Molecular and Cellular Biology: Gene Regulation, Cell Signaling, the Cell Cycle, and Cancer

Comprehensive practice flashcards reviewing eukaryotic and prokaryotic transcriptional regulation, signal transduction pathways, cell cycle transitions, apoptotic machinery, cancer biology, and molecular techniques.

Coupled Transcription and Translation

The simultaneous occurrence of transcription and translation on the same mRNA molecule in the cytoplasm of prokaryotes, contrasted with eukaryotes where transcription occurs in the nucleus and translation occurs in the cytoplasm.

Catabolite Activator Protein (CAP)

A bacterial transcriptional activator that, when bound by $\text{cAMP}$ in the absence of glucose, binds upstream of the transcription initiation site to recruit RNA polymerase to the $lac$ operon promoter.

Lac Repressor

A bacterial negative regulatory protein that binds to the operator site of the $lac$ operon to prevent transcription by RNA polymerase; it dissociates from the promoter in the presence of lactose.

$\sigma$ (Sigma) Factors

Bacterial proteins that recognize basal promoter elements (such as $-10$ and $-35$) and load RNA polymerase onto DNA at the transcription start site.

Promoter-Proximal Elements

Gene- and cell-type-specific regulatory DNA sequences located within several hundred base pairs immediately upstream or downstream of the eukaryotic transcription start site that function in a position- and orientation-dependent manner.

Enhancers

Distal eukaryotic regulatory DNA sequences located tens of kilobases upstream or downstream of the transcription start site, within introns, or within adjacent open reading frames, which function independently of position and orientation via DNA bending.

Linker Scanning Mutagenesis

An experimental technique using scrambled linker sequences to systematically substitute promoter regions and identify essential regulatory elements, such as PE-1, PE-2, and the TATA box in the thymidine kinase ($tk$) gene promoter.

Combinatorial Transcription Factor Dimerization

The mechanism by which three distinct monomeric transcription factor polypeptides form six possible dimer combinations (AA, BB, CC, AB, AC, BC) to recognize six unique DNA-binding sites, which can be negatively regulated by specific inhibitory factors.

GAL4

A model eukaryotic transcriptional activator from $S.\ cerevisiae$ with modular, separable DNA-binding and activation domains essential for inducing the expression of genes involved in galactose metabolism.

Nuclear Receptor Superfamily Response Elements

Consensus DNA sequences (such as GRE, ERE, VDRE, TRE, and RARE) recognized by homodimeric or heterodimeric nuclear receptors upon binding their specific lipid-soluble hormone ligands.

Cytoplasmic Chaperone Proteins (in Nuclear Signaling)

Proteins that associate with cytoplasmic lipid-hormone receptors to mask their nuclear localization signal (NLS), dissociating upon hormone binding to allow receptor nuclear translocation.

Pioneer Transcription Factors

Specialized regulatory proteins that directly access closed chromatin to establish and maintain an open chromatin architecture without directly activating transcription themselves.

Histone Code

The collective set of post-translational modifications (including acetylation, methylation, phosphorylation, and ubiquitination) on the protruding N-terminal tails of core histones ($\text{H2A}$, $\text{H2B}$, $\text{H3}$, and $\text{H4}$) that regulate chromatin condensation and DNA accessibility.

Silencers (Position-Dependent Repression)

Specific genomic loci that establish and maintain extensive heterochromatic regions, strongly silencing genes positioned close to or within them independently of their specific promoters.

Telomeric Silencing Complex (Rap1 and Sir Proteins)

A position-dependent repression system at yeast telomeres where Rap1 binds telomeric repeats and recruits Sir3/Sir4 corepressors and the Sir2 histone deacetylase to assemble condensed, hypoacetylated heterochromatin.

Lysine Mutational Analysis in Histone Tails

Experimental substitutions in histone tails where Lysine $\rightarrow$ Arginine (which retains positive charge and cannot be acetylated) produces permanent repression, whereas Lysine $\rightarrow$ Glutamine (which neutralizes charge mimicking acetylated lysine) produces permanent activation.

Bromo-domain

A conserved protein structural motif of approximately 110 amino acids found in transcriptional coactivators that specifically recognizes and binds to acetylated lysine residues on histone tails.

Mediator

A large multi-subunit coactivator complex that acts as a central molecular bridge organizing interactions between transcriptional activators, general transcription factors, RNA Polymerase II, histone modifiers, and chromatin remodelers.

Epigenetic Memory of Transcription

The preservation of cell-type-specific gene expression states across cell division, achieved by faithfully reconstructing DNA methylation patterns and histone modifications immediately after the passage of the replication fork.

Heterogeneous Nuclear Ribonucleoprotein (hnRNP)

Complexes of RNA and RNA-binding proteins that associate with nascent eukaryotic pre-mRNA transcripts cotranscriptionally as they are extruded from RNA Polymerase II.

SR Proteins

RNA-binding proteins containing RNA recognition motifs (RRMs) and arginine-serine-rich (RS) domains that coordinate with snRNPs to form cross-exon recognition complexes directing accurate splice site selection.

Drosophila Sex Determination Splicing Cascade

An alternative RNA splicing hierarchy in fruit flies governed by Sex-lethal (Sxl), which suppresses exon 3 inclusion; Transformer (Tra), which activates exon 4 inclusion; and Doublesex (Dsx), which produces sex-specific transcriptional regulators.

microRNA (miRNA) vs. siRNA Complementarity

Mechanistic distinction where miRNAs anneal imperfectly (often to $3'\text{-UTRs}$) to cause reversible translational inhibition, whereas siRNAs anneal with perfect complementarity to trigger permanent endonucleolytic RNA cleavage.

Dicer

An endoribonuclease that cleaves double-stranded precursor RNAs into mature $21\text{--}28\text{ bp}$ miRNAs and siRNAs; knockouts in model organisms fail to develop beyond gastrulation.

Hydrophobic vs. Hydrophilic Signal Transduction

Signaling pathway differences where hydrophobic ligands cross the plasma membrane to bind cytosolic or nuclear receptors, while hydrophilic ligands bind cell-surface receptors (such as GPCRs and RTKs) to trigger intracellular cascades.

G-Protein GTPase Switch Mechanism

A regulatory cycle where Guanine Nucleotide Exchange Factors (GEFs) activate G proteins by exchanging GDP for GTP, and GTPase-Activating Proteins (GAPs) or RGS proteins inactivate them by accelerating intrinsic GTP hydrolysis.

Heterotrimeric G-Protein Subunit Activation

The dissociation of agonist-activated GPCR-bound G proteins into an active $G_\alpha\text{-GTP}$ monomer and a $G_{\beta\gamma}$ heterodimer, both of which can modulate effector enzymes and ion channels.

Fluorescence Resonance Energy Transfer (FRET)

A biophysical technique measuring non-radiative energy transfer between two fluorophores positioned within $1\text{--}10\text{ nm}$ of each other, used to monitor receptor and G-protein subunit interactions in living cells.

HER1 (EGFR) Dimerization

Ligand-induced conformational changes in the extracellular domains of Human Epidermal Growth Factor Receptor 1 (HER1) that expose a dimerization arm, producing an active asymmetric receptor kinase dimer.

GRB2-Sos Adapter Complex

An adapter assembly in which Growth Factor Receptor-Bound Protein 2 (GRB2) uses its SH2 domain to bind autophosphorylated RTK tyrosines and its SH3 domains to recruit Son of Sevenless (Sos) to activate Ras at the plasma membrane.

SH2 and SH3 Domains

Conserved protein interaction modules where SH2 domains bind specific phosphotyrosine residues and SH3 domains bind proline-rich peptide sequences on target signaling proteins.

Ras/MAP Kinase Pathway

A phosphorylation cascade initiated by GTP-bound Ras recruiting and activating Raf (MAPKKK), which phosphorylates MEK (MAPKK), which in turn phosphorylates and activates MAP kinase (MAPK) to induce gene transcription.

14-3-3 Protein

A regulatory phospho-serine/threonine binding protein that binds inactive Raf to maintain it in an autoinhibited conformation until displaced by active GTP-bound Ras.

Cyclin-CDK Activity Waves

The programmed oscillations of individual Cyclin-CDK combinations (such as Cyclin D-CDK4, Cyclin E-CDK2, Cyclin A-CDK2, and Cyclin B-CDK1) and the APC/C that sequentially propel a eukaryotic cell through $G_1$, S, $G_2$, and M phases.

CAK (CDK-Activating Kinase)

A protein kinase that phosphorylates a conserved threonine residue located near the active site of CDKs, which is required for complete catalytic activation.

Wee1 Kinase

A dual-specificity inhibitory kinase that phosphorylates tyrosine and threonine residues on CDKs to prevent premature activation of mitotic kinases during S phase.

Cdc25 Phosphatase

A dual-specificity phosphatase that dephosphorylates the inhibitory tyrosine and threonine residues on CDKs placed by Wee1, activating mitotic and S-phase CDKs.

SCF E3 Ubiquitin Ligase

A multi-protein ubiquitin ligase that polyubiquitinylates phosphorylated CDK inhibitors, such as Sic1 in budding yeast and $p27^{KIP1}$ in mammals, targeting them for proteasomal degradation at the $G_1\text{/S}$ transition.

Sic1 Destruction Mechanism

The cooperative multisite phosphorylation of the budding yeast S-phase inhibitor Sic1 by $G_1\text{/S}$ CDKs, triggering polyubiquitinylation by SCF and proteasomal degradation to initiate DNA replication.

Anaphase-Promoting Complex (APC/C) Targets

An E3 ubiquitin ligase that degrades securin when complexed with Cdc20 ($\text{APC/C}^{\text{Cdc20}}$) to initiate sister chromatid separation at anaphase, and degrades mitotic B-type cyclins when complexed with Cdh1 ($\text{APC/C}^{\text{Cdh1}}$) to drive exit from mitosis.

Retinoblastoma (Rb) Protein

A mammalian tumor suppressor protein that binds and represses the E2F transcription factor in early $G_1$; phosphorylation by Cyclin D-CDK4/6 and Cyclin E-CDK2 triggers its release, allowing E2F-driven transcription of S-phase genes.

Pre-Replication Complex (Pre-RC)

A multi-protein initiation platform formed at replication origins by the binding of Origin Recognition Complexes (ORCs), which coordinate with Cdc6 and Cdt1 to load inactive MCM replicative helicases during $G_1$.

Apoptotic Chromatin Fragmentation

The cleavage of nuclear DNA between nucleosomes by apoptotic nucleases into fragments of less than $2\text{N}$ ($1\text{C}$) content, visible as nuclear blebbing and pyknosis under Hoechst fluorescent staining.

Nematode vs. Mammalian Apoptotic Pathways

Evolutionarily conserved cell-death cascades where nematode EGL-1, CED-9, CED-4, and CED-3 functionally correspond to mammalian BH3-only proteins, Bcl-2, Apaf-1, and Caspase-9/caspase effectors, respectively.

Caspases

Cysteinyl aspartate-specific proteases divided into initiators (such as Caspase-8, -9, and -10) that process and activate executioners, and effectors (such as Caspase-3, -6, and -7) that cleave cellular targets and activate DNA nucleases during apoptosis.

Bcl-2 Family Proteins

Regulators of outer mitochondrial membrane integrity containing BH domains, classified into pro-survival pore closers (Bcl-2, $\text{Bcl-X}_\text{L}$), pro-apoptotic channel formers (Bax, Bak), and regulatory BH3-only proteins (Bad, Bim, Puma, Bid).

Multistep Cancer Progression

The progressive acquisition of malignancy wherein precancerous cells evade apoptosis and immune killing by cytotoxic T cells, followed by loss of contact inhibition, extracellular matrix degradation, angiogenesis, and distant metastasis.

Invadopodium

A specialized actin-rich cellular projection utilized by metastatic tumor cells to degrade the basement membrane via matrix metalloproteases and migrate through the extracellular matrix toward blood vessels.

K-ras Activation in Colorectal Carcinoma

An early oncogenic driver mutation occurring on chromosome 12 during the transition from a benign polyp to an adenoma that locks Ras in a constitutively active GTP-bound signaling state.

NEU and ErbB Oncoproteins

Ligand-independent receptor oncoprotein variants generated by a transmembrane Val $\rightarrow$ Gln point mutation in HER2 (forming NEU) or by an extracellular deletion of the ligand-binding domain in EGFR (forming ErbB), causing constitutive kinase activation.

RNA Polymerase II Structural Core

A 12-subunit eukaryotic transcription complex (RPB1–RPB12) containing an RPB1 clamp domain to accommodate template DNA, a wall domain that bends DNA, a catalytic center coordinating $\text{Mg}^{2+}$, and an extrusion channel for nascent RNA.

Carboxy-Terminal Domain (CTD) of RPB1

A specialized, unstructured C-terminal tail of the RPB1 subunit of RNA Polymerase II composed of multiple heptapeptide repeats whose serine residues are dynamically phosphorylated to regulate initiation, promoter clearance, elongation, and pre-mRNA processing.

Whole Genome Sequencing Strategies

Approaches for determining an organism's complete genomic sequence by generating ordered cDNA clone maps or constructing random fragment libraries assembled via massively parallel computer alignments.

ChIP-Seq (Chromatin Immunoprecipitation-Sequencing)

A genome-wide technique combining formaldehyde cross-linking, chromatin shearing, antibody immunoprecipitation (such as anti-Pol II), cross-link reversal, and massively parallel DNA sequencing to map protein-DNA binding sites in vivo.

CpG Islands

Vertebrate promoter regions spanning roughly $70\%$ of genes that are low in nucleosome density, initiate transcription bidirectionally, and allow elongation to proceed primarily in the sense direction toward the open reading frame.

Preinitiation Complex (PIC) Assembly and Activation

The sequential assembly of general transcription factors over core promoter elements, forming a Closed PIC, an ATP-dependent Open PIC with a transcription bubble, and an Elongation Complex following CTD phosphorylation and factor release.

TFIIH

A multi-protein general transcription factor that contains an ATP-dependent DNA helicase to melt promoter DNA into a transcription bubble and a protein kinase that phosphorylates the RNA Pol II CTD to release it from the promoter.

NELF and DSIF

Negative elongation factors that associate with RNA Polymerase II downstream of the transcription initiation site to cause polymerase pausing until relieved by phosphorylation.

P-TEFb (Positive Transcription Elongation Factor b)

A CDK9/Cyclin T protein kinase complex that phosphorylates NELF and the CTD of paused RNA Polymerase II, converting DSIF into a positive elongation factor and releasing the polymerase into productive transcript elongation.

HIV Tat and TAR

A viral transcriptional elongation control mechanism where the nascent $5'$ TAR stem-loop RNA halts RNA Polymerase II until the viral Tat protein binds TAR to recruit and activate P-TEFb (CDK9/CycT), releasing the paused polymerase.