Biochemistry Protein Folding Quiz
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Questions and Answers

What is the name of the scientist who won the 1972 Nobel Prize in Chemistry for his work on ribonuclease?

  • Christian Anfinsen (correct)
  • Demis Hassabis
  • John Jumper
  • David Baker

What is the main driving force for protein folding, leading to the formation of the tertiary structure?

  • Electrostatic interactions
  • Hydrogen bonding
  • Hydrophobic interactions (correct)
  • Van der Waals forces

What type of bond is disrupted when ribonuclease loses its function?

  • Covalent bonds
  • Ionic bonds
  • Hydrogen bonds
  • Disulfide bonds (correct)

Which of the following is NOT involved in stabilizing the tertiary structure of a protein?

<p>Amino acid sequence (D)</p> Signup and view all the answers

What is the significance of AlphaFold AI's ability to predict protein structures?

<p>All of the above. (D)</p> Signup and view all the answers

What is the relationship between the primary sequence of a protein and its biological activity?

<p>The amino acid sequence determines the folding of a protein, which in turn, determines its function. (A)</p> Signup and view all the answers

What can happen if a protein folds incorrectly due to a mutation?

<p>The protein may become inactive. (C), The protein's function may be altered or lost. (E), Multiple of the above. (F), All of the above (H)</p> Signup and view all the answers

What is the primary function of chaperone proteins?

<p>To help proteins fold correctly (A)</p> Signup and view all the answers

Which of the following statements about GroEL is TRUE?

<p>GroEL is a chaperone protein that forms a chamber for protein folding. (A)</p> Signup and view all the answers

What triggers the release of a protein from the GroEL chamber?

<p>The binding of GroES to the GroEL complex (A)</p> Signup and view all the answers

What is the role of ATP hydrolysis in the GroEL system?

<p>It acts as a timer, controlling the duration of protein folding in the GroEL chamber. (B)</p> Signup and view all the answers

What is the effect of GroES binding to GroEL on the chamber structure?

<p>The chamber becomes larger, providing more space for protein folding. (B)</p> Signup and view all the answers

What is the primary function of the proteasome?

<p>To degrade misfolded proteins (D)</p> Signup and view all the answers

What is the main reason why hydrophobic residues line the GroEL chamber wall?

<p>To help the protein fold by stabilizing hydrophobic interactions. (C)</p> Signup and view all the answers

Which of the following statements about hub proteins is TRUE?

<p>Hub proteins are more likely to be essential for cell function than non-hub proteins. (C)</p> Signup and view all the answers

What is the significance of the conformational change in the GroEL complex upon GroES binding?

<p>It facilitates the release of the folded protein from the chamber. (A)</p> Signup and view all the answers

How does the cell handle proteins that fail to fold correctly despite the assistance of chaperones?

<p>Degradation by proteasomes (B)</p> Signup and view all the answers

What is primarily responsible for the conversion of normal proteins into amyloid deposits?

<p>Aβ42 overproduction and its refolding (D)</p> Signup and view all the answers

Which of the following diseases is associated with misfolded α-synuclein?

<p>Parkinson's disease (B)</p> Signup and view all the answers

What consequence does the duplication of the APP gene primarily lead to?

<p>Overproduction of Aβ42 (B)</p> Signup and view all the answers

Which of the following statements is true regarding amyloidosis?

<p>It is characterized by the presence of fibrillar amyloid deposits. (B)</p> Signup and view all the answers

What structural change does Aβ42 undergo to become toxic?

<p>It refolds into beta sheets. (B)</p> Signup and view all the answers

Which of the following is a common misfolded protein in Alzheimer's disease?

<p>Tau protein (A)</p> Signup and view all the answers

Which part of the APP is primarily responsible for the production of Aβ peptides?

<p>Gamma secretase (A)</p> Signup and view all the answers

Which condition involves the misfolding of transthyretin?

<p>Primary systemic amyloidosis (D)</p> Signup and view all the answers

Which of the following is true regarding protein misfolding diseases?

<p>They can be caused by mutations or aging. (D)</p> Signup and view all the answers

Which protein is misfolded in Type II diabetes?

<p>Amylin (A)</p> Signup and view all the answers

What is the main mode of transmission of kuru among the Fore Tribe?

<p>Ingestion of brain tissue from deceased relatives (B)</p> Signup and view all the answers

Which of the following diseases is classified as a transmissible spongiform encephalopathy (TSE)?

<p>Creutzfeldt-Jakob disease (CJD) (B)</p> Signup and view all the answers

What characteristic makes prions resistant to traditional methods of inactivation?

<p>Proteinaceous nature lacking nucleic acids (D)</p> Signup and view all the answers

Who was awarded the Nobel Prize in Physiology or Medicine in 1997 for the discovery of prions?

<p>Stanley Prusiner (B)</p> Signup and view all the answers

What is the significance of the PRNP gene in relation to prion diseases?

<p>It is associated with the presence of scrapie in affected individuals (B)</p> Signup and view all the answers

What is the significance of non-covalent bonds in protein structure?

<p>They allow flexibility and conformational changes in proteins. (B)</p> Signup and view all the answers

Which of the following is NOT a type of non-covalent interaction involved in protein structure and function?

<p>Covalent bonds (A)</p> Signup and view all the answers

What is the consequence of a single amino acid change in the primary structure of a protein, like in the case of sickle cell anemia?

<p>Can alter the protein's shape and function. (B)</p> Signup and view all the answers

What is a key characteristic of amino acids that contribute to their ability to mediate protein-DNA interactions, like in the example of histones?

<p>Their charged nature, enabling electrostatic interactions with the phosphate backbone of DNA. (A)</p> Signup and view all the answers

Which of the statements best describes how phosphorylation impacts protein function?

<p>Phosphorylation can alter a protein's conformation and therefore its activity. (A)</p> Signup and view all the answers

What is the primary role of disulfide bridges in protein structure?

<p>They contribute to the stability and rigidity of proteins. (A)</p> Signup and view all the answers

Where are disulfide bonds commonly found in proteins?

<p>Both within a single polypeptide chain and between two different polypeptide chains (A)</p> Signup and view all the answers

What is the key characteristic of amino acids that are often involved in phosphorylation?

<p>Positively charged side chains. (D)</p> Signup and view all the answers

Which of the following is NOT a consequence of non-covalent bond interactions in proteins?

<p>Determination of the primary structure of a protein. (B)</p> Signup and view all the answers

Flashcards

Tertiary structure

The three-dimensional shape of a protein formed by the folding of its polypeptide chain.

Protein folding

The process by which a protein structure acquires its functional shape.

Hydrophobic interactions

Forces that drive the folding of proteins, pushing nonpolar side chains away from water.

Primary sequence

The linear sequence of amino acids in a protein, determining its structure.

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Disulfide bonds

Covalent bonds that stabilize protein structure by linking cysteine residues.

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Noncovalent bonds

Weak attractions that help stabilize the tertiary structure of proteins.

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Ribonuclease

An RNA-cleaving enzyme that illustrates protein folding and function.

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Amyloid deposits

Fibrillar deposits of insoluble proteins that can cause disease.

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Alzheimer's disease

Neurodegenerative disease characterized by amyloid plaques and tau tangles.

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Aβ peptides

Amyloid beta peptides that accumulate in Alzheimer's disease.

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Protein misfolding

Incorrect folding of proteins, leading to disease states.

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Tau protein

A protein that forms tangles in the brains of Alzheimer's patients.

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Prion

Infectious proteins that can cause spongiform encephalopathies.

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Secretases

Enzymes that cut APP to produce Aβ40 and Aβ42.

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Aβ42 overproduction

Excessive production of Aβ42 linked to Alzheimer's disease.

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Neurodegenerative disorders

Diseases characterized by progressive loss of nerve function.

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Amyloidosis

Diseases caused by amyloid protein deposits in tissues.

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Chaperones

Proteins that assist in folding other proteins correctly.

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Hydrophobic patches

Areas on nascent polypeptides that can misfold due to water-hating residues.

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Chaperonin

A specific type of chaperone that provides a chamber for protein folding.

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GroEL complex

A chaperonin composed of two disks with two internal chambers.

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Hydrophilic residues

Water-loving residues that help protein folding in chaperonins.

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ATP hydrolysis

A chemical reaction that provides energy for protein folding.

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GroES cap

A lid that binds to GroEL, allowing protein release and folding.

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Proteasome

A complex that degrades misfolded proteins in a selective manner.

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Conformational change

Alteration in protein structure when GroES binds to GroEL.

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Nascent polypeptide

A newly synthesized polypeptide chain that is folding.

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Kuru

A fatal neurodegenerative disease characterized by progressive dementia and ataxia associated with the Fore Tribe in Papua New Guinea.

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Transmissible Spongiform Encephalopathies (TSEs)

A group of neurodegenerative diseases caused by infectious prions leading to brain damage and sponge-like degeneration.

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PrP (Prion Protein)

A normal protein encoded by the PRNP gene that can fold improperly and become pathogenic.

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Prion Hypothesis

The idea that a normal prion protein can misfold, leading to disease without involving nucleic acids.

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Hydrophobic effect

Weak attractive forces between non-polar molecules at optimal distances.

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Sickle-cell anemia

Condition caused by a single amino acid change in hemoglobin, altering cell shape.

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Histones

Proteins that bind to DNA, often with reactive amino acids.

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Phosphorylation

Addition of a phosphate group to a protein, altering its folding.

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Cysteine

An amino acid with a reactive -SH group that forms disulfide bridges.

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Charged atoms attraction

The force between atoms with positive and negative charges.

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Study Notes

Cell Biology

  • Two basic types of cells exist: prokaryotic and eukaryotic
  • Prokaryotic and eukaryotic cells differ in size and the types of organelles present
  • Both share an identical genetic language, common metabolic pathways, and several structural similarities

Prokaryotic Cells

  • Prokaryotic cells are smaller than eukaryotic cells
  • They lack membrane-bound organelles
  • The DNA is not contained in a nucleus, but forms a nucleoid
  • Parts of prokaryotic cells include a plasma membrane, cell wall, capsule, ribosomes, bacterial flagellum, and pilus

Eukaryotic Cells

  • Larger than prokaryotic cells
  • Contain membrane-bound organelles including the nucleus, endoplasmic reticulum, Golgi complex, mitochondria, lysosomes, and others (see details in diagram on page 4)
  • Parts of eukaryotic cells include cytoskeleton, flagellum, centrioles, plasma membrane, secretory vesicles, lysosomes, smooth endoplasmic reticulum (ER), peroxisomes, and mitochondria

Comparing Prokaryotic and Eukaryotic Cells

  • Both have plasma membranes
  • Both use DNA to hold genetic information
  • Both use a similar process for transcription and translation, including similar ribosomes
  • Both use common metabolic pathways and conserve chemical energy (e.g., ATP)
  • Both have similar ways of producing membrane proteins through photosynthesis (in some cells)

Eukaryotic Cell Features Not Found in Prokaryotic Cells

  • The nucleus separating the cytoplasm from the nucleus
  • Complex chromosomal structures
  • Complex membranous cytoplasmic organelles
  • Specialized organelles for aerobic respiration, photosynthesis
  • Complex cytoskeletal structures
  • Ability to ingest material through membrane vesicles
  • Cell division using a microtubule-containing spindle
  • Having two copies of genes per cells
  • Sexual reproduction needing meiosis and fertilization.

Examples of Eukaryotic Cell Organelles

  • Endosome/Lysosomes/Vacuoles: breakdown biological polymers
  • Peroxisomes: for oxidation reactions, lipid biosynthesis
  • Mitochondria: generate metabolic energy (ATP) through oxidative phosphorylation
  • Nucleus: contains chromatin, DNA, and a nucleolus
  • Plasma membrane: separates the inner cell contents from the outside (environment)
  • Endoplasmic Reticulum (ER): involved in protein synthesis and processing
  • Golgi complex: sorts proteins to lysosomes, plasma membrane, and secretion pathways
  • Cytoplasm: material within the cell excluding the nucleus

Cell Differentiation

  • Multicellular eukaryotes have different cell types with different functions
  • The number and arrangements of organelles relate to the function and activities of cells

Biological Molecules

  • Four main types: proteins, carbohydrates, lipids, and nucleic acids
  • Essential components of cell structure and function

Protein Structure and Function

  • Proteins are polypeptides made of a sequence of amino acids
  • The primary structure of a protein (amino acid sequence) determines the final folded state (and hence function)
  • The amino acid side chains have different properties that dictate how the protein folds
  • Proteins may be made of one or more domains.

Protein Folding

  • The way a protein folds is crucial for its function.
  • The structure-function relationship is critical
  • Folding reactions can be catalyzed by helpers in the cell, such as chaperones
  • Chaperones assist in protein folding and stop aggregation.
  • Conditions (like urea and mercaptoethanol) can affect protein structure, for instance, unfolding proteins
  • Noncovalent bonds like hydrogen bonds, hydrophobic interactions, and van der Waals forces drive and stabilize tertiary protein structure
  • Mutations impacting protein sequence can cause detrimental effects, such as in sickle-cell anemia

Four Major Types of Side Chains

  • Polar or charged (e.g., Asp, Glu, Lys, Arg, His)
  • Polar uncharged (e.g., Ser, Thr, Gln, Asn, Tyr)
  • Nonpolar (e.g., Ala, Val, Leu, Ile, Met, Phe, Trp, Cys, Pro)
  • Cysteines can form disulfide bridges

Protein Misfolding Diseases

  • Misfolded proteins often form aggregates, causing diseases, such as Alzheimer's disease, Parkinson's disease
  • Several misfolded proteins have similar characteristics

Prion Diseases

  • Prions cause disease by propagating abnormal protein conformations (PrPSc) that convert normal protein conformations (PrPc)
  • Misfolded proteins form aggregates and cause dysfunction
  • Prions are difficult to inactivate and are resistant to conventional methods
  • The specific mechanism of prion conversion is not fully understood, but it involves alteration in structure that leads to disease.

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Description

Test your knowledge on the intricacies of protein folding and the mechanisms involved in the tertiary structure formation. This quiz covers key concepts such as the role of ribonuclease, chaperone proteins, and the significance of AI in predicting protein structures.

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