Genetics: DNA Mutation, Transposable Elements, and Chromosome Variation

Comprehensive practice flashcards covering DNA mutation types and mechanisms, transposable elements in prokaryotes and eukaryotes, and large-scale chromosomal number and structural variations.

Mutation

A stable, heritable change in DNA structure that alters the nucleotide base sequence.

Point Mutation (Base Substitution)

A DNA mutation in which one nucleotide base is substituted for another.

Transition Mutation

A point mutation involving a substitution of a purine for another purine ($A \rightarrow G$ or $G \rightarrow A$) or a pyrimidine for another pyrimidine ($C \rightarrow T$ or $T \rightarrow C$).

Transversion Mutation

A base substitution in which a purine is replaced by a pyrimidine, or a pyrimidine is replaced by a purine.

Missense Mutation (Nonsynonymous Mutation)

A base substitution resulting in an altered codon that specifies a different amino acid; can be conservative (specifying a chemically similar amino acid) or nonconservative (specifying a chemically dissimilar amino acid).

Nonsense Mutation

A point mutation that alters a sense codon into a stop codon, signaling premature chain termination during translation.

Synonymous Mutation (Sense Mutation)

A point mutation in which a base substitution alters a codon without changing the encoded amino acid.

Frameshift Mutation

A mutation caused by the insertion or deletion of nucleotide bases in numbers not divisible by three, which shifts the reading frame during mRNA translation.

Tautomeric Shift

A reversible chemical isomerization of a nucleotide base (such as from keto to rare enol, or amino to rare imino form) that changes hydrogen-bonding properties and induces replication mispairing.

Base Analog

A chemical compound that resembles a normal nucleotide base closely enough to be incorporated into DNA during replication, frequently undergoing tautomeric shifts to cause mispairing (e.g., 5-bromouracil).

Deamination

The spontaneous or chemically induced removal of an amine group from a base, converting cytosine to uracil, adenine to hypoxanthine, or guanine to xanthine.

Depurination

The spontaneous cleavage of the glycosyl bond linking a purine base to deoxyribose, occurring at a rate of approximately $10^4$ bases per mammalian cell per day.

AP Site (Apurinic/Apyrimidinic Site)

An abasic site in a DNA strand created by the spontaneous or enzymatic loss of a purine or pyrimidine base, leaving the sugar-phosphate backbone intact.

Alkylating Agents

Chemical mutagens (such as nitrogen mustard) that add methyl or ethyl groups to nucleotide bases, modifying their base-pairing characteristics.

Intercalating Agents

Planar chemical agents (e.g., ethidium bromide, acridine orange, actinomycin D) that slide between stacked base pairs, distorting the double helix and causing frameshift insertions or deletions.

Pyrimidine Dimer

A DNA lesion induced by ultraviolet (UV) radiation where adjacent pyrimidine bases (e.g., thymines) become linked by a cyclobutyl ring, blocking DNA replication.

Base Excision Repair (BER)

A DNA repair pathway that fixes abnormal single bases, including uracil, hypoxanthine, and alkylated bases.

Nucleotide Excision Repair (NER)

A DNA repair mechanism that removes larger oligonucleotide fragments containing significant helix distortions and bulky adducts, such as pyrimidine dimers.

Transposable Elements (TEs)

Mobile genetic elements capable of excising or duplicating themselves to insert into new genomic sites, also known as controlling elements, jumping genes, or transposons.

Variegation

An irregular, sectoring or spotted pattern of pigmentation resulting from unstable somatic mutations that alter the expression of pigment-producing genes.

Dissociation ($Ds$) Locus

A non-autonomous transposable element on maize chromosome 9 identified by Barbara McClintock that breaks the chromosome at its insertion site when activated by $Ac$.

Activator ($Ac$) Locus

An autonomous transposable element in maize that encodes functional transposase, capable of moving on its own and mobilizing the non-autonomous $Ds$ element.

Autonomous Element

A transposable element that codes for all proteins (such as transposase) necessary for its own transposition as well as for the movement of non-autonomous elements.

Non-autonomous Element

A transposable element that lacks functional genes encoding transposase and requires an autonomous element elsewhere in the genome to mobilize.

Insertion Sequence (IS) Element

The simplest bacterial transposable elements, carrying only the gene encoding transposase flanked by inverted terminal repeats ($IRs$), ranging in size from $768\,\text{bp}$ to $> 5\,\text{kb}$.

Inverted Terminal Repeats (IRs)

Short DNA sequences ($9\text{--}41\,\text{bp}$) located in reverse orientation at the boundaries of transposable elements, recognized by transposase to catalyze transposition.

Composite Transposon

A bacterial transposon carrying accessory genes (such as antibiotic resistance) flanked on both sides by identical insertion sequence elements ($IS_L$ and $IS_R$) that supply transposase and terminal recognition signals.

Simple Transposon (Non-composite Transposon)

A bacterial transposon (e.g., Tn3) carrying accessory genes that ends with inverted repeats rather than full IS elements, encoding transposase and resolvase in its central region.

Replicative Transposition

A "copy and paste" transposition mechanism where the element is duplicated, retaining a copy at the original donor site while inserting a new copy into a target site.

Conservative Transposition

A non-replicative "cut and paste" transposition mechanism where the mobile element is excised from the donor site and integrated into a new target site without leaving a copy behind.

Retrotransposon (Class 1 TE)

A eukaryotic transposable element that transposes via an RNA intermediate using reverse transcriptase to synthesize a double-stranded DNA copy that inserts into the genome.

DNA Transposon (Class 2 TE)

A transposable element that transposes directly as DNA using transposase to cut and reinsert the element without an RNA intermediate.

Transposon Tagging

A genetic engineering method where a transposable element inserts into and disrupts a gene to produce a mutant phenotype, simultaneously marking the gene with a known sequence tag for cloning.

C-value Paradox

The lack of correlation between the amount of DNA in a haploid nucleus (the C-value) and the biological or morphological complexity of an organism, primarily due to varying amounts of transposable element sequences.

Synteny

The conservation of chromosomal gene content and order across evolutionary related species, such as among cereal grasses.

Aneuploidy

A chromosomal condition involving the loss or gain of one or a few individual chromosomes, rather than whole sets, arising from meiotic nondisjunction.

Euploidy

Variation in chromosome number involving changes in complete sets or exact multiples of the basic chromosome set (e.g., monoploidy, diploidy, polyploidy).

Monoploidy

The condition of possessing only a single chromosome set ($1n$) in an organism species that is typically diploid, such as male bees, wasps, and ants that develop by parthenogenesis.

Polyploidy

The condition of possessing three or more complete chromosome sets ($3n$, $4n$, $6n$, etc.), highly prevalent in plants and grasses.

Autopolyploid

A polyploid organism whose chromosome sets are derived from chromosome duplication within a single species, frequently exhibiting sterility in odd-numbered ploids ($3n$, $5n$) due to irregular meiotic pairing.

Allopolyploid

A polyploid organism arising from interspecific hybridization between closely related species followed by chromosome doubling, typically fertile because homeologous chromosomes segregate independently.

Amphidiploid

A fertile allotetraploid plant possessing the sum of the diploid chromosome numbers of two parental species due to spontaneous or induced doubling in a sterile interspecific hybrid (e.g., Raphanobrassica, $4n = 36$).

Colchicine

A toxic secondary metabolite extracted from Colchicum autumnale (autumn crocus) that binds tubulin and disrupts mitotic spindle-fiber formation, preventing chromatid migration to produce autopolyploid cells.

Homeologous Chromosomes

Partially homologous chromosomes derived from different ancestral species in an allopolyploid that typically do not synapse or pair during meiosis.

Nondisjunction

The failure of homologous chromosomes or sister chromatids to disjoin properly during meiotic or mitotic division, yielding gametes with abnormal numbers of chromosomes ($n+1$ or $n-1$).

Monosomy

An aneuploid state ($2n - 1$) characterized by the loss of a single chromosome from a diploid set, such as Turner syndrome (45,XO).

Trisomy

An aneuploid state ($2n + 1$) characterized by the presence of three copies of a particular chromosome, such as Down syndrome (Trisomy 21).

Gene Balance

The concept that a normal phenotype requires a balanced relative proportion (such as $1:1$) of interacting genes and their products throughout the genome.

Gene-Dosage Effect

A phenotypic change caused by an abnormal number of wild-type alleles, leading to developmental imbalance in aneuploids.

Terminal Deletion

A chromosomal structural alteration caused by a single break near the tip of a chromosome resulting in the loss of the terminal end segment.

Intercalary Deletion (Interstitial Deletion)

A chromosomal mutation caused by two breaks within an internal chromosomal region, leading to the loss of the internal segment and rejoining of flanking regions.

Pseudodominance

The expression of a recessive allele phenotype occurring in a heterozygote when a deletion removes the homologous chromosome region carrying the dominant wild-type allele.

Tandem Duplication

A chromosomal aberration in which an identical duplicated chromosome segment lies immediately adjacent to the original segment in the same orientation (e.g., $AB \cdot CBCDEF$).

Pericentric Inversion

A chromosomal inversion involving breaks in both chromosome arms that includes the centromere, flipping the intervening segment $180^\circ$.

Paracentric Inversion

A chromosomal inversion restricted to a single chromosome arm that excludes the centromere, rotating the segment $180^\circ$.

Reciprocal Translocation

A chromosomal rearrangement resulting from the exchange of chromosome segments between two non-homologous chromosomes, altering linkage groups without net gain or loss of genetic material.