CHAPTER 8

Mutation

CHAPTER OUTLINE
Nature of Mutations 117 Special Types of Mutations 120
Categories and Frequencies 117 Trinucleotide Repeats 120
Causes 118 DNA Repair Defects 121
Molecular Types 118 Transposable Elements 122
Effect of Mutations on Transcription, Editing,
and Translation 119

CORE CONCEPT
117
A mutation is a heritable change in the nucleotide sequence or arrangement of DNA. In the positive,
evolutionary sense, mutations are responsible for the selective advantage that one species gains over
another. In the negative sense, mutations cause or increase susceptibility to thousands of human disorders.
Three general categories of mutations exist: genome, chromosome, and gene. Genome mutations result
from missegregration (failure to properly segregate) during meiosis and produce changes in chromosome
number. Chromosome mutations are caused by rearrangements in the structure of a chromosome, such as
translocations or deletions. Gene mutations alter the base sequence of a gene. Mutations occur in germ
cells, somatic cells, and mitochondria. Germ-line mutations affect DNA in all cells and are transmitted to
offspring. Mitochondrial mutations affect mitochondrial DNA, all of which is inherited from the mother’s egg;
accordingly, they are inherited maternally. Somatic mutations affect cells in a single tissue and are not
transmitted to the next generation. Mutations act, generally, by perturbing gene expression or the function of
proteins, and they may do so from the earliest to the latest stages of life.

DNA is not static. Rather its sequence changes at a slow but measurable rate all the time.
Mutations are of central importance to all life forms, including humans. Without mutations, our
species would not have evolved over several billion years. Without mutations, humankind also
would not be faced with a myriad of spontaneous abortions, inherited disorders, or cancers.
Therefore, we must comprehend both the nature of mutations, and the effects they produce.

NATURE OF MUTATIONS
Categories and Frequencies
Three categories of mutations exist (Table 8.1): those that alter the number of chromosomes in
the cell (genome mutations); those that alter the structure of single chromosomes (chromo-
some mutations); and those that alter individual genes (gene mutations). Genome
mutations are the most common, occurring as often as 4
102 per meiotic cell division.

Human Genes and Genomes. DOI: 10.1016/B978-0-12-385212-0.00008-1

Copyright Ó 2012 Elsevier Inc. All rights reserved.
 PART 1
Introduction and Core Concepts

TABLE 8.1 Categories and Frequencies of Human Mutations

Category Mechanism Frequency
2
Genome Chromosome missegregation 2 to 4
10 per cell division
Chromosome Chromosome rearrangement 6
104 per cell division
Gene Base pair change 1010 per base pair per cell division
105 to 106 per locus per cell division

Chromosome mutations are about 100 times less common (6
104/cell division). Gene
mutations take place in about 1010 per base pair per cell division or 105 to 106 per locus per
generation (four orders of magnitude less frequent than chromosome mutations.) Genome and
chromosome mutations will be discussed further in Chapter 11. Gene mutations will be
detailed here and in Chapter 12.

Causes
Most mutations are spontaneous, that is, they occur in the absence of any known cause. We are
aware of some causes. Water, for example, can cause a purine base (G or A) to separate from
DNA’s backbone (called depurination). The DNA repair system, to be discussed later in this
chapter, may replace, for instance, G with A, thereby leading to a base change after the next
round of replication. Oxidation (the addition of oxygen to a molecule), too, can lead to base
changes. Other mutations are induced by chemicals, ultraviolet light, or radiation, all of
which can break nucleotide chains or damage nucleotide bases. The vast majority of DNA
damage is repaired by specific enzymes almost immediately and has no deleterious effects.
Those new mutations that go unrepaired are copied during subsequent rounds of replication
and may be transmitted to subsequent generations of cells.
118
Mutations that occur in cells destined to be germ cells are called germ-line mutations. Such
mutations are transmitted during meiosis and mitosis to all cells of the body. Other muta-
tions, called somatic mutations, arise in cells of only one tissue or organ. They affect,
therefore, only that organ’s structure and function and are not transmitted to the next
generation. Finally, mutations can also occur in the mitochondrial chromosome. These
mutations are transmitted, but only by the mother, because the egg is the source of the
zygote’s mitochondria.
A number of studies in flies, worms, mice, and humans have come to the same general
conclusion: a given gene mutates in about 1 in 100,000 (1
105) gametes. Because
humans have about 21,000 genes, this rate computes to 2
104
105¼ 0.2 mutations per
generation per haploid gamete. The mutation rate of some genes is decidedly higher than
105; for other genes, decidedly lower. It seems likely that diploid organisms, like humans,
can tolerate a relatively high mutation rate without ill effect because we have two alleles for
each gene.

Molecular Types
Many kinds of mutations can change the usual (called the wild-type) DNA sequence to
a mutant one (Figure 8.1). A substitution occurs when a base at a certain position on one
strand of the DNA molecule is replaced by any of the other three bases (A/G, C, or T). During
the next round of replication, the substituted base will be paired with its appropriate base-
paired partner. Substitution of one purine for another purine (for example, A to G) or of one
pyrimidine for another pyrimidine (e.g., C to T) is called a transition. Substitution of a purine
for a pyrimidine (such as A to C) is called a transversion.
Other types of mutations are more complex (and rarer) than substitutions. A deletion occurs
when one or more nucleotide pairs in a DNA molecule are lost. Most deletions remove one
 CHAPTER 8
Mutation

Starting sequence

T C T C G C A T G G T A G G T
A G A G C G T A C C A T C C A

Type of mutation and effect on base sequence

A Substitution
Transition: Purine for purine, pyrimidine for pyrimidine

T C T C G C A T A G T A G G T
A G A G C G T A T C A T C C A

Transversion: Purine for pyrimidine, pyrimidine for purine

T C A C G C A T G G T A G G T
A G T G C G T A C C A T C C A

B Insertion
A A
T T

T C T C A A G C A T G G T A G G T
A G A G T T C G T A C C A T C C A
FIGURE 8.1
Classes of mutations affecting
C Deletion
DNA structure. See text for further
T C T C T G G T A G G T definition of substitution, insertion,
A G A G A C C A T C C A deletion, and inversion.

G C
A
C G
T

D Inversion 119
Site of inversion
5′ 3′
T C T C G C A T G G T A G G T
A G A G C G T A C C A T C C A
3′ 5′

3′
G
5′ A T G C
T A C C G C
T A C 5′
A T G G
3′
5′ 3′
T C T T A C C A T G C G G G T
A G A A T G G T A C G C C C A
3′ 5′

to six nucleotides, but a few are much larger, removing whole genes or chromosomal regions.
An insertion is just the opposite: addition of one or more nucleotide pairs to the DNA
molecule. Inversions are more complex still: a 180 rotation of a segment of DNA, without
either loss or gain in nucleotide number.

Effect of Mutations on Transcription, Editing, and Translation

Mutations can, and do, affect every step in the sequence of events required for gene expression
(see Chapter 7). Most mutations eliminate or reduce gene function and are called loss-of-
function mutations. Mutations that completely eliminate function are called null or
“knockout” mutations. A mutation that reduces but doesn’t eliminate expression of a gene is
referred to as a hypomorphic one. In contrast, mutations that increase gene expression are
referred to as gain-of-function mutations (Table 8.2).
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Introduction and Core Concepts

TABLE 8.2 Classes and Distinguishing Features of Mutations

Parameter Affected Types of Mutations Major Features
Gene function Loss-of-function (null) Eliminates normal function
Hypomorphic Reduces normal function
Gain of function Increases normal function
Molecular change Nucleotide substitution (point) One base pair replaces another
Transition Purine (A or G) to purine
Pyrimidine (C or T) to pyrimidine
Transversion Purine (A or G) to pyrimidine
Insertion Addition of one or more nucleotides
Deletion Removal of one or more nucleotides
Transcription Promotor, enhancer, start site elongation, Interferes with or accelerates process
termination
Editing Changes splice sites or exone intron borders Alternate splicing produces mRNA
with changed exon structure
Translation Silent (synonymous) No change in encoded amino acid
Missense (nonsynonymous) Change in encoded amino acid
Nonsense Creates termination codon
Frameshift Shifts triplet reading out of correct phase

Loss-of-function mutations can affect transcription, editing, or translation. Many affect the
transcriptional apparatus: start sites, promoters, enhancers, termination signals. Those
affecting RNA splicing can reduce the rate of mRNA formation or inhibit splicing at a given site
entirely. If splicing is qualitatively changed, the mRNA will not contain the information to
encode precisely its polypeptide or protein. In analogous ways, translation may be altered.
120 Mutations can interfere with the ability to initiate polypeptide chain formation, can result in
incorporation of the “wrong” amino acid, can cause premature termination, or can lead to
failure to add post-translational chemical signals.
Another set of terms is used here:
l Missense mutations (or “non-synonymous” ones) are substitutions that change one
amino acid into a different one.
l Silent mutations (or synonymous ones) are substitutions in DNA that do not change the
amino acid even though they change the triplet coding for it.
l Nonsense mutations convert a triplet coding for an amino acid into a terminator codon,
thereby truncating the polypeptide.
l Frameshift mutations result from insertion or deletion of one or two nucleotides and
throw off the triplet reading frame, thereby changing all subsequent amino acid residues in
the growing polypeptide chain.

Special Types of Mutations

TRINUCLEOTIDE REPEATS
The human genome contains many trinucleotide repeats (including, but not limited to, CGG,
CGG, CGG) as part of its normal sequence. In 1992, a novel kind of mutation was discovered
by human geneticists studying an X-linked disorder called the Fragile X syndrome. They
discovered that affected males had more than 200 CGG repeats at a site on the X chromosome,
compared to less than 50 repeats in normal subjects. Mothers of the affected males had
50e100 of these repeats. Such trinucleotide expansion was not stabledit tended to increase in
length from one generation to the next (Figure 8.2). Subsequent study revealed that such
expansion of trinucleotide repeats is responsible for another 10 human disorders, and has
been found in other animals as well.
 CHAPTER 8
Mutation

Starting sequence

C G G C G G ... T A T G A C
<50
G C C G C C ... A T A C T G

Premutation FIGURE 8.2

C G G C G G C G G C G G ... T A T G A C Trinucleotide repeat expansion. The starting sequence in
>50
G C C G C C G C C G C C ... A T A C T G healthy subjects has fewer than 50 CGG/GCC repeats, while
those with triplet repeat premutations have > 50 and those
with disease-causing mutations > 100 repeats, and the size of
Mutation the expansion increases with each generation.
C G G C G G C G G C G G C G G C G G ... T A T G A C
>100
G C C G C C G C C G C C G C C G C C ... A T A C T G

The rules governing the cause, expansion, and instability of trinucleotide repeats are not
completely understood. We know the following: the larger the number of repeats at a site, the
higher the probability that expansion will occur and function as a mutation; the longer the
expansion, the earlier the onset of signs and symptoms; and large tracts of repeats affect DNA
structure such that replication errors occur, leading to aberrant starting and stopping, called
“replication stuttering.”

DNA REPAIR DEFECTS

Every minute the human genome is damaged at approximately three sites (1 per billion
nucleotides). Such damage may be produced by physical or chemical agents in the envi-
ronment or by endogenous errors in the machinery that conducts DNA replication. This
amount of DNA damage would be intolerable to the survival of the organism, so all 121
organisms are equipped with a number of different enzymatically controlled systems that
scan DNA molecules for errors and repair them. Table 8.3 summarizes some of the types of
DNA damage and the corresponding DNA repair system. For example, a base modified by
a chemical is removed by the excision-repair enzyme system. A different system, called
mismatch repair, identifies a mismatch in the double-stranded DNA (such as A/G, rather
than A/T) and corrects it.
These DNA repair systems are highly effective. They deal with damage before it becomes
a transmitted mutation. Every cell has its own complement of DNA repair enzymes. In rare
instances, however, one DNA repair system or another is, itself, mutated, resulting in unre-
paired changesdmutations throughout the genome that are deleterious. One such disorder,
xeroderma pigmentosum (XP), is characterized by a large number of skin cancers. XP results
from a specific defect in a repair enzyme that removes thymine dimers (TeT), abnormally
bonded bases caused by exposure to ultraviolet light. Such individuals must avoid exposure to

TABLE 8.3 Types of DNA Damage and Mechanism of Repair

Type of Damage Major Mechanism of Repair
Nicks in DNA strand Repaired by DNA ligase
Uracil present in DNA Uracil removed by DNA uracil glycosylase
Mismatched bases Corrected by mismatch repair (excision and resynthesis)
Apurinic or apyrimidinic site Repaired by AP endonuclease repair system
Pyrimidine dimers (from UV light) Enzymatically reversed
Damaged region of DNA Excision repair (excision and resynthesis across partner
strand)
 PART 1
Introduction and Core Concepts

sunlight to compensate for strong predisposition to cancer. Another DNA repair defect leads to
familial colon cancer.

TRANSPOSABLE ELEMENTS
In the 1940s, Barbara McClintock discovered a genetic element in maize that caused mottling
in kernels as well as breaks in chromosomes. This element did not have a constant location;
rather, it was transposed from one place to another where it caused chromosome damage.
Since then, such transposable elements (or transposons) have been found in most organ-
isms. Numerous families of transposable elements are now recognized. They are responsible
for mutagenic events in many simple plants and animals, including mammals. The human
genome contains many transposable elements with names like SINE, Alu, LINE, and LTR.
Together they constitute nearly half of genomic DNA.
Whereas transposable elements are responsible for a significant fraction of mutations up to
and including the mouse, they cause fewer than 0.5% of mutations in humans. They appear to
be evolutionary remnants, but likely retain some functional role. SINE elements may promote
translation under circumstances of stress; Alu sequences are found in abundance near coding
sequences, suggesting that there is some reason for their being there. Importantly, there is little
evidence that any of these elements are movable in humansdthat they retain their capacity to
transpose.

IMPLICATIONS: MOLECULAR BIOLOGY AND DISEASE

Pneumococcal DNA Morphs to Dodge Vaccines
For nearly 30 years researchers around the world have studied the evolution of a single strain of
122 Streptococcus pneumoniae. More than 240 samples of this strain have been characterized since 1984,
when it was first identified in Spain. Observations from laboratories in seven countries have given us
insight as to why it is so difficult to create a vaccine or antibiotic that will continue to fight this bacterium.
The answer to this question emerged with the development of new technology that allows speedy
genomic sequencing.

It was found that the DNA of Streptococcus pneumoniae is constantly mutating and that the strain has
turned over about three-quarters of its genome since it was first identified. The mutations in the DNA are
a result of both recombination, in which pieces of DNA are moved around, and substitutions, where
individual nucleotides in the DNA sequence are changed.

Vaccines and antibiotics, which target specific gene clusters in the DNA of the bacterium, are thrown off
the track and cease being effective as a result of these mutations. Any mutation in the DNA, however,
must be such that the bacteria can still be viable and infect its human host. It is, then, remarkable that
viability and pathogenicity has been sustained after so much change in the DNA.

A B C

(A) Lung tissue showing streptococcal infection; (B) & (C) Enlargement of Streptococcus pneumoniae.
 CHAPTER 8
Mutation

REVIEW QUESTIONS AND EXERCISES

1. Choose the phrase in the right column that best matches the term in the left column (each term in the left
column refers to a particular type of mutation).
a. transition 1. occur in the absence of any known cause
b. mitochondrial 2. addition of one or more bases
c. silent mutation 3. occur in tissue cells, not gametes
d. deletion 4. missegregation of chromosome(s)
e. chain terminator 5. maternally inherited
f. spontaneous 6. substitution of purine for pyrimidine
g. genomic 7. caused by environmental exposure
h. frameshift 8. does not change amino acid
i. trinucleotide repeat 9. occur in cells destined to become gametes
j. chromosomal 10. substitution of one purine for another purine
k. induced 11. removal of one or more bases
l. gene 12. affects single gene
m. germ-line 13. results in formation of terminator codon (also called nonsense)
n. insertion 14. change in a single base
o. somatic 15. results in a structural rearrangement of whole chromosome
p. substitution (missense) 16. affects triplet reading frame thereby changing all subsequent triplets
q. transversion toward the 3’ end of the mRNA
17. expansion of trinucleotide units in a gene

2. Suppose that the most common mutation in a gene responsible for a particular genetic disorder has
changed an isoleucine residue to an asparagine. Assuming single base substitution mutations:
a. How many different substitutions could change isoleucine to asparagine?
b. List the codon changes that expand your answer to part (a).
3. Describe two general forms of RNA splicing mutations and their respective effects on mRNA
formation. 123
4. Single base substitutions often cause no deleterious phenotype. Describe briefly three ways this could
occur.

5. If a highly mutable human gene has a mutation rate of 5
104 per generation and if that gene is
followed generation after generation, how many generations, on average, will it take before the gene
undergoes a mutation? Show your work.

6. As far as the genetic code is concerned, the successive triplets beyond the point of a frameshift
mutation become random.
a. Of the major classes (not categories) of mutations discussed, are there any that may not change the
reading frame?
b. How often, on average, would you expect a stop codon to appear after a frameshift mutation?

7. In some disorders caused by trinucleotide repeat expansion mutations, the mutation occurs within an
intron, in others within an exon. Speculate on the ways these different mutations could produce
phenotypic abnormalities.

8. The most common mutation causing cystic fibrosis results in deletion of a single phenylalanine residue
at position 508 of the protein involved. Describe the molecular mutation responsible.

9. The following normal amino acid sequence represents part of a protein:

elyseargehisehisetyreleue
a. What is the one double-stranded DNA sequence of the gene (of many possible ones) corresponding
to this amino acid sequence?
b. What kind of mutation would produce the following amino acid sequence?
elysegluethresereleuesere
c. What kind of mutation would produce the following amino acid sequence?
elyseargeileeileeilee
 PART 1
Introduction and Core Concepts

10. Describe how mutation in each of the following might be expected to interfere with normal gene
function.
a. Promoter
b. Initiator codon
c. DNA helicase.

124