structure of ATP & ADP
All organisms require a constant supply of energy to maintain their cells and stay alive
In all organisms this energy is required for:
Anabolic reactions (building larger molecules from smaller molecules)
Moving substances across the cell membrane or moving substances within the cell
In animals energy is also required for:
Muscle contraction – to coordinate movement at the whole-organism level
The conduction of nerve impulses
In all known forms of life, ATP from respiration is used to transfer energy in all energy-
requiring processes in cells
This is why ATP is known as the universal energy currency
Adenosine Triphosphate (ATP) is a nucleotide
The monomers of DNA and RNA are also nucleotide
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
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)
Three phosphate groups = adenosine triphosphate (ATP)
Page 8 of 34
YOUR NOTES

The structure of AMP, ADP and ATP
 Exam Tip
Don’t worry – you are not expected to know the structural formulae for the
nucleotides that make up AMP, ADP and ATP (as in the diagram above)! You just need
to learn the different groups that they are made up of ( pentose sugars and
nitrogenous bases and how many phosphate groups,).Remember that adenine is a
nitrogenous base whereas adenosine is a nucleoside (a base – adenine, attached
to a pentose sugar).
Page 9 of 34
2.3.3 DNA: Structure 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
The nitrogenous bases of each nucleotide project out from the backbone towards the
interior of the double-stranded DNA molecule
Page 10 of 34
YOUR NOTES

A single DNA polynucleotide strand showing the positioning of the ester bonds
Hydrogen bonding
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:
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 process is known as complementary base pairing and the pairs are known as
complementary base pairs
Page 11 of 34
YOUR NOTES

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
DNA is described as a double helix (this refers to the three-dimensional shape formed by
the twisting of the DNA molecule)
Page 12 of 34
YOUR NOTES

DNA molecules form a three-dimensional structure known as a DNA double helix
 Exam Tip
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 34
2.3.4 DNA Purification YOUR NOTES


DNA Purification
Practical investigations can be conducted to purify (isolate) DNA via the process of
precipitation
Isolating DNA from cells is an essential starting point for a huge range of other
investigations and so is a key research technique in the field of molecular biology
A common method used to isolate DNA is known as the 'Marmur preparation'
The method is derived from the work of Julius Marmur (1926-1996), an American
molecular biologist who made significant contributions to DNA research
The Marmur preparation involves three basic steps:
Breaking (lysing) the cells and disrupting the nuclear membranes to release the DNA
Using enzymes to denature and remove the proteins (histones) associated with the
DNA
Precipitating the DNA using an organic solvent (e.g. ethanol)
Example practical investigation: extracting DNA from onions
Onions are good to use for this investigation as their cells contain a relatively large amount
of DNA
Fruits that also have relatively large amounts of DNA in their cells, such as strawberries,
bananas and kiwis, can also be used
Equipment
Plastic syringe (1 cm³)
Plastic funnel
2 × beakers (250 cm³)
2 × Test tubes
Stirrer (e.g. stirring rod or plastic spoon)
Chopping board
Knife (for chopping onion)
Onion
Washing-up liquid (10 cm³)
Ice-cold ethanol (10 cm³)
Protease enzyme (2-3 drops)
Coffee filter paper (laboratory filter paper not suitable as the liquid takes too long to pass
through)
Water bath (60 °C)
Ice-water bath
Blender or liquidiser
Method
Place the ethanol in a freezer 24 hours before starting the investigation
The ethanol must be ice-cold, it is key to the success of the investigation
Cut up the onion into small pieces (5 mm × 5 mm)
Page 14 of 34
Add the washing-up liquid to 90 cm³ of tap water in a beaker YOUR NOTES
Add some of the onion pieces to the beaker 
Place the beaker in a water bath at 60 °C for 15 minutes
The detergent (washing-up liquid) and the heat disrupt the phospholipid bilayer of the
onion cell membranes and nuclear membranes, releasing the DNA
The heat also denatures enzymes released from the cell that would otherwise begin to
digest the DNA
Cool the mixture in an ice-water bath for 5 minutes, stirring it continually
Lowering the temperature prevents the DNA itself from breaking down, which would
occur if the high temperature from the previous step was maintained
Continual stirring ensures the whole mixture is cooled
Pour the mixture into a blender and blend for 5 seconds
Blending breaks down the cell walls and cell membranes of the onion cells even
further, releasing more DNA
The mixture is only blended for a very short time to ensure the DNA strands themselves
are not broken apart
Using the filter paper, filter the mixture into another beaker
Filtering removes cell debris and membrane fragments
The filtrate now contains the DNA and its associated proteins
Pour 10 cm³ of the filtrate into a test tube and add 2-3 drops of protease enzyme, mixing
well
The protease denatures and removes the proteins, leaving just the DNA
Carefully add the ice-cold ethanol to the test tube and wait 2-3 minutes
Nucleic acids are insoluble in ice-cold ethanol and so the DNA forms a precipitate
(white layer) at the top of the test tube mixture
Results
The DNA in the resulting white precipitate can now be extracted and used for analysis or in
further investigations
Page 15 of 34
YOUR NOTES

Page 16 of 34
YOUR NOTES

A method for isolating and extracting DNA from onion cells
Page 17 of 34
2.3.5 DNA Replication YOUR NOTES


Semi-conservative Replication of DNA
Before a (parent) cell divides, it needs to copy the DNA contained within it
Doubling the DNA ensures that the two new (daughter) cells produced will both receive
full copies of the parental DNA
The DNA is copied via a process known as semi-conservative replication (semi = half)
The process is called this because in each new DNA molecule produced, one of the
polynucleotide DNA strands (half of the new DNA molecule) is from the original DNA
molecule being copied
The other polynucleotide DNA strand (the other half of the new DNA molecule) has to
be newly created by the cell
Therefore, the new DNA molecule has conserved half of the original DNA and then
used this to create a new strand
The importance of retaining one original DNA strand
Retaining one original DNA strand ensures there is genetic continuity (i.e. genetic
information is conserved) between generations of cells
In other words, it ensures that the new cells produced during cell division inherit all their
genes from their parent cells
This is important because cells in our body are replaced regularly and therefore we need
the new cells to be able to do the same role as the old ones
Replication of DNA and cell division also occurs during growth
Semi-conservative replication
DNA replication occurs in preparation for mitosis, when a parent cell divides to produce
two genetically identical daughter cells – as each daughter cell contains the same number
of chromosomes as the parent cell, 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 (which occurs during
interphase, when a cell is not dividing)
The enzyme helicase unwinds the DNA double helix by breaking the hydrogen bonds
between the base pairs on the two antiparallel polynucleotide DNA strands 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 made from free nucleotides that are attracted to the exposed DNA bases by
base pairing
The new nucleotides are then joined together by the enzyme DNA polymerase which
catalyses condensation reactions to form a new strand
The original strand and the new strand join together through hydrogen bonding between
base pairs to form the 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
Page 18 of 34
YOUR NOTES

Semi-conservative replication of DNA

DNA polymerase
In the nucleus, there are free nucleotides which contain three phosphate groups
These nucleotides 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
Page 19 of 34
The enzyme DNA polymerase synthesises new DNA strands from the two template YOUR NOTES
strands 
It does this by catalysing condensation reactions between the deoxyribose sugar and
phosphate groups of adjacent nucleotides within the new strands, creating 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
Page 20 of 34
YOUR NOTES

Page 21 of 34
YOUR NOTES

Nucleotides are bonded together by DNA polymerase to create the new complementary
DNA strands
Mutations
The replicated DNA molecules must be an exact copy of the parent DNA molecule,
therefore the formation of the complementary strands must be a highly accurate process
Although the process is astonishingly accurate considering it is happening constantly in
cells and at a considerable speed, occasional mistakes occur in the form of:
Bases being inserted into the complementary strand in the wrong order
An extra base being inserted by accident
A base being left out by accident
These mistakes in the process of semi-conservative replication of DNA result in the
occurrence of random, spontaneous mutations (i.e. errors in the genetic code)
 Exam Tip
Make sure you don’t confuse ‘parent cell’ with ‘parent organism’. A parent cell is any
cell in the body that divides into two cells and the terminology is used to refer to the
‘original’ cell that the DNA came from before it was split and replicated semi-
conservatively.
Page 22 of 34
2.3.6 The Genetic Code YOUR NOTES


Nature of the Genetic Code
A gene is a sequence of nucleotides that forms part of a DNA molecule (one DNA molecule
contains many genes)
This sequence of nucleotides (the gene) codes for the production of a specific
polypeptide (protein)
Protein molecules are made up of a series of amino acids bonded together
The shape and behaviour of a protein molecule depends on the exact sequence of these
amino acids (the initial sequence of amino acids is known as the primary structure of the
protein molecule)
The genes in DNA molecules, therefore, control protein structure (and as a result, protein
function) as they determine the exact sequence in which the amino acids join together
when proteins are synthesised in a cell
A gene is a sequence of nucleotides that codes for the production of a specific protein
molecule (polypeptide)
The triplet code
The sequence of DNA nucleotide bases found within a gene is determined by a triplet
(three-letter) code
Each sequence of three bases (i.e. each triplet of bases) in a gene codes for one amino
acid
These triplets codes for different amino acids – there are 20 different amino acids that cells
use to make up different proteins
Page 23 of 34
For example: YOUR NOTES

CAG codes for the amino acid valine 
TTC codes for the amino acid lysine
GAC codes for the amino acid leucine
CCG codes for the amino acid glycine
Some of these triplets of bases code for start (TAC – methionine) and stop signals
These start and stop signals tell the cell where individual genes start and stop
As a result, the cell reads the DNA correctly and produces the correct sequences of
amino acids (and therefore the correct protein molecules) that it requires to function
properly
The genetic code is non-overlapping
Each base is only read once in which codon it is part of
There are four bases, so there are 64 different codons (triplets) possible (43 = 64), yet there
are only 20 amino acids that commonly occur in biological proteins
This is why the code is said to be degenerate: multiple codons can code for the same
amino acids
The degenerate nature of the genetic code can limit the effect of mutations
The genetic code is also universal, meaning that almost every organism uses the same
code (there are a few rare and minor exceptions)
The same triplet codes code for the same amino acids in all living things (meaning that
genetic information is transferable between species)
The universal nature of the genetic code is why genetic engineering (the transfer of
genes from one species to another) is possible
Codons and anticodons
Once mRNA has been formed and left the nucleus it moves to the ribosomes where it can
as a template for protein synthesis
Each triplet within the mRNA code is described as a codon
The tRNA molecules that transfer amino acids possess anticodons which are
complementary to the codons on mRNA
Page 24 of 34
YOUR NOTES

A DNA molecule with the triplet code for the mRNA codons of the start amino acid
(methionine) and valine
Page 25 of 34
Exam Tip YOUR NOTES

 Remember – each chromosome in a human cell nucleus contains one very long DNA

molecule. This DNA molecule is made up of thousands of specific nucleotide
sequences called genes that code for specific proteins. Even though these genes
are all found within the same DNA molecule and are therefore all linked up, the cell
knows where individual genes start and stop. This ensures the cell reads the DNA
correctly and can produce the correct protein molecules that it requires to function
properly.
Page 26 of 34
2.3.7 Transcription YOUR NOTES


Transcription
A gene is a sequence of nucleotide bases in a DNA molecule that codes for the
production of a specific sequence of amino acids, that in turn make up a specific
polypeptide (protein)
This process of protein synthesis occurs in two stages:
Transcription – DNA is transcribed and an mRNA molecule is produced
Translation – mRNA (messenger RNA) is translated and an amino acid sequence is
produced
Transcription
This stage of protein synthesis occurs in the nucleus of the cell
Part of a DNA molecule unwinds (the hydrogen bonds between the complementary base
pairs break)
The exposed gene can then be transcribed (the gene from which a particular polypeptide
will be produced)
A complimentary copy of the code from the gene is made by building a single-stranded
nucleic acid molecule known as mRNA (messenger RNA)
Free RNA nucleotides pair up (via hydrogen bonds) with their complementary (now
exposed) bases on one strand (the template strand) of the ‘unzipped’ DNA molecule
The sugar-phosphate groups of these RNA nucleotides are then bonded together (by
phosphodiester bonds) by the enzyme RNA polymerase to form the sugar-phosphate
backbone of the mRNA molecule
When the gene has been transcribed (when the mRNA molecule is complete), the hydrogen
bonds between the mRNA and DNA strands break and the double-stranded DNA
molecule re-forms
The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope
Page 27 of 34
YOUR NOTES

The transcription stage of protein synthesis – DNA is transcribed and an mRNA molecule is
produced
The coding strand and the template strand
In the transcription stage of protein synthesis, free RNA nucleotides pair up with the
exposed bases on the DNA molecule
RNA nucleotides only pair with the bases on one strand of the DNA molecule
This strand of the DNA molecule is known as the template strand (or the transcribed
strand) and it is used to produce the mRNA molecule
The other strand is known as the coding strand (or the non-template or non-
transcribed strand)
RNA polymerase moves along the template strand in the 3' to 5' direction
This means that the mRNA molecule grows in the 5' to 3' direction
Because the mRNA is formed by complementary pairing with the DNA template strand, the
mRNA molecule contains the exact same sequence of nucleotides as the DNA coding
strand (although the mRNA will contain uracil instead of thymine)
Page 28 of 34
YOUR NOTES

The template strand of the DNA molecule is the one that is transcribed
 Exam Tip
Be careful: DNA polymerase is the enzyme involved in DNA replication, whereas RNA
polymerase is the enzyme involved in transcription – don’t get these confused!Make
sure you can also distinguish between the DNA coding strand and the DNA template
strand. The DNA template strand acts as a 'template' for the newly forming mRNA
strand. The mRNA has the same base sequence (and therefore the same sequence
of codons) as the DNA coding strand - the only difference being that the mRNA will
contain uracil instead of thymine.
Page 29 of 34
2.3.8 Translation YOUR NOTES


Translation
Translation occurs in the cytoplasm of the cell
After leaving the nucleus via a nuclear pore, the mRNA molecule attaches to a ribosome
In the cytoplasm, there are free molecules of tRNA (transfer RNA)
These tRNA molecules have a triplet of unpaired bases at one end (known as the
anticodon) and a region where a specific amino acid can attach at the other
There are about 20 different tRNA molecules, each with a specific anticodon and
specific amino acid binding site
The tRNA molecules bind with their specific amino acids (also in the cytoplasm) and bring
them to the mRNA molecule on the ribosome
The triplet of bases (anticodon) on each tRNA molecule pairs with a complementary triplet
(codon) on the mRNA molecule
Two tRNA molecules fit onto the ribosome at any one time, bringing the amino acid they
are each carrying side by side
A peptide bond is then formed (via a condensation reaction) between the two amino acids
This process continues until a ‘stop’ codon on the mRNA molecule is reached – this acts as
a signal for translation to stop and at this point the amino acid chain coded for by the mRNA
molecule is complete
The amino acid chain then forms the final polypeptide
Page 30 of 34
YOUR NOTES

The translation stage of protein synthesis – tRNA molecules bind with their specific amino
acids
Page 31 of 34
YOUR NOTES

Page 32 of 34
YOUR NOTES

Page 33 of 34
YOUR NOTES

The translation stage of protein synthesis – an amino acid chain is formed
 Exam Tip
Make sure you learn both stages of protein synthesis fully. Don’t forget –
transcription occurs in the nucleus but translation occurs in the cytoplasm!
Page 34 of 34

2.3 Biology

Uploaded by

Document Information

Original Description:

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

2.3 Biology

Uploaded by

Copyright:

Available Formats

Head to savemyexams.

com for more awesome resources

2.3 Nucleotides & Nucleic Acids

2.3.1 Nucleotides & Phosphodiester Bonds YOUR NOTES

The basic structure of a nucleotide

An RNA nucleotide (top) compared with a DNA nucleotide (bottom)

The molecular structures of purines and pyrimidines are slightly different

Phosphodiester Bond YOUR NOTES

A section of a single polynucleotide strand showing a phosphodiester bond (and the

2.3.2 Phosphorylated Nucleotides YOUR NOTES

The structure of AMP, ADP and ATP

2.3.3 DNA: Structure YOUR NOTES

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

2.3.4 DNA Purification YOUR NOTES

A method for isolating and extracting DNA from onion cells

2.3.5 DNA Replication YOUR NOTES

Semi-conservative replication of DNA

2.3.6 The Genetic Code YOUR NOTES

For example: YOUR NOTES

Exam Tip YOUR NOTES

2.3.7 Transcription YOUR NOTES

2.3.8 Translation YOUR NOTES

The translation stage of protein synthesis – an amino acid chain is formed

You might also like