Biology The Core 2nd Edition Simon Solutions Manual

Biology The Core 2nd Edition Simon
Solutions Manual
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CHAPTER 6
DNA: The Molecule of Life
Learning Outcomes
In this chapter students will:
6.1 Describe the structure of the DNA molecule and how this structure allows for the
storage of information, the replication of DNA, and protein synthesis.
(Modules 6.1, 6.2)
6.2 List the similarities and differences between the various nucleic acid molecules.
(Modules 6.3, 6.6)
6.3 Describe the process of protein synthesis, including how the genetic information is
transferred during transcription and translation. (Modules 6.3–6.7)
6.4 Define gene expression, and describe the various ways in which cells are able to
regulate gene expression, including signal transduction. (Modules 6.8, 6.9)
6.5 Differentiate between the categories of mutations and the relative effects of each on the
expression of genes. (Modules 6.10–6.12)
6.6 Describe how certain mutations can result in cancer, and what can be done to treat
cancer or prevent it. (Module 6.12)
6.7 Describe how scientists manipulate DNA to produce genetically modified products.
(Modules 6.13–6.15)
6.8 Describe how scientists can analyze DNA profiles and how this information is applied.
(Modules 6.16–6.18)
6.9 Summarize the practice of gene therapy: what it is, how it works, its successes, and its
failures. (Module 6.19)
Module Outlines
6.1 DNA is a polymer of nucleotides.
• CORE IDEA: A molecule of DNA is a double helix made of two intertwined
polynucleotide strands. Each strand is a long string of nucleotides. Each nucleotide
consists of the same sugar and phosphate, and one of four possible bases.
A. DNA history
1. In the early 1900s, biologists hypothesized a molecule acted as a chemical basis of
inheritance.
2. By the 1950s, scientists had identified the hereditary material as DNA
(deoxyribonucleic acid) and its 3-D structure.
3. DNA is one type of nucleic acid.
B. The double helix
1. Every living cell contains chromosomes.
a. Humans have 46 chromosomes.
2. Each chromosome consists of one molecule of DNA plus organizing proteins.
3. Overall structure of DNA is a double helix.
a. Two strands wrap around each other.
Copyright © 2017 Pearson Education, Inc. 75

b. Hydrogen bonds between bases hold the two strands together.
4. The precise chemical structure of DNA is common to all life on Earth.
C. Nucleotides
1. Each molecule of DNA is made of individual subunits called nucleotides.
2. Each nucleotide is composed of the following:
a. A five-carbon sugar (deoxyribose in DNA)
i. Identical in all organisms
b. A negatively charged phosphate group
i. Identical in all organisms
c. A base
i. Varies—adenine (A), guanine (G), thymine (T), and cytosine (C)
ii. All genetic information is encoded in this four-letter alphabet.
3. Polynucleotide
a. One molecule of DNA contains two polynucleotides wrapped around each other.
i. This forms a double helix.
b. Each polynucleotide is a strand of individual nucleotides.
c. Any combination of the four bases is possible along its length.
4. Sugar-phosphate backbone
a. A polynucleotide consists of bases attached to a sugar-phosphate backbone.
b. The backbone alternates sugar and phosphate groups that form a long chain.
c. The backbone is identical among all DNA molecules.
i. It is the bases that change from one molecule to the next.
5. Base pairs
a. Each nucleotide contains one of four bases.
i. Adenine (A), guanine (G), thymine (T), and cytosine (C)
b. Each kind of base can form only hydrogen bonds with only one other kind of base.
i. A with T
ii. G with C
c. The hydrogen bonds within base pairs hold the two strands of the double helix
together.
d. Due to the base-pairing rules, the sequence of one strand dictates the identity of the
nucleotides on the other strand.
6.2 During DNA replication, a cell duplicates its chromosomes.
• CORE IDEA: Genetic instructions are passed down via DNA replication: The double
helix of a DNA molecule is peeled apart, and each separated strand serves as a template
to build a new strand following the base-pairing rules.
A. Duplicating DNA
1. For the continuity of life, a complete set of genetic instructions in the form of DNA
must pass from one generation to the next.
B. Semi-conservative replication
1. During DNA replication, the two strands of the original DNA molecule separate.
2. Each DNA strand serves as a template to guide the production of the other strand.
a. Base-pairing rules dictate that A can pair only with T, and G can pair only with C.
3. In the end, two new DNA molecules are produced.
a. Semi-conservative—each contains one newly created strand and one strand from
the original molecule.
C. The process of DNA replication
1. The double helix is peeled apart.
a. Helicase attaches to the origins of replication in the DNA.
76 INSTRUCTOR’S GUIDE FOR SIMON, BIOLOGY: THE CORE, 2e Copyright © 2017 Pearson Education, Inc.
b. Helicase peels apart the two DNA strands and forms replication bubble.
c. This exposes the bases.
2. New strands are synthesized.
a. DNA polymerase builds a new DNA molecule that is complementary to the
existing strand.
b. Base-pairing rules dictate that A can pair only with T, and G can pair only with C.
c. This happens on both original DNA strands simultaneously.
3. DNA fragments are fused together.
a. DNA polymerase creates the new DNA molecule in fragments.
b. DNA ligase joins individual fragments of DNA.
6.3 DNA directs the production of proteins via RNA.
• CORE IDEA: DNA and RNA are both nucleic acids with some common features and
some differences. Within a cell, DNA acts as the molecule of heredity by directing the
production of RNA, which in turn directs the production of proteins.
A. Nucleic acids
1. A molecule of DNA (deoxyribonucleic acid) shares many structural similarities with
a molecule of RNA (ribonucleic acid).
a. Both are nucleic acids.
b. Both are polymers of nucleotides.
i. Each nucleotide consists of a sugar, a phosphate, and a base.
2. DNA and RNA have three important structural differences.
a. Number of strands
i. DNA—double-stranded (double helix)
ii. RNA—single-stranded
b. Sugar
i. DNA—deoxyribose (missing one oxygen compared to ribose)
ii. RNA—ribose
c. Base
i. DNA—adenine (A), guanine (G), thymine (T), and cytosine (C)
ii. RNA—adenine (A), guanine (G), and cytosine (C), but uracil (U) instead of
thymine (T)
B. The flow of genetic information
1. DNA is the molecule of heredity because it directs the production of proteins.
2. DNA first directs the production of RNA.
3. RNA then controls the manufacture of proteins.
4. Proteins perform the majority of cellular functions.
a. Proteins are responsible directly or indirectly for physical traits.
6.4 Genetic information flows from DNA to RNA to protein.
• CORE IDEA: Genetic information flows from DNA to messenger RNA in the nucleus
through the process of transcription. At the ribosomes in the cytoplasm, each mRNA
codon is translated into an amino acid of a protein.
A. Every trait you were born with is encoded by the DNA of your genes.
1. DNA itself does not produce your appearance.
2. DNA directs the production of proteins.
3. Proteins are responsible for your physical traits.
B. Flow of genetic information through the cell
1. Transcription—DNA to RNA
a. This occurs in the nucleus.
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2. Translation—RNA to protein
a. RNA leaves nucleus through nuclear pores.
b. This occurs in the cytoplasm on ribosomes.
C. Transcription overview
1. Flow of genetic information starts in the nucleus with DNA.
2. DNA directs production of RNA through the process of transcription.
3. Transcription makes mRNA (messenger RNA).
4. It follows base-pairing rules:
a. C is transcribed to G, and G is transcribed to C.
b. T is transcribed to A, but A is transcribed to U (uracil).
5. mRNA exits the nucleus and travels to the ribosome.
D. Translation overview
1. In translation, mRNA serves as instructions to build a sequence of amino acids.
2. mRNA contains successive codons—a sequence of three nucleotides—which
specifies one amino acid.
3. Ribosomes read each codon and attach the proper amino acid to a growing chain.
4. The resulting string of amino acids is a polypeptide.
6.5 Transcription creates a molecule of RNA from a molecule of DNA.
• CORE IDEA: During translation, the DNA double helix separates, and one strand is
used to generate a molecule of RNA. The RNA is processed to become messenger RNA,
which then exits the nucleus via a nuclear pore.
A. Transcription
1. Transcription is the transfer of information from DNA to messenger RNA (mRNA).
2. It occurs in the nucleus of eukaryotic cells.
B. RNA polymerase binds a promoter.
1. RNA polymerase binds to the promoter (DNA sequence).
2. Promoter acts as a “start here” signal marking the beginning of a gene.
3. By controlling whether or not RNA polymerase can bind, promoters turn genes on or
off.
C. RNA polymerase synthesizes a molecule of RNA.
1. After RNA polymerase binds to the promoter, it peels open the double helix.
2. One strand serves as a template for the formation of RNA.
3. RNA polymerase moves down the DNA.
a. It follows base-pairing rules.
b. C is transcribed to G, and G is transcribed to C.
c. T is transcribed to A, but A is transcribed to U (uracil).
4. As completed RNA peels away, DNA strands rejoin.
5. Transcription ends when RNA polymerase reaches a DNA “stop” sequence—
terminator.
D. RNA splicing
1. In eukaryotic cells, the RNA is processed before it leaves the nucleus.
2. RNA splicing
a. Introns: Stretches of RNA that do not code for amino acids are removed.
b. Exons: Stretches of RNA that do code for amino acids remain in the RNA.
3. One mRNA may be spliced in multiple ways to code for multiple proteins.
4. In addition, extra nucleotides are added as a “cap” and a “tail” to the RNA.
E. The mRNA leaves the nucleus.
1. The finalized RNA molecule is now called messenger RNA (mRNA).
2. mRNA leaves the nucleus through nuclear pores.
6.6 Translation involves the coordination of three kinds of RNA.
• CORE IDEA: Translation is accomplished by ribosomes, made from rRNA and protein.
Ribosomes use two kinds of RNA to produce a string of amino acids. The genetic code
dictates the correspondence between RNA triplets and amino acids.
A. Translation
1. Translation is the process through which messenger RNA (mRNA) is used to
produce a molecule of protein.
2. Translation takes place in the cytoplasm on ribosomes.
B. Ribosomes
1. Ribosomes are cellular structures that perform the translation of mRNA
polynucleotides into amino acid polypeptides.
2. Ribosomes are made of ribosomal RNA (rRNA) and proteins.
a. Each ribosome consists of two subunits that join to form the functional ribosome.
3. Within each ribosome are binding sites for mRNA (carrying the message) and transfer
RNA (tRNA).
a. tRNA brings the amino acids that match the codon to the ribosome.
4. The ribosome reads the mRNA three nucleotides at a time—codon.
5. Each codon encodes one amino acid.
C. Transfer RNA
1. tRNAs (transfer RNAs) have an anticodon at one end.
a. Follows base-pairing rules
b. C with G, and G with C
c. U with A, and A with U
2. The other end of the tRNA holds the amino acid that corresponds to that codon.
D. The genetic code
1. The correspondence between an RNA codon and its amino acid is called the triplet
code.
2. Every RNA codon encodes just one possible amino acid.
3. A given amino acid may be encoded by multiple codons.
4. There is one start codon (AUG) that signals the start of the genetic message.
5. There are three stop codons that signal the end of the message.
6. Each codon between start and stop codons encodes one amino acid.
6.7 Translation creates a molecule of protein via the genetic code.
• CORE IDEA: Translation begins when the ribosome assembles from its subunits at the
start codon of an mRNA. Elongation then proceeds, adding one amino acid at a time.
When a stop codon is reached, the ribosome machinery disassembles.
A. Translation
1. Ribosomes use information coded in messenger RNA (mRNA) to create
corresponding amino acid polypeptides.
2. Each ribosome contains binding sites for the mRNA and molecules of transfer RNA
(tRNA).
B. Initiation—Ribosome assembles.
1. Ribosomes exist as two separate components: the large and small subunits.
2. Translation begins when mRNA binds to a small ribosomal subunit.
3. A tRNA then binds the start codon of mRNA.
a. Start codon binds to anticodon of tRNA carrying amino acid methionine.
b. Start codon is UAC.
4. Large subunit then binds, creating a complete ribosome.
C. Elongation—Polypeptide grows longer.
1. Additional amino acids are added one by one.
2. The anticodon of the incoming tRNA carrying its amino acid pairs with the mRNA
codon via the RNA base-pairing rules.
3. The new amino acid is added to the end of the growing polypeptide chain.
4. The old empty tRNA (from the previous step) exits the ribosome.
5. The ribosome moves the remaining tRNA to the spot just vacated.
6. The process continues, with each entering tRNA bringing a new amino acid to be
added.
D. Termination—Ribosome disassembles.
1. Elongation continues until the ribosome reaches a stop codon on the mRNA.
2. Stop codons do not code for amino acids, indicating the end of translation.
a. Stop codons are UAA, UAG, and UGA.
3. The completed polypeptide is freed, the ribosome splits back into subunits, and
mRNA and tRNA are released.
4. The released mRNA may then begin another round of translation, producing another
protein.
6.8 Gene expression is regulated in several ways.
• CORE IDEA: Through gene regulation (the turning on and off of genes), cells control
gene expression (the production of proteins). There are several points along the path from
DNA to RNA to protein that can be regulated.
A. Gene expression
1. Every cell in your body contains every one of your genes.
2. Each cell type looks and acts differently because each produces different proteins.
3. Gene regulation: Mechanisms that turn on and off certain genes in a particular cell.
4. Genes contain information used to produce proteins.
5. Turning a gene off means that gene expression—the flow of genetic information from
DNA to RNA to protein—is not being completed.
B. Gene regulation in action
1. If you examined genes from a set of cells, you would see that certain genes are turned
on in some cells and not others.
Gene type Intestinal cell Nerve cell White blood cell

Gene for glucose- Active Active Active
digesting enzyme
Antibody gene Active
Lactase gene Active
Hemoglobin gene
2. In the examples used, only intestinal cells produce the digestive enzyme lactase.
3. None of the cell types shown produce hemoglobin.
C. X chromosome inactivation
1. If a chromosome is condensed, the genes it contains are inaccessible and will not be
used to produce proteins.
2. X chromosome inactivation: In female mammals, one X chromosome in each body
cell is highly compacted and almost entirely inactive.
3. Ensures that males (who have only one X chromosome) and females (who have two)
have the same number of active genes.
4. The inactive X condenses down into a Barr body.
D. Control of gene expression
1. Transcription factors
a. In a typical eukaryotic cell, the majority of genes are “off”—not being used to
produce proteins.
b. Transcription factors are proteins that bind to the DNA before transcription can
begin.
2. Control of RNA
a. Before leaving the nucleus, RNA can be altered in several ways.
b. A cap and tail are added.
c. Introns (noncoding regions) are spliced out and exons (coding regions) may be
rearranged.
i. This produces several possible messenger RNAs from a single gene.
d. microRNAs (small RNA molecules) bind to mRNA, preventing them from
producing protein.
3. Protein control: Initiation, activation, breakdown
a. Translation (where messenger RNA is used to produce proteins) offers more places
for regulation.
b. The cell can control whether translation proceeds, how proteins are modified after
translation, and when proteins are broken down.
6.9 Signal transduction pathways can control gene expression.
• CORE IDEA: Cells can communicate with each other via molecules that trigger signal
transduction pathways in the receiving cell. The result is gene regulation. Such
communication is particularly important in the developing embryo.
A. Multicellular life depends on cell-to-cell signaling.
B. Signal transduction
1. Within multicellular organisms, cells typically communicate with each other by
producing signal molecules that exit one cell and bind to a receptor protein on the
outside of another cell.
2. Binding triggers a signal transduction pathway—a series of relay molecules that
convey a message from the outside of the cell into the cell’s cytoplasm and nucleus.
3. The signal usually results in the turning on or off of one or more genes.
C. Cell-to-cell signaling in a developing embryo
1. Development is the growth of an animal from an embryo into an adult.
2. It involves cell division (to increase body size) that must be carefully coordinated.
3. Chemical signals are passed between neighboring cells to properly control the
formation of organs as well as the overall organization of the body.
4. Induction occurs when one group of cells influences the development of an adjacent
group of cells.
a. It switches genes on or off in target cell.
b. Inductive signals can cause cells to change shape, migrate, or even destroy cells (as
in removal of webbing in the developing hand).
5. Homeotic genes are master control genes.
a. Homeotic genes are master control genes.
b. In developing embryos, they produce protein signals that turn groups of other genes
on or off.
b. Homeotic genes help establish the overall structure of an organism.
c. For example, specific homeotic genes direct which end of the embryo will be the
head, while others direct which body parts will develop in which locations.
i. The mutant fly has an extra set of wings due to mutation in a homeotic gene.
6.10 Mutations can have a wide range of effects.
• CORE IDEA: Mutations, changes to the nucleotide sequence of DNA, can occur
spontaneously or be caused by mutagens. Point mutations occur at a single nucleotide,
whereas insertions and deletions can affect many mRNA codons.
A. Mutations
1. A mutation is any change in the nucleotide sequence of DNA.
2. Occasionally, mutations lead to improvements that make an organism better suited to
its environment.
a. These are the raw material of evolution by natural selection.
3. More often, mutations are harmful and will not enhance the survival of the affected
organism.
4. Some mutations involve a single nucleotide change, while others affect a larger
number of nucleotides.
B. Mutagens
1. Some mutations are spontaneous.
a. Due to errors during DNA replication
2. Other mutations are caused by mutagens—physical or chemical factors in the
environment that can damage DNA.
3. Many mutagens are carcinogens—cancer-causing agents.
a. Exposure to ultraviolet radiation, X-rays, tobacco products, and high-fat foods
increases risk.
b. Avoiding mutagens can help reduce the risk of developing cancer.
i. Apply sunscreen when outdoors, and include vitamins C and E from fresh fruits
and vegetables into a daily diet.
Mutations
Point mutations Frameshift mutations
Silent Missense Nonsense Insertions Deletions
C. Point mutations
1. A point mutation is the substitution of one DNA nucleotide for another.
2. Silent mutation does not change amino acid produced, so protein is unchanged.
a. Some amino acids are encoded by more than one RNA sequence.
3. Missense mutation substitutes one amino acid for another, so protein is changed.
a. Change in protein may be small or large depending on which amino acid is
substituted.
4. Nonsense mutation changes an amino acid codon to a stop codon, producing a
shortened protein.
a. A shortened protein is almost always defective.
D. Frameshift mutations
1. After a DNA gene is transcribed in messenger RNA, it is read as a series of codons.
a. A codon is three consecutive nucleotides.
2. Insertion mutations add nucleotides.
3. Deletion mutations delete nucleotides.
4. If an insertion or deletion throws off the reading frame, it is called a frameshift
mutation.
a. They often result in completely different and usually defective proteins.
6.11 Loss of gene expression control can result in cancer.
• CORE IDEA: Cancer is caused by out-of-control cell growth due to a breakdown of the
cell cycle control system. This can occur when proto-oncogenes (such as genes that code
for growth factors and tumor suppressors) are mutated to oncogenes.
A. Cancer
1. Cell division is a normal, necessary process that produces new cells from preexisting
cells.
2. Cell cycle control system controls the rate and timing of cell division.
3. A cell occasionally loses the ability to control its cell cycle.
4. A tumor is a mass of body cells growing out of control.
5. Cancer is a tumor that spreads to other tissues.
B. Proto-oncogenes and oncogenes
1. The cell cycle control system regulates the timing of cell duplication.
2. The cell cycle control system consists of proteins that integrate information from the
environment and communicate “start” and “stop” signals to the nucleus.
3. A mutation in a gene producing one of these proteins can cause the cell to fail to
respond to one of these signals.
4. A cell with such a mutation runs through the cycle again and again, producing new
cells when it should not.
5. A proto-oncogene is a normal, necessary gene that produces a protein that properly
regulates the cell cycle.
6. An oncogene is a mutated proto-oncogene that produces an abnormal protein that fails
to regulate the cell cycle.
a. The result is out-of-control growth.
C. Growth factors
1. A proto-oncogene is a gene that produces a protein that normally regulates the cell
cycle.
2. A proto-oncogene may produce a growth factor.
a. Growth factor is a protein that stimulates cell division.
b. Growth factors normally stimulate growth only when it is appropriate.
c. A mutation in a growth factor gene can make a protein that promotes cell division
when it should not.
i. A tumor may result.
D. Tumor suppressor genes
1. Tumor suppressor genes normally code for proteins that inhibit cell division.
2. A mutation that deactivates a tumor suppressor gene may result in uncontrolled
growth.
6.12 Cancer is caused by out-of-control cell growth.
• CORE IDEA: All tumors start in a single cell. If a tumor cannot move beyond its
original location, it is benign; if it is capable of spreading, it is malignant and causes
cancer. There are several ways to prevent and treat cancer.
A. Progression of cancer
1. Cancer is caused by abnormal growth of the body’s own cells.
2. Cancer always begins when DNA within a single cell undergoes a series of mutations.
a. Proto-oncogenes mutate into oncogenes.
b. Transformation is conversion of a normal cell into a cell that multiplies
continuously.
3. If the mutated cell is not destroyed by the immune system, its descendants will form a
tumor.
4. Cancers are named for the place where they originate.
a. Lung cancer starts in the lung.
b. A cancer may spread from where it originates.
5. Metastasis is the spread of cancer cells from their site of origin through the body.
6. Types of cancer
a. Benign tumor (sometimes called a cyst or polyp) is one that cannot spread from its
original location.
i. They can be dangerous if their growth disrupts the organ in which they are
located (e.g., brain or intestine).
ii. They are not usually fatal because they do not spread.
b. A malignant tumor is one that can spread to other parts of the body.
i. Genetic and cellular changes enable it to spread.
ii. Malignant tumors are cancer.
iii. The spread of tumors is called metastasis.
B. Cancer treatment
1. Surgery
a. If a tumor is benign, surgery is often sufficient to remove it.
b. If a tumor is malignant, surgery to remove as much as possible is combined with
the next treatments.
2. Radiation therapy exposes specific areas to high-energy radiation.
a. Such radiation disrupts cell division to kill cancer cells.
b. Can also damage normal body cells.
3. Chemotherapy uses drugs to disrupt cell division.
a. Affects cells through the body.
b. May have negative side effects.
C. Cancer prevention
1. Some mutations that lead to cancer are inherited and can’t be prevented.
2. Some mutations that lead to cancer are spontaneous and can’t be prevented.
3. Most cases of cancer are caused by carcinogens.
a. Carcinogens are agents that promote the development of cancer.
4. Factors to reduce your cancer risk and increase your odds of survival if you do get it:
a. Healthy diet
b. Protection from sun—UV radiation
c. Not smoking
d. Regular screenings
e. Exercise
6.13 Genetic engineering involves manipulating DNA for practical purposes.
• CORE IDEA: Genetic engineering, the manipulation of genes for practical purposes, is
an application of biotechnology. A typical genetic engineering challenge is to clone a
gene in order to produce large quantities of a desired protein.
A. DNA can be mixed and matched.
1. A gene from one species may be cut and pasted into the DNA of a different species.
a. Chemical language of DNA is identical in all life.
B. How to clone a gene
1. Gene cloning: A gene that synthesizes the protein is . . .
a. Isolated—cut out gene of interest using restriction enzyme.
b. Inserted into a piece of bacterial DNA called a plasmid—also cut with same
restriction enzyme.
i. Cutting with the restriction enzyme produces sticky ends.
ii. Both the gene of interest and the plasmid will have complementary sticky ends.
iii. DNA ligase is used to paste together the fragments of DNA.
c. A plasmid with gene of interest inserted is called a recombinant plasmid.
2. As the bacteria multiply, large amounts of the gene, and thus protein, are produced.
3. See the human insulin example on pages 138–139.
C. Genetic engineering
1. Biotechnology is the manipulation of organisms or their components to make useful
products.
2. DNA technology is a set of methods for studying and manipulating genetic material.
3. Genetic engineering is the direct manipulation of genes for practical purposes.
D. Restriction enzymes
1. Restriction enzymes are used to cut DNA at only specific nucleotide sequences.
2. Each kind of restriction enzyme recognizes just one short sequence of DNA—
restriction site.
3. Restriction fragments have sticky ends.
4. Fragments cut with the same enzyme will have complementary sticky ends.
6.14 DNA may be manipulated in many ways within the laboratory.
• CORE IDEA: Scientists can manipulate DNA in various ways: it can be cut with
restriction enzymes, isolated from a cell and put into a genomic library, visualized using
nucleic acid probes, synthesized directly, or produced from a cell’s messenger RNA.
A. Genomic libraries
1. It is often useful to start with a whole genome—an organism’s entire set of DNA.
a. There are 3 billion nucleotides in humans.
2. From the genome, recombinant DNA—a DNA molecule containing nucleotides from
more than one source—can be made.
3. The entire genome is cut up with restriction enzymes to create a large set of
fragments.
4. Each fragment is inserted into a separate plasmid.
a. A plasmid is a small circular bit of bacterial DNA.
b. DNA ligase is used to join fragment to plasmid.
5. A genomic library is a collection of cloned DNA fragments that includes an
organism’s entire genome.
6. Once created, a genomic library can be used to hunt for and manipulate any gene from
the starting organism.
B. Nucleic acid probes
1. A researcher may wish to select just one DNA fragment from an entire genomic
library.
2. A nucleic acid probe can be used.
a. A nucleic acid probe is a complementary molecule made using radioactive or
fluorescent building blocks.
3. Because the sequence of the probe is complementary, the probe binds to the fragment
of interest and helps to visualize it.
C. DNA synthesis
1. DNA can be created from scratch using an automated DNA synthesizer.
2. These machines produce customized DNA molecules of any sequence.
3. Sequences can be joined to produce DNA molecules of any length.
D. Complementary DNA
1. Within a cell, transcription produces mRNA from the DNA.
2. The mRNA is used to produce proteins.
3. Reverse transcriptase can synthesize DNA molecules from mRNA.
4. Complementary DNA (cDNA) represents just the genes that were being transcribed
in the cell at the time.
6.15 Plants and animals can be genetically modified.
• CORE IDEA: Genetic engineers can use plasmids to create transgenic plants and
animals. While GM plants currently make up a significant part of our food supply, GM
animals do not. The use of such organisms carries risks and benefits.
A. Genetically modified organisms (GMOs)
1. Genetically modified organisms (GMOs) are ones that have acquired one or more
genes by artificial means.
2. Transgenic organism: Gene transferred from another species.
a. A goat carrying a gene from a human.
3. Production of transgenic GMOs is one of the most widespread applications of genetic
engineering.
B. Transgenic plants
1. Genetically modified food crops can be produced by inserting a desired gene into a
plasmid.
a. A plasmid is a small, circular, independently replicated piece of DNA originally
isolated from a bacterium.
b. Recombinant plasmid carries the gene of interest.
2. Plasmid acts as a temporary DNA carrier to insert a gene of interest into the genome
of a plant.
3. The genetically modified plant then expresses the trait from the newly inserted gene.
4. Genetically modified food crops are widely consumed in the United States.
5. Some agricultural scientists hope the GM crops can increase food production, pest
resistance, and the nutritional value of crops.
6. Examples
a. Bt corn has a gene for an insecticide from the bacterium Bacillus thuringiensis.
b. Golden rice contains daffodil genes that produce beta-carotene. This rice could help
with vitamin A deficiency and resulting blindness.
c. A GM papaya variety resistant to the devastating ring spot virus was introduced in
Hawaii.
C. Transgenic animals
1. There is a millennia-old tradition of selectively breeding farm animals.
2. Scientists are working on various genetic modifications to food animals to make them
healthier or more productive.
3. To date, none of these animals are in our food supply.
a. In late 2015, the Food and Drug Administration approved a transgenic salmon for
consumption. It may be years before such fish are available for consumption.
4. Pharmaceutical companies have produced various GMOs that secrete medically useful
human proteins.
a. Procedure for producing Erythropoietin in goats is diagrammed on page 143.
D. Safety and ethical concerns
1. Use of GMOs has rapidly replaced traditional plant and animal breeding programs in
agriculture.
2. Regulations are still being drafted, so it is important for all citizens to be educated
about the possible risks and benefits of this technology.
3. See the table of pros and cons on page 143.
6.16 PCR can be used to multiply samples of DNA.
• CORE IDEA: Each round of the polymerase chain reaction (PCR) uses ingredients—
heat-stable DNA polymerase enzyme, DNA nucleotides, a sample to be studied, and
primers that target a specific sequence—to precisely double the amount of DNA.
A. PCR
1. Polymerase chain reaction (PCR) is a laboratory technique by which a specific
segment of DNA can be targeted and copied quickly and precisely.
2. Using PCR, a scientist can obtain enough DNA from a trace amount of blood or tissue
to allow further analysis.
3. Starting with just a single copy, automated PCR can generate billions of copies of a
DNA segment with a high degree of accuracy.
B. The PCR technique
1. In PCR, a sample of DNA is subjected to rounds of heating and cooling in a machine
called a thermal cycler.
2. The quantity of the desired region of DNA is doubled in each round.
3. DNA polymerase, a naturally occurring enzyme, is used to synthesize a new DNA
strand that is complementary to a single-stranded DNA sample.
a. DNA polymerase used was originally isolated from hot springs bacteria so it can
tolerate the high temperatures that would inactivate other organisms’ enzymes.
4. Technique
a. A double-stranded DNA molecule starts the process.
b. The sample is heated to near boiling.
i. Heat causes the hydrogen bonds that hold the double helix together to break apart.
c. The DNA strands separate due to high heat.
d. A heat-stable DNA polymerase is used to rebuild each of the missing strands.
e. The mixture is cooled, allowing the double-helix hydrogen bonds to re-form.
f. Each cycle doubles the amount of DNA.
g. Repeat the steps for the next cycle.
C. How DNA segments are targeted and copied
1. An investigator does not copy the entire DNA sample obtained (e.g., from a crime
scene).
2. PCR copies one specific region with the DNA.
3. Primers are used to target specific regions.
a. Primer: Short, chemically synthesized, single-stranded DNA molecules with
sequences that are complementary to sequences at each end of the target DNA
sequence.
4. DNA polymerase binds the primers and synthesizes to new DNA molecules using free
nucleotides included in the mixture.
5. By adding the correct primers and other needed ingredients, a large sample of the
DNA within a specific region can be obtained.
6. The DNA produced is then used for further analysis.
6.17 DNA profiles are based on STR analysis.
• CORE IDEA: DNA profiling can prove that two DNA samples came from the same
individual. PCR creates a sample of DNA containing specific short tandem repeats that
vary widely among people. Gel electrophoresis visualizes these sites.
A. DNA profiling
1. DNA profiling is a set of laboratory techniques that allows an investigator to
determine with certainty whether two samples of DNA came from the same
individual.
B. Short tandem repeats
1. DNA profilers focus on specific sites within the genome that are known to vary
considerably from person to person.
2. Short tandem repeats (STRs) are sites where a short nucleotide sequence is repeated
many times in a row.
a. They are scattered throughout the genome.
b. Locations within the chromosome and the repeated sequences are the same from
individual to individual.
c. The number of repeats varies widely with the human population.
C. STR analysis
1. STR analysis is the current method for generating a DNA profile.
2. A comparison of the lengths of short tandem repeats is made at 13 predefined sites
within the human genome.
3. These sites vary so widely that no two humans have ever had the same number of
repeats at all 13 sites.
a. Exception: identical twins
4. Method
a. DNA is collected from the crime scene and the suspect.
b. PCR is used with specific primers to copy just the STR sites.
c. PCR produces large amounts of DNA from the STR sites.
d. Samples are analyzed by gel electrophoresis.
D. Gel electrophoresis
1. Gel electrophoresis allows visualization of DNA samples based on length.
2. DNA samples are loaded into the top of a gel.
3. Current is applied.
4. All DNA molecules are negatively charged so they migrate through the gel toward the
positive pole.
5. A dense thicket of fibers within the gel slows the migrations.
6. As a result, smaller pieces of DNA migrate toward the bottom of the gel faster than
larger pieces.
7. When the power is turned off, the DNA stops migrating.
8. Staining reveals the locations of the bands.
9. The banding pattern is compared to determine if the suspect’s sample matches the
crime scene sample.
6.18 Whole genomes can be sequenced.
• CORE IDEA: By digesting a cell’s DNA with enzymes and sequencing the fragments,
the entire genome of an organism can be determined. The human genome contains
21,000 genes that encode for 100,000 different proteins.
A. Genome sequencing
1. In 1995, a team of biologists announced that they had determined the DNA sequence
of the entire genome of Haemophilus influenza, a disease-causing bacterium.
2. This was the first successful experiment in genomics, the science of studying the
complete set of genes (genomes) and their interactions.
3. Many detailed genomes from a variety of species, including our own, have been
sequenced.
B. The Human Genome Project
1. In 2003, researchers announced that they had sequenced virtually all of the genes from
a human.
2. The Human Genome Project found that our chromosomes contain about 21,000
genes within about 3 billion DNA nucleotides.
3. Human genome can be compared with other organisms.
a. Compare the number of nucleotides.
b. Compare the number of genes: Rice has 42,000; mice have 22,000; humans have
21,000.
4. See human genome facts on page 148.
C. Whole-genome shotgun method
1. The whole-genome shotgun method sequences the entire genome of an organism
using several separate techniques.
2. Method
a. Genome(s): DNA is obtained from one or more individuals.
b. DNA fragments: DNA is digested with a variety of restriction enzymes, which chop
the DNA into small segments.
c. Sequences of DNA: Sequence of each DNA fragment is determined by an
automated sequencing machine.
d. Overlapping sequences: Computer programs use overlapping regions from each
fragment to determine the original order of the sequences.
e. Final sequence: The complete genome is uploaded to a database.
D. Proteomic
1. DNA ultimately controls cells.
2. Proteins actually perform the tasks that keep all cells functioning.
3. Proteomics is the field that examines the complete set of proteins encoded by a
genome.
4. The number of human proteins (about 100,000) far exceeds the number of genes
(about 21,000).
6.19 Gene therapy aims to cure genetic diseases.
• CORE IDEA: Human gene therapy involves the production of a recombinant retrovirus
carrying an RNA version of a normal human gene. The virus can infect bone marrow
cells, transferring the proper gene to a diseased individual.
A. Gene therapy
1. Many human diseases are caused by a mutation in a single gene.
2. Gene therapy is the alteration of a person’s genes in order to treat a disease.
3. It works in theory, and some people have been cured.
B. Obtaining a healthy gene
1. Gene therapy begins by isolating a normal gene from a healthy person.
2. Enzymes are used to produce an RNA version of the target DNA gene.
3. This RNA gene is then combined with an infectious, but harmless, retrovirus (a virus
with an RNA genome).
4. The retrovirus most commonly used is a crippled version of the cold virus.
C. Injecting the healthy gene
1. Once the recombinant retrovirus has been engineered to carry the healthy gene, that
gene needs to get inside a diseased person’s cells.
2. Bone marrow cells are ideally suited for this purpose because they multiply for a long
time.
a. Take bone marrow cells from the patient.
b. Infect bone marrow cells with recombinant retrovirus.
i. Inside the bone marrow cell, RNA for the normal gene is converted into DNA.
ii. That DNA inserts itself into the cell’s genome.
3. The goal is to cure the patient, perhaps permanently, with a single injection.
D. A case study in gene therapy
1. Severe combined immunodeficiency disease (SCID)
a. This disease is caused by the absence of an enzyme required in the immune system.
b. SCID patients must remain isolated within protective “bubbles.”
c. SCID patients succumb to infections that would be easily fought off by a normal
immune system.
2. Since 2000, gene therapy has cured 22 children with SCID.
a. Four of the patients developed leukemia and one died because the retrovirus caused
some blood cells to become cancerous.
3. Gene therapy remains promising, but there is little evidence of safe and effective
applications.
4. Research continues with new, tougher safety regulations.
Key Terms

Base Double helix Polynucleotide
Base pair Nucleic acid Sugar
Deoxyribonucleic acid Nucleotide
DNA Phosphate
DNA replication Semi-conservative
Deoxyribonucleic acid Ribonucleic acid
DNA RNA
Codon mRNA Translation
Messenger RNA Transcription
Exon RNA polymerase Transcription
Intron RNA splicing
Promoter Terminator
Anticodon rRNA Translation
Codon Start codon Triplet code
Ribosome Stop codon tRNA
Ribosomal RNA Transfer RNA
Elongation Initiation Termination
Barr body Gene regulation Transcription factor
Exon Intron X chromosome inactivation
Gene expression microRNA
Development Induction
Homeotic gene Signal transduction pathway
Carcinogen Mutation Silent mutation
Missense mutation Nonsense mutation
Mutagen Point mutation
6.11 Loss of gene expression control can result in cancer.
Cancer Oncogene Tumor suppressor gene
Cell cycle control system Proto-oncogene
Growth factor Tumor
Benign tumor Malignant tumor Radiation therapy
Chemotherapy Metastasis Surgery
Biotechnology Genetic engineering Restriction site
DNA ligase Recombinant plasmid Sticky ends
DNA technology Restriction enzyme
Gene cloning Restriction fragment
6.14 DNA may be manipulated in many ways within the laboratory.
cDNA Genome Recombinant DNA
Complementary DNA Genomic library Restriction enzyme
DNA ligase Nucleic acid probe Reverse transcriptase
Genetically modified organism Plasmid Transgenic organism
GMO Recombinant plasmid
DNA polymerase Polymerase chain reaction Thermal cycler
PCR Primer
DNA profiling Short tandem repeats STR analysis
Gel electrophoresis STR
Genome Human Genome Project Whole-genome shotgun method
Genomics Proteomics
Gene therapy
Word Roots
• Poly = much or many
• Semi = half
• Anti = against or opposite
• Micro = very small
• Proto = first
• Onco = tumor or mass
• Trans = across, beyond, or through
Student Misconceptions and Teaching Tips

○ Use the analogy of a ladder to describe the structure of DNA.
The sugar-phosphate backbone is the two sides of the ladder.
The hydrogen bonds are the rungs (or steps) of the ladder.
○ DNA replication can be described as using a copying machine. The idea is to make
identical copies.
○ Unlike a copy machine, semi-conservative replication shows each DNA helix to be half
old and half new.
○ Short movies or animations will help tremendously. You may have to watch several to
find one at an appropriate level for nonmajors. You might try turning off the sound so
that students focus on what is happening and not the complicated description and
abundance of terms.
○ DNA directs the synthesis of proteins. This may be confusing. Where do carbohydrates
and lipids come from? Proteins either are the final product or are the molecular machines
(enzymes) to make the final product. RNA is also made from the DNA (transcription).
○ Contrast replication with transcription/translation.
Replication copies DNA. It’s used only in mitosis or meiosis.
Transcription/translation makes proteins—used in every cell every second of your
life.
○ Transcription is like shorthand for those who remember that term. It’s kind of a copy of
DNA.
○ Translation is nucleic acid language being translated into the completely different
language of proteins.
○ A review of the relationship between amino acids and proteins would be helpful.
○ Short movies or animations will help tremendously. You may have to watch several to
find one at an appropriate level for nonmajors. You might try turning off the sound so
that students focus on what is happening and not the complicated description and
abundance of terms.
○ Promoters and terminators are in the DNA sequence. They mark the start and end of a
gene.
Compare to start and stop codons that are in the mRNA (Module 6.6).
○ Transcription is not a copy of the entire DNA.
mRNA is kind of a copy of DNA.
mRNA is in RNA, not DNA; it’s only one gene, not all of them; it is modified to
remove introns; and it has a “cap” and “tail” that are not from the DNA sequence.
○ Introns and exons are difficult to remember. Introns are “in between” the coding regions.
Watch for students who associate “intron” with what is kept in, or “exon” with what
is exited from the mRNA.
○ If you cover Module 6.18, refer the students to RNA splicing to explain how one gene
can make more than one protein.
○ There are three kinds of RNA: rRNA, tRNA, and mRNA. All three are made by
translation. We focus on mRNA, but tRNA and rRNA are made the same way. DNA
codes for proteins and RNA.
○ Short movies or animations will help tremendously.
You may have to watch several to find one at an appropriate level for nonmajors.
You might try turning off the sound so that students focus on what is happening and
not the complicated description and abundance of terms.
○ A glucose-digesting enzyme is part of cellular respiration. Every cell has to do cellular
respiration to make ATP to live. That gene will be turned on in every cell.
○ The hemoglobin gene is turned on only in red blood cells. Students may not know the
difference between red and white blood cells.
○ An analogy for signal transduction is the following: Someone comes to the door of the
room (signal molecule). This person can’t come in the room, so she or he passes a message
to someone standing in the doorway (receptor protein embedded in plasma membrane). The
person at the door relays this message to someone standing inside the room (relay proteins).
The message is then taken to the instructor standing at the lectern (DNA in the nucleus).
○ Mutations can be good (beneficial), bad (harmful), or nothing at all (silent).
○ A mutation can be nothing at all if it is silent. Redundancy in the genetic code covers up
for minor mutations that do not change the amino acid at all.
○ A missense mutation may change the protein very little or very much depending on the
switch.
You might show students amino acid structures just to show how some are similar
and some are very different.
Sickle-cell disease is a single nucleotide change; it changes a single amino acid,
which significantly changes the structure of hemoglobin.
○ Frameshift mutations can be illustrated using three-letter words.
Original: THE CAT ATE THE RAT.
Insertion: THE CAT ART ETH ERA T.
Deletion: THE _ATA TET HER AT.
6.11 Loss of gene-expression control can result in cancer.
○ Why would we have genes for cancer? We don’t. We have genes that control the cell
cycle. Proto-oncogenes are normal healthy genes that, if they go wrong (turn into
oncogenes), can cause cancer. Oncogenes are discovered when we find the cause of a
particular kind of cancer. Then we look for the original (unmutated) gene. That original
gene is then a proto-oncogene.
○ Growth factors can be described as the “gas pedal” for cell division. Tumor suppressor
genes are the “brakes.” Both are required to control the speed of cell division in each cell.
If one is faulty, the cell may speed out of control.
○ Students will feel they know a great deal about cancer. Encourage them to share their
knowledge and use it to guide discussion.
○ Be prepared for students who have had cancer themselves or have a family member or
friend who has had cancer.
○ The human insulin story is an excellent case history of the use of genetic engineering.
A quick Web search will reveal details students will find interesting and easy to relate to.
Many people may have or know someone who has insulin-dependent diabetes.
○ Examples of the genetically modified crops in the text would be excellent case studies.
Students will find the general information more interesting if it is tied to a story they relate to.
○ A short video or animation can be very useful in conveying the idea of PCR.
○ The fact that PCR targets specific sequences will be further explored in Module 6.17.
○ The Innocence Project makes a very interesting case study for this topic. The use of
modern DNA profiling on old cases has released many unjustly imprisoned individuals.
Do a Web search for the project’s home page.
○ Refer the students to Module 6.5 on RNA splicing to explain how one gene can make
several proteins.
○ The Human Genome Project has many interesting individuals and technological
discoveries. Bring the real face of science into the class as you describe some of the
people involved in the project.
○ A case study on SCID would bring a human face to gene therapy.
Class Activities
○ A simple diagram of DNA can be made from any Internet source. Remove the labels.
Allow students—working individually, in in-class groups, or at home with homework—
to label the parts. Use an image that is not identical to that on page 116.
○ Illustrate semi-conservative replication with strips of cloth or yarn. Larger items will have
to be used in larger lecture halls. The original two halves of the DNA helix should be in
one color. The “new” DNA should be in another color. Ask students how DNA
might be copied.
If the original DNA is blue and the new DNA is orange, will the original blue DNA
helix peel apart, copy in orange and . . . what next?
Will the two blues go together and the two oranges go together? No, that’s
conservative.
Will a blue and an orange go together? Yes, that’s semi-conservative.
○ Depending on your expectations, you might ask the students to practice the base-pairing
rules.
If I give you a strand of DNA that is ATGC, what is the matching strand? TACG
• This text does not emphasize the 3′-5′ orientation of the DNA molecule.
Many different examples can easily be made.
○ A table for comparison of DNA and RNA can be made. Include similarities as well as
differences.
○ Given a list of terms, students can (individually or in groups, in or out of class) draw the
flow of genetic information through the cell.
Terms: nucleus, cytoplasm, DNA, RNA, ribosome, protein, nuclear pore, nuclear
envelope, transcription, translation
○ From the Instructor Exchange in MasteringBiology: Students Perform a Protein Synthesis
Play. Posted on June 1, 2011, by Instructor Exchange, written by Kelly A. Hogan and
James Oh, University of North Carolina at Chapel Hill.
rules.
If I give you a strand of DNA that is ATGC, what is the matching strand of mRNA?
UACG
• This text does not emphasize the 3′-5′ orientation of the DNA molecule.
rules.
If I give you a strand of mRNA that is UAC, what is the matching anticodon on the
tRNA? AUG
• This text does not emphasize the 3′-5′ orientation of the molecules.
○ An interesting class activity would be to act out the process of translation. Use two chairs
to represent the two pockets in a ribosome. Student volunteers will be tRNA bringing in
an amino acid (amino acid name written on note card or sheet of paper). Make an mRNA
sequence. Have the students “read” the mRNA, and the appropriate tRNA brings the
amino acid and sits down. Transfer the growing amino acid chain as appropriate. You
might staple or tape the amino acids together.
○ Have students suggest other cell types or other genes that might be added to the chart on
page 128.
○ Ask students what the difference is between a duck foot and a chicken foot. Obviously,
the webbing is different. How does this benefit the chicken or duck? Chickens walk.
Having webbing would be a bad trait. Ducks swim. Having webbing is beneficial. A bird
had a mutation that never removed the webbing between its toes. Is that bad or good?
Depends on whether this is a walking bird or a swimming bird. This is a good foreshadow
of natural selection.
○ Induction is also involved in a tadpole’s tail being reabsorbed as it changes into an adult,
and in human females shedding the lining of the uterus during menstruation.
○ Different examples of mutation can be provided to students as exercises.
○ Using the table on page 133, what type of mutation is given? How much will this
mutation change the protein?
6.11 Loss of gene-expression control can result in cancer.
○ Without books or notes, ask students to predict the outcome of a mutation using the
figures for mutated oncogene, growth factor, and tumor suppressor gene.
○ Ask students why surgery cannot be used for all types of cancer. If you miss some cells or
the cancer has spread, it can return.
○ What are the side effects of radiation or chemotherapy? Hair loss, vomiting, nausea, and
so forth, are all associated with killing fast-growing cells. The goal is to kill the cancer
(the patient’s own cells gone wrong) before harming the patient too greatly.
○ Ask for suggestions on ways to prevent cancer. Be prepared for excellent suggestions and
pseudoscience.
○ Ask students to bring in examples of the use of genetic engineering in the news.
Genetically modified organisms (GMO) are often in the news. Discuss how the genetic
engineering was done. What was the source of the gene being inserted?
6.14 DNA may be manipulated many ways within the laboratory.
○ Practice the idea of complementary base pairing by having students make their own
nucleic acid probe. Pass out short DNA sequences. Ask student to create the
complementary DNA strand as a probe.
○ Consider a debate on the pros and cons of genetically modified organisms. Do a Web
search for instructions on how best to conduct a debate in class that maintains order and
civility as well as maintains scientific facts as a basis of discussion.
6.16 PCR can be used to multiple samples of DNA.
○ Model PCR.
Create a short DNA sequence down a sheet of paper. Make one copy on a sheet of
paper. Use large letters to make the activity easier. Pass out additional pieces of
paper to the class. Sheets of paper may be cut into quarters lengthwise to save paper.
Start with the original DNA sequence. Cut it in half down the DNA helix. Ask what
step this represents.
Give each half to a student. The student writes the complementary base pair
sequence on their sheet of paper. Ask what step this represents.
Both halves of the DNA are present now and hydrogen bonding would occur. Ask
what step this represents. This is the end of the first cycle.
Each student passes their DNA pieces to 2 new people who copy the DNA
sequence. This is the end of the second cycle.
Repeat for multiple cycles. How many new copies of DNA are generated at the end
the series of cycles? Are they identical to the original DNA sample?
○ Paper-based activities are available that would make excellent activities in or out of class.
Do a Web search for STR analysis or gel electrophoresis.
○ To simulate the whole-genome shotgun method, find a paragraph from any book. Copy
partial phrases from the paragraph. Make sure that parts of the phrases overlap. Pass these
phrases out to individual students or student groups in class. Have them talk to each other
to find overlapping sequences to reconstruct the paragraph.
○ As an in-class discussion or on a discussion board, ask students or teams of students to
invent their own gene therapy cure. They must choose a disease that is due to a mutation
of a single gene and explain the background and importance of their chosen disease.

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Biology The Core 2nd Edition Simon

DNA: The Molecule of Life

Copyright © 2017 Pearson Education, Inc. 75

Gene type Intestinal cell Nerve cell White blood cell

6.1 DNA is a polymer of nucleotides.

Student Misconceptions and Teaching Tips

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