Question 1

Suppose you discovered a new amino acid. Its R- group contains only hydrogen and carbon atoms. Predict the behavior of this amino acid.

Accepted Answer

A)   It is hydrophilic.
B)   Relative to the amino acids found in organisms, its interactions with water will be intermediate.
C)   Relative to the amino acids found in organisms, its interactions with water will be very high.
D)   It is hydrophobic. D

Question 2

You have isolated a previously unstudied protein, identified its complete structure in detail, and determined that it catalyzes the breakdown of a large substrate. You notice it has two binding sites. One of these is large, apparently the bonding site for the large substrate; the other is small, possibly a binding site for a regulatory molecule. What do these findings tell you about the mechanism of this protein?

Accepted Answer

A)   It is probably an enzyme that works through allosteric regulation.
B)   It is probably an enzyme that works through competitive inhibition.
C)   It is probably a structural protein that is involved in cell- to- cell adhesion.
D)   It is probably a cell membrane transport protein, like an ion channel.
E)   It is probably a structural protein found in cartilage or skeletal tissue. A

Question 3

An amino acid has an R- group that is positively charged at cellular pH. Which of the following categories would best describe it?

Accepted Answer

A)   acidic
B)   basic
C)   uncharged and polar
D)   nonpolar B

Question 4

You are studying a protein that is shaped like a doughnut. The shape is a function of which levels) of protein structure?

Accepted Answer

A)   primary, secondary, and tertiary
B)   tertiary only
C)   secondary and tertiary only
D)   secondary only
E)   primary only

Question 5

Refer to the following paragraph and Figure 3.1 to answer the following questions).
  Figure 3.1
Since structure correlates so well with function, biochemists are constantly looking for new ways to probe the complex structu proteins in order to understand what they do and how they do it. One of the most powerful techniques in existence today is X crystallography. The main difficulty with this technique is getting the protein to crystallize. Once crystallized, the protein is bombarded with X- rays to create a pattern that can be analyzed mathematically to determine the three- dimensional
structure of the protein. This analysis has been performed by Krzysztof Palczewski on the protein rhodopsin, which is a light- sensitive protein found in species ranging from ancient bacteria archaea) to humans. The structure schematically shown above, where each letter represents an amino acid) is characterized by a single polypeptide chain with several
a- helical segments that loop back and forth across the cell membrane. Another notable feature is the disulfide bond - S- S- ) that can be seen at the bottom of the third transmembrane segment. [Figure adapted from K. Palczewski et al., Science 289 2000): 739.]
-If you were reading off the sequence of amino acids in Figure 3.1 to a biologist friend, what should the first three letters be?

Accepted Answer

A)   M- N- G
B)   A- P- A
C)   It doesn't matter, since the protein has no polarity or directionality.

Question 6

Which of the following is not a major functional class of proteins?

Accepted Answer

A)   hereditary proteins
B)   motility proteins
C)   structural proteins
D)   enzymes
E)   regulatory proteins

Question 7

Refer to the following paragraph and Figure 3.1 to answer the following questions).
  Figure 3.1
Since structure correlates so well with function, biochemists are constantly looking for new ways to probe the complex structu proteins in order to understand what they do and how they do it. One of the most powerful techniques in existence today is X crystallography. The main difficulty with this technique is getting the protein to crystallize. Once crystallized, the protein is bombarded with X- rays to create a pattern that can be analyzed mathematically to determine the three- dimensional
structure of the protein. This analysis has been performed by Krzysztof Palczewski on the protein rhodopsin, which is a light- sensitive protein found in species ranging from ancient bacteria archaea) to humans. The structure schematically shown above, where each letter represents an amino acid) is characterized by a single polypeptide chain with several
a- helical segments that loop back and forth across the cell membrane. Another notable feature is the disulfide bond - S- S- ) that can be seen at the bottom of the third transmembrane segment. [Figure adapted from K. Palczewski et al., Science 289 2000): 739.]
-Refer to Figure 3.1. Which level of structure is being maintained by the disulfide bond?

Accepted Answer

A)   primary
B)   tertiary
C)   secondary
D)   quaternary

Question 8

Which of the following statements about the peptide- bonded backbone is correct?

Accepted Answer

A)   The orientation of the side chains in the backbone does not allow them to interact with each other or water.
B)   Both ends of the backbone have a free carboxyl group.
C)   Interactions only take place between C=O and N-H groups in the different peptide- bonded backbones.
D)   Both ends of the backbone have a free amino group.
E)   One end of the backbone has a free amino group while the other has a free carboxyl group.

Question 9

If the primary structure of a protein is incorrect

Accepted Answer

A)   any quaternary structure will be correct.
B)   any higher- level folding of the protein will be incorrect.
C)   the tertiary structure will be correct.
D)   the secondary structure will be correct.

Question 10

Consider the HIV enzyme called protease. The amino acid residues at the active site are highly hydrophobic. In designing a drug that would bind to the active site and jam it, researchers should use which type of molecule?

Accepted Answer

A)   charged
B)   acidic
C)   hydrophobic
D)   polar

Question 11

Which is not a role proteins play in organisms?

Accepted Answer

A)   movement and shape changes
B)   store genetic information
C)   structural support
D)   chemical signaling

Question 12

A peptide bond is

Accepted Answer

A)   a particularly unstable covalent bond.
B)   a triple covalent bond.
C)   a particularly stable, planar covalent bond.
D)   an ionic bond, not a covalent one.

Question 13

An amino acid has an R- group that is negatively charged at cellular pH. Which of the following categories would best describe it?

Accepted Answer

A)   acidic
B)   basic
C)   uncharged and polar
D)   nonpolar

Question 14

You've just sequenced a new protein found in mice and observe that sulfur- containing cysteine residues occur at regular intervals. What is the significance of this finding?

Accepted Answer

A)   It will be important to include cysteine in the diet of the mice.
B)   Cysteine residues are involved in disulfide bridges that help form tertiary structure.
C)   Cysteine causes bends, or angles, to occur in the tertiary structure of proteins.
D)   Cysteine residues are required for the formation of a- helices and fi- pleated sheets.

Question 15

At the pH found in cells about 7.0), what happens to the carboxyl group on an amino acid?

Accepted Answer

A)   It acts as a base and gains a proton, giving it a positive charge.
B)   It is oxidized and tends to act as an electron acceptor in redox reactions.
C)   It remains neutral, like water, and does not have a charge.
D)   It acts as an acid and loses a proton, giving it a negative charge.

Question 16

Which one of the following is not a component of each monomer used to make proteins?

Accepted Answer

A)   an amino functional group, NH2 
B)   an iron atom, Fe
C)   a side chain, R
D)   a carboxyl group, COOH

Question 17

Which of the following statements about peptides is correct?

Accepted Answer

A)   A peptide bond is formed by a condensation reaction between two carboxyl groups.
B)   Joining two amino acids together through a peptide bond results in the formation of a carboxyl group.
C)   As a whole, the structure of the peptide- bonded backbone is flexible.
D)   A peptide bond is formed by a condensation reaction between the carboxyl and amino group of the same amino acid.
E)   The peptide bond is capable of rotating.

Question 18

An enzyme has a total of four active sites. When you denature the molecule and study its composition, you find that each active site occurs on a different polypeptide. Which of the following hypotheses does this observation support?

Accepted Answer

A)   The enzyme requires a cofactor to function normally.
B)   The protein's structure is affected by temperature and pH.
C)   The enzyme is subject to allosteric regulation.
D)   The protein has quaternary structure.

Question 19

The aquaporin family of proteins plays a major role in the transport of water all over the body. During the folding process of these proteins, a- helices start forming as

Accepted Answer

A)   part of the quaternary structure of the protein.
B)   part of the primary structure of the protein.
C)   part of the secondary structure of the protein.
D)   part of the tertiary structure of the protein.

Question 20

Which one of the following is not a component of each monomer used to make proteins?

Accepted Answer

A)   a phosphorous atom, P
B)   a side chain, R
C)   a carboxyl group, COOH
D)   an amino functional group, NH2

Exam 3: Protein Structure and Function

Suppose you discovered a new amino acid. Its R- group contains only hydrogen and carbon atoms. Predict the behavior of this amino acid.

An amino acid has an R- group that is positively charged at cellular pH. Which of the following categories would best describe it?

You are studying a protein that is shaped like a doughnut. The shape is a function of which levels) of protein structure?

Which of the following is not a major functional class of proteins?

Which of the following statements about the peptide- bonded backbone is correct?

If the primary structure of a protein is incorrect

Consider the HIV enzyme called protease. The amino acid residues at the active site are highly hydrophobic. In designing a drug that would bind to the active site and jam it, researchers should use which type of molecule?

Which is not a role proteins play in organisms?

A peptide bond is

An amino acid has an R- group that is negatively charged at cellular pH. Which of the following categories would best describe it?

You've just sequenced a new protein found in mice and observe that sulfur- containing cysteine residues occur at regular intervals. What is the significance of this finding?

At the pH found in cells about 7.0) , what happens to the carboxyl group on an amino acid?

Which one of the following is not a component of each monomer used to make proteins?

Which of the following statements about peptides is correct?

An enzyme has a total of four active sites. When you denature the molecule and study its composition, you find that each active site occurs on a different polypeptide. Which of the following hypotheses does this observation support?

The aquaporin family of proteins plays a major role in the transport of water all over the body. During the folding process of these proteins, a- helices start forming as

Which one of the following is not a component of each monomer used to make proteins?