L6 - DNA Mutations
Learning Objectives
At the end of this section, students should be able to:
Describe a few common types of DNA mutations and how mutations in protein coding genes are predicted to affect protein function.
Describe how mutations arise spontaneously and can be induced.
Explain what a transposable element is.
Compare and contrast pathways of DNA repair.
True Statements about DNA Mutations
Which of the following is TRUE about DNA mutations? (select all that apply)
A. Mutations do not occur naturally during DNA replication. (False)
B. Some chemicals induce DNA mutations. (True)
C. Mutations can cause diseases and disorders. (True)
D. Mutations generate variation among individuals in a population. (True)
E. Studying mutations helps researchers better understand how organisms work. (True)
Effects of DNA Mutations on Phenotypes
What type of effects can DNA mutations have on organismal phenotypes? (select all that apply)
a. Detrimental
b. Beneficial
c. Neutral
Definitions of DNA Mutations
DNA mutations are defined as 'Inherited' changes in DNA sequence.
Inheritance can occur:
From one cell to another within an individual (known as somatic mutations).
Across generations (known as germ-line mutations).
Germ-line mutations can be passed on to offspring, whereas somatic mutations are not transmitted to offspring.
Types of DNA Mutations
DNA mutations consist of significant categories:
Gene and chromosomal mutations:
Not all mutations are detrimental.
Some mutations lead to variation, which can result in new, beneficial traits emerging in a population (adaptive evolution!).
Subtypes of Gene Mutations
Types of gene mutations include:
Base substitutions:
Transitions: A purine replaces a purine, or a pyrimidine replaces a pyrimidine.
Transversions: A purine replaces a pyrimidine, or a pyrimidine replaces a purine.
Insertions and deletions (Indels):
Frameshift mutations: Change the reading frame of the gene.
In-frame insertions and deletions: Do not alter the reading frame (insertion or deletion of a multiple of three nucleotides).
Expanding nucleotide repeats: Increases in the number of copies of a set of nucleotides.
Diseases Associated with Gene Mutations
Many diseases are associated with expanding nucleotide repeats, such as:
Lou Gehrig's disease (Amyotrophic lateral sclerosis; ALS): Characterized by a GGGGCC repeat in the coding region that is translated.
Fragile X syndrome: Involves a CGG repeat which is methylated, reducing gene expression.
Huntington's disease: Caused by a CAG repeat in the coding region.
Example of a Mutation Identification Scenario
Imagine you are working in a lab and identifying different types of mutations in bacteria:
Original gene sequence: 5'-TGA GTC TGA AGT CC-3'.
Mutation found: 5'-TGA GTC GGA AGT CC-3'. This mutation can be best described as:
A. Expanding nucleotide repeat
B. Transversion
C. Transition
D. Insertion
E. Deletion
F. Frameshift mutation
G. Base substitution
Effects of Substitution Mutations on Protein Function
Substitutions of DNA bases in protein coding genes can lead to various effects on the protein:
Mis-sense mutations: Not all amino acid substitutions carry the same impact (consider conservative vs. nonconservative substitutions). The relationship with amino acid structure and properties (polarity/charge) is critical.
Base substitutions can cause:
Shifts in the reading frame, leading to premature stop codons.
Examples of Specific Mutations
A mutation in a gene changes the mRNA product codon from UGU to UGA.
This example illustrates:
a) Silent mutation
b) Missense mutation
c) Synonymous mutation
d) Nonsense mutation
e) Frameshift mutation
The substitution of lysine for arginine in a protein with no detectable effect exemplifies:
A. Synonymous mutation.
B. Frameshift mutation.
C. Conservative substitution.
D. Nonconservative substitution.
Types of Gene Mutations by Phenotypic Effect
Gene mutations usually have varying effects:
Which type of gene mutation in a protein-coding gene is least deleterious?
a) Expansion of a trinucleotide repeat
b) Missense substitutions
c) Nonsense substitutions
d) Base deletions
e) Base insertions
Mutation Types and their Direction
Mutation Types:
Forward mutation: Wild type → mutant type.
Reverse mutation: Mutant type → wild type (“reversion”).
Suppressor mutation: A second mutation that hides/suppresses the effect of the first mutation, which can occur within the same gene (intra-genic suppressor) or different genes (inter-genic suppressor).
Wild Type Allele in Genetics
The term ‘wild type allele’ means:
a) Allele (gene copy) that is most common in a natural population.
b) Allele (gene copy) that has a new mutation.
c) Allele (gene copy) that produces the phenotype with the highest fitness.
Organism with a Suppressor Mutation
An organism bearing a suppressor mutation is classified as:
a) single mutant.
b) double mutant.
c) reverse mutant.
d) wild-type.
Characteristics of Different Types of Gene Mutations
Table 13.2 - Characteristics:
Base Substitution:
Transition: A purine replaces a purine or a pyrimidine replaces a pyrimidine.
Transversion: A purine replaces a pyrimidine or vice versa.
Insertions and Deletions (Indels):
Insertion: Addition of one or more nucleotides.
Deletion: Removal of one or more nucleotides.
Frame-shift mutation: Alters the reading frame of a gene.
In-frame mutation: Deletion or insertion of a multiple of three nucleotides that does not alter the reading frame.
Expanding nucleotide repeats: Increase the number of copies of a nucleotide set (e.g., CAG).
Effects of Missense and Other Mutations
Effects of mutations include:
Missense mutation: Changes sense codon, leading to a different amino acid in the protein.
Nonsense mutation: Alters a sense codon to a stop codon, causing premature termination of translation.
Silent mutation: Modifies sense codon into a synonymous codon without changing the amino acid sequence.
Neutral mutation: Alters the amino acid sequence without affecting functionality.
Lethal mutation: Results in premature death.
DNA Mutation Rates
Mutation Rates:
Surprising that they are low considering the complexities of DNA replication.
DNA replication has a high fidelity of 1 error per 1 billion nucleotides! With proofreading enzymes, mutations can be repaired through various mechanisms.
Approximately 1-10 mutations in a million gametes (ranging from to mutations per gamete). ( ext{Mutation rate} ext{ varies among species.} )
Comparative Mutation Rates of Viruses
Example:
Coronviruses, as enveloped positive-sense RNA viruses, exhibit lower mutation rates due to having a 3’ exonuclease proofreading mechanism when compared to viruses like HIV and Hepatitis C, characterized by 1-2 × 10⁻⁶ mutations/nucleotide/replication cycle.
Causes of Mutations
Factors contributing to DNA mutations:
Spontaneous mutations:
Include base substitutions, tautomeric shifts, and mispairing due to structural anomalies (e.g., wobble in flexible DNA regions).
If an error is incorporated and subsequently replicated, it becomes permanent as repair systems may not detect it.
Examples of Spontaneous mutations:
Depurination: Loss of purine.
Deamination: Loss of an amino group.
Oxidative damage.
Mechanism Behind Indels and Their Occurrence
Indels: Insertions and deletions resulting from strand slippage during DNA replication occur more frequently in than in . They tend to have a significant effect on phenotype when occurring in _ but not when occurring in due to __.
Induced Mutations
Chemical Induced Mutations:
Alkylating agents: Add alkyl groups leading to base substitutions.
Base analogs: Similar to natural bases, leading to increased mis-pairing.
Intercalating agents: Distort DNA helical structure, potentially causing indels.
Ultraviolet (UV) Light:
Prone to causing pyrimidine dimers, blocking replication and inducing structural distortions.
Utilized to kill bacteria as it stalls cellular division.
Ionizing Radiation:
High energy radiation increases mutation rates by displacing electrons, resulting in free radicals and reactive ions that alter bases and break DNA backbones, possibly causing various chromosome mutations.
Transposable Elements (TEs)
Definition:
Mobile sequences known as “jumping genes” which can insert themselves throughout the genome.
Discovery: Originated from ancient viruses integrated within genomes.
Characteristics of Transposable Elements
TEs:
Often flanked by terminal inverted repeats recognized by transposase.
Generate flanking direct repeats upon insertion that are not part of the TE itself.
Modes of Transposition:
TEs may move as DNA (cut-paste mechanism) or be transcribed to RNA and then reverse-transcribed to DNA (copy-paste mechanism).
Frequencies of Transposable Elements in the Genome
Human Genome Composition:
TEs are thought to constitute a significant percentage of the genome (e.g., options: 0%, 25%, 50%, 75%, 100%).
Mutagenic Effects of Transposable Elements
TEs can induce mutations via:
Inserting into other genes affecting either coding or regulatory regions.
Promoting DNA rearrangements through mechanisms like unequal crossing over.
Associated with a notable percentage of spontaneous mutations in Drosophila and contributing to human genetic diseases (e.g., hemophilia, cancers, tauopathies).
Chromosomal Mutations
Types of Chromosomal Mutations:
Change Structure of chromosomes: Breakage and rearrangement.
Change Number of chromosomes: Aneuploidy or polyploidy.
Change Number of Sets: Variation in haploid/diploid nature.
Survival with Mutagenic TEs
Epigenetic Silencing: Majority of TEs in the genome are silenced by:
siRNAs (small interfering RNAs) and piRNAs (piwi-interacting RNAs).
Presence: TEs can thrive, increasing in copy number without detrimental effects on the host's fitness, often located in non-functional genomic regions without expressed genes.
Examples: The Tc1 transposable element in C. elegans is silenced by siRNA, with many TEs found in heterochromatic regions, such as centromeres and introns. Some TEs become non-functional due to mutations, losing their capacity to transpose.