Bacterial and Eukaryotic Gene Regulation, Epigenetics, Noncoding RNAs, and Mutations

Comprehensive practice flashcards reviewing bacterial and eukaryotic gene regulation, epigenetic mechanisms, noncoding RNA functions, and DNA mutations based on lecture quizzes.

Transition Mutation

A point mutation where a purine base is substituted for another purine (such as adenine to guanine) or a pyrimidine is substituted for another pyrimidine.

Transversion Mutation

A base substitution involving an interchange between a purine and a pyrimidine, or vice versa (such as a $G\text{-}C$ base pair mutating to a $T\text{-}A$ base pair).

Nonsense Mutation

A single-nucleotide substitution that converts an amino-acid-encoding codon into a premature stop codon, potentially yielding a truncated protein product.

Missense Mutation

A base substitution that alters a codon so that it encodes a different amino acid.

Silent Mutation

A nucleotide alteration that changes the codon sequence without altering the encoded amino acid.

Intergenic Suppressor Mutation

A secondary mutation occurring in a completely different gene from the original mutation that compensates for the defect and restores the normal phenotype.

Intragenic Suppressor Mutation

A secondary mutation occurring within the very same gene as the initial mutation that restores wild-type function.

Somatic Mutation

A mutation that occurs in a non-reproductive cell, which can be passed to daughter cells during mitosis (potentially producing genetic mosaicism) but is not transmitted to offspring via gametes.

Depurination

A lesion in which the bond between a purine base (adenine or guanine) and deoxyribose breaks, releasing the base and producing an abasic site.

8-Oxoguanine

An oxidized form of guanine that incorrectly pairs with adenine instead of cytosine, producing a $G\text{-}C \rightarrow T\text{-}A$ transversion after DNA replication if left uncorrected.

Constitutive Gene

A gene that is expressed at an essentially constant level across all environmental conditions because its product is continuously required by the cell.

Allolactose

An inducer in the lac operon that binds the allosteric site of the lac repressor, triggering a conformational change that prevents the repressor from binding the operator.

Catabolite Repression

A bacterial mechanism where the presence of glucose causes cAMP levels to drop, preventing the cAMP-CAP complex from forming and efficiently activating the lac operon.

Diauxic Growth

A biphasic growth pattern displayed by bacteria when they preferentially consume glucose before switching to metabolize a secondary sugar such as lactose.

AraC Protein

A dual-function regulatory protein that forms a DNA loop between $araO_2$ and $araI$ to block transcription without arabinose, but collapses the loop and activates transcription from $araI$ when arabinose is bound.

Tryptophan (as a Corepressor)

A small molecule in the trp operon that, at high concentrations, binds the trp repressor to enable it to bind the operator and shut down transcription of tryptophan biosynthesis genes.

Attenuation (trp Operon)

A regulatory mechanism dependent on physical coupling of bacterial transcription and translation, where ribosome positioning on the trpL leader sequence governs mRNA stem-loop formation and premature transcription termination.

Antisense RNA

An RNA molecule complementary to a target mRNA that base-pairs with it to form a double-stranded structure, physically preventing translation by ribosomes (e.g., micF RNA regulating ompF mRNA).

Riboswitch

An RNA molecule that directly binds a small molecule (such as TPP) and undergoes a conformational change to regulate expression without requiring any protein intermediate.

Operon

A group of two or more genes under the transcriptional control of a single promoter, transcribed together into a single polycistronic mRNA to allow coordinate regulation.

Feedback Inhibition

A posttranslational mechanism where the final product of a pathway binds to a regulatory allosteric site on an early pathway enzyme, inhibiting catalytic activity without altering gene expression.

Zinc Finger Motif

A transcription factor DNA-binding motif composed of one alpha helix and two beta sheets held together by a coordinated zinc ($Zn^{2+}$) ion, allowing recognition of DNA in the major groove.

Glucocorticoid Hormone Signaling

A pathway in which lipid-soluble steroid hormones diffuse directly across the plasma membrane into the cytosol to bind intracellular receptors, functioning without cell-surface receptors.

TFIID

A general eukaryotic transcription factor that binds the TATA box and serves as a primary intermediary through which regulatory transcription factors indirectly influence RNA polymerase II.

Mediator

A multi-protein eukaryotic complex that bridges upstream regulatory transcription factors to RNA polymerase II.

Combinatorial Control

The eukaryotic regulatory mechanism in which an individual gene is controlled by the combined, coordinated action of multiple activator and repressor proteins.

Alternative Splicing

A process where a single pre-mRNA is spliced differently across tissues by varying which exons are included, generating distinct protein isoforms (e.g., alpha-tropomyosin containing exon 2 in smooth muscle but exon 3 in striated muscle).

AU-Rich Elements (AREs)

Destabilizing sequence elements found within the 3'-UTR of certain mRNAs that are recognized by cellular proteins to promote rapid mRNA degradation and shorten transcript half-life.

RNA Interference (RNAi)

A post-transcriptional gene-silencing process discovered by Fire and Mello where injecting double-stranded RNA matching a target gene (such as mex-3 in C. elegans) eliminates target mRNA far more potently than antisense RNA alone.

Epigenetics

The study of heritable changes in gene expression that occur without any alteration to the underlying DNA sequence, such as through DNA methylation and histone modifications.

ATP-Dependent Chromatin Remodeling Complexes

Enzyme complexes that utilize ATP hydrolysis to alter chromatin architecture by repositioning nucleosomes, evicting histones, or substituting variant histones without changing the DNA sequence.

Histone Code Hypothesis

A hypothesis proposed by Strahl, Allis, and Turner suggesting that combinatorial patterns of histone modifications (acetylation, methylation, phosphorylation) act like a language specifying distinct chromatin states.

CpG Islands

Cytosine- and guanine-rich regions near promoters that are typically unmethylated in housekeeping genes to ensure consistent, broad transcriptional activity across cell types.

Maintenance Methylation

The enzymatic restoration of full methylation onto hemimethylated CpG sites following DNA replication, faithfully transmitting DNA methylation patterns to daughter cells.

CTCF

A regulatory protein that binds unmethylated insulator (ICR) and DMR sites near Igf2 and H19, forming a DNA loop that blocks the H19 enhancer from activating Igf2.

Barr Body

The condensed, transcriptionally silenced X chromosome in female mammalian cells, maintained by heavy CpG DNA methylation and specialized histone variants like macroH2A.

Genomic Imprinting

An epigenetic phenomenon causing monoallelic expression of a gene depending on parent of origin, maintained by DNA methylation marks that are erased and reset each generation according to parental sex.

Histone Variant H2A.Bbd

A specialized histone variant whose incorporation into a chromosomal region correlates with open chromatin and favors active gene transcription.

Histone Variant H1.0

A specialized linker histone variant whose incorporation into chromatin tends to condense chromatin and repress gene expression.

Insulator

A DNA sequence element that serves as a boundary between genes, blocking the spread of chromatin modifications or shielding a gene from activation by a neighboring enhancer.

HOTAIR

A long noncoding RNA transcribed from the HOXC cluster on human chromosome 12 that represses transcription by acting as a scaffold for PRC2 and LSD1.

PRC2 (Polycomb Repressive Complex 2)

A histone-modifying complex brought to target genes by HOTAIR that deposits the repressive $H3K27me3$ mark to promote transcriptional silencing.

LSD1

A histone demethylase enzyme scaffolded by HOTAIR that removes activating $H3K4me1/me2$ marks at target genes to facilitate gene repression.

Cosuppression

The unexpected silencing of both an introduced transgene and the homologous endogenous gene (such as chalcone synthase in petunias), triggered when sense and antisense RNAs form double-stranded RNA.

MicroRNA (miRNA)

Small noncoding RNAs that bind with imperfect complementarity to target mRNAs in animals, causing translational repression and mRNA destabilization across multiple targets.

Small Interfering RNA (siRNA)

Small noncoding RNAs that typically pair nearly perfectly with a single specific mRNA target to trigger precise cleavage and degradation.

Dicer

An endonuclease in the RNAi pathway that cleaves hairpin pre-miRNA or double-stranded pre-siRNA precursors into short double-stranded duplexes of roughly $20\text{--}25$ base pairs.

C/D Box snoRNA

A class of small nucleolar RNAs that assemble snoRNPs and guide the site-specific $2'\text{-}O\text{-}\text{methylation}$ of ribose sugars on ribosomal RNA in the nucleolus.

H/ACA Box snoRNA

A class of small nucleolar RNAs that base-pair with ribosomal RNA in the nucleolus to guide the conversion of uridine to pseudouridine.

SRP RNA (7SL RNA)

The noncoding RNA component of the signal recognition particle that serves as a scaffold for SRP proteins and stimulates GTP hydrolysis to facilitate SRP release and recycling.

Cas1 and Cas2

Endonucleases responsible for Stage 1 (adaptation) of CRISPR-Cas defense, capturing foreign viral DNA fragments and integrating them as spacers into the CRISPR locus.

Protospacer Adjacent Motif (PAM)

A short DNA sequence immediately adjacent to the viral target sequence that Cas9 must recognize before unwinding and cleaving the foreign DNA.

miR-200 Family

A family of microRNAs that suppresses the epithelial-mesenchymal transition (EMT) and maintains E-cadherin expression; its down-regulation promotes cancer invasion and metastasis.