9.

1 Manipulating DNA

KEY CONCEPT
Biotechnology relies on cutting DNA at specific
places.
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Scientists use several techniques to manipulate DNA.

• Chemicals, computers, and bacteria are used to work
with DNA.
• Scientists use these tools in genetics research and
biotechnology.
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Restriction enzymes cut DNA.

• Restriction enzymes act as “molecular scissors.”
– come from various types of bacteria
– allow scientists to more easily study and manipulate
genes
– cut DNA at a specific nucleotide sequence called a
restriction site
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• Different restriction enzymes cut DNA in different

ways.
– each enzyme has a different restriction site
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– some cut straight across and leave “blunt ends”

– some make staggered cuts and leave “sticky ends”
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Restriction maps show the lengths of DNA fragments.

• Gel electrophoresis is used to separate DNA fragments
by size.
– A DNA sample is cut with restriction enzymes.
– Electrical current pulls DNA fragments through a gel.
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– Smaller fragments move faster and travel farther

than larger fragments.
– Fragments of different
sizes appear as bands
on the gel.
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• A restriction map shows the lengths of DNA fragments

between restriction sites.
– only indicate size, not
DNA sequence
– useful in genetic
engineering
– used to study
mutations
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KEY CONCEPT
The polymerase chain reaction rapidly copies
segments of DNA.
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PCR uses polymerases to copy DNA segments.

• PCR makes many copies of a specific DNA sequence in a
few hours.

target sequence of DNA

• PCR amplifies DNA samples.

• PCR is similar to DNA replication.
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PCR is a three-step process.

• PCR uses four materials.
– DNA to be copied
– DNA polymerase
– A, T, C, and G nucleotides
– two primers

DNA strands

primer 1

polymerase

primer 2
nucleotides
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• The three steps of PCR occur in a cycle.

– heat is used to separate double-stranded DNA
molecules
– primers bind to each DNA strand on opposite ends of
the segment to be copied
– DNA polymerase binds nucleotides together to form
new strands of DNA

DNA strands

primer 1

polymerase

primer 2
nucleotides
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• Each PCR cycle doubles the number of DNA molecules.

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KEY CONCEPT
DNA fingerprints identify people at the molecular
level.
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A DNA fingerprint is a type of restriction map.

• DNA fingerprints are based on parts of an individual’s
DNA that can by used for identification.
– based on noncoding regions of DNA
– noncoding regions have repeating DNA sequences
– number of repeats differs between people
– banding pattern on a gel is a DNA fingerprint
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DNA fingerprinting is used for identification.

• DNA fingerprinting depends on the probability of a
match. (mother) (child 1) (child 2) (father)

– Many people have the

same number of
repeats in a certain
region of DNA.
– The probability that two
people share identical
numbers of repeats in
several locations is
very small.
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– Individual probabilities are multiplied to find the

overall probability of two DNA fingerprints randomly
matching.
1 1 1 1
500 x 90 x 120 = 5,400,000 =
1 chance in 5.4 million people

– Several regions of DNA are

used to make DNA fingerprints.
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• DNA fingerprinting is used in several ways.

– evidence in criminal
cases
– paternity tests
– immigration requests
– studying biodiversity
– tracking genetically
modified crops
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KEY CONCEPT
DNA sequences of organisms can be changed.
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Entire organisms can be cloned.

• A clone is a genetically identical copy of a gene or of an
organism.
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• Cloning occurs in nature.

– bacteria (binary fission)
– some plants (from roots)
– some simple animals (budding, regeneration)
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• Mammals can be cloned through a process called nuclear

transfer.
– nucleus is removed from an egg cell
– nucleus of a cell from the animal to be cloned is
implanted in the egg
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• Cloning has potential benefits.

– organs for transplant into humans
– save endangered species
• Cloning raises concerns.
– low success rate
– clones “imperfect” and less healthy than original animal
– decreased biodiversity
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New genes can be added to an organism’s DNA.

• Genetic engineering involves changing an organism’s
DNA to give it new traits.
• Genetic engineering is based on the use of
recombinant DNA.
• Recombinant DNA contains genes from more than one
organism.

(bacterial DNA)
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• Bacterial plasmids are often used to make

recombinant DNA.
– plasmids are loops of
DNA in bacteria
– restriction enzymes cut
plasmid and foreign DNA
– foreign gene inserted into
plasmid
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Genetic engineering produces organisms with new

traits.
• A transgenic organism has one or more genes from
another organism inserted into its genome.
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• Transgenic bacteria can be used to produce human

proteins.
– gene inserted into plasmid
– plasmid inserted into bacteria
– bacteria express the gene
• Transgenic plants are common in agriculture.
– transgenic bacteria
infect a plant
– plant expresses
foreign gene
– many crops are now
genetically modified
(GM)
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• Transgenic animals are used to study diseases and

gene functions.
– transgenic mice used to study development and
disease
– gene knockout mice used to study gene function
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• Scientists have concerns about some uses of genetic

engineering.
– possible long-term health effects of eating GM foods
– possible effects of GM plants on ecosystems and
biodiversity
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KEY CONCEPT
Entire genomes are sequenced, studied, and
compared.
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Genomics involves the study of genes, gene functions,

and entire genomes.
• Genomics is the study of genomes.
– can include the sequencing of the genome
– comparisons of genomes within and across species
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• Gene sequencing is determining the order of DNA

nucleotides in genes or in genomes.
• The genomes of several
different organisms have
been sequenced.
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• The Human Genome Project has sequenced all of the

DNA base pairs of human chromosomes.
– analyzed DNA from a
few people
– still working to identify
and map human genes
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Technology allows the study and comparison of both
genes and proteins.
• Bioinformatics is the use of computer databases to
organize and analyze biological data.
• DNA microarrays are used to study the expression of
many genes at once.

• Proteomics is the study and comparison of proteins.

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KEY CONCEPT
Genetics provides a basis for new medical
treatments.
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Genetic screening can detect genetic disorders.

• Genetic screening involves the testing of DNA.
– determines risk of having DMD N
or passing on a genetic
disorder
– used to detect specific
genes or proteins
– can detect some genes
related to an increased
risk of cancer
– can detect some genes
known to cause genetic
disorders
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Gene therapy is the replacement of faulty genes.

• Gene therapy replaces defective or missing genes, or
adds new genes, to treat a disease.
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• Several experimental techniques are used for gene

therapy.
– genetically engineered viruses used to “infect” a
patient’s cells
– insert gene to stimulate immune system to attack
cancer cells
– insert “suicide” genes into cancer cells that activate
a drug
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• Gene therapy has many technical challenges.

– inserting gene into correct cells
– controlling gene expression
– determining effect on other genes