Eukaryotic Cell Bio Unit 2

What are the main functions of organelles?

They concentrate molecules, separate incompatible reactions, and provide specialized environments for cellular processes.

How do organelles help cells become specialized?

Different cell types contain different amounts and sizes of organelles based on their functions.

Which organelles are especially abundant in liver and pancreatic cells?

Extensive endoplasmic reticulum (ER).

Why do cardiac muscle cells have extensive smooth ER and mitochondria?

Smooth ER stores calcium, while mitochondria supply energy.

How did internal membranes and the endomembrane system evolve?

Through protrusions of the cell surface membrane.

What evidence supports the endosymbiotic origin of mitochondria and chloroplasts?

They have double membranes and their own DNA.

Why do larger cells need specialized compartments?

Simple diffusion alone is insufficient to support all reactions throughout a larger cell.

What is the mitochondrial intermembrane space used for?

It holds a high concentration of H⁺ created by the electron transport chain.

How does ATP synthase produce ATP in mitochondria?

H⁺ flows down its concentration gradient through F-type ATP synthase, providing energy to add phosphate to ADP and form ATP.

What structures make up the endomembrane system?

The nuclear envelope, ER, Golgi apparatus, and lysosomes.

What are the functions of the secretory and endocytic pathways?

They move, package, and transport proteins and lipids within the cell and to or from the cell surface.

What is the difference between an organelle and a biomolecular condensate?

Organelles are membrane-bound; biomolecular condensates are membrane-less regions of cellular organization.

What types of interactions hold biomolecular condensates together?

Weak, fluctuating interactions between molecules.

What are scaffold and client molecules in a condensate?

Scaffold molecules help organize the condensate; client molecules are recruited into it.

Why are biomolecular condensates described as biochemical factories?

They concentrate molecules to support specific cellular reactions.

What is the nucleolus responsible for?

Producing the large and small ribosomal subunits using proteins and rRNA.

How can condensates form multiple regions?

Different scaffold molecules can form separate regions or multilayer structures, with one region surrounding another.

What can trigger biomolecular condensate assembly?

Phosphorylation, other post-translational modifications, and changes in pH, temperature, or osmolarity.

What are stress granules, and what do they do?

Condensates containing ribosomes and RNA-binding proteins that form during cellular stress and stalled translation, helping stall and protect cellular components rather than degrade them.

What are the five ways proteins move between cellular compartments?

Protein translocation, gated transport, vesicular transport, engulfment, and movement within biomolecular condensates.

What is protein translocation?

Movement of proteins across a membrane, such as from the cytosol into mitochondria, plastids, peroxisomes, or the ER.

What is gated transport?

Selective movement of proteins and RNA through nuclear pores between the cytosol and nucleus.

What happens to a protein during membrane translocation?

It usually unfolds and passes through a translocator into the next compartment.

What is a translocator?

A protein complex that guides another protein through a membrane.

How does vesicular transport preserve membrane orientation?

The cytosolic side remains facing the cytosol, while the noncytosolic side faces the vesicle lumen or the outside of the cell.

What is engulfment, and what is one example?

A process in which membranes surround material; autophagy uses this process to digest and degrade organelles.

How does the nuclear envelope reform after mitosis?

ER tubes wrap around the chromosomes and fuse to form the envelope.

What is a signal sequence?

A linear chain of amino acids, typically near the N-terminus, that directs a protein to a particular destination.

What is a signal patch?

A three-dimensional arrangement of amino acids that serves as a recognition signal.

How are signal sequences and signal patches recognized?

Specific receptors bind them and guide the protein to its destination.

What can happen to a signal sequence after targeting?

It may be cleaved by a signal peptidase or remain part of the functional protein.

What did the pyruvate kinase localization experiment demonstrate?

Adding a nuclear localization signal (NLS) and GFP to normally cytosolic pyruvate kinase directed it into the nucleus.

What are the main functions of the ER?

Protein and lipid biosynthesis, calcium storage, and production of transmembrane proteins and lipids for cellular membranes.

How is the ER connected to the nuclear envelope?

The ER is continuous with the outer nuclear envelope.

What is the ER lumen?

The single internal space enclosed by the ER membrane.

What is the main function of smooth ER?

Synthesis of lipids and steroids.

Which proteins are commonly destined for the ER pathway?

Proteins destined for the ER, Golgi, lysosomes, endosomes, secretory vesicles, peroxisomes, and plasma membrane.

What is co-translational translocation?

A protein is synthesized by a ribosome while it is being moved into or across the ER membrane; no extra energy input is required beyond protein synthesis.

What is post-translational translocation?

A protein is inserted into an organelle after synthesis is complete; it must unfold and requires additional energy.

Where does post-translational translocation occur according to the lecture?

In mitochondria and chloroplasts, and in the ER of yeast.

What is the role of HSP chaperones during post-translational translocation?

They prevent proteins from folding prematurely or aggregating in the cytosol.

What is a polyribosome?

Multiple ribosomes translating the same mRNA.

What happens to ribosomes during ER-directed protein synthesis?

The ribosome and mRNA are directed to the ER; after translation, the ribosome dissociates and returns to the cytosolic pool.

What is the ER signal sequence recognized by SRP?

A hydrophobic amino acid sequence, usually near the N-terminus of the protein.

What is the signal recognition particle (SRP)?

An RNA-and-protein complex that binds the ER signal sequence and ribosome to direct them to the ER.

What happens when SRP binds the signal sequence and ribosome?

Translation temporarily pauses.

What is the role of the SRP receptor?

It is embedded in the ER membrane and binds the SRP–ribosome complex.

What happens after the SRP–ribosome complex binds the SRP receptor?

The protein translocator docks, SRP and its receptor release, and protein synthesis resumes.

What is the Sec61 complex?

A protein translocator that forms an aqueous channel through the ER membrane.

What is the function of the Sec61 lateral gate?

It allows hydrophobic segments of a protein to move sideways into the ER membrane.

What happens to an ER signal sequence after it enters the Sec61 translocator?

It can exit through the lateral gate and be cleaved by signal peptidase.

How does post-translational translocation through the ER work?

The Sec61–Sec63 complex helps move the protein through the translocator, while BiP uses ATP to bind the unfolded chain and prevent backward movement.

How are transmembrane segments recognized during ER insertion?

Hydrophobic amino acid regions are recognized and moved through the Sec61 lateral gate into the membrane.

How are multipass transmembrane proteins inserted into the ER membrane?

Multiple hydrophobic regions pass through the lateral gate and become embedded in the membrane in alternating orientations.

What is a GPI anchor?

A glycolipid anchor made of a hydrocarbon tail connected to phosphate and sugar groups.

How is a GPI-anchored protein formed?

A transamidase cleaves the protein's C-terminal end and attaches it to a preformed GPI anchor.

How can GPI-anchored proteins be released from the membrane?

They can be cleaved by phospholipases.

What happens to proteins as they enter the ER lumen?

They enter unfolded and begin folding with the help of chaperone proteins.

What is the role of BiP in the ER?

BiP binds exposed hydrophobic regions, prevents aggregation, and helps proteins fold properly using ATP-dependent binding and release.

What is a disulfide bond?

A covalent bond between two cysteine amino acids.

What is the function of protein disulfide isomerase (PDI)?

It helps form or break disulfide bonds and is an oxidoreductase.

Why are disulfide bonds rare in the cytosol?

The cytosol has a reducing environment.

What is glycosylation?

The addition of sugar chains to proteins, producing glycoproteins.

What is the difference between N-linked and O-linked glycosylation?

N-linked sugars attach to asparagine; O-linked sugars attach to serine in the lecture's example.

What is the role of dolichol in ER glycosylation?

It anchors the oligosaccharide sugar chain to the membrane.

What enzyme transfers the sugar chain to a protein?

Oligosaccharyl transferase, which associates with the translocon.

What do calnexin and calreticulin do in the ER?

They bind newly made proteins that retain one glucose, help with folding, and keep them in the ER; they require calcium to function.

What happens when the final glucose is removed from a properly folded protein?

The protein can leave the ER and is no longer associated with calnexin.

What happens if a protein is still improperly folded?

Glucosyl transferase can add a terminal glucose back, allowing another round of quality control.

How are persistently misfolded proteins recognized for degradation?

Mannosidase trims a specific mannose, signaling that the protein has remained in the ER too long.

How are misfolded proteins removed from the ER?

They are recognized by ER retrotranslocation lectins, kept from aggregating by chaperones, unfolded or adjusted by disulfide isomerase, pulled through by an AAA-ATPase, tagged with ubiquitin, and degraded by the proteasome.

What energy source is used during misfolded protein removal?

ATP

What triggers the unfolded protein response (UPR)?

Accumulation of unfolded proteins in the ER.

What does the unfolded protein response do?

It stimulates gene transcription to improve protein folding, increase chaperones, support retrotranslocation, and expand the ER.

What are the three UPR pathways?

IRE1, PERK, and ATF6.

How are UPR pathways normally regulated?

Chaperone proteins usually inhibit them; cellular stress causes chaperones to dissociate and activates the pathways.

Which diseases associated with protein misfolding were listed in the lecture?

Alzheimer's disease, Parkinson's disease, prion disease, and ALS.

What is the main function of peroxisomes?

Oxidative reactions, including fatty acid breakdown and detoxification.

What toxic substance is produced during peroxisomal oxidation?

Hydrogen peroxide (H₂O₂).

What is the major enzyme in peroxisomes?

Catalase

What does catalase do?

Converts hydrogen peroxide into water and oxygen.

What is beta-oxidation?

The breakdown of fatty acids into acetyl-CoA.

What are plasmalogens, and why are they important?

Lipids that are components of brain myelin.

Why can peroxisomal disorders cause neurological problems?

Peroxisomes are involved in forming plasmalogens, which are important for brain myelin.

Where are most peroxisomal proteins made?

In the cytosol; some are made in the ER.

What signal sequence targets cytosolic proteins to peroxisomes?

A C-terminal signal sequence: serine-lysine-leucine (SKL).

How do ER-made transmembrane proteins reach peroxisomes?

They are transported in vesicles that fuse with the peroxisome.

How do cytosolic proteins enter peroxisomes?

Through membrane translocators that recognize their signal sequences.

Can fully folded proteins enter peroxisomes?

Yes. Peroxisomes can import fully folded proteins.

What structural feature do mitochondria and chloroplasts share?

Both are double-membrane organelles.

Do mitochondria and chloroplasts have their own DNA?

Yes. They encode some of their own proteins, but most proteins are encoded by nuclear DNA.

What percentage of mitochondrial and chloroplast proteins are made from their own DNA, according to the lecture?

Approximately 1%.

How do mitochondria and chloroplasts reproduce?

By fission.

What determines where proteins are transported within mitochondria and chloroplasts?

Their signal sequences.

What type of protein translocation occurs in mitochondria and chloroplasts?

Post-translational translocation.

What is the TOM complex?

The translocator in the outer mitochondrial membrane that helps import nucleus-encoded proteins from the cytosol.

What does MIM1 do?

Inserts proteins with a single alpha helix into the outer mitochondrial membrane.

What does the SAM complex do?

Inserts and folds beta-barrel proteins, such as porins, into the outer mitochondrial membrane.

What does TIM23 do?

Inserts proteins into the inner mitochondrial membrane or transports them into the matrix.

What does TIM22 do?

Inserts proteins into the inner mitochondrial membrane, especially proteins that span the membrane multiple times.