This document discusses silent mutations, which are DNA mutations that do not change the amino acid sequence of a protein. It defines silent mutations and describes their causes and types. While silent mutations do not alter the primary protein structure, they can impact secondary and tertiary protein structures as well as mRNA structure and stability. The document provides examples of research using silent mutations for vaccine development and their implications in mental disorders.

1. Shahjalal University of Science & Technology,
Sylhet
Assignment on:
Silent Mutation
Course name: Seminar and Oral
Course code: BMB 300
Submitted by:
Name: Sadaqur Rahman
Reg. No.: 2010433022
Semester: 3/2
Department of Biochemistry & Molecular Biology

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Contents
1. Introduction:...........................................................................................................................3
2. Mutation:................................................................................................................................4
Causes of mutation.............................................................................................................................4
I. Spontaneous mutation..................................................................................................................4
II. Error prone replication by-pass ..................................................................................................4
III. Errors introduced during DNA repair .......................................................................................5
IV. Induced mutation ......................................................................................................................5
Mutation types: ..................................................................................................................................6
I. Point mutation..............................................................................................................................6
 Missense mutation:..................................................................................................6
 Nonsense mutation: .................................................................................................6
 Insertion mutation:...................................................................................................7
 Deletion mutation:...................................................................................................7
 Silent mutaion:.........................................................................................................8
II. Frameshift mutation ...................................................................................................................8
III. Repeat expansion: .....................................................................................................................9
3. Silent mutation:....................................................................................................................10
4. Structural consequences of silent mutations........................................................................11
I. Primary structure...........................................................................................................................11
II. Secondary structure......................................................................................................................11
III. Tertiary structure.........................................................................................................................11
5. Research and clinical applications.......................................................................................12
6. References:...........................................................................................................................13

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Figures
Figure 1: Missense mutation......................................................................................................6
Figure 2: Nonsense mutation .....................................................................................................6
Figure 3: Insertion mutation.......................................................................................................7
Figure 4: Deletion mutation.......................................................................................................7
Figure 5: Silent mutaion.............................................................................................................8
Figure 6: Frameshift mutation ...................................................................................................8
Figure 7: Repeat expansion mutation ........................................................................................9
Tables
Table 1: Codon Chart.............................................................................................................................. 9

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1. Introduction:
A gene mutation is a permanent change in the DNA sequence that makes up a gene.
Mutations range in size from a single DNA building block (DNA base) to a large segment of
a chromosome.
Gene mutations occur in two ways: inherited from a parent & acquired during a person’s
lifetime.
Mutations that are passed from parent to child are called hereditary mutations or germline
mutations (because they are present in the egg and sperm cells, which are also called germ
cells). This type of mutation is present throughout a person’s life in virtually every cell in the
body.
Acquired or somatic mutations occur in the DNA of individual cells at some time during a
person’s life. These changes can be caused by environmental factors such as ultraviolet
radiation from the sun, or can occur if a mistake is made as DNA copies itself during cell
division. Acquired mutations in somatic cells (cells other than sperm and egg cells) cannot be
passed on to the next generation.
Some genetic changes are very rare; others are common in the population. Genetic changes
that occur in more than 1 percent of the population are called polymorphisms. They are
common enough to be considered a normal variation in the DNA. Polymorphisms are
responsible for many of the normal differences between people such as eye color, hair color,
and blood type. Although many polymorphisms have no negative effects on a person’s
health, some of these variations may influence the risk of developing certain disorders.
Mutation can result in several different types of change in sequences. Mutations in genes can
either have no effect, alter the product of a gene, or prevent the gene from functioning
properly or completely.
Mutations can occur in non-coding regions (outside of genes within introns), or they may
occur within exons. When they occur within exons they either do not result in a change to the
amino acid sequence of a protein. So the change can not be found in the phenotype. This type
of mutation is termed as silent mutation.

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2. Mutation:
A mutation is a change of the nucleotide sequence of the genome of an organism. Mutations
result from unrepaired damage to DNA or to RNA genomes (typically caused by radiation or
chemical mutagens), errors in the process of replication, or from the insertion or deletion of
segments of DNA by mobile genetic elements. Mutations may or may not produce
discernible changes in the observable characteristics (phenotype) of an organism. Mutations
play a part in both normal and abnormal biological processes including: evolution, cancer,
and the development of the immune system.
Causes of mutation
A mutation occurs whenever there is a change in the genetic information of an organism, due
to a variety of causes. They can be classified into four classes, They are:
(1) spontaneous mutations (molecular decay)
(2) mutations due to error prone replication by-pass of naturally occurring DNA damage (also
called error prone translesion synthesis)
(3) errors introduced during DNA repair
(4) induced mutations caused by mutagens.
I. Spontaneous mutation
Spontaneous mutations on the molecular level can be caused by:
• Tautomerism — A base is changed by the repositioning of a hydrogen atom, altering the
hydrogen bonding pattern of that base, resulting in incorrect base pairing during replication.
• Depurination — Loss of a purine base (A or G) to form an apurinic site (AP site).
• Deamination — Hydrolysis changes a normal base to an atypical base containing a keto
group in place of the original amine group. Examples include C → U and A → HX
(hypoxanthine), which can be corrected by DNA repair mechanisms; and 5MeC (5-
methylcytosine) → T, which is less likely to be detected as a mutation because thymine is a
normal DNA base.
• Slipped strand mispairing — Denaturation of the new strand from the template during
replication, followed by renaturation in a different spot ("slipping"). This can lead to
insertions or deletions.
II. Error prone replication by-pass
There is increasing evidence that the majority of spontaneously arising mutations are due to
error prone replication (translesion synthesis) past a DNA damage in the template strand.
DNA damage (naturally occurring), naturally occurring DNA damages arise about 60,000 to

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100,000 times per day per mammalian cell. In mice, the majority of mutations are caused by
translesion synthesis. Likewise, in yeast, Kunz et al. found that more than 60% of the
spontaneous single base pair substitutions and deletions were caused by translesion synthesis.
III. Errors introduced during DNA repair
Although naturally occurring double-strand breaks occur at a relatively low frequency in
DNA (see DNA damage (naturally occurring)) their repair often causes mutation. Non-
homologous end joining (NHEJ) is a major pathway for repairing double-strand breaks.
NHEJ involves removal of a few nucleotides to allow somewhat inaccurate alignment of the
two ends for rejoining followed by addition of nucleotides to fill in gaps. As a consequence,
NHEJ often introduces mutations.
IV. Induced mutation
Induced mutations on the molecular level can be caused by:-
• Chemicals
• Hydroxylamine NH2OH
• Base analogs (e.g., BrdU)
• Alkylating agents (e.g., N-ethyl-N-nitrosourea) These agents can mutate both
replicating and non-replicating DNA. In contrast, a base analog can mutate the DNA only
when the analog is incorporated in replicating the DNA. Each of these classes of chemical
mutagens has certain effects that then lead to transitions, transversions, or deletions.
• Agents that form DNA adducts (e.g., ochratoxin A metabolites)
• DNA intercalating agents (e.g., ethidium bromide)
• DNA crosslinkers
• Oxidative damage
• Nitrous acid converts amine groups on A and C to diazo groups, altering their
hydrogen bonding patterns, which leads to incorrect base pairing during replication.
• Radiation
• Ultraviolet radiation (nonionizing radiation). Two nucleotide bases in DNA —
cytosine and thymine — are most vulnerable to radiation that can change their properties. UV
light can induce adjacent pyrimidine bases in a DNA strand to become covalently joined as a
pyrimidine dimer. UV radiation, in particular longer-wave UVA, can also cause oxidative
damage to DNA.

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Mutation types:
There are two classes of mutation: point mutations and frameshift mutations.
I. Point mutation
A point mutation is a change in one or a few base pairs in a gene. Point mutations can be
divided into general categories:
 Missense mutation:
This type of mutation is a change in one DNA base pair that results in the substitution of one
amino acid for another in the protein made by a gene.
Figure 1: Missense mutation
 Nonsense mutation:
A nonsense mutation is also a change in one DNA base pair. Instead of substituting one
amino acid for another, however, the altered DNA sequence prematurely signals the cell to
stop building a protein. This type of mutation results in a shortened protein that may function
improperly or not at all.
Figure 2: Nonsense mutation

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 Insertion mutation:
An insertion changes the number of DNA bases in a gene by adding a piece of DNA. As a
result, the protein made by the gene may not function properly.
Figure 3: Insertion mutation
 Deletion mutation:
A deletion changes the number of DNA bases by removing a piece of DNA. Small deletions
may remove one or a few base pairs within a gene, while larger deletions can remove an
entire gene or several neighboring genes. The deleted DNA may alter the function of the
resulting protein(s).
Figure 4: Deletion mutation

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 Silent mutaion:
This type of mutation is a change in one DNA base pair but that does not result in an amino
acid change in a polypeptide.
Figure 5: Silent mutaion
II. Frameshift mutation
This type of mutation occurs when the addition or loss of DNA bases changes a gene’s
reading frame. A reading frame consists of groups of 3 bases that each code for one amino
acid. A frameshift mutation shifts the grouping of these bases and changes the code for amino
acids. The resulting protein is usually nonfunctional. Insertions, deletions, and duplications
can all be frameshift mutations.
Figure 6: Frameshift mutation

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There are some other kind of mutation:
III. Repeat expansion:
Nucleotide repeats are short DNA sequences that are repeated a number of times in a row.
For example, a trinucleotide repeat is made up of 3-base-pair sequences, and a tetranucleotide
repeat is made up of 4-base-pair sequences. A repeat expansion is a mutation that increases
the number of times that the short DNA sequence is repeated. This type of mutation can
cause the resulting protein to function improperly.
Figure 7: Repeat expansion mutation

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3. Silent mutation:
Silent mutations are DNA mutations that do not result in a change to the amino acid
sequence of a protein. Silent mutations can occur in non-coding regions (outside of genes
within introns), or they may occur within exons. When they occur within exons they either do
not result in a change to the amino acid sequence of a protein or result in the insertion of an
alternative amino acid with similar properties to that of the original amino acid, and in either
case there is no significant change in phenotype.
The cause is that most amino acids are specified by multiple codons demonstrating that the
genetic code is degenerate. Codons that code for the same amino acid are termed synonyms
(Table 1). Silent mutations are base substitutions that result in no change of the amino acid or
amino acid functionality when the altered messenger RNA (mRNA) is translated. For
example, if the codon AAA is altered to become AAG, the same amino acid--lysine—will be
incorporated into the peptide chain.
Table 1: Codon Chart

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4. Structural consequences of silent mutations
I. Primary structure
A nonsynonymous mutation that occurs at the genomic or transcriptional levels is one that
results in an alteration to the amino acid sequence in the protein product. A protein’s primary
structure refers to its amino acid sequence. A substitution of one amino acid for another can
impair protein function and structure, or its effects may be minimal or tolerated depending on
how closely the properties of the amino acids involved in the swap correlate. The premature
insertion of a stop codon, a nonsense mutation, can alter the primary structure of a protein. In
this case, a truncated protein is produced. Protein function and folding is dependent on the
position in which the stop codon was inserted and the amount and composition of the
sequence lost.
Conversely, silent mutations are mutations in which the amino acid sequence is not altered.
Silent mutations lead to a change of one of the letters in the triplet code that represents a
codon, but despite the single base change, the amino acid that is coded for remains
unchanged or similar in biochemical properties. This is permitted by the degeneracy of the
genetic code.
II. Secondary structure
Silent mutations alter the secondary structure of mRNA. mRNA has a secondary structure
that is not necessarily linear like that of DNA, thus the shape that accompanies
complementary bonding in the structure can have significant effects. For example, if the
mRNA molecule is relatively unstable, then it can be rapidly degraded by enzymes in the
cytoplasm. If the RNA molecule is highly stable, and the complementary bonds are strong
and resistant to unpacking prior to translation, then the gene may be underexpressed. Codon
usage influences mRNA stability.
If the oncoming ribosome pauses because of a knot in the RNA, then the polypeptide could
potentially have enough time to fold into a non-native structure before the tRNA molecule
can add another amino acid. Silent mutations may also affect splicing, or transcriptional
control.
III. Tertiary structure
Silent mutations affect protein folding and function. Recent research suggests that silent
mutations can have an effect on subsequent protein structure and activity. The timing and rate
of protein folding can be altered, which can lead to functional impairments.

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5. Research and clinical applications
Silent mutations have been employed as an experimental strategy and can have clinical
implications.
Steffen Mueller at the Stony Brook University designed a live virus vaccine for polio in
which the pathogen was engineered to have synonymous codons replace naturally-occurring
ones in the genome. As a result, the virus was still able to infect and reproduce, albeit more
slowly. Mice that were vaccinated with this vaccine and exhibited resistance against the
natural polio strain.
In molecular cloning experiments, it can be useful to introduce silent mutations into a gene of
interest in order to create or remove recognition sites for restriction enzymes.
Mental disorders can be caused by silent mutations. One silent mutation causes the dopamine
receptor D2 gene to be less stable and degrade faster, underexpressing the gene.
A silent mutation in the multidrug resistance gene 1 (MDR1), which codes for a cellular
membrane pump that expels drugs from the cell, can slow down translation in a specific
location to allow the peptide chain to bend into an unusual conformation. Thus, the mutant
pump is less functional.
Deviations from average pain sensitivity (APS) are caused by both an ATG to GTG mutation
(nonsynonymous), and a CAT to CAC mutation (synonymous). Ironically, these two
mutations are both shared by the Low pain sensitivity (LPS) and High pain sensitivity (HPS)
gene. LPS has an additional CTC to CTG silent mutation, while HPS does not and shares the
CTC sequence at this location with APS

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6. References:
1. Mutation- Wikipedia, the free encyclopedia:
http://en.wikipedia.org/wiki/Mutation
2. Silent mutation- Wikipedia, the free encyclopedia:
http://en.wikipedia.org/wiki/Silent_mutation
3. Synonymous substitution- Wikipedia, the free encyclopedia:
http://en.wikipedia.org/wiki/Synonymous_substitution
4. "Silent" mutations are not always silent | The Scientist Magazine®:
http://www.the-scientist.com/?articles.view/articleNo/24630/title/-Silent--mutations-are-not-
always-silent/
5. Mutations and Health- Genetics Home Reference.
http://ghr.nlm.nih.gov/handbook/mutationsanddisorders
6. Beckman (2006) The Sound of a Silent Mutation.
https://courses.marlboro.edu/pluginfile.php/18898/mod_page/content/1/The_Sound_of_a_Sil
ent_Mutation.pdf
7. Strachan T, Read AP (1999). Human Molecular Genetics. 2nd edition.
8. Teng S, Madej T, Panchenko A, Alexov E (March 2009). "Modeling effects of human
single nucleotide polymorphisms on protein-protein interactions". Biophys. J. 96 (6): 2178–
88.
9. Angov E (June 2011). "Codon usage: nature's roadmap to expression and folding of
proteins". Biotechnol J 6 (6): 650–9.
10. Czech A, Fedyunin I, Zhang G, Ignatova Z (October 2010). "Silent mutations in sight: co-
variations in tRNA abundance as a key to unravel consequences of silent mutations". Mol
Biosyst 6 (10): 1767–72.
11. Komar AA (August 2007). "Silent SNPs: impact on gene function and phenotype".
Pharmacogenomics 8 (8): 1075–80.
12. Kimchi-Sarfaty C, Oh JM, Kim IW, et al. (January 2007). "A "silent" polymorphism in
the MDR1 gene changes substrate specificity". Science 315 (5811): 525–8.
13. Komar, A. A. "GENETICS: SNPs, Silent But Not Invisible." Science 315.5811 (2007):
466-67.