Mutations and genetic analysis Flashcards
Describe the types, effects and nomenclature of mutations
- Types of Mutations
A. Point Mutations (Single-Nucleotide Variants)
Point mutations involve a change in a single nucleotide of the DNA sequence. These mutations are classified based on the nature of the change:
Substitution Mutations:
A single nucleotide is replaced by another.
Can be further classified as:
Transitions: A purine is substituted for another purine (A ↔ G) or a pyrimidine is substituted for another pyrimidine (C ↔ T).
Transversions: A purine is substituted for a pyrimidine (A ↔ C or G ↔ T) or vice versa.
Effects of Substitutions:
Silent Mutation: The mutation does not change the amino acid due to the redundancy in the genetic code (e.g., a change from GAA to GAG, both of which code for glutamic acid).
Missense Mutation: The mutation changes one amino acid in the protein, potentially affecting its function (e.g., sickle cell anemia caused by a substitution of valine for glutamic acid at position 6 in the hemoglobin protein).
Nonsense Mutation: The mutation creates a premature stop codon, leading to a truncated, usually nonfunctional protein (e.g., Duchenne muscular dystrophy).
Insertion/Deletion Mutations (Indels):
Insertion: Addition of one or more nucleotides into the DNA sequence.
Deletion: Loss of one or more nucleotides from the DNA sequence.
Effects of Indels:
Frameshift Mutation: Insertion or deletion of nucleotides (not in multiples of 3) causes a shift in the reading frame of the codons, which leads to a completely altered protein sequence downstream of the mutation. This often results in a nonfunctional protein.
In-Frame Mutation: Insertion or deletion of a multiple of 3 nucleotides, which adds or removes one or more amino acids but maintains the reading frame.
B. Larger Mutations
Duplication:
A segment of DNA is duplicated, leading to multiple copies of the same gene or region.
Can affect gene expression or cause diseases (e.g., Charcot-Marie-Tooth disease type 1A caused by duplication of a portion of chromosome 17).
Inversion:
A segment of DNA is reversed (flipped end to end) within the chromosome.
It may or may not have significant effects on gene function depending on whether important genes or regulatory elements are disrupted.
Translocation:
A segment of DNA from one chromosome is transferred to another chromosome.
Reciprocal translocation: Exchange of chromosomal segments between two chromosomes.
Can lead to cancer if the translocation disrupts genes involved in cell cycle regulation (e.g., Philadelphia chromosome in chronic myelogenous leukemia).
2. Effects of Mutations
A. Phenotypic Effects
Mutations can have a variety of phenotypic outcomes depending on their type and the gene or protein affected. The effects can be classified as:
Silent Mutation:
No change in the protein because the mutation does not alter the amino acid sequence due to the redundancy in the genetic code.
Usually neutral, though in some cases, the mutation may affect gene expression or RNA stability.
Loss-of-Function Mutation:
The mutation results in a nonfunctional or partially functional protein, often leading to a disease phenotype.
Can be caused by nonsense mutations, frameshift mutations, or large deletions.
Example: Cystic fibrosis is caused by mutations in the CFTR gene, leading to a nonfunctional chloride channel.
Gain-of-Function Mutation:
The mutation results in a protein with an enhanced or new function.
Often associated with dominant diseases.
Example: Oncogenes in cancer, such as mutations in the RAS gene, which can lead to uncontrolled cell division.
Dominant Negative Mutation:
The mutated gene product interferes with the normal gene product, leading to a loss of function.
Example: Mutations in the p53 gene, where the mutated p53 protein disrupts the function of the normal p53 tumor suppressor protein.
Conditional Mutation:
The effect of the mutation depends on environmental factors or specific conditions (e.g., temperature-sensitive mutations).
Example: The heat-sensitive mutation of the Sickle Cell Anemia allele, which shows symptoms under low oxygen conditions.
3. Nomenclature of Mutations
The nomenclature of mutations describes their exact nature and location in the genome. The format is standardized to ensure consistency in mutation reporting.
A. Nomenclature for Point Mutations
Gene Name: The name of the gene affected (e.g., CFTR for cystic fibrosis).
Mutation Type: Describes the change at the DNA level (e.g., c.35delG means a deletion of a guanine at position 35 in the gene).
Protein Change: Describes the change in the protein sequence (e.g., p.Glu6Val for the sickle cell mutation, where glutamic acid at position 6 is replaced by valine).
The nomenclature is often written as:
c. (coding DNA level)
p. (protein level)
For example:
c.76A>T: A change from adenine (A) to thymine (T) at position 76 in the coding sequence of the gene.
p.Arg100His: An arginine (Arg) to histidine (His) change at position 100 in the protein.
B. Nomenclature for Inversions, Duplications, and Translocations
The notation will describe the chromosomal location of the mutation.
Example: A reciprocal translocation between chromosomes 9 and 22 is written as t(9;22), often associated with the Philadelphia chromosome in chronic myelogenous leukemia (CML).
4. Causes of Mutations
Mutations can arise due to a variety of factors, including:
Spontaneous mutations: Errors during DNA replication, such as mispairing of bases.
Environmental factors:
Physical: Radiation (e.g., UV light or X-rays), which can cause DNA damage (e.g., thymine dimers).
Chemical: Mutagens like benzene, tobacco smoke, or certain chemicals used in chemotherapy.
Biological: Viral infections or the action of transposons (jumping genes) can cause genetic changes.
Summary
Types of Mutations:
Point mutations (substitutions, insertions, deletions).
Larger mutations (duplications, inversions, translocations).
Effects of Mutations:
Can lead to silent, loss-of-function, gain-of-function, or dominant-negative effects.
May result in disease or altered traits depending on the mutation.
Nomenclature:
Mutations are described using standardized formats that specify their location at both the DNA and protein levels.
Describe the application of molecular genetic technology to identify genetic mutations associated with disease.
Summary of Applications in Disease Diagnosis
PCR-based methods: Targeted mutation detection and carrier screening (e.g., for CFTR, sickle cell anemia, and Tay-Sachs).
NGS: Whole genome or exome sequencing for rare or complex diseases (e.g., cystic fibrosis, cancer).
Sanger sequencing: Confirming mutations in single genes (e.g., BRCA1/2 testing for breast cancer risk).
Microarray: Detecting copy number variations and SNPs for diseases like autism and cancer.
CRISPR-Cas9: Potential for gene correction in genetic diseases and creating disease models.
Southern blotting: Detecting large-scale DNA rearrangements (e.g., in Huntington’s disease).
