Cell Biology: Cytoskeleton, Chromatin, DNA Replication, and Transcription

Vocabulary practice flashcards covering eukaryotic cellular architecture, cytoskeletal elements (microtubules, microfilaments, intermediate filaments), chromatin structure, DNA repair and telomeres, and eukaryotic transcription and RNA processing.

RXR Retention Tag

An Arg-X-Arg sequence (where $X$ is any amino acid) found on certain proteins localized to the endoplasmic reticulum that prevents them from escaping the ER and aids in retrieving them from the Golgi apparatus.

Endocytosis

A membrane transport process unique to eukaryotic cells in which external materials are internalized through vesicles formed from the plasma membrane.

Exocytosis

A membrane transport process unique to eukaryotic cells where secretory vesicles fuse with the plasma membrane to release their contents outside the cell.

Endoplasmic Reticulum Functional Variation

The cellular adaptation whereby cells actively synthesizing secretory proteins possess prominent rough ER networks, while cells producing steroid hormones contain extensive smooth ER networks.

Microtubules

The largest cytoskeletal elements, structured as hollow tubes composed of alternating $\alpha$-tubulin and $\beta$-tubulin heterodimers that possess polarity, grow primarily at their plus end, and mediate chromosome segregation and intracellular transport.

Microfilaments

Cytoskeletal polymers approximately $7\,\text{nm}$ in diameter assembled from actin monomers with defined polarity, whose assembly is regulated by ATP and which function in whole-cell locomotion and muscle contraction.

Intermediate Filaments

Durable, non-polar cytoskeletal fibers approximately $8\text{--}12\,\text{nm}$ wide made of tissue-specific fibrous protein subunits wrapped into reinforced coils to provide high mechanical strength to cells and tissues.

Microtubule Assembly Phases

The three-stage kinetic process of microtubule polymerization starting with a lag phase (nucleation of dimers into oligomers and protofilaments), followed by an elongation phase (rapid assembly of growing microtubules), and culminating in a plateau phase where subunit addition and loss reach equilibrium.

G-actin vs. F-actin

G-actin represents the individual globular monomeric building block that binds ATP, whereas F-actin is the fibrous, filamentous polymer formed when G-actin subunits assemble into a microfilament.

Treadmilling

A steady-state phenomenon occurring in cytoskeletal filaments when free subunit concentration permits simultaneous polymer assembly at the plus end and disassembly at the minus end.

Dynamic Instability and Microtubule Catastrophe

The rapid switching between growth and shrinkage at the microtubule plus end; loss of the protective GTP cap via GTP hydrolysis causes rapid filament depolymerization termed a catastrophe.

Taxol

A chemotherapeutic drug originally derived from a rare tree that binds to and stabilizes microtubules, preventing their disassembly and arresting cancer cells in division, used in breast cancer treatment.

Colchicine

A chemical compound that inhibits microtubule assembly and promotes disassembly, blocking mitotic spindle formation and preventing cellular division.

Microtubule Organizing Center (MTOC)

A specialized cellular anchor site, such as a centrosome or basal body, containing specialized $\gamma$-tubulin that nucleates and directs the growth of microtubules.

Lamellipodia

Broad, sheet-like protrusions composed of dense, branched actin networks extended at the leading edge of crawling cells, organized through activation of Rac GTPase.

Filopodia

Thin, finger-like cellular extensions containing concentrated parallel bundles of actin filaments pushed against the plasma membrane, regulated by CDC42 GTPase.

Microvilli

Finger-like surface projections on intestinal mucosal cells supported internally by bundled, crosslinked actin filaments that maximize membrane surface area for nutrient absorption.

Rho GTPases

A family of molecular switches (including Rho, Rac, and CDC42) active when bound to GTP and inactive when bound to GDP that signal and direct actin cytoskeletal remodeling.

Nuclear Lamins

Intermediate filament proteins lining the inner nuclear membrane to provide structural reinforcement for the nucleus; mutations in these proteins can cause muscular dystrophy.

Nucleosome Bead

The fundamental structural repeating unit of eukaryotic chromatin consisting of approximately $146$ base pairs of DNA coiled around an octamer core of eight histone molecules (two each of H2A, H2B, H3, and H4), forming a structure roughly $10\,\text{nm}$ wide.

Histone H1

A linker histone protein that binds to linker DNA adjacent to the nucleosome core particle to facilitate higher-order packing of chromatin fibers.

Telomeres

Repetitive noncoding DNA sequences located at chromosome termini (such as $100\text{ to }1500$ copies of $5'\text{-TTAGGG-}3'$ in humans) that prevent loss of essential genetic information during lagging-strand end replication.

Telomerase

A specialized ribonucleoprotein reverse transcriptase carrying its own RNA template (such as $3'\text{-AACCCC-}5'$ in Tetrahymena) that synthesizes complementary DNA repeat sequences (such as $5'\text{-TTGGGG-}3'$) onto the ends of chromosomes.

Nonhomologous End-Joining (NHEJ)

An error-prone double-strand DNA break repair pathway that utilizes proteins such as Ku70/Ku80 to bind and join broken ends together directly, frequently leading to the loss of nucleotides.

Homologous Recombination

An accurate, high-fidelity double-strand break repair mechanism that uses an intact homologous chromosome as a template for strand invasion and DNA synthesis, resolving through a crossed Holliday junction.

Gene Conversion

An outcome of homologous recombination in which a damaged DNA sequence is repaired using an intact homologue as a template without reciprocal genetic exchange, causing the repaired region to match the undamaged strand sequence.

Degenerate Genetic Code

The feature of the genetic code wherein $64$ nucleotide triplet codons encode only $20$ standard amino acids, meaning individual amino acids can be specified by more than one triplet.

Nonoverlapping Reading Frame

The structural property of the genetic code in which translation advances sequentially three nucleotides at a time, without sharing nucleotides between adjacent codons.

TATA Box

An evolutionarily conserved promoter sequence enriched in adenine and thymine bases located upstream of the transcription start site that facilitates DNA unwinding due to fewer hydrogen bonds between A and T.

TFIID

A eukaryotic basal transcription factor containing TATA-binding protein (TBP) that initiates pre-initiation complex assembly by binding directly to the promoter TATA box and recruiting TFIIA, TFIIB, and RNA Polymerase II.

RNA Polymerase I

The eukaryotic enzyme localized to the nucleolus that is dedicated to the synthesis of ribosomal RNA (rRNA) precursors.

RNA Polymerase II

The eukaryotic RNA polymerase that transcribes all protein-coding genes into pre-mRNA (hnRNA) and uses its C-terminal domain as a scaffold for RNA processing machinery.

RNA Polymerase III

The eukaryotic enzyme responsible for synthesizing transfer RNAs (tRNAs), 5S rRNA, and various other small non-coding functional RNAs.

5' Cap

A modified 7-methylguanosine residue added to the 5' end of eukaryotic pre-mRNA shortly after initiation that identifies the transcript as mRNA, protects it against cellular nucleases, and positions it on ribosomes for translation.

Poly(A) Tail

A stretch of $50\text{ to }250$ adenine residues appended to the cleaved 3' end of pre-mRNA by poly(A) polymerase that prevents transcript degradation, aids ribosomal recognition, and is required for export to the cytoplasm.

Polyadenylation Signal

The consensus sequence AAUAAA located upstream of the 3' pre-mRNA cleavage site that, together with a downstream GU- or U-rich element, directs endonucleolytic cleavage and poly(A) tail addition.

Introns

Intervening sequences present within pre-mRNA primary transcripts that do not appear in mature, functional mRNA molecules and are excised and destroyed during RNA splicing.

Exons

The transcribed nucleotide sequences of a primary RNA transcript that are retained and joined together during RNA splicing to form the mature mRNA exported for protein translation.

Alternative Splicing

A post-transcriptional process in which specific splice sites or exons within a single pre-mRNA transcript are differentially included or skipped, allowing a single gene to encode multiple distinct protein isoforms.