Case 6

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Questions and Answers

Which type of interaction primarily drives the clustering of nonpolar amino acids in a protein?

Ionic bonds

Hydrogen bonding

Hydrophobic effect (correct)

Metal bridges

What is the role of hydrogen bonds in protein structure?

They are only important in quaternary structure.

They primarily form between nonpolar amino acids.

They stabilize protein structure by occurring between polar side chains. (correct)

They provide a covalent bond between side chains.

Which of the following proteins is an example of quaternary structure?

Keratin

Myoglobin

Hemoglobin (correct)

Insulin

Which force is the main contributor to the stability of tertiary structure in proteins?

Hydrophobic interactions Signup and view all the answers

What type of bonds form between positively and negatively charged side chains in proteins?

Ionic bonds Signup and view all the answers

Which component is released into the environment when nonpolar amino acids cluster together?

Water molecules Signup and view all the answers

What primarily distinguishes quaternary structure from tertiary structure?

Interactions between multiple polypeptide chains Signup and view all the answers

Which type of protein interaction is denoted as acting like ‘safety pins’ to connect polypeptide parts?

Salt bridges Signup and view all the answers

What is the primary role of disulfide bonds in proteins?

They provide significant stabilization for extracellular proteins. Signup and view all the answers

Which type of interaction primarily drives the clustering of hydrophobic side chains in proteins?

Hydrophobic interactions Signup and view all the answers

How do chaperone proteins assist in protein folding?

By stabilizing nascent polypeptides and preventing improper interactions Signup and view all the answers

What effect does the hydrophobic effect have on protein folding?

It leads to a release of structured water molecules into the solvent. Signup and view all the answers

In the context of protein folding, what is conformational entropy?

The order that increases as a protein folds. Signup and view all the answers

Which of the following is NOT a force stabilizing quaternary interactions in proteins?

Ribosomal interactions Signup and view all the answers

What is the role of heat shock proteins (HSPs) in protein folding?

They bind to hydrophobic regions of nascent proteins to prevent aggregation. Signup and view all the answers

What is the primary function of chaperonins such as GroEL/GroES?

To provide a protected environment for protein folding Signup and view all the answers

Which of the following is a role of mitochondrial Hsp70 (mt-Hsp70)?

It refolds incoming protein chains Signup and view all the answers

What happens when protein folding is not performed correctly?

Misfolded proteins accumulate and lead to diseases Signup and view all the answers

In which form must proteins pass through the mitochondrial membranes?

In an unfolded form Signup and view all the answers

Which common post-translational modification involves adding a phosphate group?

Phosphorylation Signup and view all the answers

What is N-linked glycosylation specifically associated with?

Attachment of carbohydrate groups to asparagine residues Signup and view all the answers

What role do chaperonins play in mitochondrial protein processing?

They assist with folding proteins inside a special chamber Signup and view all the answers

Which enzyme is responsible for deactivating a phosphorylated protein?

Phosphatase Signup and view all the answers

What is the primary enzyme that is deficient in Gaucher's disease?

Glucocerebrosidase Signup and view all the answers

What accumulates in cells affected by Gaucher's disease?

Glucocerebroside Signup and view all the answers

What is the genetic cause of I-Cell disease?

Mutation in the GNPTAB gene Signup and view all the answers

What is the consequence of missing mannose-6-phosphate tags in I-Cell disease?

Enzymes are secreted outside the cell Signup and view all the answers

What are the enlarged macrophages filled with lipids in Gaucher's disease called?

Gaucher cells Signup and view all the answers

What type of proteins are transported to the nucleus?

Proteins with nuclear localization signals Signup and view all the answers

Which of the following proteins is involved in transporting proteins into the mitochondria?

Msf1 (Mitochondrial import stimulation factor 1) Signup and view all the answers

What is the primary function of ER-bound ribosomes?

Synthesizing secreted proteins and plasma membrane proteins Signup and view all the answers

What role does the signal sequence play in protein synthesis?

It binds to the cytoplasmic signal recognition particle (SRP) Signup and view all the answers

Which type of transport is involved in moving proteins into the nucleus?

Gated/pore transport Signup and view all the answers

How do free ribosomes and ER-bound ribosomes differ in their function?

ER-bound ribosomes produce proteins for secretion and membrane integration. Signup and view all the answers

What is the consequence if a protein lacks a signal sequence?

It will remain in the cytosol. Signup and view all the answers

Which organelle is NOT involved in post-translational transport?

Vesicle Signup and view all the answers

What is primarily determined by the primary structure of a protein?

The sequence of amino acids in the polypeptide chain Signup and view all the answers

Which type of secondary structure is characterized by hydrogen bonds between parts of the backbone, giving rise to a helical structure?

α helix Signup and view all the answers

In a β pleated sheet, which interactions hold the structure together?

Hydrogen bonds between the backbone's carbonyl and amino groups Signup and view all the answers

What is a key characteristic of the tertiary structure of a protein?

It is the overall three-dimensional structure of the polypeptide Signup and view all the answers

Which of the following statements about polypeptide chain interactions is true?

Interactions can be influenced by the chemical properties of side chains Signup and view all the answers

If a polypeptide fails to fold properly, which of the following is a potential consequence?

It could lead to loss of function or disease Signup and view all the answers

The sequence of amino acids in a protein can lead to a massive number of potential proteins. How many unique proteins can be formed from 60 amino acids using 20 different amino acids?

20^60, equaling approximately 10^78 different proteins Signup and view all the answers

Which structural feature is NOT typically involved in the stabilization of tertiary structure in proteins?

Phosphodiester bonds Signup and view all the answers

What sequences are critical for importing proteins into mitochondria?

Mitochondrial targeting sequences Signup and view all the answers

Which of the following statements about co-translational transport is correct?

Ribosomes bind to the ER through a signal recognition particle. Signup and view all the answers

What is the primary role of mannose-6-phosphate tagging in the Golgi apparatus?

To determine the localization of proteins to lysosomes. Signup and view all the answers

Which type of secretion is characterized by proteins being stored and released in response to specific signals?

Regulated secretion Signup and view all the answers

What is required for proteins to enter peroxisomes?

Proteins need to be folded properly. Signup and view all the answers

What is the fate of proteins in the endocytic pathway?

They are degraded in lysosomes or recycled to the plasma membrane. Signup and view all the answers

Which statement accurately describes the processing of secretory proteins in the Golgi apparatus?

They are sorted for different cellular destinations. Signup and view all the answers

What triggers the movement of secretory vesicles toward the plasma membrane?

Regulated secretion signals from the cytoplasm. Signup and view all the answers

What is the primary purpose of signal recognition particles (SRPs) during protein synthesis?

To halt translation and direct proteins to the endoplasmic reticulum Signup and view all the answers

Which targeting signal is necessary for proteins to be imported into mitochondria?

Mitochondrial targeting sequence Signup and view all the answers

What distinguishes gated transport from other forms of protein transport?

It occurs through membranes with pores allowing free diffusion Signup and view all the answers

What role does Msf1 play in mitochondrial protein import?

It guides specific proteins to translocase complexes Signup and view all the answers

What type of proteins do free ribosomes in the cytoplasm synthesize?

Both cytoplasmic and nuclear proteins Signup and view all the answers

Which mechanism primarily transports proteins into the endoplasmic reticulum?

Co-translational transport involving SRPs Signup and view all the answers

What happens to a protein if it lacks a peroxisomal targeting sequence?

It will be degraded in the cytoplasm Signup and view all the answers

What is a significant characteristic of proteins synthesized by ER-bound ribosomes?

They include secretory and membrane proteins Signup and view all the answers

What is the primary function of ubiquitin in the context of protein degradation?

To mark proteins for destruction Signup and view all the answers

Which pathway is activated when there is an accumulation of misfolded proteins in the endoplasmic reticulum?

Unfolded Protein Response (UPR) Signup and view all the answers

What happens to misfolded proteins if they cannot be refolded by chaperones?

They are retro-translocated to the cytosol for degradation Signup and view all the answers

Which component of the proteasome is specifically responsible for degrading ubiquitin-tagged proteins?

Catalytic subunits Signup and view all the answers

What initiates the process of protein degradation by the proteasome?

Covalent attachment of ubiquitin chains Signup and view all the answers

What is a potential outcome if the Unfolded Protein Response fails to restore normal protein folding?

Cell apoptosis Signup and view all the answers

What role do chaperone proteins play in protein degradation?

They assist in refolding or marking proteins for degradation Signup and view all the answers

What is the primary function of ubiquitin ligases within the ubiquitin-proteasome pathway?

To attach ubiquitin to targeted proteins Signup and view all the answers

What happens to the signal sequence once the polypeptide passes into the lumen of the rough ER?

It is cleaved off by a signal peptidase. Signup and view all the answers

Which coat protein is responsible for vesicular transport from the ER to the cis part of the Golgi apparatus?

COPII Signup and view all the answers

What is the primary role of Rab proteins in vesicular transport?

To assist in the fusion of vesicles with their target membranes. Signup and view all the answers

What is the main purpose of protein degradation within a cell?

To remove damaged or unneeded proteins. Signup and view all the answers

Which of the following proteins is commonly known for assisting in protein quality control by preventing aggregation?

Hsp70 Signup and view all the answers

In the process of endocytosis, which factor is vital for recognizing correct transportation due to modification?

Phosphatidyl-inositol-phosphates (PIP) Signup and view all the answers

Which type of vesicle is primarily utilized for the process of endocytosis?

Clathrin-coated vesicles Signup and view all the answers

What occurs to misfolded proteins that cannot be corrected by chaperones?

They are tagged for degradation. Signup and view all the answers

Study Notes

Protein Structure

Primary Structure: Amino acid sequence of a polypeptide chain.
Secondary Structure: Local folding patterns within a polypeptide chain, including alpha-helices and beta-sheets, stabilized by hydrogen bonds.
Tertiary Structure: Three-dimensional structure of a single polypeptide chain, stabilized by various interactions such as hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bonds, and van der Waals forces.
Quaternary Structure: Arrangement of multiple polypeptide chains (subunits) in a protein, stabilized by the same interactions that stabilize tertiary structure.
- Hemoglobin is an example of a protein with quaternary structure.

Protein Folding

Hydrophobic effect: Non-polar amino acids cluster together to avoid water, increasing the system's entropy. This drives protein folding.
Chaperones: Proteins that assist in protein folding, preventing aggregation and ensuring correct folding.
- Molecular chaperones: Bind to nascent or partially folded polypeptides, preventing improper interactions.
- Chaperonins: Provide a protected environment for protein folding, preventing aggregation and allowing for proper folding within a chamber, like the GroEL/GroES system in bacteria.
Mitochondrial Protein Folding: Proteins destined for the mitochondrial matrix must pass through both the inner and outer mitochondrial membranes in an unfolded form.
- Mitochondrial Hsp70 (mt-Hsp70) helps guide proteins across the membrane and refolds them once they reach the matrix.
- Hsp60/Hsp10 chaperonins also assist in folding proteins within the mitochondria.

Post-Translational Modifications

Phosphorylation: Addition of a phosphate group to a protein by kinases, regulating cellular processes.
Glycosylation: Attachment of carbohydrate groups to a protein, modifying its function.
- N-linked glycosylation: Occurs on asparagine residues.
- O-linked glycosylation: Occurs on serine or threonine residues.

Protein Transport

Nucleus: Proteins enter the nucleus through nuclear pores using gated transport.
Mitochondria: Proteins enter mitochondria through translocators, which move between environments with different properties.
- Msf1 (Mitochondrial import stimulation factor 1) acts as a chaperone directing certain mitochondrial outer membrane proteins to the TOM complex.
Endoplasmic Reticulum (ER): Ribosomes attached to the rough ER synthesize proteins destined for the ER, Golgi apparatus, lysosomes, plasma membrane, or secretion, depending on their signal sequences.
- Co-translational transport: Proteins are synthesized and transported into the ER simultaneously.
- Signal sequence: A short sequence of hydrophobic amino acid residues at the amino end of proteins bound for the ER.
- Signal Recognition Particle (SRP): Binds to the signal sequence and halts translation until the ribosome reaches the ER membrane.

Protein Diseases

Gaucher's disease: A genetic disorder caused by a deficiency in Glucocerebrosidase enzyme, leading to the accumulation of glucocerebroside in macrophages, resulting in Gaucher cells (enlarged, lipid-filled macrophages).
I-Cell disease: A rare lysosomal storage disorder resulting from a defect in the tagging of enzymes for transport to lysosomes.
- The GNPTAB gene, responsible for tagging lysosomal enzymes with a mannose-6-phosphate (M6P) marker, is defective.
- Without the M6P tag, lysosomal enzymes are secreted instead of directed to the lysosomes, causing an accumulation of undigested materials within lysosomes.

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Explore the intricacies of protein structure and folding in this quiz. From the primary to the quaternary structure, understand the roles of various forces and chaperones in maintaining the integrity of proteins. Test your knowledge on how these concepts contribute to protein function.