Principles of Life
Hillis • Sadava • Heller • Price
Instructor’s Manual
Chapter 9: DNA and Its Role in Heredity
OVERVIEW
Chapter 9 covers DNA in depth and opens with a description of the classic experiments
that first confirmed that DNA is the genetic material and then determined its structure;
included is a crucial X-ray diffraction experiment. A portion of the chapter covers DNA
replication, including the topography of replication and the contributions of many
different proteins. The importance of accurate DNA replication is discussed as are the
mechanisms that repair DNA damage. An introduction to PCR (the Polymerase Chain
Reaction) technique that revolutionized molecular biology is included. The chapter ends
with an overview of genetic mutations, including both nucleotide base changes and larger
chromosomal changes, and the possible phenotypic effects of mutations.
KEY CONCEPTS/ CHAPTER OUTLINE
9.1 DNA Structure Reflects Its Role as the Genetic Material
• Circumstantial evidence suggested that DNA was the genetic material
• Experimental evidence confirmed that DNA is the genetic material
• The discovery of the three-dimensional structure of DNA was a milestone in biology
• The nucleotide composition of DNA was known
• Watson and Crick described the double helix
• Four key features define DNA structure
• The double-helical structure of DNA is essential to its function
Scientists used two types of evidence to show that DNA is the genetic material:
circumstantial and experimental. Further experiments allowed for the correct model of
the helical structure to be described. The special structure of the DNA molecule is
essential for its function as the genetic material.
9.2 DNA Replicates Semiconservatively
• DNA polymerases add nucleotides to the growing chain
• The two DNA strands grow differently at the replication fork
• Telomeres are not fully replicated in most eukaryotic cells
• Errors in DNA replication can be repaired
• The basic mechanisms of DNA replication can be used to amplify DNA in a test tube
Experimental evidence supports the semiconservative replication of DNA. DNA
replication takes place in two general steps: the double helix is unwound and DNA
polymerases add nucleotides to the exposed strands. Telomeres are not fully replicated
and they grow shorter with each division. Errors in replication are repaired most of the
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time, and knowing the basic elements of replication allows the use of PCR to amplify
DNA for study.
9.3 Mutations Are Heritable Changes in DNA
• Mutations can have various phenotypic effects
• Chromosomal mutations are extensive changes in the genetic material
• Mutations can be spontaneous or induced
• Some base pairs are more vulnerable than others
• Mutations have both benefits and costs
Mutations in DNA are often expressed as abnormal proteins. However, the result may not
be easily observable phenotypic changes. Chromosomal mutations (deletions,
duplications, inversions, or translocations) involve large regions of a chromosome, while
point mutations result from alterations in single base pairs of DNA. Mutations can be
spontaneous or induced, and may be good or deleterious to the individual; mutations are
the raw material of evolution.
LECTURE OUTLINE
Chapter 9 Opening Question
What can we learn from ancient DNA?
Concept 9.1 DNA Structure Reflects Its Role as the Genetic Material
Scientists had criteria for DNA to be accepted as the genetic material, including that it:
• Be present in the cell nucleus and in chromosomes
• Doubles in the cell cycle
• Is twice as abundant in diploid cells
• Has same the pattern of transmission as its genetic information
DNA was found in the nucleus by Miescher.
He isolated cell nuclei and treated them chemically.
A fibrous substance came out of the solution and he called it “nuclein”.
DNA was found in chromosomes using dyes that bind specifically to DNA.
FIGURE 9.1 DNA in the Nucleus and in the Cell Cycle
IN-TEXT ART, p.166
Dividing cells were stained and passed through a flow cytometer, confirming two other
predictions for DNA:
• Nondividing cells have the same amount of nuclear DNA.
• After meiosis, gametes have half the amount of DNA.
Chromosomes contain DNA, but also contain proteins, so scientists had to determine
whether proteins carried genetic information.
Viruses, such as bacteriophages, contain DNA and a little protein.
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When a virus infects a bacterium, it injects only its DNA into it, and changes the genetic
program of the bacterium.
This provides further evidence for DNA, and not protein, as the genetic material.
(ANIMATED TUTORIAL 9.1 The Hershey-Chase Experiment)
FIGURE 9.2 Viral DNA and Not Protein Enters Host
Transformation experiments showed that DNA from one strain of bacteria could
genetically transform another strain.
DNA can be made to pass through any cell membrane, including egg cells.
It can genetically transform an organism, resulting in a transgenic version of that
organism.
FIGURE 9.3 Transformation of Eukaryotic Cells
After identifying DNA as the genetic material, scientists hoped to answer two questions
about the structure:
1. How is DNA replicated between cell divisions?
2. How does it direct the synthesis of specific proteins?
DNA structure was discovered through the work of many scientists.
One crucial piece of evidence came from X-ray crystallography.
A purified substance can be made to form crystals; the pattern of diffraction of X rays
passed through the crystallized substance shows position of atoms.
Rosalind Franklin:
Prepared crystallographs from uniformly oriented DNA fibers—her images suggested a
spiral model
FIGURE 9.4 X-Ray Crystallography Helped Reveal the Structure of DNA
Chemical composition also provided clues:
DNA is a polymer of nucleotides: deoxyribose, a phosphate group, and a nitrogencontaining base.
The bases form the differences:
• Purines: adenine (A), guanine (G)
• Pyrimidines: cytosine (C), thymine (T)
(See Figure 3.1)
In 1950 Erwin Chargaff found that in the DNA from many different species:
Amount of A = amount of T
Amount of C = amount of G
Or, the abundance of purines = the abundance of pyrimidines—Chargaff’s rule.
IN-TEXT ART, p. 169
Model building is the assembly of 3-D models of possible molecular structures.
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Francis Crick and James Watson used model building and combined all the knowledge of
DNA to determine its structure.
Franklin’s X-ray crystallography convinced them the molecule was helical.
Modeling also showed that DNA strands are anti-parallel.
(VIDEO 9.1 Deoxyribonucleic acid: A three-dimensional model)
FIGURE 9.5 DNA IS a Double Helix
Watson and Crick suggested that:
• Nucleotide bases are on the interior of the two strands, with a sugar-phosphate
backbone on the outside.
• Per Chargaff’s rule, a purine on one strand is paired with a pyrimidine on the other.
These base pairs (A-T and G-C) have the same width down the helix.
Four key features of DNA structure:
• It is a double-stranded helix of uniform diameter.
• It is right-handed.
• It is antiparallel.
• Outer edges of nitrogenous bases are exposed in the major and minor grooves.
(See Figure 3.4)
Grooves exist because the backbones of the DNA strands are not evenly spaced relative
to one another.
The exposed outer edges of the base pairs are accessible for hydrogen bonding.
Surfaces of A-T and G-C base pairs are chemically distinct.
Binding of proteins to specific base pair sequences is key to DNA–protein interactions,
and necessary for replication and gene expression.
(See Figure 9.5B)
FIGURE 9.6 Base Pairs in DNA Can Interact with Other Molecules
DNA has four important functions—double-helical structure is essential:
• Storage of genetic information—millions of nucleotides; base sequence encodes huge
amounts of information
• Precise replication during cell division by complementary base pairing
• Susceptibility to mutations—a change in information—possibly a simple alteration to a
sequence
Expression of the coded information as the phenotype—nucleotide sequence is
transcribed into RNA and determines sequence of amino acids in proteins
(LINK Transcription and translation are described in more detail in Concepts 10.2 and
10.4)
(See Chapter 3)
(See Figure 3.5)
Concept 9.2 DNA Replicates Semiconservatively
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Semiconservative replication means that each parental strand serves as a template for a
new strand.
Conservative replication would show that the intact parental DNA (both strands) serves
as a template.
Evidence from radioactively-labeled strands supports semiconservative replication.
(ANIMATED TUTORIAL 9.2 Experimental Evidence for Semi-Conservative DNA
Replication)
Two steps in DNA replication:
The double helix is unwound, making two template strands available for new base
pairing.
New nucleotides form base pairs with template strands and linked together by
phosphodiester bonds. Template DNA is read in the 3′-to-5′ direction.
(VIDEO 9.2 Cell Visualization: From DNA to chromosomes)
During DNA synthesis, new nucleotides are added to the 3′ end of the new strand, which
has a free hydroxyl group (—OH).
Deoxyribonucleoside triphosphates (dNTPs), or deoxyribonucleotides, are the building
blocks—two of their phosphate groups are released and the third bonds to the 3′ end of
the DNA chain.
(ANIMATED TUTORIAL 9.3 DNA Replication, Part 1: Replication of a Chromosome
and DNA Polymerization)
(See Concept 3.1)
(See Figure 3.2)
FIGURE 9.7 Each New DNA strand Grows by the Addition of Nucleotides to Its 3′ End
DNA replication begins with the binding of a large protein complex—the pre-replication
complex—to a specific site on the DNA molecule.
The complex contains DNA polymerase, which catalyzes addition of nucleotides.
The complex binds to a region on the chromosome called the origin of replication (ori).
(VIDEO 9.3 Cell Visualization: DNA replication)
When the pre-replication complex binds to ori, the DNA unwinds and replication
proceeds in two directions.
The replication fork is the site where DNA unwinds to expose bases.
Eukaryotic chromosomes are linear and have multiple origins of replication, which speed
up replication.
FIGURE 9.8 The Origin of DNA Replication
DNA replication begins with a short primer—a starter strand.
The primer is complementary to the DNA template.
Primase—an enzyme—synthesizes DNA one nucleotide at a time.
DNA polymerase adds nucleotides to the 3′ end.
FIGURE 9.9 DNA FORMS WITH A PRIMER
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DNA polymerases are larger than their substrates, the dNTPs, and the template DNA.
The enzyme is shaped like an open right hand—the “palm” brings the active site and the
substrates into contact.
The “fingers” recognize the nucleotide bases.
FIGURE 9.10 DNA POLYMERASE BINDS TO THE TEMPLATE
A single replication fork opens up in one direction.
• The two DNA strands are antiparallel—the 3′ end of one strand is paired with the 5′ end
of the other.
• DNA replicates in a 5′-to-3′ direction.
FIGURE 9.11 The Two New Strands Form in Different Ways
One new strand, the leading strand, is oriented to grow at its 3′ end as the fork opens.
The lagging strand is oriented so that its exposed 3′ end gets farther from the fork.
Synthesis of the lagging strand occurs in small, discontinuous stretches—Okazaki
fragments.
(ANIMATED TUTORIAL 9.4 DNA replication, Part 2: Coordination of Leading and
Lagging Strand Synthesis)
(APPLY THE CONCEPT DNA replicates semiconservatively)
Each Okazaki fragment requires its own primer, synthesized by the primase.
DNA polymerase adds nucleotides to the 3′ end, until reaching the primer of the previous
fragment.
A different DNA polymerase then replaces the primer with DNA.
The final phosphodiester linkage between fragments is catalyzed by DNA ligase.
FIGURE 9.12 The Lagging Strand Story
DNA polymerase works very fast:
It is processive—it catalyzes many sequential polymerization reactions each time it binds
to DNA
(See Chapter 3)
Okazaki fragments are added to RNA primers to replicate the lagging strand.
When the last primer is removed no DNA synthesis occurs because there is no 3′ end to
extend—a single-stranded bit of DNA is left at each end.
These are cut after replication and the chromosome is slightly shortened after each cell
division.
FIGURE 9.13 Telomeres and Telomerase
Telomeres are repetitive sequences at the ends of eukaryotic chromosomes.
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These repeats prevent the chromosome ends from being joined together by the DNA
repair system.
Telomerase contains an RNA sequence—it acts as a template for telomeric DNA
sequences.
Telomeric DNA is lost over time in most cells, but not in continuously dividing cells like
bone marrow and gametes.
DNA polymerases can make mistakes in replication, but most errors are repaired.
Cells have two major repair mechanisms:
• Proofreading—as DNA polymerase adds nucleotides, it has a proofreading function
and if bases are paired incorrectly, the nucleotide is removed.
• Mismatch repair—after replication other proteins scan for mismatched bases missed
in proofreading, and replace them with correct ones.
FIGURE 9.14 DNA Repair Mechanisms
Copies of DNA sequences can be made by the polymerase chain reaction (PCR)
technique, which uses:
• A double-stranded DNA sample
• Two short primers complementary to the ends of the sequence to be amplified
• The four dNTPs
• A DNA polymerase that works at high temperatures
• Salts and a buffer to maintain pH
(INTERACTIVE TUTORIAL 9.1 Polymerase Chain Reaction (PCR): Identifying
Pathogens)
FIGURE 9.15 The Polymerase Chain Reaction
Mutations are changes in the nucleotide sequence of DNA that are passed on from one
cell, or organism, to another.
Mutations occur by a variety of processes.
Errors that are not corrected by repair systems are passed on to daughter cells.
(See Chapter 8)
Mutations are of two types:
Somatic mutations occur in somatic (body) cells—passed on by mitosis but not to
sexually produced offspring.
Germ line mutations occur in germ line cells that give rise to gametes. A gamete passes
a mutation on at fertilization.
Concept 9.3 Mutations Are Heritable Changes in DNA
Most genomes include genes and regions of DNA that are not expressed:
• Genes are transcribed into RNAs, for translation into amino acid sequences or into
RNAs with catalytic functions.
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The coding regions of a gene contain sequences within the transcribed region that are
translated.
• Genomes also contain regions of DNA that are not expressed.
(See Chapters 10 through 12)
Mutations are discussed in terms of their effects on protein-coding gene function:
• Silent mutations do not affect protein function.
• Loss of function mutations affect protein function and may lead to structural proteins
or enzymes that no longer work—almost always recessive.
(LINK Silent mutations are a source of neutral alleles in evolution; see Concept 15.2)
(See Figure 8.1)
• Gain of function mutations lead to a protein with altered function.
• Conditional mutations cause phenotypes under restrictive conditions, such as
temperature, but are not detectable under permissive conditions.
(See Figure 8.9)
FIGURE 9.16 Mutation and Phenotype
At the molecular level there are two categories of mutations:
A point mutation results from the gain, loss, or substitution of a single nucleotide.
Chromosomal mutations are more extensive—they may change the position or cause a
DNA segment to be duplicated or lost.
Point mutations change single nucleotides.
They can be due to errors in replication or to environmental mutagens.
Point mutations in the coding regions of DNA usually cause changes in the mRNA, but
may not affect the protein.
(LINK The genetic code explains why some point mutations in the coding regions of DNA
are silent; see Figure 10.11)
Other mutations result in altered amino acid sequences and have drastic phenotypic
effects:
• Sickle-cell disease—allele differs from normal by one base pair
• A gain-of-function mutation as in the TP53 gene, which gains cancer-causing function
(VIDEO 9.4 Normal human red blood cells and sickle-cells)
(See In-Text Art, Ch. 3, p. 37)
Chromosomal mutations:
• Deletions—result in the removal of part of the genetic material and can have severe or
fatal consequences.
• Duplications—homologous chromosomes break in different places and recombine
with wrong partners; one may have two copies of segment and the other may have none
FIGURE 9.17 Chromosomal Mutations
Chromosomal mutations:
Inversions—result from breaking and rejoining, but segment is “flipped”
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Translocations—segment of DNA breaks off and is inserted into another chromosome;
this can lead to duplications and deletions
(LINK Another way mutations can occur is through mobile DNA elements called
transposons; see Figure 12.6)
Mutations are caused in two ways:
Spontaneous mutations occur with no outside influence, and are permanent.
Induced mutations are due to an outside agent, a mutagen.
Spontaneous mutations—several mechanisms that alter DNA:
• Errors in replication by DNA polymerase —most errors are repaired but some become
permanent
• Nucleotide bases can have different structures—may form tautomers; a rare tautomer
can pair with the wrong base
Spontaneous mutations:
• Chemical reactions may change bases (e.g., loss of amino group—deamination)
• Imperfect meiosis—nondisjunction of homologous chromosomes may occur
• Gene sequences can be disrupted—random chromosome breakage and rejoining
(See Concept 7.4)
FIGURE 9.18 Spontaneous and Induced Mutations
Induced mutation—caused by mutagens:
• Chemicals can alter nucleotide bases (e.g., nitrous acid can cause deamination)
• Some chemicals add other groups to bases (e.g., benzopyrene adds a group to guanine
and prevents base pairing). DNA polymerase will then add any base there.
Radiation damages DNA:
Ionizing radiation, such as X rays, creates free radicals—highly reactive—can change
bases, break sugar phosphate bonds
UV radiation (from sun or tanning beds) is absorbed by thymine, causing it to form
covalent bonds with adjacent nucleotides—disrupts DNA replication
DNA sequencing revealed that mutations occur most often at certain base pairs.
If 5-methylcytosine loses an amino acid, it becomes thymine, a natural base for DNA.
During mismatch repair, it is repaired correctly only half of the time.
(See Chapter 11)
FIGURE 9.19 5-Methylcytosine in DNA Is a “Hotspot” for Mutations
Mutations can be artificial or natural:
• Human-made chemicals (e.g., nitrites) or naturally occurring substances (e.g., molds)
• Radiation from nuclear reactions, bombs, or from the sun
(See Chapter 28)
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Mutations can have benefits:
• Provide the raw material for evolution in the form of genetic diversity
• Diversity may benefit the organism immediately—if mutation is in somatic cells
• May cause an advantageous change in offspring
Possible costs of mutations:
• Some germ line and somatic cell mutations are harmful or lethal.
• Mutations in oncogenes stimulate cell division in cancer, and mutations in tumor
suppressor cells fail to inhibit growth.
• Public health policy includes bans on ozone-depleting chemicals and on cigarette
smoking, which cause mutations that lead to cancer.
(APPLY THE CONCEPT Mutations are changes in DNA)
(See Chapter 7)
Answer to Opening Question
Ancient DNA is usually destroyed—but can still be studied in samples found frozen or
from the interior of bones.
The PCR reaction is used to amplify tiny amounts of DNA.
DNA from Neanderthals has been sequenced and is over 99% identical to our human
DNA.
Comparisons between humans and Neanderthals are interesting:
Some Neanderthals may have had red hair and fair skin, due to a point mutation in the
gene MC1R.
Neanderthals may have been capable of speech, as their vocalization gene FOXP2 was
identical to humans.
DNA sequences suggest interbreeding of humans and Neanderthals.
FIGURE 9.20 A Neanderthal Child
KEY TERMS
anti-parallel
bacteriophage
base pairs
chromosomal mutations
conditional mutations
deletions
deoxyribonucleoside triphosphates
DNA ligase
DNA polymerase
dNTPs
duplications
gain-of-function mutations
germline mutations
helical
induced mutations
inversions
lagging strand
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leading strand
loss-of-function mutations
mutagens
Okazaki fragments
origin of replication (ori)
PCR
point mutation
polymerase chain reaction
primase
primer
processive
replication forks
semiconservative replication
silent mutations
somatic mutations
spontaneous mutations
telomerase
telomeres
template
transformation
transgenic
translocations
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