Nuclear structure – Study guide

A set of practice flashcards covering key concepts from the Nuclear Structure study guide, including nuclear components, chromosome organization, gene gating, GFP applications, lamin function, Progeria, NPC structure, nuclear import mechanics, Ran GTPase cycle, and related assays.

What subnuclear structures are highlighted in the basic nuclear organization (e.g., nucleolus, nuclear lamina, nuclear pore) and what are their general derivations or origins?

Nucleolus: site of rRNA transcription and ribosome assembly; Nuclear lamina: a fibrous network of lamins beneath the inner nuclear membrane that supports the nuclear envelope and organizes chromatin; Nuclear pore: large protein complexes (NPCs) spanning the nuclear envelope, formed by nucleoporins, that regulate transport.

What are the organizing principles for chromosomes in the eukaryotic nucleus and how does chromosomal organization relate to gene activity?

Chromosomes occupy distinct territories (chromosome territories). Gene-rich regions tend to be more interior and transcriptionally active, while heterochromatin regions localize toward the periphery or lamina-associated domains (LADs) and are generally repressed; organization correlates with transcriptional activity.

What is the gene gating hypothesis?

Active genes associate with nuclear pore complexes to couple transcription with mRNA export, thereby increasing transcriptional efficiency and coordination between transcription and export.

How is GFP technology used to track the behavior of genes in response to transcriptional activation?

GFP-tagged gene loci or GFP-based reporters enable live-cell visualization of transcriptional activation and gene movement; systems like MS2-GFP label nascent RNA to monitor transcription dynamics in real time.

What is the primary function of lamins?

Lamins provide structural support to the nuclear envelope, help organize chromatin, and participate in nuclear envelope reassembly after cell division.

What molecule is defective in individuals with Progeria, and why does mislocalization of specific chromosomal structures lead to Progeria?

Progeria involves a defect in LMNA producing progerin; this defective lamin A disrupts the nuclear lamina, causing mislocalization/altered organization of chromatin and nuclear morphology, which contributes to premature aging.

Describe the structure of the nuclear pore and the relevance of nucleoporins.

The nuclear pore complex consists of ~30 different nucleoporins (Nups) forming a central transport channel; FG-Nups create a selective barrier; cytoplasmic filaments and the nuclear basket coordinate transport.

What is the basis of nuclear import including how differently sized cargos would behave (i.e., what size cargos are gated, which diffuse freely with no gating)?

Small cargos (< about 40–60 kDa) diffuse freely through the NPC; larger cargos require active transport via nuclear localization signals (NLS) and transport receptors (importins) for gated translocation.

Explain GTPase cycles and the effect of accessory factors in nuclear transport.

Ran GTPase cycle: Ran-GTP is enriched in the nucleus (maintained by RCC1 as GEF); Ran-GDP is enriched in the cytoplasm (via RanGAP). Accessory factors (e.g., RanBP1, NTF2) regulate cargo binding/release and receptor recycling during import and export.

Describe the nuclear import cycle (NLS, carriers, release) and the role of Ran asymmetry in concerted transport. What assays were developed to elucidate the process?

Cargo with an NLS binds importins to form a transport complex, translocates through the NPC, and in the nucleus, Ran-GTP binds the importin causing cargo release; the importin-Ran-GTP complex is recycled to the cytoplasm where GTP is hydrolyzed. Assays include in vitro nuclear import with permeabilized cells or Xenopus egg extracts, fluorescence-based transport assays, and FRAP to study dynamics.

What roles do nucleoporins play beyond forming the pore structure?

Nucleoporins mediate recognition and translocation of cargo, contribute to the selective permeability barrier (via FG repeats), and regulate transport cycles through interactions with transport receptors.