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Chapter 15
Lecture Outline

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 Chapter 15
Mutation, DNA Repair,
and Cancer
Key Concepts:
• Consequences of Mutations
• Causes of Mutations
• DNA Repair
• Cancer

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 Cancer-causing pollutants

During the past two decades, over 25% of the beluga whales in Canada’s St.
Lawrence Seaway have died of cancer. Biologists speculate that these deaths are
caused by cancer-causing pollutants, such as polycyclic aromatic hydrocarbons.

© McGraw-Hill Education ©Yvette Cardozo/Workbook Stock/Getty Images 3

 Mutation
• A heritable change in the genetic material
• Essential to the continuity of life
Source of variation for natural selection
• New mutations are more likely to be harmful
than beneficial
• DNA repair systems reverse DNA damage
• Cancer is a disease caused by gene mutations

© McGraw-Hill Education 4
 Point mutation examples
• Base substitution
5’ – CCCGCTAGATA – 3’ 5’ – CCCGCGAGATA – 3’
→
3’ – GGGCGATCTAT – 5’ 3’ – GGGCGCTCTAT – 5’

• Add or delete a single base pair

5’ – GGCGCTAGATC – 3’ 5’ – GGCAGCTAGATC – 3’
→
3’ – CCGCGATCTAG – 5’ 3’ – CCGTCGATCTAG – 5’

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 Table 15.1
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Table 15.1 Consequences of Point Mutations

Within the Coding Sequence of a
Protein-Encoding Gene
Mutation in Effect on
the DNA polypeptide Example*
None None

Base Silent—causes
substitution no change

Base Missense—
substitution changes one
amino acid in
the polypeptide
Base Nonsense—
substitution changes a normal
codon to a stop
codon
Addition Frameshift—
of a single produces a
base different amino
acid sequence
*
DNA sequence in the coding strand. This sequence is the same as the mRNA sequence except that
RNA contains uracil (U) instead of thymine (T).

© McGraw-Hill Education 6
 Gene mutations may affect amino acid
sequences 1

• Silent mutation
Does not alter the amino acid sequence
Due to degeneracy of genetic code
• Missense mutation
Changes a single amino acid in a polypeptide
May not alter function if a substituted amino acid is
similar in chemistry to original
But significant in Sickle-cell disease

© McGraw-Hill Education 7
 Gene mutations may affect amino acid
sequences 2

• Nonsense mutation
Change from a normal codon to a stop codon
Produces a truncated polypeptide
• Frameshift mutation
Addition or deletion of nucleotides (excluding
multiples of 3)
Completely different amino acid sequence
downstream from mutation

© McGraw-Hill Education 8
 A missense mutation in sickle cell disease

© McGraw-Hill Education a: ©Mary Martin/Science Source; b: ©Science Source; c: Courtesy of Thomas Wellems and Robert Josephs. Electron Microscopy and Image Processing Laboratory, University of Chicago 9
 Gene mutations outside of coding
sequences
• A mutation may alter the sequence within a
promoter and affect the rate of transcription
May enhance or inhibit transcription
• Mutations may occur in other regulatory
elements or operator sites
Mutation may alter DNA sequence of operator so
that repressor protein does not bind

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 Effects of Mutations Outside of the Coding
Sequence of a Gene
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Sequence Effect of mutation

Promoter May increase or decrease the rate of
transcription
Transcriptional regulatory May alter the regulation of transcription
element/operator site
Splice sites May alter the ability of pre-mRNA to be
properly spliced
Translational regulatory May alter the ability of mRNA to be
element translationally regulated
Intergenic region Not as likely to have an effect on gene
expression

© McGraw-Hill Education 11
 Germ-line or somatic cell mutations
• The time and location of a mutation
determines its severity and the heritability
• Germ-line cells give rise to gametes
Mutation can occur in sperm or egg cell, or in
gamete progenitor cells
• Somatic cells are all other body cells
Can occur early or late in development
Gives a genetic mosaic with patches of mutant
tissue

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 Germ line vs somatic mutations

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 Somatic mutation

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 Spontaneous or induced mutations
• Spontaneous mutations
From abnormalities in biological processes
Rates vary from species to species and gene to gene
Background mutation rate approximately 1 mutation /
million genes
• Induced mutations
Caused by environmental agents
Higher rate than spontaneous mutations
Mutagens – chemical or physical agents that alter DNA

© McGraw-Hill Education 15
 Table 15.4

Table 15.4 Some Common Causes of Gene Mutations

Common causes of Description
mutations
Spontaneous
Errors in DNA replication A mistake by DNA polymerase may cause a point mutation.
Toxic metabolic products The products of normal metabolic processes may be reactive
chemicals such as free radicals that can alter the structure of D NA.
Changes in nucleotide On rare occasions, the linkage between a purine and deoxyribose
structure can spontaneously break. Changes in base structure (isomerization)
may cause mispairing during D NA replication.
Transposons As discussed in Chapter 21, transposons are small segments of D NA
that can insert at various sites in the genome. If they insert into a
gene, they may inactivate the gene.
Induced
Chemical agents Chemical substances, such as benzo(a)pyrene, a chemical found in
cigarette smoke, may cause changes in the structure of D NA.
Physical agents Physical agents such as U V (ultraviolet) light and X-rays can damage
DNA.

© McGraw-Hill Education 16
 Examples of Mutagens
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Mutagen Effect(s) on DNA structure

Chemical
Nitrous acid Deaminates bases
5-Bromouracil Acts as a base analogue
2-Aminopurine Acts as a base analogue
Nitrogen mustard Alkylates bases
Ethyl methanesulfonate (EMS) Alkylates bases
Benzo α  pyrene Inserts between bases in the DNA
double helix and causes additions or
deletions
Physical
X-rays Causes base deletions, single nicks
in DNA strands, crosslinking, and
chromosomal breaks
UV light Promotes pyrimidine dimer formation,
which involves covalent bonds between
adjacent pyrimidines (C and T)

© McGraw-Hill Education 17
 Mutagens alter DNA
Disruption of base-pairing
Some modify nucleotide structure
• Nitrous acid deaminates bases, changing C to U, so that it
pairs with the wrong nucleotide
• Mustard gas or EMS alkylate bases, adding methyl or ethyl
groups
Base analogues substitute into DNA

Disruption of replication
Some insert between the bases and distort the helix
• Benzopyrene, found in cigarettes and charbroiled food

© McGraw-Hill Education 18
 Deamination and mispairing of modified base

© McGraw-Hill Education 19
 Physical mutagens
Radiation damage
Ionizing radiation has high energy and penetrates
deeply to create free radicals
• X rays and gamma rays
• Cause deletions or breaks in one or both DNA strands
Nonionizing radiation has less energy and can only
penetrate the surface
• UV rays can cause formation of thymine dimers, causing
gaps or incorporation of incorrect bases

© McGraw-Hill Education 20
 Formation of a thymine dimer

© McGraw-Hill Education 21
 Ames test
• Uses Salmonella typhimurium that cannot
synthesize histidine due to a point mutation
Bacteria cannot grow unless histidine is added to
medium
Or, a second mutation occurs that fixes the original,
allowing synthesis of histidine
• Test monitors rate at which second mutation
occurs
Allows us to test and quantify mutagenicity

© McGraw-Hill Education 22
 Ames test for mutagenicity

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 DNA Repair
• All living organisms require the ability to
repair damage to DNA in order to minimize
mutation
• Two components:
Detection of damage
Repair of damage

© McGraw-Hill Education 24
 Types of repair
• Direct repair
A repair enzyme recognizes an incorrect structure in the DNA
and directly converts it back.
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• Nucleotide excision repair

Portion of DNA strand containing an abnormal nucleotide is
removed and replaced.

• Methyl-directed mismatch repair

A base pair mismatch is detected, and a strand of
© McGraw-Hill Education 25
 Common Types of DNA Repair Systems*

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System Description

Direct repair A repair enzyme recognizes an incorrect

structure in the DNA and directly restores the
correct structure.

Base excision and An abnormal base or nucleotide is recognized, and a

nucleotide excision repair portion of the strand containing the abnormality is
removed. The complementary DNA strand is then used as
a template to synthesize a normal DNA strand.

Methyl-directed mismatch Similar to excision repair except that the DNA defect is a
repair base pair mismatch in the DNA, not an abnormal
nucleotide. The mismatch is recognized, and a strand of
DNA in this region is removed. The complementary strand
is used to synthesize a normal strand of DNA.

*Other types of repair systems exist; these are common examples.

© McGraw-Hill Education 26
 Nucleotide Excision Repair (NER)
• Most common DNA repair system
• Region encompassing several nucleotides in
the damaged strand is removed from the DNA
• Intact undamaged strand is used as a
template for resynthesis of a normal
complementary strand
• Found in all eukaryotes and prokaryotes

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 Nucleotide excision repair in E. Coli

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 NER and human genetic disease
• NER was discovered in humans from genetic
diseases that affect DNA repair
Xeroderma pigmentosum (XP)
Cockayne’s syndrome (CS)
PIBIDS
• Photosensitivity is a common characteristic in
all three syndromes because of an inability to
repair UV-induced lesions

© McGraw-Hill Education 29
 Xeroderma pigmentosum

© McGraw-Hill Education ©Barcroft Media/Getty Images 30

 General information on cancer
• Disease of multicellular organisms
• Characterized by uncontrolled cell division
• Approximately 1.5 million Americans are diagnosed
with cancer each year
• Over 0.5 million will die from the disease
• In about 10% of cancers, a higher predisposition to
develop the disease is an inherited trait
• Most cancers, about 90%, do not involve heritable
genetic changes

© McGraw-Hill Education 31
 Carcinogens
• About 80% of all human cancers are related to
exposure to carcinogens – agents that increase the
likelihood of developing cancer
• Most carcinogens, such as UV light and certain
chemicals in cigarette smoke, are mutagens that
promote genetic changes in somatic cells
• DNA alterations can lead to effects on gene
expression that ultimately affect cell division, and
thereby lead to cancer

© McGraw-Hill Education 32
 Cancer 1

• Cancers originate from a single cell

• Cell and its offspring mutate so cells grow
abnormally
• Tumor – an overgrowth of cells with no useful
purpose
• Tumor may begin as benign or pre-cancerous
Do not invade or spread
• May become malignant

© McGraw-Hill Education 33
 Cancer 2

• Malignant stage
Lost normal growth regulation
Invasive – can invade healthy tissue
Metastatic – can migrate to other parts of the body
• Left untreated, malignant cells will cause the
death of the organism

© McGraw-Hill Education 34
 Cancer: Typical progression and effects

a) Progression of cancer b)Normal lung (left) and cancerous lung (right)

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© McGraw-Hill Education b: ©St. Bartholomew’s Hospital/Science Source 35

 Oncogenes
Cell division regulated by hormones called growth factors
Bind to cell surface and initiate cascade, activating specific
genes, leading to cell division
Mutations in genes for cell growth signaling proteins can
change them into oncogenes – producing abnormally high
level of activity
An oncogene may promote cancer by keeping the cell
division signaling pathway in a permanent “on” position
• In some cancers the amount of gene product is too high
• In others the gene produces a functionally hyperactive protein

© McGraw-Hill Education 36
 Examples of Genes That Encode Signal Transduction Proteins and Can Become Oncogenes

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Gene* Cellular function of encoded protein

erbB Growth factor receptor for EGF (epidermal growth factor)
ras Intracellular signaling protein
raf Intracellular signaling protein
src Intracellular signaling protein
fos Transcription factor
jun Transcription factor
*The genes described in this table are found in humans as well as other vertebrate species. Most
of the genes have been given three-letter names that are abbreviations for the type of cancer the
oncogene causes or the type of virus in which the gene was first identified.

© McGraw-Hill Education 37
 Transduction pathway of a growth factor leading to cell division

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© McGraw-Hill Education 38
 Ras
• Intracellular signaling
protein that hydrolyses
GTP
• When GTP is bound, Ras
promotes cell division
• Oncogenic mutations
may decrease ability of
Ras to hydrolyze GTP or
exchange GDP/GTP
faster
• Both keep signaling
pathway constantly on

© McGraw-Hill Education 39
 Proto-oncogene
Normal gene that, if mutated, can become
an oncogene
Four common genetic changes
• Missense mutations
• Gene amplifications
• Chromosomal translocations
• Retroviral insertions

© McGraw-Hill Education 40
 Missense mutations
Chemical mutagens have been shown to cause
missense mutations leading to cancer

Example- Ras gene mutation changes a specific glycine to valine, decrease the
ability of the Ras protein to hydrolyze GTP
© McGraw-Hill Education 41
 Gene amplifications
Increase in copy number results in too much protein
Many human cancers are associated with
amplification of particular proto-oncogenes

Example-myc gene which encodes transcription factor myc is amplified in

human leukemia
© McGraw-Hill Education 42
 Chromosomal translocations
Two chromosomes break and switch ends
Very specific translocations associated with certain
types of tumors
Can create chimeric genes

© McGraw-Hill Education 43
 Example of a fused gene found in some forms of leukemia

© McGraw-Hill Education 44
 Retroviral insertions
Viral DNA inserts into a
chromosome, putting a viral
promoter next to a proto-
oncogene
• If proto-oncogene
becomes
overexpressed, it will
promote cancer
Some viruses cause
cancer because they
carry an oncogene
in the viral genome

© McGraw-Hill Education 45
 Some cancers caused by viruses
• Majority of cancers are caused by mutagens
• A few viruses are known to cause cancer in
plants, animals, and humans
• Some viruses may cause cancer by modifying
host DNA
• Others carry oncogenes in the viral genome

© McGraw-Hill Education 46
 Examples of Viruses That Cause Cancer

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distribution without the prior written consent of McGraw-Hill Education.

Virus Description
Rous sarcoma virus Causes sarcomas in chickens
Simian sarcoma virus Causes sarcomas in monkeys
Abelson leukemia Causes leukemia in mice
virus
Hardy-Zuckerman 4 Causes sarcomas in cats
feline sarcoma virus
Hepatitis B Causes liver cancer in several species,
including humans

© McGraw-Hill Education 47
 Tumor-suppressor genes
Normal role to prevent cancerous growth
Typical functions:
• Maintain genome integrity by monitoring and/or
repairing DNA damage
• Checkpoint proteins check the integrity of the
genome and prevent a cell from progressing past a
certain point in the cell cycle
• Inhibitors of cell division
• Necessary to properly halt cell division otherwise
division becomes abnormally accelerated

© McGraw-Hill Education 48
 Functions of Selected Tumor-Suppressor Genes
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Gene

Maintenance of genome integrity

p53 p53 is a transcription factor that acts as a sensor of DNA damage. It

can promote DNA repair, prevent the progression through the cell
cycle, and promote apoptosis.

BRCA-1 BRCA-1 and BRCA-2 proteins are both involved in the cellular
BRCA-2 defense against DNA damage. They play a role in sensing DNA
damage and facilitate DNA repair. These genes are mutant in
persons with certain inherited forms of breast cancer.

XPD This represents one of several different genes whose products

function in DNA repair. These genes are defective in patients with
xeroderma pigmentosum.

Negative regulation of cell division

Rb The Rb protein is a negative regulator that represses the

transcription of genes required for DNA replication and cell
division.

NF1 The NF1 protein stimulates Ras to hydrolyze its GTP to GDP. Loss of
NF1 function causes the Ras protein to be overactive, which
promotes cell division.

P16 The p16 protein is a negative regulator of cyclin-dependent kinases

(cdks).

© McGraw-Hill Education 49
 Checkpoint proteins
• Proteins called cyclins and cyclin-dependent
protein kinases (cdks) are responsible for
advancing a cell through the four phases of
the cell cycle
• Formation of activated cyclin/cdk complexes
can be stopped by checkpoint proteins
• p53 – about 50% of all human cancers are
associated with defects in this gene

© McGraw-Hill Education 50
 p53 1

G1 checkpoint protein
• DNA damage induces expression to prevent cell from
progressing from G1 to S phase
• If DNA is repaired, cell may proceed

© McGraw-Hill Education 51
 p53 2

• If the DNA damage is too severe, the p53 protein

will also activate other genes that promote
programmed cell death or apoptosis
• Caspases function as proteases that digest
selected cellular proteins causing the cell to break
down
• It is beneficial for a multicellular organism to kill
an occasional cell with cancer causing potential

© McGraw-Hill Education 52
 Mutation of p53
• When checkpoint genes are broken by mutation, the division
of normal healthy cells may not be affected
• For example, mice that are missing the p53 gene are born
healthy
Cell division leading to normal growth is regulated properly
Checkpoint proteins such as p53 are not necessary for normal cell growth
and division

• However, these mice are very sensitive to mutagens and

easily develop cancer
Loss of checkpoint protein function makes it more likely that genetic
changes will occur that could cause cancerous growth

© McGraw-Hill Education 53
 Negative regulators of cell division
• Second category of a tumor-suppressor gene
• Example: Rb (retinoblastoma)
First tumor-suppressor gene to be identified in
humans by studying patients with the disease
retinoblastoma
Some people have an inherited form that occurs
early
Other forms caused by environmental agents occur
later in life

© McGraw-Hill Education 54
 “Two-hit” model for retinoblastoma
• People have two copies of the Rb gene, one from each parent
• Individuals with the inherited form of the disease have one
mutant gene already from one parent
One additional mutation will cause disease
Tends to occur early in life

• People with the noninherited form of the disease must have

two mutations in the same retinal cell to cause the disease
Two rare events are far less likely than a single event, so the noninherited
form of this disease is expected to occur only
rarely and late in life

© McGraw-Hill Education 55
 Rb protein
• Rb protein inhibits the 1. When E2F is bound to Rb, E2F
is inhibited, and cell division is

transcription factor E2F, prevented.

which activates genes for G1

to S phase cell cycle 2. When a cell is supposed to divide,
Rb is phosphorylated via cyclin-
dependent kinase, causing Rb to
progression dissociate from E2F.

• Binding of functional Rb 3. Unbound E2F becomes activated and

can then bind to DNA, causing target

protein inhibits E2F and gene transcription. Note: If Rb is

inactivated by mutation, E2F will
always be active, thereby promoting
prevents cell division cell division.

• If both copies of Rb are

defective, E2F protein is
always active, resulting in
uncontrolled cell division

© McGraw-Hill Education 56
 Loss of tumor-suppressor gene
function
• Three common ways
Mutation within a tumor-suppressor gene to
inactivate its function
Chromosome loss may contribute if the missing
chromosome carries one or more tumor-suppressor
genes
Abnormal methylation of CpG islands near
promoter regions of the tumor-suppressor gene

© McGraw-Hill Education 57
 Cancer is a series of changes
• Cancer usually requires multiple genetic
changes to the same cell
• Begin with a benign genetic alteration that,
over time and with additional mutations,
leads to malignancy
• Malignancy can continue to accumulate
genetic changes that make it even more
difficult to treat

© McGraw-Hill Education 58
 Lung cancer 1

• Diagnosed in approximately 170,000 people each year in the

U.S.
• Worldwide, more than 1.2 million cases are diagnosed
• Nearly 90% of these cases are caused by smoking and are
thus preventable
• Unlike other cancers for which early diagnosis is possible, lung
cancer is usually detected late, after it has become advanced
and is difficult, if not impossible, to cure
• Five-year survival rate for lung cancer is only approximately
15%

© McGraw-Hill Education 59
 Lung cancer 2

• Most lung cancers are carcinomas – epithelial cell cancers

• Mutations accumulate in basal cells and their numbers
increase – hyperplasia
• As more mutations accumulate, the basal cells develop more
abnormal morphologies – dysplasia
• In early stages, the abnormal basal cells are precancerous
If the source of chronic irritation (like cigarette smoke) is eliminated, the
abnormal cells are likely to disappear
But if smoking continues, these abnormal cells may accumulate
additional genetic changes and lose the ability to stop dividing
These cells are cancerous – patient has basal cell carcinoma

© McGraw-Hill Education 60
 Metastasis
• Metastasis of these cells to other parts of the
body will typically kill the patient within a year
of being diagnosed

© McGraw-Hill Education 61
 Progression of changes leading to lung cancer

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© McGraw-Hill Education (photos): ©Dr. Oscar Auerbach, reproduced with permission 62

 Mutations in Approximately 300 Human Genes
May Promote Cancer
• Not all of these mutant genes found in
cancers have been directly shown to affect
the growth rate of cells
• But such mutations are likely to be found in
tumors because they provide some type of
growth advantage for the cell population
from which the cancer developed
• Over 1% of our genes have potential to
promote cancer if they are mutated
© McGraw-Hill Education 63
 Genetic changes
• Another common genetic change associated with cancer is
abnormal chromosome structure and number
• Comparing cells in normal and tumor cells, there are bizarre
chromosomal abnormalities
• If tumor-suppressor genes are on missing chromosomes,
their function is lost as well
• Extra chromosomes may result in over expression of
oncogenes
• Translocations can result in chimeric genes

© McGraw-Hill Education 64