MODULE 3: Chapter 4.3 Flashcards
What determines the three-dimensional structure and biochemical function of a protein?
The amino acid sequence of a protein.
How do newly synthesized polypeptide chains fold into a stable three-dimensional structure?
They are flexible molecules that are constantly moving and fluctuating.
What influences the way a protein folds into its final three-dimensional structure?
The surrounding solvent.
For cytosolic proteins, what is the solvent that influences protein folding?
Water.
What drives hydrophobic residues toward the interior of the protein during folding?
Hydrogen bonds formed with water.
What are the three general principles about the formation of stable tertiary structures?
- Limited folding pathways 2. Favorable free energy difference (ΔG < 0) 3. In vivo vs. in vitro folding differences.
Who first pointed out that protein folding must follow some energy minimization path?
Cyrus Levinthal in 1968.
What is the equation that relates free energy change (ΔG) to enthalpy (ΔH) and entropy (ΔS)?
ΔG = ΔH − TΔS.
What is the major driving force for protein folding?
The entropic contribution from the hydrophobic effect.
What role do chaperones play in protein folding?
- Help newly synthesized proteins fold 2. Rescue misfolded proteins 3. Disrupt protein aggregates.
What are intrinsically disordered proteins?
Proteins that function despite having significant structural variability.
Give an example of an intrinsically disordered protein.
BRCA1.
What is a key feature of intrinsically disordered proteins?
Their dynamic flexibility.
What can cause large structural alterations in proteins according to Robert Sauer’s studies?
Small changes in the polypeptide sequence.
How is protein unfolding often studied in vitro?
By disrupting noncovalent interactions using heat, pH, or chemicals.
What is the temperature (Tm) related to in protein unfolding studies?
The temperature where 50% of proteins are folded and 50% are unfolded.
True or False: Unfolding of a protein is a cooperative process.
True.
What did Christian Anfinsen demonstrate about protein folding?
That all biochemical information required for protein folding resides in the amino acid sequence.
What was used to denature ribonuclease A (RNaseA) in Anfinsen’s experiments?
8 M urea and reducing agent β-mercaptoethanol (BME).
Fill in the blank: The formation of hydrogen bonds, ionic interactions, and van der Waals interactions provide sources of favorable _______ contributions.
enthalpic.
What is the impact of the hydrophobic effect on protein folding?
It increases the disorder of surrounding water molecules.
Who was awarded a share of the 1972 Nobel Prize in Chemistry for their work on protein folding?
Anfinsen
What compound did Anfinsen use to denature purified RNaseA?
8 M urea
What does urea do to proteins during denaturation?
Disrupts polar interactions without altering covalent structure
What was the result when Anfinsen removed urea and BME simultaneously?
The protein refolded correctly, regaining full enzymatic activity
What happened when BME was removed before urea under oxidizing conditions?
The protein was only 1% active due to incorrect disulfide bond formation
What does the 1:100 ratio of active to inactive RNaseA proteins indicate?
The probability of forming the correct disulfide bonds among eight cysteines
What additional step did Anfinsen take to demonstrate the importance of amino acid sequence in protein folding?
Added trace amounts of BME to scrambled proteins to allow refolding
What is the significance of Alan Fersht in protein folding studies?
Pioneered studies predicting folding pathways for small globular proteins
What did Fersht’s group suggest about the initial formation of protein structures?
Secondary structures initially form as independent α helices
What are the three proposed models for protein folding?
- Hydrophobic collapse model
- Framework model
- Nucleation model
What does the hydrophobic collapse model propose about protein folding?
Hydrophobic residues form the interior first, leading to secondary and tertiary structures
In the framework model, how do secondary and tertiary structures form?
Local secondary structures form independently before tertiary structures
What does the nucleation model suggest about the formation of protein structures?
Random interactions create a localized region of correct structure that seeds further folding
What does a protein folding funnel illustrate?
The varied paths and energetic states in protein folding
What does the width of the protein folding funnel represent?
The entropy of the polypeptide chain
What does the height of the protein folding funnel indicate?
The overall energy difference between folded and unfolded states
What are chaperone proteins and their primary function?
Assist in protein folding in vivo
What are the two most common types of chaperone proteins?
- Clamp-type chaperones
- Chamber-type chaperones
What is the best-characterized clamp-type chaperone protein?
Heat shock protein 70 (Hsp70)
What role does ATP play in the function of Hsp70?
Induces conformational changes for binding and releasing misfolded proteins
What is the GroEL–GroES protein complex?
A chamber-type chaperone that aids in protein folding
How many subunits does the GroEL component consist of?
14 identical polypeptide subunits
What is the molecular mass of the GroEL–GroES complex?
850 kDa
What is the role of GroES in the GroEL–GroES complex?
Acts as a cap for the GroEL chaperone
What percentage of synthesized proteins may need refolding or degradation?
Up to 30%
What are the two outcomes of misfolded proteins in cells?
- Degraded (loss of function)
- Form protein aggregates (gain of function)
Name a disease associated with protein folding defects.
Alzheimer’s disease
True or False: Misfolded proteins can interfere with the function of normal proteins.
True
Fill in the blank: Chaperone proteins are highly ________ throughout evolution.
conserved
What is the cause of Phenylketonuria?
Deficiency of phenylalanine hydroxylase
This enzyme is crucial for the metabolism of phenylalanine, an amino acid.
What is the main consequence of Tay–Sachs disease?
Deficiency of hexosaminidase
This leads to the accumulation of GM2 gangliosides, causing neurodegeneration.
What type of mutation is associated with Cystic Fibrosis?
Loss-of-function mutation
It results in the degradation of cystic fibrosis transmembrane conductance regulator protein.
What is the genetic cause of Huntington’s disease?
Expansion of CAG triplet nucleotides in the huntingtin gene
This results in a polyglutamine track expansion.
What type of mutation characterizes protein aggregation diseases like Huntington’s?
Gain-of-function mutation
The mutated protein acquires new, harmful functions.
What are amyloid plaques associated with?
Alzheimer’s disease
They contain aggregates of amyloid β protein.
What is the role of prion protein (PrP) in transmissible spongiform encephalopathies (TSEs)?
Formation of large protein aggregates in the brain
Misfolded PrP can lead to neurodegenerative diseases.
What does the prion hypothesis propose?
Normal prion protein (PrPc) can be converted to a misfolded, infectious form (PrPSc)
This conversion is a key mechanism in prion diseases.
What is the role of chaperone proteins?
Facilitate the formation of stable three-dimensional structures
They assist in protein folding.
Define intrinsically disordered protein.
A protein lacking a stable, folded three-dimensional structure under certain conditions
Despite this, it can still perform biological functions.
What is a molten globule?
An intermediate stage in globular protein folding
Characterized by initial hydrophobic residue clustering.
What are heat shock proteins (Hsp70)?
A family of proteins that help refold denatured proteins
They are crucial for cellular recovery from stress.
What is the significance of amyloid plaques in Alzheimer’s disease?
They are hallmarks of the disease and indicate neuronal cell death
Found in brain regions affected by the disease.
What is the transition curve midpoint (Tm)?
Condition where 50% of proteins are folded and 50% are unfolded
It indicates the stability of protein folding.
What does the term polyglutamine track expansion refer to?
Gene mutation with multiple CAG repeats encoding glutamine
Associated with neurodegenerative diseases like Huntington’s.
True or False: Misfolded proteins can lead to gain-of-function mutations.
True
This can result in new, harmful activities for the cell.
What is the role of circular dichroism (CD) in studying proteins?
Measures differences in absorption of circularly polarized light
Used to study protein folding and conformation.
Fill in the blank: Cystic fibrosis is caused by mutations in the _______.
cystic fibrosis transmembrane conductance regulator protein
This protein functions as a chloride ion channel.
