Regulation of Gene Expression in Eukaryotes

Vocabulary practice flashcards covering eukaryotic gene expression regulation across DNA structure/epigenetics, transcription, mRNA processing and degradation, translation, and post-translational protein regulation.

Central Dogma of Molecular Biology

The framework describing the transfer of genetic sequence information, $DNA \rightarrow RNA \rightarrow \text{Protein}$, where gene regulation can occur at any step along the pathway.

Epigenetic Modifications

Heritable changes that regulate gene expression independently of alterations to the primary DNA nucleotide sequence.

Euchromatin

A loosely packaged, uncoiled form of chromatin that allows transcription machinery access to DNA, promoting active gene expression.

Heterochromatin

A highly condensed, densely packaged form of chromatin that renders DNA inaccessible to transcriptional machinery, keeping genes suppressed.

Histone Acetyltransferases (HATs)

Chromatin-modifying enzymes that add acetyl groups ($\text{Ac}$) to histone tails, which loosens chromatin structure and promotes euchromatin formation.

Histone Deacetylases (HDACs)

Chromatin-modifying enzymes that remove acetyl groups ($\text{Ac}$) from histone ends, leading to chromatin compaction into heterochromatin and transcriptional silencing.

DNA Methyltransferases (DNMTs)

Enzymes that transfer a methyl group ($\text{CH}_3$) from $SAM$ to cytosine nucleotides to generate $5'\text{ Methyl-cytosine}$ and $SAH$, creating a heritable mark that suppresses transcription.

DNA Methylation

The enzymatic addition of methyl groups to cytosines in promoter regions, functioning as an epigenetic mark that typically silences gene transcription.

Proximal Control Elements

Noncoding DNA sequence elements situated near the gene promoter that assist in regulating transcription.

Enhancers

Distal control DNA elements located far upstream or downstream from a promoter and gene that bind activator proteins to stimulate transcription.

Activators

Specific regulatory proteins that bind to distal control elements within enhancers to stimulate gene transcription.

General Transcription Factors

Proteins that bind to the promoter region (such as the TATA box) to assemble the transcription initiation complex and recruit RNA polymerase II.

Combinatorial Control

A mechanism of transcriptional regulation wherein unique combinations of activator proteins drive the simultaneous, coordinate activation of multiple distinct genes.

Alternative RNA Splicing

A post-transcriptional mechanism where different exon combinations from a single primary RNA transcript (such as Troponin T) are joined, yielding diverse mRNA and protein products.

Ccr4/Pop2/Not Complex

A cytoplasmic multiprotein complex responsible for shortening the $3'$ poly(A) tail during mRNA degradation.

Dcp1/2 Decapping Enzyme

An enzyme complex that removes the $7\text{-methyl guanosine cap}$ from the $5'$ end of mRNA after poly(A) shortening has taken place.

Xrn1p Exonuclease

A cytoplasmic exonuclease that degrades decapped mRNA transcripts processively in the $5' \rightarrow 3'$ direction.

Exosome

A multiprotein ribonuclease complex responsible for degrading poly(A)-shortened mRNA transcripts in the $3' \rightarrow 5'$ direction.

Noncoding RNAs (ncRNAs)

Transcripts that do not code for proteins or typical rRNA/tRNA molecules, functioning instead to control gene expression via chromatin configuration and translational repression.

MicroRNAs (miRNAs)

Small double-stranded RNA molecules that are processed into single strands to bind complementary target mRNAs, blocking translation or triggering cleavage.

RNA Interference (RNAi)

A biological process wherein small RNA molecules (siRNAs or miRNAs) specifically inhibit gene expression by degrading complementary mRNA transcripts or disrupting protein synthesis.

Drosha

A nuclear RNase enzyme that processes long double-stranded precursor RNA (dsRNA) into shorter fragments prior to cytoplasmic export.

Dicer

A cytoplasmic RNase enzyme that cleaves double-stranded RNA into small interfering RNAs (siRNAs) or microRNAs (miRNAs) measuring $21\text{--}25$ base pairs in length.

RNA-Induced Silencing Complex (RISC)

A ribonucleoprotein complex incorporating single-stranded siRNA or miRNA that binds to complementary mRNA, directing Argonaute to cleave the target transcript.

Competitive Inhibition

An enzyme inhibition mechanism where an inhibitor directly binds to the active site, competing directly with the substrate for binding.

Noncompetitive Inhibition

An enzyme inhibition mechanism where an inhibitor binds to an allosteric site rather than the active site, inducing a conformational change that prevents the substrate from binding.

Uncompetitive Inhibition

An enzyme inhibition mechanism where an inhibitor binds to an allosteric site only after the enzyme-substrate complex has formed, increasing the time required to catalyze the substrate.

Ubiquitin

A regulatory protein ubiquitously expressed in eukaryotic cells that attaches covalently to target proteins, tagging them for destruction and recycling.

Proteasome

A large multi-subunit cellular complex that recognizes ubiquitinated proteins, degrading them into peptide fragments while recycling intact ubiquitin molecules.