Module 3: Mutations, and the Cis and Trans paradigm

A comprehensive set of practice flashcards covering mutations, cis/trans paradigm, allele/locus concepts, zygosity, mutation types and effects, hotspots, and reversal/suppression concepts from the lecture notes.

What is a mutation?

A change in the nucleotide sequence of DNA.

What is an allele?

A unique sequence variant of a gene occupying a given locus on a chromosome (an alternative form of a gene).

What is a locus?

Position on a chromosome where a particular gene resides; a locus may be occupied by any one of the gene's alleles.

What is the difference between an allele and a locus?

An allele is a variant form of a gene; a locus is the physical position of the gene on the chromosome.

What does ‘diploid’ mean?

Having two copies of each chromosome (two alleles per gene per cell).

What is zygosity?

The degree of similarity between alleles on homologous chromosomes.

What are homozygotes?

Two identical alleles for a gene (e.g., two wild-type or two mutant copies).

What are heterozygotes?

Two different alleles for a gene (e.g., one wild-type and one mutant).

What is a cis-acting site?

A DNA sequence that controls expression of adjacent DNA and does not influence the homologous allele.

What is a trans-acting product?

A gene product (RNA or protein) that can act on multiple alleles across the genome.

What does ‘cis-configuration’ mean for mutations?

Two mutations on the same allele; they are in cis.

What does ‘trans-configuration’ mean for mutations?

Mutations on different homologous chromosomes; they are in trans.

What is a transition mutation?

A substitution where a purine is replaced by a purine (A↔G) or a pyrimidine by a pyrimidine (C↔T).

What is a transversion mutation?

A substitution where a purine is replaced by a pyrimidine or vice versa (e.g., A↔C, G↔T).

What is an insertion or deletion (indel)?

Addition or loss of DNA bases; can shift reading frame or disrupt function; may arise from transposable elements or genome editing like CRISPR.

What is a mutation hotspot?

A base pair site with a much higher mutation frequency than expected, often due to chemically modified bases.

Which base modification commonly creates hotspots via deamination?

5-methylcytosine deaminates to thymine, increasing hotspot mutation frequency.

What does deamination of cytosine produce?

Uracil, leading to a C→T transition after replication.

What is a loss-of-function mutation?

A mutation where the gene product has none or reduced activity.

What is a hypomorph?

A loss-of-function mutation with reduced activity of the gene product.

What is a gain-of-function mutation?

A mutation that increases activity or confers a new function (hypermorph).

What is a null mutation?

A mutation that completely eliminates the gene's function; used to test gene essentiality.

What is a silent mutation?

A mutation with no observable effect on phenotype.

What is a missense mutation?

A base change that alters one amino acid in the protein (e.g., M to D).

What is a nonsense mutation?

A base change that creates a premature stop codon, truncating the protein.

What is a frameshift mutation?

An insertion or deletion that shifts the reading frame of the ORF, altering downstream amino acids.

What is a true reversion?

Reversion that restores the original sequence and function; can occur by a compensatory change or true reversion at the same site.

What is a suppression mutation?

A mutation at a second site (another gene) that suppresses the effect of the original mutation, revealing pathway interactions.

What is a forward mutation?

A mutation that changes the wild-type to a mutant phenotype.

What is a back (reversion) mutation?

A mutation that reverts a mutated gene back toward the wild-type sequence or function.

What is a direct vs an indirect way to correct a mutation or phenotype?

Direct: repair/edit the mutated gene (e.g., gene therapy). Indirect: bypass or suppress the defect (e.g., suppression mutations or pathway compensation).