Deck 3: Protein Structure and Function

Question 1

In solution, why do hydrolysis reactions occur more readily than condensation reactions?

A) Hydrolysis raises G, or Gibbs free energy.
B) Hydrolysis increases entropy and is exothermic.
C) Hydrolysis decreases entropy and is exothermic.
D) Hydrolysis increases entropy and is endothermic.

Answer 1

B

Question 2

How does the structure of an amino acid enable it to play its most important roles in cells?

A) Because each amino acid contains a variety of functional groups, they can participate in a wide variety of chemical reactions.
B) It can serve a wide variety of functions in a cell, because it contains the atoms most commonly found in organisms C, H, N, and O).
C) The presence of carboxyl and amino groups gives it the ability to form peptide bonds, and its side chain gives it unique chemical properties.
D) Because both carboxyl and amino groups are present, polymerization is exergonic. In addition, the presence of a side chain makes the molecule water soluble.

Answer 2

C

Question 3

An amino acid has an R- group that does not have a positive or a negative charge but has an oxygen atom. Which of the following categories would best describe it?

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

Answer 3

C

Question 4

Which is not a role proteins play in organisms?

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

Question 5

When polymerization of a protein is complete, but the protein is still completely linear, what is the highest level of structure that has been completed?

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

Question 6

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

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

Question 7

Which of the following statements about peptides is correct?

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 8

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

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

Question 9

Three important functions of proteins are cell

A) information coding, conversion, and transfer.
B) movement, signaling, and reaction catalysis.
C) wall composition, cushioning, and membrane fluidity.

Question 10

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

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 11

An amino acid has an R- group that is composed of only carbon and hydrogen atoms. Which of the following categories would best describe it?

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

Question 12

A peptide bond is

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

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

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.

Question 14

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

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

Question 15

Which of the following involves an increase in entropy?

A) polymerization
B) chemical evolution
C) condensation
D) hydrolysis

Question 16

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

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

Question 17

Amino acid side chains R groups) with what characteristics) dissolve best in water?

A) at least one ring structure
B) small sizes and simple structures
C) polarity or charged structures
D) the presence of sulfur

Question 18

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

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 19

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

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

Question 20

Why are polymerization reactions endergonic?

A) They release heat, making the reactant monomers move faster.
B) Because the condensation and hydrolysis reactions are equally spontaneous.
C) Because polymers are energetically more stable and have lower potential energy than monomers do.
D) They reduce entropy.

Question 21

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?

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.

Question 22

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?

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 23

What is the location of the C- terminus of the protein in Figure 3.1?

A) nucleus
B) cytoplasm
C) extracellular
D) embedded within the membrane

Question 24

Identify the location of the disulfide bond in Figure 3.1. What is the name of the amino acids that are forming this bond?

A) cytosine
B) glycine
C) cysteine
D) aspartic acid

Question 25

What type of interaction is directly responsible for the formation of secondary structure?

A) peptide bonds between adjacent amino acids
B) peptide bonds between nonadjacent amino acids
C) hydrogen bonds between side chains of amino acids
D) hydrogen bonds between sections of the polypeptide backbone

Question 26

Which of the following best describes primary structure in proteins?

A) It is the sequence of amino acids in the complete protein.
B) It is the number of a- helices and fi- pleated sheets in the complete protein.
C) It is the number of amino acids present in the complete protein.
D) It is the number of peptide bonds in the complete protein.

Question 27

When, and by whom, was the lock- and- key model of enzyme specificity developed?

A) 1974 by Haldane and Oparin
B) 1894 by Fischer
C) 1956 by Fischer
D) 1894 by Miller
E) 1936 by Fischer

Question 28

Recent technological advances have made it more feasible than ever to work out the three- dimensional structure of proteins. There is intense interest in this research field, called structural biology. Why?

A) Understanding structure can help in the design of drugs that alter the function of certain proteins.
B) Understanding structure should help us understand function.
C) Solving a protein's 3- D structure can lead to a better understanding of how the molecule works-for example, by identifying the active site and determining if there are regulatory sites.
D) All of the above apply.

Question 29

If the primary structure of a protein is incorrect

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 30

A series of hydrophobic side chains will congregate together as a protein folds in an aqueous solution and be stabilized by

A) van der Waals interaction.
B) disulfide bonds.
C) hydrogen bonds.
D) quaternary structure bonds.

Question 31

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

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

Question 32

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.]
How many times does the protein in Figure 3.1 cross the cell membrane?

A) 1
B) 3
C) 4
D) 7

Question 33

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?

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

Question 34

Which of the following observations is the strongest argument in favor of the hypothesis that protein structure and function are correlated?

A) Denatured unfolded) proteins do not function normally.
B) Enzymes tend to be globular in shape.
C) Proteins have four distinct levels of structure and many functions.
D) Proteins function best at certain temperatures.

Question 35

Interactions between side chains R- groups) in a polypeptide are most important in stabilizing which of the following?

A) the secondary structure of a protein
B) a fi- sheet
C) the primary structure of a protein
D) the tertiary structure of a protein
E) an a- helix

Question 36

Refer to Figure 3.1. Which level of structure is being maintained by the disulfide bond?

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

Question 37

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

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

Question 38

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?

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

Question 39

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

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 40

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?

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.