Question 1

What is the difference between clamp-type and chamber-type chaperone proteins?

Accepted Answer

A)  One uses ATP and the other does not. 
B)  One folds proteins, whereas the other just protects them from unfolding. 
C)  They are shaped differently. 
D)  One type is found extracellularly and one intracellularly. 
A)  One uses ATP and the other does not. 
B)  One folds proteins, whereas the other just protects them from unfolding. 
C)  They are shaped differently. 
D)  One type is found extracellularly and one intracellularly.

Question 2

At what point does the isoelectric point or pI occur?

Accepted Answer

A)  when all of the acidic protons are neutralized with base 
B)  at pH = 7.0 
C)  at the pH when all negative charges on a zwitterion counter the positive charges 
D)  when the molecule has a single electric charge 
A)  when all of the acidic protons are neutralized with base 
B)  at pH = 7.0 
C)  at the pH when all negative charges on a zwitterion counter the positive charges 
D)  when the molecule has a single electric charge

Question 3

Use the table below and the following RNA sequence to determine which reading frame would give rise to the shortest peptide, or which reading frame gives rise to the first stop codon.
Frame: 1 2 3
RNA: GCG CCC CCU AAC AGG UAG CUG CGG UUC CUG

Accepted Answer

Frame 3: Beginning w

Question 4

What is the pI of the dipeptide shown? (Use the pK as given.)

Accepted Answer

A)  0 
B)  5 
C)  9 
D)  10.5 
A)  0 
B)  5 
C)  9 
D)  10.5

Question 5

Draw the resonance structures that stabilize the peptide bonds found in proteins.

Accepted Answer

The answer of Draw the resonance structures that stabilize the...

Question 6

Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace?

Accepted Answer

A)  NCCNCC 
B)  NCCONCCO 
C)  NCONCO 
D)  CNCCNC 
A)  NCCNCC 
B)  NCCONCCO 
C)  NCONCO 
D)  CNCCNC

Question 7

What is the minimum number of amino acids needed to make one turn of an $\alpha$-helix?

Accepted Answer

A)  3 
B)  4 
C)  6 
D)  7 
A)  3 
B)  4 
C)  6 
D)  7

Question 8

Which of the following statements about the clamp-type chaperone protein Hsp70 is correct?

Accepted Answer

A)  Hsp70 uses ATP binding and hydrolysis energy to assist in the folding of a protein. 
B)  Hsp70 is a multi-subunit protein shaped like a large barrel, inside of which the folding protein is protected. 
C)  Hsp70 is most active during cell division phases. 
D)  Hsp70 assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds. 
A)  Hsp70 uses ATP binding and hydrolysis energy to assist in the folding of a protein. 
B)  Hsp70 is a multi-subunit protein shaped like a large barrel, inside of which the folding protein is protected. 
C)  Hsp70 is most active during cell division phases. 
D)  Hsp70 assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds.

Question 9

Describe the proposed model of globular protein folding called the nucleation model.

Accepted Answer

In the nucleation model of globular prot

Question 10

The essential amino acids in adult humans are those that are required in our diet because of a lack of the biosynthetic pathway in our cells. The single-letter abbreviations for these amino acids are WVMILKFHT. Name these amino acids.

Accepted Answer

Tryptophan, valine, methionine

Question 11

What is a current hypothesis that explains the infectious nature of prion diseases?

Accepted Answer

A)  The virus responsible for prion diseases is transmissible. 
B)  Unfavorable environmental factors negatively influence healthy cells. 
C)  The small molecule denaturants found in infected cells are passed on to healthy cells. 
D)  The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins. 
A)  The virus responsible for prion diseases is transmissible. 
B)  Unfavorable environmental factors negatively influence healthy cells. 
C)  The small molecule denaturants found in infected cells are passed on to healthy cells. 
D)  The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins.

Question 12

What is believed to be the underlying cause of prion protein plaque formation?

Accepted Answer

A)  The PrPSc proteins are misfolded and aggregated from PrPc proteins. 
B)  The unstructured N-terminal region of PrPc is thought to remain unfolded. 
C)  The normal PrPc proteins are aggregated. 
D)  The PrPSc protein adheres to and inhibits cell membranes. 
A)  The PrPSc proteins are misfolded and aggregated from PrPc proteins. 
B)  The unstructured N-terminal region of PrPc is thought to remain unfolded. 
C)  The normal PrPc proteins are aggregated. 
D)  The PrPSc protein adheres to and inhibits cell membranes.

Question 13

Of the 20 common amino acids, how many have a chiral $\alpha$-carbon?

Accepted Answer

A)  0 
B)  1 
C)  19 
D)  20 
A)  0 
B)  1 
C)  19 
D)  20

Question 14

The peptide bond

Accepted Answer

A)  is most stable in the cis configuration. 
B)  has a mix of single and double bond characters. 
C)  can rotate around the carbonyl and N bond but not around the $\alpha$-carbon and N bond. 
D)  can function as a weak acid and weak base. 
A)  is most stable in the cis configuration. 
B)  has a mix of single and double bond characters. 
C)  can rotate around the carbonyl and N bond but not around the $\alpha$-carbon and N bond. 
D)  can function as a weak acid and weak base.

Question 15

Christian Anfinsen showed in a famous experiment that it is possible to unfold a protein and refold it to obtain a functional protein. Which two reagents were used in this experiment to unfold the protein?

Accepted Answer

A)  detergent and salt 
B)  urea and $\beta$-mercaptoethanol 
C)  acid and base 
D)  ethanol and $\beta$-mercaptoethanol 
A)  detergent and salt 
B)  urea and $\beta$-mercaptoethanol 
C)  acid and base 
D)  ethanol and $\beta$-mercaptoethanol

Question 16

In the multi-subunit protein family called immunoglobulins, the different subunits are held together by both covalent and noncovalent forces. What are the covalent forces that hold subunits together in immunoglobulins?

Accepted Answer

Cysteine disulfide b

Question 17

Using the pKas shown, what is the isoelectric point of the amino acid tyrosine?

Accepted Answer

A)  <1.0 
B)  5.5 
C)  7.0 
D)  9.75 
A)  <1.0 
B)  5.5 
C)  7.0 
D)  9.75

Question 18

The common protein fold shown below is the fold.

Accepted Answer

A)  "Greek key" 
B)  "Rossman" 
C)  "FERM domain" 
D)  "$\alpha$/$\beta$ barrel" 
A)  "Greek key" 
B)  "Rossman" 
C)  "FERM domain" 
D)  "$\alpha$/$\beta$ barrel"

Question 19

Use the two-stranded antiparallel $\beta$-sheet below and drawn in a $\beta$-turn.

Accepted Answer

The answer of Use the two-stranded antiparallel $\beta$-sheet below and...

Question 20

All of the following are stabilizing forces in maintaining a stable protein tertiary (3$\degree$) structure, EXCEPT

Accepted Answer

A)  H bonds. 
B)  temperature. 
C)  hydrophobic interactions. 
D)  electrostatic attractions. 
A)  H bonds. 
B)  temperature. 
C)  hydrophobic interactions. 
D)  electrostatic attractions.

Exam 4: Protein Structure

What is the difference between clamp-type and chamber-type chaperone proteins?

At what point does the isoelectric point or pI occur?

Use the table below and the following RNA sequence to determine which reading frame would give rise to the shortest peptide, or which reading frame gives rise to the first stop codon. Frame: 1 2 3 RNA: GCG CCC CCU AAC AGG UAG CUG CGG UUC CUG

What is the pI of the dipeptide shown? (Use the pK as given.)

Draw the resonance structures that stabilize the peptide bonds found in proteins.

Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace?

What is the minimum number of amino acids needed to make one turn of an α\alphaα -helix?

Which of the following statements about the clamp-type chaperone protein Hsp70 is correct?

Describe the proposed model of globular protein folding called the nucleation model.

The essential amino acids in adult humans are those that are required in our diet because of a lack of the biosynthetic pathway in our cells. The single-letter abbreviations for these amino acids are WVMILKFHT. Name these amino acids.

What is a current hypothesis that explains the infectious nature of prion diseases?

What is believed to be the underlying cause of prion protein plaque formation?

Of the 20 common amino acids, how many have a chiral α\alphaα -carbon?

The peptide bond

Christian Anfinsen showed in a famous experiment that it is possible to unfold a protein and refold it to obtain a functional protein. Which two reagents were used in this experiment to unfold the protein?

In the multi-subunit protein family called immunoglobulins, the different subunits are held together by both covalent and noncovalent forces. What are the covalent forces that hold subunits together in immunoglobulins?

Using the pKas shown, what is the isoelectric point of the amino acid tyrosine?

The common protein fold shown below is the fold.

Use the two-stranded antiparallel β\betaβ -sheet below and drawn in a β\betaβ -turn.

All of the following are stabilizing forces in maintaining a stable protein tertiary (3 °\degree° ) structure, EXCEPT

Principles of Biochemistry

Physical Biochemistry: Energy Conversion, Water, and Membranes

Nucleic Acid Structure and Function

Methods in Protein Biochemistry

Protein Function

Enzyme Mechanisms

Cell Signaling Systems

Glycolysis: a Paradigm of Metabolic Regulation

The Citrate Cycle

Oxidative Phosphorylation

Photosynthesis

Carbohydrate Structure and Function

Carbohydrate Metabolism

Lipid Structure and Function

Lipid Metabolism

Amino Acid Metabolism

Nucleotide Metabolism

Metabolic Integration

DNA Replication, Repair, and Recombination

RNA Synthesis, Processing, and Gene Silencing

Protein Synthesis, Posttranslational Modification, and Transport

Gene Regulation

Filters

What is the minimum number of amino acids needed to make one turn of an $\alpha$ -helix?

Of the 20 common amino acids, how many have a chiral $\alpha$ -carbon?

Use the two-stranded antiparallel $\beta$ -sheet below and drawn in a $\beta$ -turn. $Use the two-stranded antiparallel \beta -sheet below and drawn in a \beta -turn.$

All of the following are stabilizing forces in maintaining a stable protein tertiary (3 $\degree$ ) structure, EXCEPT