MCB2050 Final Exam: Lectures 17–22 (Nucleus, ER & Protein Trafficking)

[L17] Which nuclear subdomain is the site of rDNA transcription, rRNA processing, and initial ribosomal subunit assembly?

A) Nuclear speckle
B) Nucleolus
C) Transcription factory
D) Inter-chromosomal channel

B) Nucleolus

[L17] A cell sharply increases its protein synthesis. What happens to its nucleoli?

A) Fewer and smaller nucleoli
B) Nucleoli dissolve into speckles
C) Larger and more numerous nucleoli
D) Same size, but fewer nucleoli

C) Larger and more numerous nucleoli

[L17] Nuclear speckles are best described as dynamic subdomains that:

A) Store histones for chromatin assembly
B) Transcribe rDNA into rRNA
C) Separate neighbouring chromosome territories
D) Concentrate mRNA splicing factors

D) Concentrate mRNA splicing factors

[L17] Which statement about the outer nuclear membrane is TRUE?

A) It is continuous with the RER
B) It is lined by the nuclear lamina
C) It has a unique, non-ER protein makeup
D) Its lumen is sealed off from the ER

A) It is continuous with the RER

[L17] Nuclear lamins (A, B, C) are related to which cytoskeletal proteins?

A) Tubulin microtubules
B) Actin microfilaments
C) Myosin motor proteins
D) Intermediate filaments

D) Intermediate filaments

[L17] What causes Hutchinson-Gilford Progeria Syndrome?

A) Loss of FG nucleoporins in the NPC
B) Inactivating mutation in the RCC1 gene
C) Truncating point mutation in LAMIN A
D) Defective importin beta binding to Ran

C) Truncating point mutation in LAMIN A

[L17] FG nucleoporins are best described as:

A) Disordered Nups forming a mesh in the channel
B) Membrane Nups anchoring the NPC scaffold
C) Structural Nups forming the nuclear basket
D) Small GTPases that power NPC transport

A) Disordered Nups forming a mesh in the channel

[L17] What is the approximate size limit for free diffusion through the NPC?

A) About 4 kDa
B) About 40 kDa
C) About 400 kDa
D) About 4000 kDa

B) About 40 kDa

[L18] A classic NLS consists of:

A) A leucine-rich LxxLxxL motif
B) 8-15 hydrophobic N-terminal residues
C) An N-x-S/T glycosylation sequence
D) A short stretch of basic residues

D) A short stretch of basic residues

[L18] Pyruvate kinase (normally cytoplasmic) moves to the nucleus when an NLS is attached. This shows the NLS is:

A) Necessary
B) Cleaved
C) Sufficient
D) Bipartite

C) Sufficient

[L18] Mutating a nuclear protein's NLS leaves the protein in the cytoplasm. This shows the NLS is:

A) Necessary
B) Sufficient
C) Cleaved
D) Bipartite

A) Necessary

[L18] Which subunit of importin directly binds the NLS of a cargo protein?

A) Importin beta
B) Importin alpha
C) Exportin 2
D) Ran-GTP

B) Importin alpha

[L18] What triggers release of the cargo from importin inside the nucleus?

A) Ran-GTP binding importin beta
B) RanGAP1 hydrolysing Ran-GTP
C) Signal peptidase cleaving the NLS
D) Kinases phosphorylating importin alpha

A) Ran-GTP binding importin beta

[L18] What are the location and function of RCC1?

A) Cytoplasmic GAP, Ran-GTP to Ran-GDP
B) Nuclear GAP, Ran-GTP to Ran-GDP
C) Cytoplasmic GEF, Ran-GDP to Ran-GTP
D) Nuclear GEF, Ran-GDP to Ran-GTP

D) Nuclear GEF, Ran-GDP to Ran-GTP

[L18] If RanGAP1 were inactivated, what would most likely happen?

A) The Ran-GTP gradient would collapse
B) Nuclear Ran-GTP would drop sharply
C) Importin alpha would bind NLSs tighter
D) NPCs would lose their FG mesh

A) The Ran-GTP gradient would collapse

[L18] How does importin alpha get back to the cytoplasm after import?

A) Free diffusion through the NPC
B) Carried out by importin beta
C) Degraded and resynthesized
D) Carried out by exportin 2

D) Carried out by exportin 2

[L18] What is the most common type of NES?

A) Basic KKQRKK motif
B) Leucine-rich LxxLxxL motif
C) C-terminal KDEL motif
D) N-x-S/T glycosylation motif

B) Leucine-rich LxxLxxL motif

[L18] A shuttling protein has both an NLS and an NES, and its NLS is stronger. Where is it found at steady state?

A) Mostly in the cytoplasm
B) Equally in both
C) Mostly in the nucleus
D) Mostly in the ER

C) Mostly in the nucleus

[L18] In a co-IP with anti-Myc beads, importin alpha pulls down with Myc-ARC1 but NOT with Myc-ARC1 NLS-mut. What does this mean?

A) Importin alpha binds regardless of the NLS
B) The anti-Myc antibody failed to bind
C) Importin alpha binds through an NES
D) The NLS is required for importin b…

D) The NLS is required for importin binding

[L19] How is a microscope's resolution improved (smaller resolvable distance)?

A) Longer wavelength, lower NA
B) Shorter wavelength, higher NA
C) Shorter wavelength, lower NA
D) Longer wavelength, higher NA

B) Shorter wavelength, higher NA

[L19] Why does electron microscopy give far better resolution than light microscopy?

A) Electrons have a much shorter wavelength
B) EM lenses provide higher magnification
C) EM uses oil to raise numerical aperture
D) EM samples are fixed and stained

A) Electrons have a much shorter wavelength

[L19] What is the major limitation of brightfield microscopy?

A) Too much photodamage
B) Too little magnification
C) Poor specimen contrast
D) Too slow to image

C) Poor specimen contrast

[L19] Which organelle is NOT part of the endomembrane system?

A) Mitochondrion
B) Golgi apparatus
C) Peroxisome
D) Nuclear envelope

A) Mitochondrion

[L19] Which feature is unique to regulated (vs constitutive) secretion?

A) Golgi-to-PM vesicle transport
B) Vesicle fusion with the PM membrane
C) Release of cargo by exocytosis
D) Signal-triggered granule release

D) Signal-triggered granule release

[L19] During vesicle formation and budding, what role do vesicle coat proteins play?

A) Power vesicle fusion with the target
B) Select cargo and drive vesicle budding
C) Link vesicles to cytoskeletal tracks
D) Return escaped proteins to the donor

B) Select cargo and drive vesicle budding

[L20] The yeast sec12 mutant has a large, expanded ER. Which class is it, and what is defective?

A) Class A, translocation into the ER
B) Class D, vesicle budding from Golgi
C) Class B, vesicle budding from the ER
D) Class E, vesicle fusion with the PM

C) Class B, vesicle budding from the ER

[L20] A Class A sec mutant accumulates secretory proteins in the:

A) ER
B) Golgi
C) Secretory vesicles
D) Cytosol

D) Cytosol

[L20] A Class B + Class D double mutant looks like a Class B mutant. What does this tell you?

A) ER budding happens before Golgi budding
B) Golgi budding happens before ER budding
C) The two budding steps are independent
D) The Class D defect is dominant

A) ER budding happens before Golgi budding

[L20] Reticulons are ER membrane proteins that:

A) Form the Sec61 translocon channel
B) Shape ER membrane curvature
C) Cleave N-terminal signal sequences
D) Fold proteins in the ER lumen

B) Shape ER membrane curvature

[L20] Which function belongs to the SER rather than the RER?

A) Ca2+ storage and hormone synthesis
B) Protein synthesis on bound ribosomes
C) Co-translational protein translocation
D) Cleavage of N-terminal signal sequences

A) Ca2+ storage and hormone synthesis

[L20] The ER signal sequence is:

A) A basic stretch at the C-terminus
B) A leucine-rich internal motif
C) 8-15 hydrophobic N-terminal residues
D) An N-x-S/T sequence for sugars

C) 8-15 hydrophobic N-terminal residues

[L20] What strengthens the binding of SRP to the SRP receptor, and what releases them?

A) ATP binding, then ATP hydrolysis
B) GTP binding, then GTP hydrolysis
C) Ran-GTP binding, then RanGAP1 action
D) Ca2+ binding, then Ca2+ release

B) GTP binding, then GTP hydrolysis

[L21] How does the Sec61 translocon stay sealed to ions and small molecules?

A) A hydrophobic pore ring and helix plug
B) FG-repeat mesh filling the channel
C) Signal peptidase blocking the pore
D) BiP plugging the cytosolic opening

A) A hydrophobic pore ring and helix plug

[L21] What drives the polypeptide through the Sec61 translocon in co-translational translocation?

A) ATP hydrolysis by BiP
B) The Ran-GTP gradient
C) Ongoing translation
D) GTP hydrolysis by SRP

C) Ongoing translation

[L21] Signal peptidase is:

A) A cytosolic protease that cleaves NLSs
B) An ER protease with a lumenal active site
C) A subunit of the signal recognition particle
D) A Golgi protease that cleaves ATF6

B) An ER protease with a lumenal active site

[L21] A Type I membrane protein has which features and final topology?

A) Cleaved signal sequence + STA; N lumen
B) Internal SA, flipped; N cytosol
C) Internal SA, not flipped; N lumen
D) Several SAs and STAs; varied topology

A) Cleaved signal sequence + STA; N lumen

[L21] A Type II membrane protein has which features and final topology?

A) Cleaved signal sequence + STA; N lumen
B) Internal SA, flipped; N cytosol
C) Internal SA, not flipped; N lumen
D) C-terminal lipid anchor; N cytosol

B) Internal SA, flipped; N cytosol

[L21] Under the "positive-outside rule," positively charged residues next to a signal-anchor face the:

A) ER lumen
B) Nucleoplasm
C) Cytosol
D) Golgi lumen

C) Cytosol

[L21] How does a Type III membrane protein differ from a Type II?

A) It has a cleaved N-terminal signal
B) It contains several TMDs
C) It is targeted without SRP
D) Its + residues are C-terminal to the SA

D) Its + residues are C-terminal to the SA

[L21] Multi-pass (Type IV) membrane proteins contain:

A) Only an N-terminal signal sequence
B) Internal SA and STA sequences
C) Only internal STA sequences
D) A C-terminal lipid anchor

B) Internal SA and STA sequences

[L22] In N-linked glycosylation, the core oligosaccharide attaches to:

A) Serine in S-x-N/T
B) Threonine in T-x-N/S
C) Asparagine in N-x-S/T
D) Glutamine in Q-x-S/T

C) Asparagine in N-x-S/T

[L22] Tunicamycin causes misfolding of ER proteins because it:

A) Blocks the first glycosylation step
B) Inhibits protein disulfide isomerase
C) Prevents SRP from binding signals
D) Inhibits the cytosolic proteasome

A) Blocks the first glycosylation step

[L22] What is the role of UGGT in ER quality control?

A) Trims mannose from folded proteins
B) Re-adds glucose to misfolded proteins
C) Forms disulfide bonds in new proteins
D) Ubiquitinates proteins for degradation

B) Re-adds glucose to misfolded proteins

[L22] Protein disulfide isomerase (PDI) helps proteins fold by:

A) Adding glucose to the core
B) Pulling proteins into cytosol
C) Binding exposed hydrophobic patches
D) Forming disulfide bonds

D) Forming disulfide bonds

[L22] In ERAD, what is p97's role?

A) Pulls misfolded proteins into the cytosol
B) Attaches ubiquitin to misfolded proteins
C) Forms the lid of the proteasome
D) Senses ER stress in the lumen

A) Pulls misfolded proteins into the cytosol

[L22] Poly-ubiquitination vs mono-ubiquitination signals:

A) Poly-UB: ER retention; mono-UB: export
B) Poly-UB: endosomes; mono-UB: proteasome
C) Poly-UB: proteasome; mono-UB: endosomes
D) Poly-UB: nucleus; mono-UB: cytoplasm

C) Poly-UB: proteasome; mono-UB: endosomes

[L22] Under normal (unstressed) conditions, what keeps the UPR sensors PERK and ATF6 inactive?

A) Phosphorylated eIF2alpha
B) Bound Ran-GDP
C) Attached ubiquitin
D) Bound BiP

D) Bound BiP

[L22] When activated, PERK relieves ER stress by:

A) Moving to the Golgi to be cleaved
B) Phosphorylating eIF2alpha to cut translation
C) Splicing XBP1 mRNA with its RNase domain
D) Acting directly as a transcription factor

B) Phosphorylating eIF2alpha to cut translation

[L22] When activated, ATF6 relieves ER stress by:

A) Dimerizing and splicing XBP1 mRNA
B) Phosphorylating eIF2alpha to cut translation
C) Being cleaved in the Golgi to make a TF
D) Pulling misfolded proteins into the cytosol

C) Being cleaved in the Golgi to make a TF

[L22] When activated, IRE1 relieves ER stress by:

A) Phosphorylating eIF2alpha to cut translation
B) Being cleaved in the Golgi to make a TF
C) Ubiquitinating misfolded proteins
D) Splicing XBP1u mRNA into XBP1s

D) Splicing XBP1u mRNA into XBP1s