Unit 3 Exam: Nucleus and Protein Processing/Sorting

Nuclear envelope

A structure composed of two concentric membranes—an inner and outer nuclear membrane—that encloses the nucleus, with the outer membrane being continuous with the rough endoplasmic reticulum.

Perinuclear space

The lumenal space situated between the inner and outer nuclear membranes of the nuclear envelope.

Nuclear lamina

A structural protein network positioned directly underneath the inner nuclear membrane that provides mechanical support to the nucleus and serves as an attachment site for DNA.

Nuclear localization signal (NLS)

A specific sequence of amino acid motifs on a protein destined to enter or exit the nucleus that is recognized and bound by nuclear transport receptors to direct import through the nuclear pore.

Importin

A nuclear transport receptor that binds an NLS-bearing cargo protein in the cytoplasm, carries it through the nuclear pore, and releases it upon binding Ran-GTP in the nucleus.

Exportin

A nuclear transport receptor that binds cargo proteins containing a nuclear export signal in a complex with Ran-GTP and escorts them out through the nuclear pore into the cytoplasm.

Ran-GAP

A cytoplasmic GTPase-activating protein that stimulates Ran-GTP to hydrolyze its bound GTP to Ran-GDP and inorganic phosphate causing the release of exported cargo from exportin or releasing importin.

Ran-GEF

A nuclear guanine nucleotide exchange factor bound to chromatin that converts Ran-GDP back into Ran-GTP by catalyzing the exchange of GDP for GTP.

NTF2

A nuclear transport factor that specifically binds Ran-GDP in the cytoplasm and shuttles it back into the nucleus.

Exporter complex

A specialized protein complex that binds mature mRNAs to facilitate their transport through the nuclear pore into the cytoplasm in a pathway that does not involve Ran.

Chromosome territories

Distinct, nonrandom spatial domains within the nucleus occupied by individual chromosomes and chromatin.

Lamina-associated domains (LADs)

Regions of genomic heterochromatin attached/localized to the nuclear lamina that are generally transcriptionally inactive/repressed.

Nucleolus-associated domains (NADs)

Heterochromatic regions of DNA physically associated with the nucleolus that remain generally transcriptionally inactive.

Topologically associating domains (TADs)

Looped regions of euchromatin bounded by CTCF and cohesin that permit RNA polymerase and transcription factor access when transcription is needed.

Nucleolus

A subnuclear body where rRNA transcription, pre-rRNA processing, and assembly of pre-ribosomal particles take place. Ribosome production factory.

Endoplasmic reticulum (ER)

The largest organelle of most eukaryotic cells, comprising approximately $10\%$ of total cell volume, divided into rough and smooth regions.

Rough endoplasmic reticulum

Ribosome-studded ER membranes dedicated to cotranslational protein processing, folding, and sorting into the secretory pathway.

Smooth endoplasmic reticulum

Ribosome-free ER tubules dedicated to lipid and phospholipid synthesis, as well as the production of steroid hormones.

Signal sequence

A short sequence of hydrophobic amino acids located at the N-terminus of a growing polypeptide chain that recruits the translating ribosome-mRNA complex to the rough ER. Stops translation and recruits rRNA. Determines where mRNA will be translated.

Signal recognition particle (SRP)

A ribonucleoprotein particle that recognizes and binds the N-terminal signal sequence emerging from a ribosome, pauses translation, and escorts the complex to the SRP receptor on the rough ER.

SRP receptor

A rough ER membrane receptor that binds the SRP complex, triggering GTP hydrolysis and the release of SRP from the signal sequence.

Translocon

A membrane protein conducting channel in the rough ER that allows nascent polypeptides to enter the ER lumen or integrate laterally into the lipid bilayer.

Signal peptidase

An ER membrane enzyme that cleaves the N-terminal signal sequence from a nascent polypeptide as translation resumes into the lumen.

BiP

An ER lumenal molecular chaperone that binds to newly translocated unfolded polypeptide chains to facilitate proper protein folding.

GPI anchor

A glycolipid structure added post-translationally to the C-terminus of target proteins by GPI transamidase in the rough ER lumen to attach them to the membrane.

ER-associated degradation (ERAD)

A quality-control pathway wherein misfolded lumenal ER proteins are retrotranslocated to the cytosol, ubiquitinated, and degraded by the proteasome.

Flippases

Enzymes that facilitate the transfer of newly synthesized phospholipids from the cytosolic half of the ER membrane to the lumenal half, allowing balanced growth of both leaflets.

Golgi apparatus

A compartmentalized organelle consisting of cis, medial, trans, and trans-Golgi network regions that processes, sorts, and packages ER-derived proteins and synthesizes complex polysaccharides in plants.

COPII

A vesicle coat protein complex that drives the formation of transport vesicles traveling anterograde from the rough ER toward the ERGIC and cis-Golgi.

COPI

A coat protein complex that drives the formation of retrograde transport vesicles returning membrane components and proteins back from the Golgi to the ER.

Clathrin

A coat protein that forms a basketlike meshwork around budding vesicles operating between the trans-Golgi network, endosomes, and plasma membrane.

SNAREs

Complementary pairs of transmembrane proteins on transport vesicles and target membranes that interact and twist tightly together to drive membrane fusion.

Lysosomes

Membrane-enclosed organelles containing acid hydrolases that degrade biological polymers including proteins, nucleic acids, carbohydrates, and lipids.

Autophagy

A catabolic pathway in which a cell degrades its own components by sequestering organelles or cytoplasm inside a double-membrane autophagosome that fuses with a lysosome.

Molecular Chaperones

Keep proteins linear until entire protein is made. They assist in protein folding, unfolding, assembly, and translocation of other proteins without becoming part of the final structure.