Question 1

Why is the amino acid proline not commonly found in $\alpha$-helices or $\beta$-sheets? In what secondary structure might proline be commonly found?

Accepted Answer

Because of its cyclic nature, proline has more restricted $\Psi$ and $\Psi$ angles. Also, because of its lack of an NH group on its backbone amine, proline cannot hydrogen bond to stabilize the helices or sheets. Proline can often be found in turns or loops connecting helices or strands.

Question 2

Which stabilizing force in protein tertiary structures is a covalent bonding force?

Accepted Answer

A)  ionic bonding 
B)  disulfide bonding 
C)  hydrophobic interactions 
D)  van der Waals bonding 
A)  ionic bonding 
B)  disulfide bonding 
C)  hydrophobic interactions 
D)  van der Waals bonding B

Question 3

It is important for cells to degrade misfolded proteins. If misfolded proteins are not degraded, the misfolded proteins may

Accepted Answer

A)  waste excessive ATP in attempts to refold them. 
B)  aggregate and interfere with normal cellular function. 
C)  eventually refold, but not until excessive and sometimes fatal levels of cellular energy are spent. 
D)  be excreted from the cell rather than recycled for building blocks. 
A)  waste excessive ATP in attempts to refold them. 
B)  aggregate and interfere with normal cellular function. 
C)  eventually refold, but not until excessive and sometimes fatal levels of cellular energy are spent. 
D)  be excreted from the cell rather than recycled for building blocks. B

Question 4

Which amino acid contains a hydroxyl group?

Accepted Answer

A)  valine 
B)  cysteine 
C)  threonine 
D)  aspartate 
A)  valine 
B)  cysteine 
C)  threonine 
D)  aspartate

Question 5

At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer?

Accepted Answer

A)  glutamate-aspartate. 
B)  leucine-aspartate. 
C)  glutamate-lysine. 
D)  phenylalaninelysine. 
A)  glutamate-aspartate. 
B)  leucine-aspartate. 
C)  glutamate-lysine. 
D)  phenylalaninelysine.

Question 6

Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure?

Accepted Answer

A)  mutant globule 
B)  hydrophobic collapse model 
C)  framework model 
D)  nucleation model 
A)  mutant globule 
B)  hydrophobic collapse model 
C)  framework model 
D)  nucleation model

Question 7

Which amino acid has the highest pKa?

Accepted Answer

A)  glutamate 
B)  asparagine 
C)  cysteine 
D)  lysine 
A)  glutamate 
B)  asparagine 
C)  cysteine 
D)  lysine

Question 8

Which linear sequence of bonded atoms can be found in the backbone of polypeptides?

Accepted Answer

A)  C-N-N-C 
B)  C-C-N-C 
C)  N-C-C-C 
D)  C-O-C-N 
A)  C-N-N-C 
B)  C-C-N-C 
C)  N-C-C-C 
D)  C-O-C-N

Question 9

In the Anfinsen experiment with the unfolding of RNaseA, what order could the chemical reagents be removed in order to achieve an inactive protein?

Accepted Answer

A)  Remove denaturant first and reductant second. 
B)  Simultaneously remove denaturant and reductant. 
C)  Remove reductant first, denaturant second, and then finally add back reductant. 
D)  Remove reductant first and denaturant second. 
A)  Remove denaturant first and reductant second. 
B)  Simultaneously remove denaturant and reductant. 
C)  Remove reductant first, denaturant second, and then finally add back reductant. 
D)  Remove reductant first and denaturant second.

Question 10

Which class of protein structures does the protein shown below fit into?

Accepted Answer

A)  predominantly $\alpha$-helical 
B)  predominantly $\beta$-sheet 
C)  intermixed $\alpha$-helix and $\beta$-sheet 
D)  domains of $\alpha$-helix adjacent to domains of $\beta$-sheet 
A)  predominantly $\alpha$-helical 
B)  predominantly $\beta$-sheet 
C)  intermixed $\alpha$-helix and $\beta$-sheet 
D)  domains of $\alpha$-helix adjacent to domains of $\beta$-sheet

Question 11

Use the theoretical Ramachandran plot at the top to evaluate the two experimental plots on the bottom. Describe the likely secondary structures found in each experimental plot.

Accepted Answer

The middle Ramachandran plot is consiste

Question 12

The chirality of naturally occurring amino acids in proteins is

Accepted Answer

A)  R. 
B)  L. 
C)  D. 
D)  the same as glyceraldehyde. 
A)  R. 
B)  L. 
C)  D. 
D)  the same as glyceraldehyde.

Question 13

Identify the four images below, which represent the four classes of protein structures commonly identified across MOST structures found in the Protein Data Bank.

Accepted Answer

(a) Predominantly @#LAT-DLM&-helical, (b

Question 14

In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT

Accepted Answer

A)  hydrogen bonds. 
B)  electrostatic interactions. 
C)  hydrophobic interactions. 
D)  peptide bonds. 
A)  hydrogen bonds. 
B)  electrostatic interactions. 
C)  hydrophobic interactions. 
D)  peptide bonds.

Question 15

Which of the following statements about Ramachandran plots is true?

Accepted Answer

A)  They are good predictors of protein tertiary structure. 
B)  They are needed to determine the secondary structure of a protein. 
C)  They show equal distributions of $\phi$ and $\Psi$angles for $\alpha$-helical and $\beta$-sheet containing proteins. 
D)  They show that$\beta$-sheets and $\alpha$-helices occupy different $\phi$and $\Psi$ angles. 
A)  They are good predictors of protein tertiary structure. 
B)  They are needed to determine the secondary structure of a protein. 
C)  They show equal distributions of $\phi$ and $\Psi$angles for $\alpha$-helical and $\beta$-sheet containing proteins. 
D)  They show that$\beta$-sheets and $\alpha$-helices occupy different $\phi$and $\Psi$ angles.

Question 16

Use the table below and write out the amino acid sequence coded by the following RNA sequence: AUG_CAC_AGG_UGA.

Accepted Answer

The answer of Use the table below and write out...

Question 17

Which interaction largely stabilizes protein secondary (2$\degree$) structures?

Accepted Answer

A)  disulfide bonds 
B)  hydrogen bonding 
C)  hydrophobic packing 
D)  metal ions 
A)  disulfide bonds 
B)  hydrogen bonding 
C)  hydrophobic packing 
D)  metal ions

Question 18

The points in the Ramachandran plot are derived by

Accepted Answer

A)  counting the number of amino acids and placing points in allowed regions. 
B)  measuring the $\phi$and $\Psi$angles in an experimentally determined protein crystal structure. 
C)  placing each amino acid in regions commonly occupied by that amino acid. 
D)  experimentally measuring the optical rotation of polarized light. 
A)  counting the number of amino acids and placing points in allowed regions. 
B)  measuring the $\phi$and $\Psi$angles in an experimentally determined protein crystal structure. 
C)  placing each amino acid in regions commonly occupied by that amino acid. 
D)  experimentally measuring the optical rotation of polarized light.

Question 19

The amino acid with the neutral side chain at neutral pH is

Accepted Answer

A)  asparagine. 
B)  aspartate. 
C)  arginine. 
D)  glutamate. 
A)  asparagine. 
B)  aspartate. 
C)  arginine. 
D)  glutamate.

Question 20

How many $\beta$-turns or $\beta$-loops are required to construct a $\beta$-sheet composed of four antiparallel strands?

Accepted Answer

A)  0 
B)  3 
C)  4 
D)  5 
A)  0 
B)  3 
C)  4 
D)  5

Exam 4: Protein Structure

Why is the amino acid proline not commonly found in α\alphaα -helices or β\betaβ -sheets? In what secondary structure might proline be commonly found?

Which stabilizing force in protein tertiary structures is a covalent bonding force?

It is important for cells to degrade misfolded proteins. If misfolded proteins are not degraded, the misfolded proteins may

Which amino acid contains a hydroxyl group?

At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer?

Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure?

Which amino acid has the highest pKa?

Which linear sequence of bonded atoms can be found in the backbone of polypeptides?

In the Anfinsen experiment with the unfolding of RNaseA, what order could the chemical reagents be removed in order to achieve an inactive protein?

Which class of protein structures does the protein shown below fit into?

Use the theoretical Ramachandran plot at the top to evaluate the two experimental plots on the bottom. Describe the likely secondary structures found in each experimental plot.

The chirality of naturally occurring amino acids in proteins is

Identify the four images below, which represent the four classes of protein structures commonly identified across MOST structures found in the Protein Data Bank.

In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT

Which of the following statements about Ramachandran plots is true?

Use the table below and write out the amino acid sequence coded by the following RNA sequence: AUG_CAC_AGG_UGA.

Which interaction largely stabilizes protein secondary (2 °\degree° ) structures?

The points in the Ramachandran plot are derived by

The amino acid with the neutral side chain at neutral pH is

How many β\betaβ -turns or β\betaβ -loops are required to construct a β\betaβ -sheet composed of four antiparallel strands?

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

Why is the amino acid proline not commonly found in $\alpha$ -helices or $\beta$ -sheets? In what secondary structure might proline be commonly found?

Which interaction largely stabilizes protein secondary (2 $\degree$ ) structures?

How many $\beta$ -turns or $\beta$ -loops are required to construct a $\beta$ -sheet composed of four antiparallel strands?