Molecular Genetics: Mutations, Gene Regulation, Epigenetics, and Non-Coding RNAs

Comprehensive vocabulary flashcards covering mutation types, bacterial trp operon attenuation, eukaryotic transcription factors and chromatin remodeling, epigenetic inheritance, and the mechanisms of non-coding RNAs and CRISPR-Cas systems.

Replica Plating

A microbiological technique where bacterial colonies are transferred from a master plate to selective and non-selective plates using velvet, preserving the spatial colony pattern to demonstrate that mutations arise spontaneously before exposure to selective agents (such as phage T1).

Single Point Mutation (Sickle Cell Anemia)

A single base change in the coding sequence of hemoglobin (changing a GAG codon for glutamic acid to GTG for valine) that causes hemoglobin molecules to crystallize at low oxygen levels, leading red blood cells to sickle and occlude small blood vessels.

Up Mutation

A mutation occurring within the core promoter region of a gene that increases the rate of transcription and overall gene expression.

Down Mutation

A mutation located in the core promoter that decreases transcription efficiency and lowers gene expression levels.

Conditional Mutation

A mutation that affects the phenotype of an organism only under a specific set of environmental conditions, such as a temperature-sensitive allele.

Suppressor Mutation

A second mutation occurring at a distinct site that counteracts the phenotypic consequences of an initial mutation, restoring the wild-type phenotype without changing the first mutant genotype back.

Intragenic Suppressor

A suppressor mutation whose second altered site is situated within the very same gene as the initial inactivating mutation (e.g., restoring transporter function).

Intergenic Suppressor

A suppressor mutation occurring in a completely different gene from the first mutation, functioning through redundant proteins, common metabolic pathways, multimeric protein subunit interactions, or transcription factor alterations.

Germ-Line Mutation vs. Somatic Mutation

Germ-line mutations occur before fertilization in gametes, distribute to every cell in the body, and pass to $50\%$ of gametes in offspring; somatic mutations occur after fertilization in embryonic cells, form a localized patch whose size depends on developmental timing, produce genetic mosaics, and cannot be passed to future generations.

Genetic Mosaic

An individual possessing somatic regions that are genotypically distinct from one another as a result of somatic mutations occurring after fertilization.

Transition

A molecular point mutation that substitutes a purine for a different purine ($\text{A} \leftrightarrow \text{G}$) or a pyrimidine for a different pyrimidine ($\text{C} \leftrightarrow \text{T}$); it has 4 possible changes and occurs more frequently than transversions.

Transversion

A base substitution where a purine is interchanged with a pyrimidine (or vice versa); it has 8 possible changes, occurs less commonly, and is more likely to alter an amino acid and be purged by natural selection.

trp Operon

A repressible polycistronic operon in Escherichia coli containing five structural genes required for tryptophan biosynthesis (trpE, trpD, trpC, trpB, and trpA) that is repressed when tryptophan levels are high.

TrpR Repressor

An aporepressor protein that cannot bind the trp operator alone, but becomes activated upon binding corepressor tryptophan, thereby binding the operator DNA sequence to block transcription.

Attenuation (trp Operon)

A fine-tuning regulatory mechanism in prokaryotes that couples transcription and translation in the cytoplasm; alternative hairpin conformations formed by Regions 1, 2, 3, and 4 in the 162-bp trpL leader sequence prematurely arrest or permit transcription depending on tryptophan-charged tRNA abundance.

Anti-Terminator Hairpin

The stem-loop structure formed between Region 2 and Region 3 of the trpL leader mRNA when low tryptophan levels cause the ribosome to stall at tandem Trp codons in Region 1, preventing the terminator loop and allowing transcription to proceed.

Intrinsic Terminator Hairpin

The 3–4 stem-loop structure in trpL mRNA followed by a run of uracils that forms when high tryptophan allows the ribosome to cover Region 2, signaling RNA polymerase to dissociate and arrest transcription.

Alternative Sigma Factors

Bacterial transcription factors—such as $\sigma^H$ (heat shock), $\sigma^E$ (extracytoplasmic stress), $\sigma^S$ (stationary phase), $\sigma^F$ (flagellar), $\sigma^{19}$ (ferric citrate), and $\sigma^N$ (low nitrogen)—that direct RNA polymerase to distinct sets of promoters during specific physiological states alongside primary $\sigma^{70}$.

Gal4p

The eukaryotic transcriptional activator in yeast that binds constitutively as a zinc finger protein to the Upstream Activating Sequence ($\text{UAS}_G$) to recruit the transcription initiation complex in the presence of galactose.

Gal80p

A negative regulatory protein in yeast that directly binds to the activation domain of Gal4p in the absence of galactose, inhibiting transcriptional activation.

Gal3p

An allosteric regulator that binds galactose and ATP to sequester Gal80p in the cytoplasm, releasing Gal4p to stimulate transcription of GAL structural genes.

Mediator Complex

A multi-protein eukaryotic coactivator complex discovered by Roger D. Kornberg that bridges regulatory transcription factors and RNA Polymerase II, promoting phosphorylation of the Carboxyl-Terminal Domain (CTD) to trigger the switch from transcription initiation to elongation.

CREB Protein

cAMP Response Element-Binding protein; a transcription factor phosphorylated by Protein Kinase A in response to elevated intracellular cAMP, allowing it to recruit CREB Binding Protein (CBP) and stimulate gene expression.

Histone Eviction

An ATP-dependent chromatin remodeling activity (carried out by complexes such as SWI/SNF) that completely removes histone octamers from DNA, creating nucleosome-free regions for transcriptional access.

Histone Acetyltransferases (HATs)

Enzymes that append acetyl groups to positively charged lysines on histone amino-terminal tails, neutralizing charge to weaken histone-DNA interactions, create open chromatin, and activate transcription.

Histone Deacetylases (HDACs)

Enzymes that remove acetyl groups from histone lysine residues, restoring positive charges, strengthening histone-DNA binding, condensing chromatin into a closed state, and repressing transcription.

Insulator

A specific DNA sequence that isolates a gene from surrounding chromosomal context by blocking the spreading of condensed heterochromatin or shielding promoters from inappropriate activation by neighboring enhancers.

Iron Regulatory Protein (IRP)

An RNA-binding protein that regulates iron metabolism post-transcriptionally by binding Iron Response Elements (IREs): stabilizing transferrin receptor mRNA when bound to its 3' UTR under low iron, or blocking ferritin mRNA translation initiation when bound to its 5' UTR.

Cis- vs. Trans-Epigenetic Changes

Cis-epigenetic changes are localized modifications restricted to a specific DNA site on one homolog (where cell fusion maintains independent expression patterns), whereas trans-epigenetic changes are mediated by diffusible factors that act on all homologous alleles throughout the nucleoplasm (causing both genes to become expressed following cell fusion).

Genomic Imprinting

An epigenetic modification established during gametogenesis (oogenesis or spermatogenesis) via cytosine methylation that marks an allele according to parent of origin, leading to monoallelic expression in offspring.

Igf2 Imprinting

A non-Mendelian inheritance phenomenon in mice where only the paternally inherited Igf2 allele is expressed to produce insulin-like growth factor 2, while the maternally inherited allele is silenced regardless of its functional or mutant status.

ICR and DMR Regulation

During oogenesis, the Imprinting Control Region (ICR) and Differentially Methylated Region (DMR) remain unmethylated, allowing repressive CTC factors to bind and form a chromatin loop that blocks the downstream enhancer from activating Igf2; during spermatogenesis, methylation across ICR and DMR prevents CTC factor binding, permitting enhancer-driven Igf2 expression.

Prader-Willi and Angelman Syndromes

Two distinct human neurodevelopmental disorders arising from the exact same chromosomal deletion ($\text{del 15q11}$); maternal imprinting silences SNRPN (causing Prader-Willi syndrome when inherited with a paternal deletion), whereas paternal imprinting silences UBE3A (causing Angelman syndrome when inherited with a maternal deletion).

Dosage Compensation

The physiological balancing of X-linked gene expression between female mammals (XX) and male mammals (XY) through the transcriptional inactivation of one female X chromosome.

Barr Body

A highly condensed, transcriptionally inactive X chromosome visible as a dark heterochromatic mass located against the inner nuclear membrane during interphase in female mammalian somatic cells, first identified in 1949 by Murray Barr and Ewart Bertram.

Lyon Hypothesis

The principle formulated in 1961 stating that one of the two X chromosomes is randomly inactivated in somatic cells during early female mammalian embryogenesis, with the chosen inactivation pattern clonally maintained in all descendant cells.

Xist

X-inactive specific transcript; a long non-coding RNA transcribed from the X-inactivation center (Xic) that progressively spreads along the chromosome to coat the DNA, recruit repressive proteins, and mediate chromatin compaction into a Barr body.

Tsix

A non-coding antisense RNA transcribed complementary to Xist that protects the active X chromosome from silencing by blocking Xist accumulation.

Trithorax Group (TrxG)

A conserved family of epigenetic regulatory protein complexes that promote developmental gene activation by catalyzing trimethylation of lysine 4 on histone H3 ($\text{H3K4me3}$).

Polycomb Repressive Complex 2 (PRC2)

A repressive chromatin complex recruited to Polycomb Response Elements (PREs) that silences target genes by catalyzing the trimethylation of lysine 27 on histone H3 ($\text{H3K27me3}$), which directly inhibits RNA polymerase and recruits PRC1.

Polycomb Repressive Complex 1 (PRC1)

A multi-protein complex recruited by $\text{H3K27me3}$ tags that executes gene silencing through nucleosome compaction into dense knot-like structures, monoubiquitination of histone H2A, and direct physical inhibition of transcription factor TFIID.

Avy (Agouti Viable Yellow) Allele

A mouse variant containing an upstream transposable element promoter that drives ectopic transcription of the Agouti gene; maternal dietary supplementation with methyl donors (folate, B12, choline, betaine) hypermethylates the transposon promoter, shifting coat color from yellow to pseudo-agouti.

Protobiont

A hypothesized non-living precursor to the first biological cells, consisting of an organized aggregate of macromolecules enclosed by a boundary (such as a lipid bilayer) maintaining a distinct internal chemical environment.

RNA World Hypothesis

The evolutionary proposal that self-replicating ribonucleic acid molecules served as the ancestral basis of life, simultaneously performing dual roles: storing genetic information (like DNA) and catalyzing enzymatic chemical reactions (like protein ribozymes).

Non-Coding RNA (ncRNA) Interactions

Molecules that do not encode proteins, yet account for approximately $80\%$ of cellular transcription; their intramolecular stem-loops allow them to bind DNA via base-pairing, bind other RNAs, insert into pockets on protein surfaces, or coordinate small molecules.

Ribozyme

An RNA molecule possessing organic enzymatic catalytic activity without requiring protein components, such as self-splicing group I and II introns, the 23S/28S rRNA peptidyl transferase, or RNase P.

RNase P

A catalytic ribozyme endonuclease (characterized by Sidney Altman) responsible for cleaving the extended 5' leader segment of precursor tRNAs to produce mature, functional tRNA ends.

Small Nucleolar RNA (snoRNA)

Non-coding RNAs abundant in the nucleolus that act as scaffolds and guides within snoRNPs; C/D box snoRNAs direct 2'-O-methylation of ribose, while H/ACA box snoRNAs direct pseudouridylation of specific uracils on rRNA.

micF

A bacterial non-coding antisense RNA induced in Escherichia coli under high osmolarity that base-pairs directly over the Shine-Dalgarno sequence and start codon of ompF mRNA to physically block ribosomal docking and translation.

DsrA

An 85-nucleotide trans-acting bacterial ncRNA that uses the Hfq chaperone to repress translation of hns mRNA by masking its ribosome-binding site, while activating translation of rpoS mRNA by unwinding an inhibitory stem-loop.

HOTAIR

A 2.2-kb human long non-coding RNA transcribed antisense to the HoxC locus that binds PRC2 at its 5' end and LSD1 at its 3' end, guiding these repressive histone modifiers to GA-rich chromosomal regions to shut down transcription.

RNA Interference (RNAi)

A sequence-specific gene silencing process discovered in Caenorhabditis elegans by Andrew Fire and Craig Mello in 1998, in which double-stranded RNA (dsRNA) targets complementary mRNAs for cleavage or translational repression.

MicroRNAs (miRNAs)

Endogenous, non-coding regulatory RNAs (typically 20–25 nucleotides) processed from genomic transcripts that base-pair imperfectly with target mRNAs to mediate translational repression, degradation, or sequestration in P-bodies.

Small Interfering RNAs (siRNAs)

Short regulatory RNAs generated from exogenous sources (such as viruses or transposons) that form exact complementary matches with target RNAs, leading to catalytic cleavage by Argonaute within RISC.

Drosha

A nuclear RNase enzyme that crops primary microRNA transcripts (pri-miRNAs) into ~70-nucleotide hairpin precursors (pre-miRNAs) prior to export to the cytoplasm via Exportin 5.

Dicer

A cytoplasmic endoribonuclease complex that processes pre-miRNAs and foreign double-stranded RNAs into mature 20–25 base-pair double-stranded RNA duplexes.

Argonaute

The catalytic core endonuclease protein within the RNA-Induced Silencing Complex (RISC) responsible for using the guide RNA strand to recognize and cleave target mRNAs displaying perfect sequence complementarity.

piRNAs (PIWI-Interacting RNAs)

Germ-line non-coding RNAs in animals that complex with PIWI family proteins (such as Drosophila piRISC) to suppress transposable elements through cytoplasmic mRNA degradation or nuclear chromatin silencing.

Simple Transposition

A 'cut-and-paste' conservative mechanism of transposable element mobility wherein a transposase enzyme excises the element from its original genomic location and inserts it into a new target site without an RNA intermediate.

Retrotransposition

A 'copy-and-paste' transposition mechanism wherein a transposable element is transcribed into an RNA intermediate, reverse-transcribed into double-stranded DNA by reverse transcriptase, and inserted elsewhere, increasing genomic copy number.

CRISPR Array

A prokaryotic genomic locus containing short, repeated palindromic DNA sequences separated by unique 20–50 base-pair spacer sequences derived from past infections by bacteriophages or plasmids, serving as a heritable molecular immune memory.

Cas1-Cas2 Complex

The conserved bacterial integrase-endonuclease complex responsible for the adaptation phase of CRISPR immunity, excising protospacer fragments from foreign DNA and inserting them adjacent to the leader sequence of the CRISPR array.

Protospacer Adjacent Motif (PAM)

A short, conserved DNA sequence immediately flanking the target protospacer in foreign phage or plasmid DNA that is recognized by Cas nucleases (such as Cas9); its absence in the host CRISPR array prevents self-targeting and autoimmune cleavage.

Anti-CRISPR Proteins (Acr)

Bacteriophage-encoded inhibitor proteins (such as AcrIIA4) that counteract host prokaryotic CRISPR-Cas defense systems by directly mimicking DNA or blocking Cas nuclease binding and cleavage.