MODULE 3: Chapter 4.3

Question 1

What determines the three-dimensional structure and biochemical function of a protein?

Answer 1

The amino acid sequence of a protein.

Question 2

How do newly synthesized polypeptide chains fold into a stable three-dimensional structure?

Answer 2

They are flexible molecules that are constantly moving and fluctuating.

Question 3

What influences the way a protein folds into its final three-dimensional structure?

Answer 3

The surrounding solvent.

Question 4

For cytosolic proteins, what is the solvent that influences protein folding?

Answer 4

Water.

Question 5

What drives hydrophobic residues toward the interior of the protein during folding?

Answer 5

Hydrogen bonds formed with water.

Question 6

What are the three general principles about the formation of stable tertiary structures?

Answer 6

1. Limited folding pathways 2. Favorable free energy difference (ΔG < 0) 3. In vivo vs. in vitro folding differences.

Question 7

Who first pointed out that protein folding must follow some energy minimization path?

Answer 7

Cyrus Levinthal in 1968.

Question 8

What is the equation that relates free energy change (ΔG) to enthalpy (ΔH) and entropy (ΔS)?

Answer 8

ΔG = ΔH − TΔS.

Question 9

What is the major driving force for protein folding?

Answer 9

The entropic contribution from the hydrophobic effect.

Question 10

What role do chaperones play in protein folding?

Answer 10

1. Help newly synthesized proteins fold 2. Rescue misfolded proteins 3. Disrupt protein aggregates.

Question 11

What are intrinsically disordered proteins?

Answer 11

Proteins that function despite having significant structural variability.

Question 12

Give an example of an intrinsically disordered protein.

Answer 12

BRCA1.

Question 13

What is a key feature of intrinsically disordered proteins?

Answer 13

Their dynamic flexibility.

Question 14

What can cause large structural alterations in proteins according to Robert Sauer’s studies?

Answer 14

Small changes in the polypeptide sequence.

Question 15

How is protein unfolding often studied in vitro?

Answer 15

By disrupting noncovalent interactions using heat, pH, or chemicals.

Question 16

What is the temperature (Tm) related to in protein unfolding studies?

Answer 16

The temperature where 50% of proteins are folded and 50% are unfolded.

Question 17

True or False: Unfolding of a protein is a cooperative process.

Answer 17

True.

Question 18

What did Christian Anfinsen demonstrate about protein folding?

Answer 18

That all biochemical information required for protein folding resides in the amino acid sequence.

Question 19

What was used to denature ribonuclease A (RNaseA) in Anfinsen’s experiments?

Answer 19

8 M urea and reducing agent β-mercaptoethanol (BME).

Question 20

Fill in the blank: The formation of hydrogen bonds, ionic interactions, and van der Waals interactions provide sources of favorable _______ contributions.

Answer 20

enthalpic.

Question 21

What is the impact of the hydrophobic effect on protein folding?

Answer 21

It increases the disorder of surrounding water molecules.

Question 22

Who was awarded a share of the 1972 Nobel Prize in Chemistry for their work on protein folding?

Answer 22

Anfinsen

Question 23

What compound did Anfinsen use to denature purified RNaseA?

Answer 23

8 M urea

Question 24

What does urea do to proteins during denaturation?

Answer 24

Disrupts polar interactions without altering covalent structure

Question 25

What was the result when Anfinsen removed urea and BME simultaneously?

Answer 25

The protein refolded correctly, regaining full enzymatic activity

Question 26

What happened when BME was removed before urea under oxidizing conditions?

Answer 26

The protein was only 1% active due to incorrect disulfide bond formation

Question 27

What does the 1:100 ratio of active to inactive RNaseA proteins indicate?

Answer 27

The probability of forming the correct disulfide bonds among eight cysteines

Question 28

What additional step did Anfinsen take to demonstrate the importance of amino acid sequence in protein folding?

Answer 28

Added trace amounts of BME to scrambled proteins to allow refolding

Question 29

What is the significance of Alan Fersht in protein folding studies?

Answer 29

Pioneered studies predicting folding pathways for small globular proteins

Question 30

What did Fersht's group suggest about the initial formation of protein structures?

Answer 30

Secondary structures initially form as independent α helices

Question 31

What are the three proposed models for protein folding?

Answer 31

* Hydrophobic collapse model * Framework model * Nucleation model

Question 32

What does the hydrophobic collapse model propose about protein folding?

Answer 32

Hydrophobic residues form the interior first, leading to secondary and tertiary structures

Question 33

In the framework model, how do secondary and tertiary structures form?

Answer 33

Local secondary structures form independently before tertiary structures

Question 34

What does the nucleation model suggest about the formation of protein structures?

Answer 34

Random interactions create a localized region of correct structure that seeds further folding

Question 35

What does a protein folding funnel illustrate?

Answer 35

The varied paths and energetic states in protein folding

Question 36

What does the width of the protein folding funnel represent?

Answer 36

The entropy of the polypeptide chain

Question 37

What does the height of the protein folding funnel indicate?

Answer 37

The overall energy difference between folded and unfolded states

Question 38

What are chaperone proteins and their primary function?

Answer 38

Assist in protein folding in vivo

Question 39

What are the two most common types of chaperone proteins?

Answer 39

* Clamp-type chaperones * Chamber-type chaperones

Question 40

What is the best-characterized clamp-type chaperone protein?

Answer 40

Heat shock protein 70 (Hsp70)

Question 41

What role does ATP play in the function of Hsp70?

Answer 41

Induces conformational changes for binding and releasing misfolded proteins

Question 42

What is the GroEL–GroES protein complex?

Answer 42

A chamber-type chaperone that aids in protein folding

Question 43

How many subunits does the GroEL component consist of?

Answer 43

14 identical polypeptide subunits

Question 44

What is the molecular mass of the GroEL–GroES complex?

Answer 44

850 kDa

Question 45

What is the role of GroES in the GroEL–GroES complex?

Answer 45

Acts as a cap for the GroEL chaperone

Question 46

What percentage of synthesized proteins may need refolding or degradation?

Answer 46

Up to 30%

Question 47

What are the two outcomes of misfolded proteins in cells?

Answer 47

* Degraded (loss of function) * Form protein aggregates (gain of function)

Question 48

Name a disease associated with protein folding defects.

Answer 48

Alzheimer's disease

Question 49

True or False: Misfolded proteins can interfere with the function of normal proteins.

Answer 49

True

Question 50

Fill in the blank: Chaperone proteins are highly ________ throughout evolution.

Answer 50

conserved

Question 51

What is the cause of Phenylketonuria?

Answer 51

Deficiency of phenylalanine hydroxylase ## Footnote This enzyme is crucial for the metabolism of phenylalanine, an amino acid.

Question 52

What is the main consequence of Tay–Sachs disease?

Answer 52

Deficiency of hexosaminidase ## Footnote This leads to the accumulation of GM2 gangliosides, causing neurodegeneration.

Question 53

What type of mutation is associated with Cystic Fibrosis?

Answer 53

Loss-of-function mutation ## Footnote It results in the degradation of cystic fibrosis transmembrane conductance regulator protein.

Question 54

What is the genetic cause of Huntington's disease?

Answer 54

Expansion of CAG triplet nucleotides in the huntingtin gene ## Footnote This results in a polyglutamine track expansion.

Question 55

What type of mutation characterizes protein aggregation diseases like Huntington's?

Answer 55

Gain-of-function mutation ## Footnote The mutated protein acquires new, harmful functions.

Question 56

What are amyloid plaques associated with?

Answer 56

Alzheimer’s disease ## Footnote They contain aggregates of amyloid β protein.

Question 57

What is the role of prion protein (PrP) in transmissible spongiform encephalopathies (TSEs)?

Answer 57

Formation of large protein aggregates in the brain ## Footnote Misfolded PrP can lead to neurodegenerative diseases.

Question 58

What does the prion hypothesis propose?

Answer 58

Normal prion protein (PrPc) can be converted to a misfolded, infectious form (PrPSc) ## Footnote This conversion is a key mechanism in prion diseases.

Question 59

What is the role of chaperone proteins?

Answer 59

Facilitate the formation of stable three-dimensional structures ## Footnote They assist in protein folding.

Question 60

Define intrinsically disordered protein.

Answer 60

A protein lacking a stable, folded three-dimensional structure under certain conditions ## Footnote Despite this, it can still perform biological functions.

Question 61

What is a molten globule?

Answer 61

An intermediate stage in globular protein folding ## Footnote Characterized by initial hydrophobic residue clustering.

Question 62

What are heat shock proteins (Hsp70)?

Answer 62

A family of proteins that help refold denatured proteins ## Footnote They are crucial for cellular recovery from stress.

Question 63

What is the significance of amyloid plaques in Alzheimer's disease?

Answer 63

They are hallmarks of the disease and indicate neuronal cell death ## Footnote Found in brain regions affected by the disease.

Question 64

What is the transition curve midpoint (Tm)?

Answer 64

Condition where 50% of proteins are folded and 50% are unfolded ## Footnote It indicates the stability of protein folding.

Question 65

What does the term polyglutamine track expansion refer to?

Answer 65

Gene mutation with multiple CAG repeats encoding glutamine ## Footnote Associated with neurodegenerative diseases like Huntington's.

Question 66

True or False: Misfolded proteins can lead to gain-of-function mutations.

Answer 66

True ## Footnote This can result in new, harmful activities for the cell.

Question 67

What is the role of circular dichroism (CD) in studying proteins?

Answer 67

Measures differences in absorption of circularly polarized light ## Footnote Used to study protein folding and conformation.

Question 68

Fill in the blank: Cystic fibrosis is caused by mutations in the _______.

Answer 68

cystic fibrosis transmembrane conductance regulator protein ## Footnote This protein functions as a chloride ion channel.