MCB*2050 Practice Questions: 2nd Half

Give three examples of ER chaperone proteins.

- BiP - calnexin - calreticulin

Given three examples of reticuloplasmins.

- BiP - calnexin - calreticulin

What are the 2 functions of the nuclear lamina?

1. Support structure for nuclear envelope 2. Scaffold for chromatin & nuclear matrix (maybe?) attachment

Name the component of the NPC that forms the central channel.

Central scaffold

__________________ serve(s) as the docking site for the incoming SRP

Cytosolic-facing domains of the SRP-receptor.

True or False: "The SRP-receptor is a G-protein, but the SRP is not."

False, they're *both* G-proteins.

True or False: "Membrane asymmetry can be altered at any point in the endomembrane system to match the function of the compartment."

False. Protein and lipid asymmetry is established in the ER and maintained throughout the endomembrane system.

How is the SRP released from the receptor after the ribosome has been docked on the translocon?

GTP-hydrolysis (causes a conformational change in BOTH the SRP and the SRP-receptor).

Describe the structure of the nuclear lamina.

It is a thin meshwork of long filament-like proteins.

Which end of a protein emerges from the translocon into the ER lumen first, the N-terminus, or the C-terminus?

N-terminus

True or False: "Tubules/ Cisternae of the endoplasmic reticulum can undergo fusion and fission with each other."

True, they are in constant flux.

Which of the following is NOT a G-protein? a) SRP b) SRP receptor c) Ran d) Arc1

d) Arc1

How many subdomains does the nucleus have?

over 30

What is the name of the protein that mediates the shape of ER tubules and cisternae? How does it accomplish this?

reticulons; have hairpin (V-shaped) secondary structure that regulate ER membrane curvature.

Briefly describe the regulated secretory pathway.

**Occurs only in specialized cells ER-derived materials -> Golgi -> secretory granules (storage) Later, when signal arrives: - secretory granules release cargo by exocytosis

Give 5 examples of ER subdomains.

- SER - RER - ERES - outer nuclear membrane - MAM & PAM

Assuming the nuclear matrix exists, what are its functions?

- Structural role -> maintains shape of nucleus - Scaffold -> organizes nuclear subdomains & anchoring protein factors

List three functions of oligosaccharides on glycoproteins.

- assist in binding with other macromolecules - assist in protein folding - important in intracellular trafficking (specifically targeting proteins to subcellular destinations)

List the 4 main contents of the nucleus

- chromatin - nucleoplasm - nuclear matrix (maybe?) - nucleolus

List the three components of the nuclear envelope.

- nuclear membrane - nuclear lamina - nuclear pores

Briefly describe the endocytic pathway.

- operates in the opposite direction of the secretory pathway (i.e., moves materials INTO the cell). - materials from plasma membrane -> endosomes -> lysosomes/ vacuoles

Describe the structure/ composition of Nups in the NPC's central channel.

- proteins that contain a large number of phenylalanine-glycine repeats - unique, highly disordered secondary structure

What is the function of the nucleolus?

- ribosome biogenesis; site of ribosomal DNA (rDNA) gene transcription and RNA processing AND - initital stages of ribosomal subnit assembly

What are the 2 stages of N-linked glycosylation?

1) Core glycosylation 2) Core modification

What are the 2 main sites of protein synthesis/ translation in the cell?

1. *Cytosol*: Free ribosomes 2. *ER*: ER-bound ribosomes

What are the four general steps of vesicle transport?

1. Cargo-containing vesicle buds off donor membrane 2. Nascent vesicle is transported through cytosol to recipient membrane -> moves along cytoskeleton. 3. Vesicle fuses w/ proper recipient membrane compartment 4. Process of budding is repeated in reverse

What are the two main functions of the nucleus?

1. Compartmentalization of the cellular genome & its activities 2. Coordinating cellular activities

What are the 2 types of secretory pathways?

1. Constitutive secretion 2. Regulated secretion

What are the two mechanisms for maintaining membrane asymmetry?

1. Lipid composition 2. Modification & orientation of integral membrane proteins

State 5 structural differences between prokaryotes and eukaryotes

1. Prokaryotes have a nucleoid instead of a nucelus; eukaryotes have an enclosed nucleus 2. Prokaryotes only synthesize proteins on free ribosomes; eukaryotes synthesize protein on free ribosomes & those attached to the RER. 3. Prokaryotes do not have an endomembrane system, whereas eukaryotes have a very extensive endomembrane system. 4. Prokaryotes do not have any mitochondria/ chloroplasts, eukaryotes do. 5. Prokaryotes are typically much smaller than eukaryotes

List three functions of the nuclear envelope.

1. Separates nuclear content from cytoplasm 2. Acts as selective barrier: - regulates passage of molecules into/ out of the nucleus) - establishes the composition of the nucleus and regulates gene expression 3. Binds nuclear lamina -> structural framework for nucleus

What are the 4 final steps in the co-translational translocation pathway, i.e., processing done in the ER lumen? (a.k.a what else happens to the peptide in the ER after it is translated into the ER?)

1. Signal sequence cleavage 2. Initial stages of glycosylation (N-linked only) 3. Protein folding & assembly 4. Quality control/ getting rid of damaged proteins

How thick is the intermembrane space, between leaflets of the nuclear envelope?

10 - 50 nm

What is the diameter of the nucleus?

10 micrometers

How many small molecules can diffuse through a NPC per minute? (i.e., what is the rate of diffusion of small solutes through a nuclear pore?)

100 molecules/min./pore

What is the approximate diameter of a 'naked' nuclear pore?

120 nm

How many nuclear localization signals are there?

2

What is the functional diameter of nuclear pores (i.e., diameter w/ the NPC in place)?

20 - 30 nm

How many nuclear lamins make up the nuclear lamina?

3 (A, B, C)

Approximately how many nuclear pores are there per nucleus?

3000 - 4000

The nuclear pore complex limits the diffusion of molecules larger than ___________ kDa.

40 kDa

What percentage of a eukaryotic cell's volume is taken up by the nucleus?

5 - 10%

How many large molecules can the NPC import/ export per minute? (i.e., what is the rate at which regulated molecules can enter or leave the nucleus, per pore?)

6 molecules/min./pore

What type of amino acids make up the signal sequence? How many amino acids are in the signal sequence?

8 - 15 hydrophobic amino acids = ER targeting signal

What is nucleoplasmin?

A nuclear protein.

After translation is stalled by the binding of the SRP, how does it resume?

After the ribosome binds to sec61 (the translocon), translation continues.

What is the sequence of the *Classic* NLS?

Amino acid sequence = KKQRKK

What is the sequence of the *Bipartite* NLS?

Amino acid sequence on either side of "spacer" = KR[SPACER]KKKK

What are transcription factories?

Assemblies of active genes on chromatin from different subdomains that has extended into the interchromosomal channels, where transcription factors are located.

Where is the nuclear lamina located in a cell?

Attached to the inner membrane of the nuclear envelope.

What is the *primary* difference between prokaryotes and eukaryotes?

Eukaryotes have a membrane-bound nucleus; prokaryotes do not (they just have a 'region' where the chromosome is located, called the nuceloid).

What is the name of the proteins that line the central channel of the NPC?

FG nucleoporins (Nups)

______________________ form(s) a hydrophobic mesh in the central channel of the nuclear pore complex.

FG nups

True or False: "Many variations of the nuclear pore complex exist across mammals, with some species not containing any NPCs at all."

False, NPC structure is highly conserved among all eukaryotes.

True or False: "Ribosomes cannot pass through nuclear pore complexes because they are much bigger than the NPCs."

False, NPCs are 30x bigger than ribosomes. Ribosomes cannot fit through once fully assembled because of the reduced functional diameter of the nuclear pore.

True or False: "The nuclear pore complex has bilateral symmetry."

False, it has octagonal symmetry of overall structure.

True or False: "Unlike the nucleus, the nucleolus is bound by a single membrane instead of a double membrane."

False, it is not bound by a membrane at all

True or False: "Nuclear speckles tend to have fixed positions in cells."

False, they are highly dynamic (can move quickly & grow/ shrink depending on the needs of the cell).

True or False: "The nucleolus has a dense, regular shape (spherical)."

False. Although it *is* dense nad granular in appearance, it is *irregular* in shape, not spherical.

True or False: "The nucleus contains several membrane-bound subdomains, such as the nucleolus."

False. Although it does contain subdomains, they are NOT membrane-bound.

True or False: "All proteins destined to locate to the nucleus require an NLS."

False. If a protein doesn't have its own NLS, it can 'piggyback' into the nucleus by binding to a protein that *does* have an NLS.

True or False: "The inner and outer leaflets of the nuclear envelope are continuous with each other, and thus share a high degree of symmetry."

False. They *are* continuous with each other, but integral components cannot pass b/w leaflets due to the nuclear pore complexes. The inner and outer membranes of the nuclear envelope are distinct.

______________causes the pore ring of sec61 (translocon) to widen, and the plug to be displaced.

Interaction of the signal sequence on the nascent polypeptide w/ the interior of the translocon.

How does the signal sequence lead to widening of the translocon pore and displacement of the plug?

Interaction of the signal sequence with the interior of the translocon causes conformational changes in the translocon subunits leading to opening/ widening of the pore ring & displacement of the plug.

What shape is the nucleus?

It has an irregular shape

What are the 2 critical aspects to consider when defining an NLS?

It has to be both *sufficient* and *necessary* (i.e., it has to be enough to get the protein to the nucleus w/o other signals, and it has to be required for transport to the nucleus -- protein cannot get in without it).

Briefly describe the SRP-receptor structure.

It is a hetero-dimeric integral membrane protein complex. Is a G-protein.

How does a defective lamin A gene (LMNA) cause progeria?

It results in destabilization of the nuclear lamina, which causes deviant changes in the functioning and morphology of the nuclear envelope.

Transport receptors that carry proteins in/ out of the nucleus are called...?

Karyopherins (e.g., importins & exportins)

Briefly describe the composition/ structure of the signal recognition particle (SRP).

Made up of 6 proteins + 1 small RNA. Is a G-protein.

Briefly describe the constitutive secretory pathway.

Material derived from ER -> Golgi -> PM (exocytosis)

Briefly describe the biosynthetic pathway

Material transport occurs: ER -> Golgi -> Endosomes -> Lysosomes/PM

Which end of a protein comes out of the ribosome first (i.e., which end is synthesized first): the N-terminus, or the C-terminus?

N-terminus

Which end of a nascent peptide contains the signal sequence?

N-terminus (b/c that's the end of the protein that is synthesized by the ribosome first).

Where in the nucleus are nuclear speckles often found?

Next to transcription factories, in interchromosomal channels.

What are nuclear speckles?

Nuclear subdomains where mRNA splicing factors are concentrated.

Are more actively transcribed genes found in the middle, or at the periphery of a chromosomal subdomain?

Periphery

Give an example of a disease caused by a defective lamin gene.

Progeria (lamin A gene mutation)

What is a nuceloid?

Region in a prokaryotic cell where the chromosome is located

What is a transmembrane domain?

Region of a polypeptide that serves as "stop transfer" signal in the translocons (sec61) of the RER. A TMD is typically an alpha-helix made up of 16-25 hydrophobic amino acids.

What are interchromosomal channels?

Regions between subdomains that serve as barriers to prevent unwanted DNA-DNA and/or DNA-protein interactions.

What are the 2 classic ER subdomains?

Smooth ER & Rough ER

What is glycosylation?

The addition of oligosaccharides to proteins to form glycoproteins

How is the topology (orientation) of an integral membrane protein determined? What is the signal?

The amino acids upstream (closer to the N-terminal) of the TMD determine orientation, since the rule is "positive outside". -> if there are +vely charged AAs upstream of the TMD, the N-terminus will be in the cytosol.

_________________________ is the starting point for the secretory and biosynthetic pathways.

The endoplasmic reticulum (ER)

What is nucleoplasm?

The highly organized, fluid-filled interior of the nucleus

How does a TMD stop the transfer of a growing peptide through sec61 (translocon)?

The hydrophobic residues of the TMD interact with the hydrophobic pore ring of the translocon.

Briefly describe the MAM & PAM ER subdomain.

The mitochindria & plasma membrane-associated membranes (MAM & PAM) are regions of the ER that make direct contact with mitochondria or the plasma membrane; they are involved in membrane lipid exchange.

True or False: "A gene's location is often related to its activity."

True

True or False: "It is possible for cells to have up to 5 nucleoli in one nucleus."

True

True or False: "The SRP is a G-protein."

True

True or False: "As an integral membrane protein moves through the endomembrane system, its cytoplasmic domain will always remain in the cytoplasm."

True.

Does the transport of molecules into the nucleus require energy input (i.e., does nuclear import use energy)?

Yes

Which of the following molecules require regulated movement through nuclear pores? [Select all that apply]. [ ] solutes [ ] histones [ ] rRNA [ ] nucleotides [ ] tRNA [ ] proteins [ ] mRNA

[ ] solutes [ ] histones [✔] rRNA [ ] nucleotides [✔] tRNA [✔] proteins [✔] mRNA

Which of the following molecules can diffuse freely through nuclear pores, via passive diffusion? [Select all that apply]. [ ] solutes [ ] histones [ ] rRNA [ ] nucleotides [ ] tRNA [ ] proteins [ ] mRNA

[✔] solutes [✔] histones [ ] rRNA [✔] nucleotides [ ] tRNA [ ] proteins [ ] mRNA

Where is nucleoplasmin synthesized? a) cytoplasm b) nucleoplasm c) ER

a) cytoplasm

Nuclear lamins are related to _______________. a) cytosolic intermediate filaments b) collagen c) extracellular matrix proteins d) aortic elastin e) microfilaments

a) cytosolic intermediate filaments

Which of the following is NOT true of the SRP-receptor? a) it is a G-protein b) it is an integral membrane protein c) it a homodimer d) It is located at the RER

c) it a homodimer [it is actually a heterodimer]

Which of the following does not need to be selectively imported/ exported through the nuclear pore complex? a) RNA b) proteins c) nucleotides

c) nucleotides [small enough to pass through w/o help]

What are reticuloplasmins?

chaperone proteins that operate in the ER

What cytosolic structure is the nuclear matrix analogous to?

cytoskeletal network (e.g., microtubules, actin microfilaments, intermediate filaments)

Which organelle has the most surface area?

endoplasmic reticulum

Why do more metabolically active cells contain more/ bigger nucleoli?

increased metabolic activity = increased protein synthesis = increased nucleoli

Is the signal peptidase that cleaves the signal sequence from polypeptides in the ER a soluble protein, or an integral protein?

integral (located next to translocon).

What is the name of the region in the nucleus, between subdomains, that serve as barriers to prevent unwanted DNA-DNA and/ or DNA-protein interactions?

interchromosomal channels

Assuming the nuclear matrix exists, what is its structure like?

network of insoluble fibrillar-like proteins -> mesh distributed throughout the cytoplasm

What is the name of the protein structure that fills the nuclear pore?

nuclear pore complex (NPC)

What is the name of the nuclear subdomains where mRNA splicing factors are concentrated?

nuclear speckles

What is the name of the highly organized, fluid-filled interior of the nucleus?

nucleoplasm

What is the largest organelle?

nucleus

How many nuclei are in a typical eukaryotic cell?

one

The ________________ (of the nucleus) is continuous with the ER.

outer membrane of the nuclear envelope

How many ER subdomains are there?

over 20

What is the name of the translocon protein that is involved in co-translational transport of proteins into the ER?

sec61

What is the name of the enzyme that cleaves the signal sequence off of peptides in the ER?

signal peptidase

What is the name of the molecule that recognizes the signal sequence, and binds to the ribosome to stop translation?

signal recognition particle (SRP)

What is the name of the signal that targets proteins to the ER?

signal sequence

What happens at the ERES subdomain of the ER?

the ER exit sites are where vesicles bud off of the Er on their way to the Golgi.

The size & number of nucleoli in a cell's nucleus depends on ...?

the metabolic activity of the cell.

What is the name of the most obvious nuclear subdomain?

the nucleolus

What is the name of the structure formed when similar active genes (chromatin) from different subdomains extend into interchromosomal channels where transcription factors needed to transcribe them are located?

transcription factories.

What are reticulons?

unique ER integral membrane proteins that possess a 'hair-pin' (V-shaped) secondary structure and regulate ER membrane curvature ('bending').

How does the lamina connect to the inner membrane of the nuclear envelope?

via integral membrane proteins in the inner membrane