BIO315: Life & Death of a Protein, Protein Trafficking, and ER Translocation

Vocabulary practice flashcards covering protein folding, chaperone mechanisms, the ubiquitin-proteasome degradation system, nucleocytoplasmic transport, and endoplasmic reticulum translocation pathways.

Exon Junction Complex (EJC)

A protein complex deposited on mRNA at sites where splicing has occurred; it stimulates translation and acts as a landmark during nonsense-mediated mRNA degradation.

Nonsense-Mediated mRNA Degradation (NMD)

A cellular surveillance pathway that detects and degrades abnormal transcripts containing premature in-frame stop codons upstream of an exon junction complex (EJC).

Upf Proteins

Proteins recruited by an exon junction complex (EJC) situated downstream of a premature stop codon; they interact with the premature stop codon and trigger mRNA degradation via ribonucleases.

Molten Globule

A folding intermediate that begins forming as soon as the N-terminal domain of a nascent polypeptide emerges from the ribosome before fine side-chain positioning occurs.

Hsp70

A molecular chaperone that acts co-translationally by binding with ATP to $7$ hydrophobic amino acid residues to prevent aggregation; it dissociates from the protein upon ATP hydrolysis to ADP.

Hsp60 (Chaperonin)

A barrel-shaped chaperone complex that mediates post-translational folding by capturing proteins with hydrophobic residues on its lip, stretching them upon GroES cap and ATP binding, and releasing them following ATP hydrolysis and binding of a second ATP.

20S Core Cylinder

The hollow catalytic core of the proteasome composed of $4$ rings containing $7$ subunits each ($28$ subunits total) with internal active sites to prevent indiscriminate cleavage of cytosolic proteins.

Unfoldase Ring

A hexameric ring of $6$ AAA protein subunits in the proteasome cap that couples ATP hydrolysis to conformational changes that pull and feed the unfolded polypeptide into the 20S core.

Ubiquitin (Ub)

A $76$-amino-acid protein covalently attached to lysine residues of target proteins; it contains $7$ internal lysine residues that can themselves receive additional ubiquitin molecules.

K48-Linked Polyubiquitylation

A specific polyubiquitin chain linkage formed via lysine-$48$ of successive ubiquitin molecules that signals for target protein degradation by the proteasome.

E1 Ubiquitin-Activating Enzyme

An ATP-dependent enzyme that forms an AMP-ubiquitin intermediate, releasing pyrophosphate, and covalently attaches ubiquitin to its own cysteine side chain via a high-energy thioester linkage.

E2 Ubiquitin-Conjugating Enzyme

An enzyme that receives activated ubiquitin onto its cysteine residue from E1 and pairs with E3 to transfer ubiquitin to a target protein lysine.

E3 Ubiquitin Ligase

An enzyme or multi-subunit complex that recognizes specific degradation signals on target proteins and positions them close to E2 for ubiquitin attachment.

SCF Ubiquitin Ligase

A multi-subunit ubiquitin ligase complex containing an F-box protein that brings target proteins into close proximity to the E2 ligase for ubiquitylation.

Topological Equivalence

The property shared by intracellular compartments whose lumina or exterior environments can communicate and exchange molecules via transport vesicles or pores without crossing a membrane.

Gated Transport

Bidirectional transport between topologically equivalent compartments (cytosol and nucleus) via nuclear pore complexes that does not involve crossing a membrane or protein unfolding.

Transmembrane Transport

Anterograde transport of proteins requiring unfolding to translocate directly across a membrane from the cytosol into topologically distinct organelle compartments (e.g., ER lumen).

Vesicular Transport

Transport mediated by membrane-enclosed vesicles that bud from one compartment and fuse with another without unfolding cargo proteins or crossing biological membranes.

Nuclear Lamina

A protein meshwork underlying the inner nuclear membrane that provides structural support to the nuclear envelope and anchors chromatin.

Nuclear Pore Complex (NPC)

An octagonal aqueous assembly of $500\text{--}1000$ protein molecules spanning the nuclear envelope that allows passive diffusion of macromolecules $<5\,\text{kDa}$ while selectively gating larger cargo.

Nuclear Localization Signal (NLS)

A sorting sequence rich in positively charged lysine and arginine residues on the surface of a cargo protein that is recognized by import receptors for transport into the nucleus.

Ran GTPase

A monomeric GTPase that coordinates the directionality of nucleocytoplasmic transport, adopting a GTP-bound conformation in the nucleus and a GDP-bound conformation in the cytosol.

Ran-GEF

A nuclear guanine nucleotide exchange factor that catalyzes the exchange of GDP for GTP on Ran, maintaining high nuclear levels of Ran-GTP.

Ran-GAP

A cytosolic GTPase-activating protein that stimulates Ran to hydrolyze its bound GTP to GDP, maintaining high cytosolic levels of Ran-GDP.

Calcineurin

A calcium-activated protein phosphatase that dephosphorylates the transcription factor NF-AT, unmasking its NLS and blocking its NES to promote nuclear import during T-cell activation.

SREBP (Sterol Regulatory Element-Binding Protein)

A latent membrane-bound transcription factor in the ER that is escorted by SCAP to the Golgi under low cholesterol conditions, where proteases cleave it to release an active nuclear domain.

Microsomes

Small, closed vesicles spontaneously formed from fragmented endoplasmic reticulum membranes during tissue homogenization, separated experimentally via sucrose gradient centrifugation.

Signal-Recognition Particle (SRP)

A cytosolic ribonucleoprotein complex consisting of $6$ polypeptide chains and $1$ RNA molecule that binds an N-terminal hydrophobic signal sequence using a methionine pocket and arrests translation via its pause domain.

Sec61 Complex

The core heterotrimeric ER translocator whose $\alpha$ subunit forms a $10$-helix central aqueous pore gated centrally by a flexible short helix plug and gated laterally to release transmembrane segments.

BiP

An ER lumenal Hsp70-family chaperone and ATPase that binds translocating nascent polypeptides and utilizes cycles of ATP hydrolysis to pull them into the eukaryotic ER lumen.

SecA

A bacterial motor protein and ATPase that associates with the cytosolic face of the SecY translocator and uses ATP-driven conformational shifts to push polypeptides through the membrane.

Signal Peptidase

An ER translocator-associated protease that cleaves N-terminal leader signal peptides from translocating proteins before releasing the mature protein into the ER lumen.

KDEL Signal

A C-terminal tetrapeptide retention signal ($-\text{Lys-Asp-Glu-Leu-COO}^-$) present on soluble ER resident proteins, preventing their permanent loss through the secretory pathway.

Protein Disulfide Isomerase (PDI)

An ER resident enzyme that catalyzes the oxidation of free sulfhydryl groups to generate disulfide bonds in proteins entering the secretory pathway.

Oligosaccharyl Transferase

A membrane-bound ER enzyme with its catalytic site facing the ER lumen that transfers a pre-assembled $14$-sugar oligosaccharide from dolichol to the $\text{-NH}_2$ group of an asparagine in an $\text{Asn-X-Ser/Thr}$ motif.

Dolichol

A membrane-anchored polyisoprenoid lipid that holds the growing precursor oligosaccharide via a high-energy pyrophosphate bond that energizes oligosaccharide transfer to nascent proteins.

Calnexin and Calreticulin

ER chaperone proteins (transmembrane and soluble, respectively) that bind specifically to glycoproteins containing a single terminal glucose residue to facilitate folding and retain unfolded proteins in the ER.

Glucosyl Transferase

An ER enzyme that recognizes misfolded or incompletely folded glycoproteins and adds a terminal glucose residue back onto the N-linked oligosaccharide to renew calnexin/calreticulin chaperone binding.

Get3 ATPase

A cytosolic targeting ATPase that binds the hydrophobic C-terminus of tail-anchored proteins and delivers them to the Get1-Get2 membrane receptor complex for ER membrane insertion.