👎 Week 11 - Mutations

Mutations and DNA Repair: Section Outline

• Mutation – the source of all genetic variability

• Types of gene mutations

• Functional effects of mutations

• Suppressor mutations

• Mutation rates

• Molecular mechanisms of mutation

• Mechanisms of DNA repair

Learning Objectives: Mutations and DNA Repair

 Explain why DNA mutations are the source of phenotypic variation
 Explain why many DNA mutations do not affect phenotype
 List three ways DNA mutations can occur
 Identify how mutations are detected and repaired
 Recognize that mutations often pass through an intermediate stage that can be repaired to avoid mutation
 Describe the types of chromosomal rearrangements

Mutations

Definition
 Change in the nucleotide sequence of an organism’s genome
 Source of all genetic variability

Causes
 Agents that damage DNA: UV light, certain chemicals, viruses
 Random errors during DNA replication

Effects on Phenotype
 Generate nonfunctional proteins
 Alter protein function
 Change when and where a gene is expressed

Mutant
 Organism carrying one or more mutations in its genetic material

Mutations

Occurrence
 Spontaneous – occur naturally at low rates
 Induced – caused by mutagens

Effects
 Change DNA sequence
 May alter or eliminate encoded proteins
 Phenotypic consequences may or may not occur

Genetic Variation and Mutation

Mutation
 Occurs in all organisms with genetic material, from viruses to humans
 Source of all genetic variation

Natural Selection
 Preserves gene combinations that are best adapted to the environment
 Drives evolution

Recombination During Meiosis
 Homologous chromosomes exchange segments
 Rearranges genetic variability into new gene combinations

Key Point
 Mutation is the fundamental source of all genetic variability

Types of Mutations

Somatic Mutations
 Occur in somatic (body) cells
 Affect only the descendants of that cell
 Not transmitted to offspring

Germinal (Germ Line) Mutations
 Occur in germ-line (reproductive) cells
 Transmitted to progeny through gametes

Types of Mutations

A. Base Substitutions
 Transition
  Replacement of a purine with another purine (A ↔ G) or a pyrimidine with another pyrimidine (C ↔ T)
 Transversion
  Replacement of a purine with a pyrimidine or vice versa

B. Insertions and Deletions
 Frameshift Mutations
  Addition or loss of nucleotides that shifts the reading frame
 In-Frame Insertions and Deletions
  Addition or loss of nucleotides in multiples of three, preserving the reading frame

C. Tautomeric Shifts
 Movement of hydrogen atoms within bases
 Can cause mispairing during DNA replication

Base Substitutions - 12 Possibilities

Transition (same base type switch)
 Replaces a pyrimidine with another pyrimidine (C ↔ T) or a purine with another purine (A ↔ G)

Transversion (opposite base type switch)
 Replaces a pyrimidine with a purine or a purine with a pyrimidine

Frameshift Mutations

Definition
 Insertion or deletion of one or two base pairs that changes the reading frame of the gene

Effect on Protein
 Protein sequence changes dramatically after the site of the mutation

Tautomeric Shifts

Definition
 Reversible change in the location of a hydrogen atom in a molecule
 Alters the molecule from one isomer to another
 Specifically, movement of H⁺ atoms within purine or pyrimidine bases

Occurrence
 Rare and can happen spontaneously during DNA replication
 Alters base pairing and can cause spontaneous mutations

Tautomeric Shifts

Effect on Base Pairing
 Can generate rare A:C and G:T base pairs during DNA replication

Mechanism
 Occurs when bases adopt their rare enol or imino forms

Tautomeric Shift Mutations: Example Mechanism

Normal Base
 Guanine (G) in its normal keto form pairs correctly with cytosine (C)

Rare Tautomeric Form
 Guanine shifts to its rare enol form (G*)
 This form mispairs with thymine (T) during DNA replication

Replication Process
 Parental DNA contains G in normal keto form
 During replication, G* pairs with T instead of C
 First-generation progeny contains half normal half G paired with T
 Second-generation contains ¾ normal and ¼ mutant since G paired with C correctly from first-gen progeny parent but T paired with A which wasn’t there before

Result
 A single base change occurs: G → A transition mutation
 Mutation appeared in second gen progeny

Tautomeric Shifts

Definition
 Bases have two isomers called tautomers
 When a base temporarily adopts its rare tautomeric form, it can pair with the wrong base
 This leads to a mismatch during DNA replication

Types of Point Mutations

Missense Mutation
 Codon change results in a different amino acid

Nonsense Mutation
 Codon change converts a sense codon into a stop codon

Silent Mutation
 Codon change results in a synonymous codon, amino acid remains the same

Functional Effects of Mutations

Missense Mutation
 Base substitution changes an amino acid in the protein

Nonsense Mutation
 Base substitution converts a sense codon into a stop codon (UAG, UGA, UAA)

Silent Mutation
 Base substitution changes the codon but still specifies the same amino acid

Key Point
 Mutations are classified based on how they affect gene or protein function

Silent Point Mutation

Definition
 Result from the gain, loss, or substitution of a single DNA base pair

Effect in Coding Regions
 May be silent or may change the amino acid sequence of the protein

Silent Point Mutation
 Occurs at a redundant (synonymous) site of a codon
 Expression of the wild-type gene sequence is NOT maintained

Missense Point Mutation

Effects on Protein
 May change a single amino acid (missense)
 May cause loss of amino acids at the carboxyl terminus

Missense Point Mutation
 Occurs at a nonsynonymous site of a codon
 Changes the identity of a single amino acid
 Amino acid properties can change (e.g., negatively charged → nonpolar/hydrophobic)

Missense vs. Nonsense Mutations

Missense Point Mutation
 Occurs at a nonsynonymous site of a codon
 Changes a single amino acid in the protein

Nonsense Point Mutation
 Converts a sense codon into a stop codon
 Causes premature termination of translation
 Shortens the polypeptide

General Effect
 Point mutations may change an amino acid or cause loss of amino acids at the carboxyl terminus of the protein

Point Mutations in Coding Regions

Frame-Shift Point Mutation
 Insertion or deletion changes the reading frame
 Drastically alters the sequence of the resulting polypeptide

Loss-of-Stop Mutation
 Eliminates the normal stop codon
 Translation continues until a new stop codon is reached
 Can extend or alter the C-terminal end of the protein

Effects of Single Base Mutations

Silent Mutation
 No effect on protein sequence
 Example: AGG → Arginine, AGA → Arginine

Nonsense Mutation
 Changes a codon to a stop codon
 Results in truncation of the protein
 Example: TGA = stop

Missense Mutation
 Changes one amino acid in the protein
 Can be conserved (similar properties, e.g., AAA → Lysine)
 Or non-conserved (different properties, e.g., AGT → Serine)

Types and Effects of Gene Mutations

Base Substitutions (Point Mutations)
 Can be transitions or transversions
 Silent Mutation – Codon changes but still specifies the same amino acid, no effect on protein
 Missense Mutation – Codon changes to a different amino acid
  Can be conserved (similar properties, e.g. AAA → Lysine)
  Or non-conserved (different properties, e.g. AGT → Serine)
 Nonsense Mutation – Codon changes to a stop codon (UAG, UGA, UAA)
  Causes premature termination, truncating the polypeptide

Frameshift Mutations
 Insertion or deletion of one or two nucleotides
 Alters the reading frame
 Drastically changes amino acid sequence downstream

Loss-of-Stop Mutation
 Eliminates normal stop codon
 Translation continues to next stop codon, extending or altering the C-terminal end

Insertions and Deletions (In-Frame)
 Addition or loss of nucleotides in multiples of three
 Preserves reading frame
 Adds or removes amino acids without shifting downstream sequence

Tautomeric Shifts
 Bases temporarily adopt rare forms (enol or imino)
 Mispairing occurs during DNA replication (e.g., A:C, G:T)
 Can result in point mutations like transitions or transversions

A. Base Substitutions
 Transition
  Replacement of a purine with another purine (A ↔ G) or a pyrimidine with another pyrimidine (C ↔ T)
 Transversion
  Replacement of a purine with a pyrimidine or vice versa

B. Insertions and Deletions
 Frameshift Mutations
  Addition or loss of nucleotides that shifts the reading frame
 In-Frame Insertions and Deletions
  Addition or loss of nucleotides in multiples of three, preserving the reading frame

C. Tautomeric Shifts
 Movement of hydrogen atoms within bases
 Can cause mispairing during DNA replication

Functional Effects of Mutations

Silent Mutations
 Do not affect protein function

Loss-of-Function Mutations
 Prevent gene transcription or produce nonfunctional proteins
 Usually recessive

Gain-of-Function Mutations
 Produce a protein with altered or new function
 Usually dominant
 Common in cancer cells

Point Mutations
 Forward Mutation – Wild-type sequence changes to mutant
 Reverse Mutation – Mutant sequence changes back to wild-type

Types of Functional Mutations

Neutral Mutation
 A missense mutation changes an amino acid to one with similar chemical properties (e.g., glycine → alanine)
 No observable effect on protein function

Loss-of-Function Mutation
 Mutations cause complete or partial loss of normal protein function
 Example: cystic fibrosis caused by loss-of-function mutation in the CF gene

Gain-of-Function Mutation
 Mutations produce a protein with a new or abnormal function
 Example: mutation in a cell surface growth receptor that stimulates growth without the growth factor

Conditional Mutation
 Mutation is expressed only under specific conditions
 Example: temperature-sensitive mutation observable only at extreme temperatures

Gain-of-Function Mutation (GOF) *Don’t memorize name

Example
 A transcription factor normally active only in stem cells for larval leg development is mistakenly expressed in stem cells for larval antenna development
 Example gene: Antennapedia

Effect
 Causes a new or abnormal function, such as leg structures forming where antennae should develop

Conditional Mutation

Temperature-Sensitive Allele
 Functional only under certain temperatures
 Example: Fruit fly with a mutation in a wing development gene
 Protein is non-functional at low temperatures (cold-sensitive)
 Protein is functional at warmer temperatures

Conditional Mutations

Definition
 Affect the phenotype only under specific environmental conditions
 Wild-type phenotype is expressed under other conditions

Example
 Coat color in some cats and rabbits
 Temperature-sensitive mutant protein is inactive in warmer body regions → pale fur
 Protein is active in cooler extremities (ears, nose, feet) → dark fur

Lethal Mutation

Definition
 Mutation that causes premature cell death

Chromosomal Mutations

Definition
 Extensive changes in genetic material involving long DNA sequences

Significance
 Can provide genetic diversity for evolution by natural selection
 Often deleterious

Mechanism
 Chromosomal rearrangements involve double-strand breaks
 Aberrant crossover between homologous or nonhomologous chromosomes can cause rearrangements
 Radiation can induce double-strand breaks, and repair may join non-homologous ends

Effect on Cell
 Multiple chromosome breaks can cause cell death due to loss of DNA fragments or triggering of apoptosis

Chromosomal Rearrangements: Deletions and Duplications

Deletion
 Loss of a chromosome segment
 Can have severe or fatal consequences

Duplication
 A portion of a chromosome is replicated, creating multiple copies
 Occurs when homologous chromosomes break at different positions and reconnect incorrectly
 One chromosome loses the segment, the other gains two copies
 Extra copies can lead to overexpression of genes

Chromosomal Rearrangements: Inversions and Translocations

Inversion
 A chromosome segment breaks and rejoins in the reverse orientation (“flipped”)
 Can result in loss-of-function mutations

Translocation
 A chromosome segment breaks off and inserts into another non-homologous chromosome
 Often involves reciprocal exchange of segments between chromosomes
 Can place a gene next to a new control region, altering its expression

Forward and Reverse Mutations

Forward Mutation
 Change from wild-type to mutant form

Reversion Mutation
 A second mutation that restores the wild-type phenotype
 True Reversion – Converts the mutant nucleotide sequence back to the original wild-type sequence

Suppressor Mutation
 A second mutation that compensates for the effect of the original mutation without restoring the original nucleotide sequence
 Intragenic Suppressor – Occurs within the same gene
 Intergenic Suppressor – Occurs in a different gene

Original and Suppressor Mutations

Original Mutation
 The initial change in the DNA sequence that causes a problem
 Example: produces a nonfunctional protein

Suppressor Mutation
 A second mutation elsewhere in the genome
 Does not revert the original mutation
 Compensates for the defect caused by the original mutation
 Example: restores some protein function, helps the cell compensate, or alters interactions to reduce negative effects

Intragenic Suppressor Mutations

Definition
 A second-site mutation that hides or suppresses the effect of the first mutation
 Not a reverse mutation

Types
 Intragenic Suppressor – Occurs within the same gene as the original mutation
 Intergenic Suppressor – Occurs in a different gene (implied from earlier notes)

Intergenic Suppressor Mutations

Intergenic Suppressor
 A suppressor mutation that occurs in a different gene from the original mutation

Mechanism
 The second mutation can be a gain-of-function mutation
 Example: a mutated tRNA acquires a novel function, such as binding to a stop codon to suppress a nonsense mutation

Relationship to Reverse and Suppressor Mutations

Forward Mutation
 Changes the wild-type gene into a mutant phenotype

Reverse Mutation
 Restores the wild-type gene and phenotype

Suppressor Mutation
 Occurs at a different site than the original mutation
 Individual carries both the original mutation and the suppressor mutation
 Phenotype appears wild-type despite the original mutation

Example Genotype
 Wild type: A⁺ B⁺
 Forward mutation produces a mutant
 Suppressor mutation restores the wild-type phenotype without changing the original mutant nucleotide sequence

Example of Reversion and Suppressor Mutations

Harlequin Norway Maple Trees
 Mutation affects chlorophyll production, resulting in partly albino leaves

Revertants
 Occasionally, all-green leaves appear
 Result of a secondary mutation that restores the wild-type phenotype
 Masks the effect of the original mutation

Summary of Mutation Types

Base Substitution
 Change of a single DNA nucleotide

Transition
 Purine ↔ purine or pyrimidine ↔ pyrimidine

Transversion
 Purine ↔ pyrimidine

Insertion
 Addition of one or more nucleotides

Deletion
 Loss of one or more nucleotides

Frameshift Mutation
 Insertion or deletion that alters the reading frame of a gene

In-Frame Deletion or Insertion
 Deletion or insertion in multiples of three nucleotides
 Does not change the reading frame

Expanding Nucleotide Repeats *NOT ON EXAM
 Increase in the number of copies of a nucleotide sequence

Forward Mutation
 Changes wild-type phenotype to mutant

Reverse Mutation
 Restores mutant phenotype back to wild-type

Missense Mutation
 Sense codon changes to a different sense codon
 Incorporates a different amino acid

Nonsense Mutation
 Sense codon changes to a stop codon
 Causes premature translation termination

Silent Mutation
 Codon changes but amino acid sequence remains unchanged

Neutral Mutation
 Changes amino acid without affecting protein function

Loss-of-Function Mutation
 Complete or partial loss of normal protein function

Gain-of-Function Mutation
 New trait or function appears
 Can be expressed at inappropriate tissue or time

Lethal Mutation
 Causes premature death

Suppressor Mutation
 Suppresses effect of an earlier mutation at a different site

Intragenic Suppressor Mutation
 Suppresses effect of a mutation within the same gene

Intergenic Suppressor Mutation
 Suppresses effect of a mutation in a different gene