Proteins – Theme 1 Module 3 (Endomembrane System, Structure, and Synthesis)

A comprehensive set of practice questions (Question and Answer format) covering protein roles, structure, synthesis, folding, and the endomembrane system based on Theme 1 Module 3 notes.

What are the four levels of protein structure?

Primary, secondary, tertiary, and quaternary structure.

Name three general roles of proteins in the cell as highlighted in the notes.

Transport across membranes, enzymes (catalysis), and structural/motility roles (including signaling and immune defense like antibodies).

What structural feature do porin proteins have that enables water transport across the membrane?

A hydrophilic pore formed by their structure.

What is a common structural trait of most soluble cellular proteins?

Globular shapes with a hydrophobic interior and a hydrophilic exterior.

What are two common representations of protein structure used by scientists?

Space-filling models and ribbon diagrams.

Where are ribosomal RNA (rRNA) molecules transcribed and assembled into ribosomal subunits?

In the nucleolus.

What is the role of nuclear pore complexes?

They regulate traffic between the nucleus and cytoplasm, allowing RNA and ribosomal subunits to exit and importing essential materials into the nucleus.

How is transcription related to translation in prokaryotic cells?

Transcription and translation are tightly linked; translation begins while the mRNA is still being transcribed.

In eukaryotic cells, where is the primary RNA transcript processed to mRNA?

In the nucleus.

What mediates targeting of ribosomes to the endoplasmic reticulum for proteins destined for the endomembrane system?

A signal sequence on the nascent protein, which is recognized by the signal recognition particle (SRP) and SRP receptor (SRPR) in the ER membrane.

What happens to the signal sequence once the polypeptide enters the ER lumen?

It is removed.

Where does glycosylation occur during protein processing?

In the lumen of the endoplasmic reticulum and in the Golgi apparatus.

How are proteins sorted to their destinations after the Golgi apparatus?

They are packaged into transport vesicles with destination-specific tags that direct them to membranes, lysosomes, the cell membrane, etc.

What cellular structure provides tracks for vesicle transport and which motor proteins move them?

Microtubules; kinesin and dynein move the vesicles along them.

Where are proteins destined for mitochondria, chloroplasts, and peroxisomes synthesized?

On free ribosomes in the cytosol.

What is the primary structure of a protein?

The unique sequence of amino acids in the polypeptide.

What bond joins amino acids to form a polypeptide chain?

A peptide bond (formed by a condensation reaction).

Which molecule brings the correct amino acid to the growing polypeptide during translation?

Transfer RNA (tRNA).

What determines the functional three-dimensional shape of a protein?

Interactions among the amino acid side chains (R-groups) and backbone, including hydrophobic/hydrophilic interactions.

What are the two main secondary structures in proteins?

Alpha helices and beta-pleated sheets.

What stabilizes an alpha helix?

Hydrogen bonds between the carbonyl of one amino acid and the amide of another four residues away.

What kinds of interactions contribute to a protein's tertiary structure?

Hydrogen bonds, ionic bonds, covalent disulfide bonds, hydrophobic interactions, and Van der Waals interactions.

What cellular mechanisms assist in protein folding?

Molecular chaperones and chaperonins.

What is the quaternary structure of a protein?

The assembly of multiple polypeptide subunits into a functional protein (e.g., hemoglobin).

Which disease is linked to malfunction of the CFTR ion channel, and what does CFTR stand for?

Cystic fibrosis; CFTR stands for cystic fibrosis transmembrane conductance regulator.

What is an aquaporin and what is its structural organization?

A membrane channel that transports water; it is a tetramer composed of four subunits forming four water pores.

What structural feature enables bacterial porins to form a channel in membranes?

A beta-barrel formed by beta sheets with a hydrophobic exterior and hydrophilic interior.

What is the role of the endomembrane system?

To compartmentalize the cell and process/traffic proteins through the ER, Golgi, lysosomes, and related components.

Where does most glycosylation of proteins occur?

In the ER lumen and the Golgi apparatus.

How do vesicles know where to go and how do they deliver their cargo?

Vesicles carry destination-specific tags; they dock and fuse with the correct membrane to deliver their contents.

What is the role of the nucleolus in ribosome biogenesis?

Transcribes rRNA and assembles ribosomal subunits with proteins, which are then exported to the cytoplasm.

What is the difference between free and bound ribosomes?

Free ribosomes synthesize cytosolic/organellar proteins; bound ribosomes synthesize proteins destined for secretion or ER lumen.

What is the role of the Golgi apparatus in protein processing?

Further modify proteins (e.g., glycosylation) and sort them for delivery to their final destinations.

What happens during co-translational translocation into the ER lumen?

A signal sequence directs the ribosome to the ER, SRP guides it to the ER membrane, and the polypeptide enters the ER lumen where the signal sequence is removed and processing occurs.

What is contained in the endomembrane system?

Nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, and related vesicular transport systems.

What is a key selective feature of aquaporin channels?

A pore lined with hydrophilic residues that allows selective water movement while embedded in a hydrophobic membrane.

How can CFTR mutations affect respiratory health?

They disrupt chloride ion transport, leading to thick mucus buildup and increased risk of infections.

What is the relationship between protein structure and function as illustrated by aquaporins and porins?

Protein structure (primary to quaternary) dictates how residues and overall architecture create selective channels and gates that determine function.