BI 203 CH 10 **good**

What are the two membranes of the nuclear envelope?

Inner and outer nuclear membranes, consisting of two phospholipid bilayers separated by the perinuclear space.

How is the outer nuclear membrane connected to the ER?

The outer nuclear membrane is continuous with the endoplasmic reticulum.

What is the function of the LINC complex?

Connects the inside of the nucleus to the cytoskeleton outside the nucleus.

What is the nuclear lamina?

A supporting meshwork of lamin proteins underneath the inner nuclear membrane.

What are lamins?

Fibrous proteins that form coiled-coil structures and provide mechanical support to the nucleus.

What are the main functions of the nuclear lamina?

Maintains nuclear shape, provides mechanical support, organizes chromatin, and supports the nuclear envelope.

How is the nuclear lamina anchored?

Through protein-protein interactions with the inner nuclear membrane.

What can mutations in lamin genes cause?

Weakened nuclear structure, altered gene regulation, and inherited tissue-specific diseases.

What disease is associated with mutations in lamin genes?

Hutchinson-Gilford progeria syndrome, characterized by accelerated aging.

What is the nuclear pore complex (NPC)?

The channel responsible for transport into and out of the nucleus.

What are FG-NUPs?

Nucleoporins that form a selective barrier within the nuclear pore.

How do small molecules enter and exit the nucleus?

By diffusion through nuclear pore complexes.

How do large molecules move through nuclear pores?

Through regulated transport involving transport receptors.

What is a nuclear localization signal (NLS)?

An amino acid sequence signaling that a protein should be imported into the nucleus.

Which amino acids are abundant in NLS sequences?

Basic amino acids, especially lysine and arginine.

What is a bipartite NLS?

An NLS consisting of two amino acid sequences separated by non-NLS amino acids.

What are importins?

Transport receptor proteins that recognize NLS-containing cargo and bring it into the nucleus.

What regulates importin-mediated nuclear transport?

The GTP-binding protein Ran.

What happens first during nuclear protein import?

Importin binds an NLS-containing cargo protein in the cytoplasm.

What causes importin to release its cargo inside the nucleus?

Ran-GTP binds importin, causing cargo release.

What happens to importin after releasing its cargo?

Importin binds Ran-GTP and returns to the cytoplasm.

What does Ran-GAP do in the cytoplasm?

Promotes conversion of Ran-GTP to Ran-GDP, leading to dissociation of Ran from importin.

What does Ran-GEF do in the nucleus?

Promotes exchange of GDP for GTP on Ran, regenerating Ran-GTP.

What is the complete importin transport cycle?

Importin binds NLS cargo in cytoplasm → enters nucleus → Ran-GTP releases cargo → importin-Ran-GTP exits → Ran-GAP produces Ran-GDP → importin is released.

What are exportins?

Transport receptors that recognize nuclear export signals and move cargo from the nucleus into the cytoplasm.

What is a nuclear export signal (NES)?

An amino acid sequence recognized by exportins to direct nuclear export.

What role does Ran-GTP play in nuclear export?

Ran-GTP binds exportin and helps form the exportin-Ran-GTP-cargo complex for nuclear export.

What happens to the export complex in the cytoplasm?

Ran-GAP promotes GTP hydrolysis, allowing the export complex to dissociate.

What is the nuclear protein export sequence?

Exportin recognizes NES cargo → Ran-GTP binds → complex exits nucleus → Ran-GAP converts Ran-GTP to Ran-GDP → complex dissociates.

How does Ran-GTP function differently in import versus export?

Import: Ran-GTP triggers cargo release from importin. Export: Ran-GTP promotes exportin-cargo complex formation.

What are karyopherins?

A family of nuclear transport receptors that includes different import and export transporters.

What is the function of NTF2?

Binds Ran-GDP in the cytoplasm and transports it back into the nucleus.

How is Ran-GDP converted back into Ran-GTP?

Ran-GEF in the nucleus facilitates GDP-to-GTP exchange.

Is mRNA nuclear export Ran-dependent?

No. mRNA export uses a distinct transport complex and is Ran-independent.

What ensures one-way movement during mRNA export?

A helicase on the cytoplasmic side releases mRNA from the export complex, promoting unidirectional transport.

What is the purpose of the snRNA transport cycle?

snRNA temporarily leaves the nucleus to associate with proteins and then returns as an snRNP.

What protein exports snRNA from the nucleus?

Crm1, an exportin.

What happens to snRNA in the cytoplasm?

Proteins bind the snRNA, forming an snRNP.

What protein imports snRNPs back into the nucleus?

Snurportin, an importin.

What is the complete snRNA transport cycle?

snRNA exits nucleus via Crm1 → proteins associate with snRNA to form snRNP → snurportin imports snRNP into nucleus.

How does IκB regulate NF-κB?

IκB binds NF-κB and masks its NLS, preventing nuclear import.

What triggers NF-κB nuclear import?

Extracellular stimulation leads to IκB phosphorylation and degradation, exposing the NF-κB NLS.

What does NF-κB do after entering the nucleus?

Activates transcription of target genes.

What is the effect of Pho4 phosphorylation near its NLS?

Phosphorylation of a nearby serine blocks importin binding and prevents nuclear import.

What happens when Pho4 is dephosphorylated?

Importin can recognize its NLS, allowing Pho4 to enter the nucleus and activate target gene transcription.

What is the key difference between NF-κB and Pho4 regulation?

NF-κB is regulated by an inhibitor masking its NLS; Pho4 is regulated by phosphorylation near its NLS.

Are chromosomes randomly distributed inside the nucleus?

No. Individual chromosomes occupy distinct chromosome territories.

What are chromosome territories?

Distinct regions of the nucleus occupied by individual chromosomes.

Where is heterochromatin commonly located?

Near the nuclear periphery and in nucleolus-associated regions.

What are lamina-associated domains (LADs)?

Chromatin regions that associate with the nuclear lamina.

What are nucleolus-associated domains (NADs)?

Chromatin regions associated with the nucleolus.

Where are actively transcribed genes often located within chromosome territories?

Toward the periphery of chromosome territories, within organized chromatin domains.

What are topologically associated domains (TADs)?

Regions of chromatin organized into domains with frequent internal physical contacts.

Is chromatin structure static or dynamic?

Dynamic; chromatin organization and interactions can change.

What does chromosome conformation capture measure?

Which DNA regions are physically close together inside the nucleus.

What are the steps of chromosome conformation capture?

Fix and crosslink nearby DNA → fragment and ligate crosslinked DNA pieces → detect contacts using PCR.

Why is crosslinking used in chromosome conformation capture?

To preserve nearby DNA contacts before fragmentation.

What is the difference between euchromatin and heterochromatin?

Euchromatin appears lighter and is more widely distributed; heterochromatin appears darker and is commonly near the nuclear envelope.

What is fluorescence in situ hybridization (FISH)?

A technique using complementary fluorescent DNA or RNA probes to locate specific sequences inside cells.

What can FISH visualize?

Specific DNA loci or chromosome territories directly in nuclei.

What is the key difference between FISH and chromosome conformation capture?

FISH visualizes where a DNA sequence is located; chromosome conformation capture identifies which DNA regions are physically close.

What are replication factories?

Nuclear regions where DNA replication proteins concentrate and DNA synthesis occurs.

What experiments revealed replication factories?

BrdU and PCNA experiments.

What are transcription factories?

Nuclear hubs where different active DNA regions loop together and share transcription machinery for RNA synthesis.

What are Polycomb bodies?

Membraneless nuclear assemblies concentrating repressed chromatin and Polycomb complexes involved in gene silencing.

What is the role of PRC2 in gene silencing?

Deposits the repressive histone modification H3K27me3.

What is the role of PRC1 in gene silencing?

Recognizes the repressive mark and promotes chromatin compaction.

How do PRC1 and PRC2 work together?

PRC2 deposits H3K27me3 → PRC1 recognizes the mark → chromatin becomes compacted, promoting transcriptional repression.

What are nuclear bodies?

Organized, membraneless structures within the nucleus.

What are the three main functions of the nucleolus?

rRNA synthesis, rRNA processing, and ribosomal subunit assembly.

What is the sequence of ribosomal subunit assembly in the nucleolus?

rRNA transcription → pre-rRNA processing → ribosomal proteins assemble on pre-rRNA → additional proteins and 5S rRNA associate → pre-ribosomal particles form.

What is the function of Cajal bodies?

Support snRNP maturation and modification and participate in telomerase RNP assembly.

What is the function of nuclear speckles?

Organize and store RNA-processing and splicing factors near transcriptionally active chromatin.

How are the nucleolus, Cajal bodies, and nuclear speckles different?

Nucleolus: rRNA and ribosome assembly; Cajal bodies: snRNP maturation and telomerase RNP assembly; nuclear speckles: splicing factor organization.