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B8 Nucleic Acids HL
Essential idea: DNA is the genetic
material that expresses itself by
controlling the synthesis of proteins
by the cell.
Nature of Science
 Scientific method—the discovery of the structure
of DNA is a good example of different approaches
to solving the same problem. Scientists used
models and diffraction experiments to develop the
structure of DNA. (1.3)
 Developments in scientific research follow
improvements in apparatus—double helix from Xray diffraction provides explanation for known
functions of DNA. (3.7)
Understandings
B.8.U1 Nucleotides are the condensation products of a pentose
sugar, phosphoric acid and a nitrogenous base—adenine (A), guanine
(G), cytosine (C), thymine (T) or uracil (U).
B.8.U2 Polynucleotides form by condensation reactions.
B.8.U3 DNA is a double helix of two polynucleotide strands held
together by hydrogen bonds.
B.8.U4 RNA is usually a single polynucleotide chain that contains
uracil in place of thymine, and a sugar ribose in place of deoxyribose.
B.8.U5 The sequence of bases in DNA determines the primary
structure of proteins synthesized by the cell using a triplet code,
known as the genetic code, which is universal.
B.8.U6 Genetically modified organisms have genetic material that
has been altered by genetic engineering techniques, involving
transferring DNA between species.
Applications and Skills
B.8.AS1 Explanation of the stability of DNA in terms of
the interactions between its hydrophilic and hydrophobic
components.
B.8.AS2 Explanation of the origin of the negative charge on
DNA and its association with basic proteins (histones) in
chromosomes.
B.8.AS3 Deduction of the nucleotide sequence in a
complementary strand of DNA or a molecule of RNA from a
given polynucleotide sequence.
B.8.AS4 Explanation of how the complementary pairing
between bases enables DNA to replicate itself exactly.
B.8.AS5 Discussion of the benefits and concerns of using
genetically modified foods.
Guidance
 Structures of the nitrogenous bases and ribose
and deoxyribose sugars are given in the data
booklet in section 34.
 Knowledge of the different forms of RNA is not
required.
 Details of the process of DNA replication are not
required.
 Limit expression of DNA to the concept of a
four-unit base code determining a twenty-unit
amino acid sequence. Details of transcription and
translation are not required.
Nucleic Acid
 Living cells contain two different types of nucleic
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acids
DNA (deoxyribose nucleic acid)
RNA (ribose nucleic acid)
Nucleic Acids are condensation polymers made up
of Nucleotides which contain three smaller types of
molecules that are covalently bound together under
enzyme control
Phosphate
Pentose sugar
Base
Nucleotides: Phosphate
 The phosphate group is a chemically reactive
functional group that allows new molecules to
be added via a condensation reaction.
 Hence, nucleotides can form long chains (linear
polymers).
 The phosphate groups are ionized and partially
responsible for the solubility of nucleic acids in
water
Phosphate
 Component 1 of a
nucleotide is the
phosphate
Phosphoric acid can dissociate in aqueous
solutions freeing H ions and leaving the
phosphate negatively charged
Pentose Sugar
 The second component, pentose sugar, is a 5-
carbon monosaccharide known as deoxyribose in
DNA and ribose in RNA
 These sugars are chemically reactive and are
involved in bonding different nucleotides together
via condensation reactions with –OH groups at
carbons 1 and 5
Pentose Sugar
 Component 2 of a
nucleotide is the
pentose sugar
Nucleic Acids: Base
 The base, the third component, is covalently
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bonded to the pentose sugar via the carbon atom in
position 1 of the ring.
Four different bases are found in DNA:
Adenine (A) Nitrogenous bases are derived from amines-derivatives of
by replacement of one or more H atoms by
Thymine (T) ammonia
organic groups
Guanine (G)
Cytosine (C)
Cells continuously synthesize nucleotides and these
form a ‘pool’ in the cytoplasm from which nucleotides
can be used by the cell for synthesizing DNA
Bases
 Component 3 of a nucleotide is the base present
Nucleic Acid
 Polymer chain of repeating nucleotides which consist
of a phosphate group, a pentose sugar and an organic
nitrogenous base.
 The sequence of the bases in DNA and RNA are the
key to storage of genetic information.
 Only a few simple nucleotides
 Adenine (A)
 Guanine (G)
 Cytosine (C)
A and G are purines with a double-ringed
structure.
 Thymine (T) C, T and U are pyrimidines with a single-ringed
structure.
 Uracil (U)
Components of Nucleic Acids
Components of Nucleic Acids
Purines
Two-ringed
structures
Components of Nucleic Acids
Pyrimidines
One-ringed
structures
Components of Nucleic Acids
Present in DNA
A, C, G, T
Components of Nucleic Acids
Present in RNA
A, C, G, U
Components of Nucleic Acids
Deoxyribose
The 5-carbon sugar
in DNA
Components of Nucleic Acids
Ribose
The 5-carbon sugar
in RNA
General Structure of a Nucleotide
Nitrogenous
Base
Phosphate
Group
5-Carbon
Sugar
Condensation Reaction
Ester Bond Using the
Condensation Reaction
A phosphoester bond is a bond between the
phosphorous atom of a phosphate group and an
oxygen atom.
Phosphodiester
Linkage Using
Condensation
Reaction
Phosphoester bond forms between
OH (the H is used) of C3 of one
nucleotide and OH (this OH is
used) of C5 of another nucleotide=
phosphodiester bonds (bonds
between two sugar groups and a
phosphate group
Putting them all together
 Nucleotides are formed from all three
components, a phosphate, pentose sugar, and base
 Many polynucleotide chains form by the condensation
reactions
So that bases can face each other and pair
Structure of
DNA Polymer
Primary Structure
Sequence of nucleotides
Syllabus Statement
Explain the double helical structure of DNA.
Double Helix
 Secondary Structure
 Two strands of nucleic acids that interact
through hydrogen bonding between bases
attached to the strands.
 Complementary Pairs
 A-T
 C-G
Hydrogen
Bonding
Only the
combination of a
purine with a
pyrimidine allows
the bases to be
close enough to
hydrogen bond.
DNA
 The DNA nucleotides are
linked together by
covalent bonds into a
single strand.
 The bonds between the
phosphate group and the
sugar are covalent. They
make up the “backbone”
of the DNA’s ladder
shape.
 The nitrogenous bases
are attached to the
sugar.
DNA Structure
 The double helix shape is
formed using complementary
base pairing and hydrogen
bonds.
 Adenine bonds with Thymine
and Cytosine bonds with
Guanine.
 Hydrogen bonds form in the
center of the helix. They
join the complementary base
pairs.
DNA Structure
 The double
helix forms
from two
nucleic acid
strands that
spiral around a
central axis.
Hydrogen Bonding and the
Double Helix
 The following slides answer the Nature of Science
points:
-different approaches (the use of models and diffraction)
to discover the structure of DNA
-developments in scientific research follow
improvements in apparatus=X ray diffraction provides
explanation for known functions of DNA
A1 Crick and Watson’s elucidation of the
structure of DNA using model-making
 http://www.nature.com/scitable/topicpage/discovery-of-dnastructure-and-function-watson-397
 Go to the website above and read the following
article answering the questions below
1. For each of the following scientists below write
down the contributions each made towards DNA
structure and how they made such discoveries.
- Friedrich Miescher
- Phoebus Levene
- Erwin Chargraff
- Rosalind Franklin and Maurice Wilkins
- James Watson and Frances Crick
Replication
Only certain pairings of bases are possible. Adenine always pairs with
thymine, and guanine always pairs with cytosine. Therefore, the two strands
of the double helix are complementary, each the predictable counterpart of
the other.
Since the two strands of DNA are complimentary, they can separate from
one another and each can serve as a template for building a new partner (if
you know the sequence of one DNA strand then you can easily figure out the
sequence of the other strand).
Thus, DNA replication is semi-conservative, with each of the two daughter
DNA molecules having one old strand derived from the parent and one newly
made strand.
The complementary base pairing results in the two daughter DNA molecules
being identical.
 Nitrogenous bases-mainly hydrophobic
 Phosphate groups-almost completely ionised
(negatively charged) at physiological pH 7.4 and are
hydrophilic
 Intermolecular bonds formed between hydrophilic
and hydrophobic parts of polynucleotide strand
stabilise DNA an make it resistant to chemical cleavage
Nucleosomes
 Analysis of chromosomes has shown that they are
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made up of DNA and protein.
The total length of DNA in a human cell is about 2.2
m.
To pack this into a nucleus means that the total length
must be shortened to about 0.2mm.
This means that the length is reduced by a factor of
about 8000, which needs good organisation.
DNA is wrapped around special proteins called histone
proteins forming a structure called a Nucleosome.
Nucleosomes
 A nucleosome consists of DNA wrapped around 8
histone proteins and a 9th histone protein to tie it off.
The negatively charged DNA is
attracted to the positively charged
proteins.
Histones are
highly alkaline proteins
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Histones contain a large proportion of
the positively charged (basic) amino
acids, lyseine and arginine in their
structure.
DNA is negatively charged due to the
phosphate groups on its backbone. These
result of these opposite charges is
strong attraction and therefore high
binding affinity between histones and
DNA.
Hydrogen bonding involving hydroxyl
amino acids in the histone peptide and
the phosphodiester backbone of DNA
and are also important in further
stabilizing the structure.
One of the advantages of histones
interacting mainly with the backbone of
DNA is it means the interaction is not
sequence dependent. This means that
despite an apparent preference of
histones to some sequences of DNA,
they are able to bind anywhere.
Nucleosome Organisation
 For DNA to
reduce its
length, coiling
and super coiling
of the chromatin
must occur.
 Nucleosomes are
an essential part
of this
organisation.
Ref: Advanced Biology, Roberts, Reiss & Monger
Nucleosome Organisation
Ref: Advanced Biology, Kent
Understandings
B.8.U4 RNA is usually a single polynucleotide chain
that contains uracil in place of thymine, and a sugar
ribose in place of deoxyribose.
DNA vs RNA
 Both DNA and RNA molecules are polynucleotides
 RNA is considerably shorter than DNA molecules
 In RNA, all of the nucleotides include ribose
 In RNA, bases are adenine cytosine (C), guanine (G),
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adenine (A), and uracil (U). (T only in rRNA)
In living cells, three main functional types of RNA, all
are directly involved in protein synthesis
Messenger RNA (mRNA)
Transfer RNA (tRNA) (single/double helix)
Ribosomal RNA (rRNA) (single/double helix)
Comparing Nucleic Acids
DNA
RNA
2 Strands
1 Strand
Thymine, Adenine,
Cytosine, Guanine
Uracil, Adenine,
Cytosine, Guanine
Deoxyribose sugar
Ribose sugar
Syllabus Statement
Describe the role of DNA as the repository of
genetic information, and explain its role in
protein synthesis.
Repository of Genetic
Information
 Role of DNA
 Reproduce itself
 Carry information which encodes the proteins in an
organism.
 The DNA is the genetic information that defines the
organism.
 Gene
 Section of a DNA molecule that codes for a protein.
 Contains many nucleotides with a specific sequence of
the four bases, A, C, G ant T.
 The sequence of bases in each gene specifies the
amino acid sequence of the protein.
Protein Synthesis
 20 Amino acids coded by triplets of DNA
 Transcription from DNA  messenger RNA
 Translation of mRNA  Amino Acid Sequence
Transcription, Translation
 DNA is the genetic material that an individual
inherits from its parents.
 It directs mRNA synthesis (transcription) and,
through mRNA, directs protein synthesis
(translation) using a triplet code.
 Transcription/ translation video
The Role of DNA
 The DNA molecules in the nucleus of the cell hold
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the genetic code for protein synthesis.
Each gene is responsible for the production of a
single protein
The genetic information is coded in DNA in the
form of a specific sequence of bases within a gene
The synthesis of proteins involves two steps
Transcription
Translation
Transcription
 RNA is a single-stranded molecule that is formed by
transcription from DNA
 The DNA molecule separates into two strands
(under enzyme control) to reveal its bases, as in
replication.
 BUT NOW its free ribonucleotides (and not
deoxyribonucleotides) that base-pair to it and form
an RNA molecule
 The RNA molecule, known as mRNA, is transported
out of the nucleus of the cell and attaches to a
cell organelle known as a ribosome.
Translation
 Ribosomes are formed from protein and RNA,
and are the sites at which proteins are
synthesized from amino acids.
 This process is called Translation
 Messenger RNA is responsible for converting the
genetic code of DNA into protein
The Triplet Code
 The primary structure of a protein consists of a chain
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of amino acids connected by peptide links (10 AA’s)
The structure of DNA is from four bases A,G,C,T
The code for an amino acid (called a codon) is a
sequence of 3 bases
There are then 64 (34) different ‘triplets’
Some amino acids are encoded by +1 codons
Of the 64 codons, 61 code for amino acids and three
act as ‘stop’ signals to terminate the protein synthesis
when the end of the polypeptide chain is reached
Translation and Ribosomes
 Protein synthesis takes place in ribosomes located in
the cytoplasm.
 One end of an mRNA molecule binds to a ribosome,
which moves along the mRNA strand three bases at a
time (next slide)
 Molecules of another type of RNA, called transfer
RNA (tRNA), bind to free amino acids in the
cytoplasm
 tRNA molecules carry specific AA’s, and have their
own base triplet, known as anticodon, which binds via
hydrogen bonding to the complementary codon
triplet on the mRNA.
Summary
Genetic Modified Foods
 Genetic modified foods (GM foods) are foods
produced from genetically modified organisms
that have had changes introduced into their DNA
through genetic engineering.
 Genetic engineering allows DNA to be transferred
from one species to another.
 An example is corn that has has been genetically
modified to express a protein taken from bacteria
that acts as a natural pesticide.
Activity
 Draw a table that outlines the Benefits and
Disadvantages of GM Foods.
 Research and read Benefits and Disadvantages
of GM Foods (Do not write)
 Write down what you can remember to complete
your table.
 Discuss your findings with the person next to you
(or in a group) and add to your table.
Benefits of GM Foods
 Increased crop yields: which could help by feeding
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more people in developing countries.
Improved Food Quality: a tomato was genetically
engineered to stay fresher for longer, extending shelf
life in the supermarket.
Increased resistance to disease or pests: thereby
reducing the use of pesticides.
Increased resistance to adverse weather: such as
droughts.
Engineered to have a high content of a specific
nutrient: that is lacking in the diet of a local
population group.
Concerns Over GM Foods
 The ability of a GM food to trigger an allergy in
humans: genes used in GM technology might be taken
from a food that causes allergies in certain people.
 Lack of information regarding the long term
effects of GM foods.
 Other organisms in the ecosystem could be harmed:
which could lead to a lower level of biodiversity.
 GM foods can be modified using bacteria and
viruses: there is a concern regarding the emergence
of new diseases.