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Year 12 Chemistry: Chapter 13 DNA
13.1 The biological importance of DNA
Within the nucleus of almost every one of your cells, 46 DNA (deoxyribonucleic acid)
molecules or chromosomes contain approximately 20 000 to 25 000 genes that act as a
blueprint directing which proteins are to be synthesised by the cell. DNA is unique
among molecules because its structure allows it to manufacture another molecule,
identical to itself, and in doing so transmit its genetic code from parents to their
children and from one cell to another as new cells are formed.
13.2 The structure of DNA
DNA is a condensation polymer constructed from four monomers known as nucleotides.
Each nucleotide consists of a:
 phosphate group
 deoxyribose sugar group and
 one of the four bases:
o adenine (A)
o cytosine (C)
o guanine (G)
o thymine (T)
Purine bases
Fig 13.2
 adenine
 guanine
Pyrimidine bases
 cytosine
 thymine
The base forms a covalent bond to the carbon atom labelled C1 in the deoxyribose
molecule. The phosphate group bonds to the carbon atom labelled C5. A water molecule is
produced when each bond is formed.
A simplified diagram of the formation of a nucleotide. Ensure you look at figure 13.5 (pg
206).
Primary Structure of the Polymer
Covalent bonds are responsible for producing the primary structure of DNA. A covalent
bond is formed between the 5’-phosphate group on one nucleotide and the 3’-hydroxy
group on the deoxyribose of another nucleotide. One end of the DNA strand has a
hydroxy group and is the 3’ end. The end of the polymer with the phosphate group called
the 5’ end. Nucleotides undergo condensation polymerisation to form a long chain of
nucleotides.
A base is also covalently bonded to the sugar group at the C1 site via a condensation
reaction.
Secondary Structure of the polymer
Hydrogen bonding is responsible for maintaining the secondary structure of DNA.
 For a given species, the percentage of each of the four bases is the same in all
cells and is characteristic of the organism.
 The mole amounts of thymine (a purine) and adenine (a pyrimidine) are equal.
 The mole amounts of cytosine (a pyrimidine) and guanine (a purine) are equal.
Base pairs
 Adenine & thymine
 Cytosine & guanine
For adenine and thymine it is possible for two hydrogen bonds to form between the on the nitrogen and oxygen atoms and the + on the hydrogen atoms on the adjacent
base. The base pairs cytosine and guanine, three hydrogen bonds can form between the
- on the nitrogen and the oxygen atoms of one base pair and the + on hydrogen atoms
on the adjacent base.
The secondary structure of DNA is a pair of DNA nucleotide strands held together by
hydrogen bonding between the bases adenine-thymine and cytosine-guanine. The
structure twists around to form a right-handed double helix. The pairing of bases A-T
and C-G is referred to as complementary base pairing. The DNA strands align in
opposite directions. The orientation of one strand 5’  3’ while the orientation of the
other is 3’  5’.
Tertiary Structure
The phosphate groups in the backbone of the double helix give DNA molecules a negative
charge, and this enables the molecules to interact with a group of proteins called
histones. It wraps around the histone forming a structure known as chromosomes.
Replication
The division of plant and animal cells involves a mechanism that generates an exact copy
of their DNA.
The DNA double helix partially unwinds, as hydrogen bonds between the two DNA stands
are broken. Enzymes catalyse this process.
Separate strands then act as templates to which new nucleotides attach by hydrogen
bonds between complementary base pairs C & G and T & A. These bases then undergo a
condensation polymerisation reaction catalysed by the enzyme DNA polymerase to form
two exact copies of the original DNA double helix.
13.3 How does DNA control biochemical processes?
Within a population, alternative sequences of nucleotides can occur at specific positions
on a given chromosome. Alternative sequences are referred to as ___________ . Alleles
give rise to most of the variation we see between people, but even the smallest change in
the nucleotides in a gene can have dramatic consequences.
A sequence of three DNA bases codes for a particular amino acid. This is known as the
triplet code. For example, the base sequence CCT codes for glutamic acid while the base
sequence AAA codes for phenylalanine. Another nucleic acid, ribonucleic acid (RNA)
decodes the information on DNA in the nucleus of the cell and transfers the information
to the part of cell where protein synthesis takes place. Another type of RNA controls
the selection and sequencing of the amino acids that form proteins.
DNA transcription RNA translation proteins
A tiny change in DNA can lead to a variation in the sequence of amino acids in a protein,
resulting in major health problems.
Case Study: sickle-cell anaemia
Sickle-cell anaemia is a heritable disease in which the red blood cells deform into a
sickle shape when oxygen concentration is low. One nucleotide in the gene is incorrect,
the base thymine is replaced by adenine.
Case Study: cystic fibrosis
Cystic fibrosis is a heritable disease caused by a tiny error in the DNA sequence of
coding allele on chromosome 7. Of the 6100 nucleotides in the gene that codes for this
protein, a person with the defective allele has a sequence of just three nucleotides
missing. This results in one amino acid, phenylalanine, being omitted.
Questions: 1, 2, 3, 4, 6, 7 & 8.
13.4 Forensic applications
Electrophoresis is an analytical technique used in creating DNA fingerprint. It is a little
like chromatography and is the best method for the separating and qualitative analysis
of very large molecules that have an overall charge such as DNA and proteins.
A solution of the sample to be analysed is place in wells in gel. The gel contains an
electrolyte so it can conduct an electric current. This causes the ions in the sample to
migrate towards the oppositely charged electrode. Smaller ions move faster than larger
ones.
Electrolyte: ________________________________________________________
__________________________________________________________________
All fragments of DNA polymer chains have a negative charge due to the phosphate
groups. The rate at which they move depends on their molecular mass, which is
proportional to the number of base pairs in the fragment. The distance the DNA copies
have travelled through the gel is compared with the distance travelled by known
standards.
The separated components are made visible by using various methods including:
 Adding a dye that binds them and fluoresces (glows) in UV light.
 Adding radioactive probes that bind to them: the radiation is then used to expose
a photographic plate.
 Shining lasers onto fragments that have a fluorescent dye incorporated into their
structure.
DNA profiling
In DNA profiling, the number of repeats in ten locates across various chromosome pairs
is considered to provide sufficient information to identify an individual accurately.
A DNA profile or fingerprint can be used to identify suspects if they leave behind a
biological sample, perhaps skin or blood under the nails of a victim. Forensic scientists
also use DNA profiling data to:
 Provide experimental data in court cases involving disputed paternity and identity.
 Help in identifying bodies recovered after natural disasters.
 Identify the species of a plant or animals. Eg birds being smuggled.
DNA fingerprinting is a technology that provides a unique identification of individuals
with the exception of identical twins.
Forensic techniques
DNA profiling involves the isolation of a sample of DNA and treating this with
restriction enzymes. Restriction enzymes act like molecular scissors, cutting DNA
molecules everywhere a particular base sequence is encounted.
Read: Chemistry in Action: Immigration status challenged (pg 215).
Polymerase chain reaction (PCR)
The polymerase chain reaction (PCR) is a technique that takes advantage of DNA’s
ability to produce an identical replica molecule. By alternately heating and cooling the
sample containing DNA.
PCR has enabled forensic scientists to work with extremely small samples of DNA. PCR is
used to duplicate DNA fragments:
1.Denaturation: the sample is heated to 95 C for 1 to 5 minutes. Hydrogen bonding
between the DNA strands is broken.
2. Annealing: the mixture is cooled to 55 C for about 1 minute. Primers bond to the
start and end of the sequence to be copied.
3. Elongation: the mixture is heated to 72 C for about 1 minute. Complementary base
pairs are added to the single DNA strands to form a double strand of DNA. This
reaction is catalysed by the enzyme polymerase and involves the formation of hydrogen
bonds.
Each heating and cooling cycle doubles the number of copies of each DNA fragment. A
fluorescent dye is added to the DNA fragment during this process. The fragments are
separated into bands according to their length by using gel electrophoresis. Today DNA
profiling is automated.
Questions: 5, 11, 12, 13, 16 (read ext pg 218), 17, 18.