Chapter 13 - DNA
DNA
• Within the nucleus of almost all of your cells 46 DNA
molecules or chromosomes contain approx. 20-25000
genes.
• These genes act as a blueprint directing which proteins
are to be synthesised by the cell.
• By controlling cell functioning, DNA is able to
determine the characteristics of a person.
• 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.
Structure of DNA
• DNA is a condensation polymer constructed from four monomers
known as nucleotides.
• Each nucleotide consists of a phosphate group, a deoxyribose sugar
group and one of the four bases.
• The four bases are adenine (A), cytosine (C), thymine (T) and
Guanine (G).
• Adenine and Guanine are derivatives of the organic compound
purine and as a results are referred to as purine bases.
• Cytosine and thymine are derivatives of another compound,
pyrimidine, and are referred to as pyrimidine bases.
• 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.
* Indicates the site
where the base bonds
to the C1 deoxyribose
carbon atom.
• A simplified
presentation of the
condensation
reaction between
nucleotides to
form a section of
DNA.
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 on the deoxyribose of another.
• One end of the DNA strand has a hydroxyl group and is called the 3’
end.
• The end of the polymer with the phosphate group is called the 5’
end.
• In this way, 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.
• It is the sequence of bases along the sugar-phopshate backbone
that forms the primary structure and is the basis for the genetic
code.
Secondary Structure of the Polymer
• As is the case in proteins, 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.
Secondary Structure of the
Polymer cont…
• By considering the structures of the base pair A and
T, it can be seen that they are able to fit together.
• It is possible for two hydrogen bonds to form
between the dipole negative on the nitrogen and
oxygen atoms and the dipole positive on hydrogen
atoms on the adjacent base.
• With base pairs C and G three hydrogen bonds can
form between the nitrogen and oxygen atoms of one
base and the hydrogen atoms on the adjacent base.
Secondary Structure of the
Polymer cont…
• The secondary structure of DNA is a pair of DNA
polynucleotide strands held together by hydrogen
bonding between the bases A-T and C-G.
• The structure twists around to form a right-handed
double helix.
• The sugar-phosphate backbone forms the handrails
and the pairs of bases the steps.
• The pairing of bases is referred to as complementary
base pairing.
• The DNA strands align in opposite direction.
Tertiary Structure of the Polymer
• 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.
• The DNA molecules wrap around histones and
become super coiled.
• This allows the DNA to be very tightly and
efficiently packaged, each molecule forming a
structure known as a chromosome.
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 strands are broken.
• Enzymes catalyse this process.
• The bases exposed on the separated strands then act as a
template to which new nucleotides attach by hydrogen bonds
between complementary base pair, C and G, A and T.
• 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.
How does DNA control biochemical
processes?
• Alternative sequences of nucleotides can occur at specific
positions on a given chromosome.
• The alternative sequences are referred to as alleles.
• Alleles give rise to most of the variation we see between
people.
• Triple code – a sequence of three DNA bases codes for an
amino acid.
• RNA decodes the information on DNA in the nucleus of the
cell where protein synthesis takes place.
• Another type of RNA controls the selection and sequencing of
the amino acids that form proteins.
Read Sickle-Cell Anaemia and Cystic Fibrosis
Forensic Applications Electrophoresis
• Electrophoresis is an analytical technique,
similar to chromatography, that allows large
charged molecules, DNA and proteins, to be
separated and quantitively determined.
• In electrophoresis the sample solution is
placed into a “well” in a block of conducting
electrolytic gel, sitting between (+) and (-)
electrodes.
Forensic Applications –
Electrophoresis cont…
• negative ions, such as DNA fragments, in the sample move
toward the positive electrode.
• The rate of travel depends on their size, how many base pairs
there are.
• for DNA analysis, the sample “well” is placed near the
negative electrode, as DNA fragments, with their HPO4phosphate linkages, are always negatively charged.
• the distance the fragments move is compared against the
distance travelled by known standards.
• the separated components can be made visible by adding
fluorescent dyes or radioactive markers.
Forensic Applications – DNA
Profiling
• The sections of DNA that do not code for the
production of proteins, non-coding regions are more
useful for forensic scientists because they differ
significantly from person to person
• Of particular interest is the number of times a
particular sequence of bases may be repeated eg. on
chromosome 5 the sequence AGAT is repeated
between 7 and 15 times, depending on the person.
• When you examine 10 different chromosome sites,
counting the number of base sequence repeats, an
accurate DNA profile identification is assured.
Forensic Applications – Polymerase
Chain Reaction (PCR)
• a major problem with early DNA forensics was
obtaining a big enough biological sample,
blood, skin, semen etc. to analyse.
• PCR has enabled forensic scientists to produce
a DNA profile from an extremely small sample
• PCR utilizes DNA’s ability to replicate itself,
making multiple copies of the sections of the
DNA of interest
•
Forensic Applications - PCR
• PCR involves 3 steps …
1. Denaturation … heating breaks the H-bonding between DNA
strands
2. Annealing … the sample is cooled and primers are added to
bond to the start and end of the base sequence to be copied
3. Elongation … the sample is warmed and polymerase enzyme
catalyst assists the addition of complementary base pairs and
the formation of H-bonds between the DNA strands
• The amplified DNA fragments are then separated using gel
electrophoresis and the analysis of the number of base
sequence repeats for 10 different chromosome locations
performed automatically.