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Chapter 3
Protein Structure and Function
Biological Science, 3e (Freeman)
1) Which is not a role proteins play in organisms?
A) store genetic information
B) movement and shape changes
C) chemical signaling
D) structural support
Answer: A
Diff: 1
Reference: Section 3.1
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
2) Three important functions of proteins are cell
A) wall composition, cushioning, and membrane fluidity.
B) movement, signaling, and reaction catalysis.
C) information coding, conversion, and transfer.
Answer: B
Diff: 1
Reference: Section 3.1
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
3) In experiments that successfully simulate chemical evolution, why must at least some small,
reduced molecules be present?
A) They act as proton donors in acid-base reactions.
B) They act as proton acceptors in acid-base reactions.
C) They act as electron acceptors in redox reactions.
D) They act as electron donors in redox reactions.
Answer: D
Diff: 2
Reference: Section 3.2
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
4) What is the process component of the theory of chemical evolution?
A) Acid-base reactions resulted in the formation of large, complex organic molecules.
B) Kinetic energy was transformed into chemical energy.
C) During polymerization reactions, hydrolysis competed with condensation.
D) The process occurred at black smokers, in the atmosphere and oceans, and in outer space.
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Answer: B
Explanation: B) This is a great question to use in class to remind students of the big picture of
chemical evolution.
Diff: 2
Reference: Section 3.2
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
5) What is the pattern component of the theory of chemical evolution?
A) Both heat and electrical discharges are required for chemical evolution to occur.
B) Most chemical evolution occurred at black smokers.
C) The process occurred at black smokers, in the atmosphere and oceans, and in outer space.
D) Increasingly complex carbon-containing molecules formed early in Earth history.
Answer: D
Diff: 2
Reference: Section 3.2
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
6) Which of the following best describes the first living entity–the one responsible for the origin
of life?
A) It was a monomer.
B) It was large and extremely complex.
C) It could make a copy of itself.
Answer: C
Diff: 1
Reference: Section 3.2
Question Type: Factual
Skill/Objective: Recall
Source/Use: Exam or In-Class
7) In interstellar space, millions of ice-encrusted dust particles contain simple carbon-containing
compounds. When particles like these are exposed to solar radiation, more complex organic
molecules form on the surfaces of the dust. What is the significance of these findings?
A) Chemical evolution occurs only in outer space and was not possible on Earth.
B) Life began in outer space.
C) Life exists in outer space.
D) Chemical evolution occurs readily in outer space.
Answer: D
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Diff: 2
Reference: Section 3.2
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
8) Consider the experiment that Stanley Miller did to simulate chemical evolution. Recall that a
glass flask held the reduced gases NH3, CH4, and H2 and that the gases were exposed to
electrical sparks. What is the null hypothesis in the experiment?
A) Chemical evolution does not occur.
B) Chemical evolution requires the presence of reduced molecules.
C) Chemical evolution requires continuous heating.
D) Chemical evolution requires a source of kinetic energy.
E) Chemical evolution occurs only on Earth.
Answer: A
Diff: 2
Reference: Section 3.2
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
9) What prediction does the chemical evolution hypothesis make?
A) Nothing will happen–meaning that no new types of molecules will appear.
B) Molecules with carbon-carbon bonds will form.
C) Proteins will be produced before any other macromolecule.
D) A self-replicating macr
macromolecule.
Answer: B
Diff: 2
Reference: Section 3.2
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
10) Suppose that Miller repeated his chemical evolution experiment but without a source of
electrical sparks. What would be the purpose?
A) to test if kinetic energy is required for chemical evolution
B) to test the hypothesis that reduced molecules are required for chemical evolution
C) to test the hypothesis that both reduced molecules and kinetic energy are required for
chemical evolution
D) to make sure that the glassware had not been contaminated, and that any new molecules
found were actually produced by chemical evolution
Answer: A
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Diff: 2
Reference: Section 3.2
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
11) Which one of the following is not a component of each monomer used to make proteins?
A) a phosphorous atom, P
B) an amino functional group, NH2
C) a side chain, R
D) a carboxyl group, COOH
Answer: A
Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
12) Amino acid side chains (R groups) with what characteristic(s) dissolve best in water?
A) small sizes and simple structures
B) at least one ring structure
C) polarity or charged structures
D) the presence of sulfur
Answer: C
Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
13) Why are polymerization reactions endergonic?
A) They reduce entropy.
B) They release heat, making the reactant monomers move faster.
C) Because the condensation and hydrolysis reactions are equally spontaneous.
D) Because polymers are energetically more stable and have lower potential energy than
monomers do.
Answer: A
Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
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14) At the pH found in cells (about 7.0), what happens to the amino group on an amino acid?
A) It acts as a base and gains a proton, giving it a positive charge.
B) It acts as an acid and loses a proton, giving it a negative charge.
C) It is reduced, and tends to act as an electron donor in redox reactions.
D) It remains neutral, like water, and does not have a charge.
Answer: A
Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
15) 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 acts as an acid and loses a proton, giving it a negative charge.
C) It is oxidized, and tends to act as an electron acceptor in redox reactions.
D) It remains neutral, like water, and does not have a charge.
Answer: B
Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
16) How does the structure of an amino acid enable it to play its most important roles in cells?
A) 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).
B) Because both carboxyl and amino groups are present, polymerization is exergonic. In
addition, the presence of a side chain makes the molecule water soluble.
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 each amino acid contains a variety of functional groups, they can participate in a
wide variety of chemical reactions.
Answer: C
Explanation: C) Some may prefer to use this question in class only, because it involves
consideration of a great deal of information.
Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
17) Which of the following involves an increase in entropy?
A) hydrolysis
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B) condensation
C) polymerization
D) chemical evolution
Answer: A
Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
18) In solution, why do hydrolysis reactions occur more readily than condensation reactions?
A) Hydrolysis increases entropy and is exothermic.
B) Hydrolysis raises G, or Gibbs free energy.
C) Hydrolysis decreases entropy and is exothermic.
D) Hydrolysis increases entropy and is endothermic.
Answer: A
Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
19) 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 hydrophobic.
B) It is hydrophilic.
C) Relative to the amino acids found in organisms, its interactions with water will be
intermediate.
D) Relative to the amino acids found in organisms, its interactions with water will be very high.
Answer: A
Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
20) An isomer of a particular molecule is
A) a molecule that has the same structure as the target molecule, but a different formula.
B) a molecule that is the same except it has an additional side group.
C) another copy of the same molecule.
D) a molecule that has the same formula, but a different structure.
Answer: D
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Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
21) A peptide bond is
A) an ionic bond, not a covalent one.
B) a triple covalent bond.
C) a particularly stable, planar covalent bond.
D) a particularly unstable covalent bond.
Answer: C
Diff: 2
Reference: Section 3.3
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
22) 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) primary
B) secondary
C) tertiary
D) quaternary
Answer: A
Diff: 1
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
23) Which of the following best describes primary structure in proteins?
A) It is the number of amino acids present in the complete protein.
B) It is the number of peptide bonds in the complete protein.
C) It is the sequence of amino acids in the complete protein.
D) It is the number of -helices and -pleated sheets in the complete protein.
Answer: C
Diff: 1
Reference: Section 3.4
Question Type: Factual
Skill/Objective: Recall
Source/Use: Exam or In-Class
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24) You are studying a protein that is shaped like a doughnut. The shape is a function of which
level(s) of protein structure?
A) primary only
B) secondary only
C) tertiary only
D) secondary and tertiary only
E) primary, secondary, and tertiary
Answer: E
Diff: 2
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
25) 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 is subject to allosteric regulation.
B) The enzyme requires a cofactor to function normally.
C) The protein's structure is affected by temperature and pH.
D) The protein has quaternary structure.
Answer: D
Diff: 3
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
26) Which of the following observations is the strongest argument in favor of the hypothesis that
protein structure and function are correlated?
A) Proteins function best at certain temperatures.
B) Proteins have four distinct levels of structure and many functions.
C) Enzymes tend to be globular in shape.
D) Denatured (unfolded) proteins do not function normally.
Answer: D
Explanation: D) This is a good in-class discussion question to get students to apply their
knowledge about protein structure and function.
Diff: 2
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
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27) 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) Cysteine residues are required for the formation of -helices and -pleated sheets.
B) It will be important to include cysteine in the diet of the mice.
C) Cysteine residues are involved in disulfide bridges that help form tertiary structure.
D) Cysteine causes bends, or angles, to occur in the tertiary structure of proteins.
Answer: C
Diff: 2
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
28) Recent technological advances have made it more feasible than ever to work out the threedimensional structure of proteins. There is intense interest in this research field, called structural
biology. Why?
A) Understanding structure should help us understand function.
B) Understanding structure can help in the design of drugs that alter the function of certain
proteins.
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.
Answer: D
Diff: 2
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
29) 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 sections of the polypeptide backbone
D) hydrogen bonds between side chains of amino acids
Answer: C
Diff: 2
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
30) A series of hydrophobic side chains will congregate together as a protein folds in an aqueous
solution and be stabilized by
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A) disulfide bonds.
B) van der Waals interaction.
C) hydrogen bonds.
D) quaternary structure bonds.
Answer: B
Diff: 2
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
31) If the primary structure of a protein is incorrect
A) the secondary structure will be correct.
B) the tertiary structure will be correct.
C) any quaternary structure will be correct.
D)
Answer: D
Explanation: D) This question goes to the hierarchical structure of protein folding (purple
thematic text) and introduces prion discussion–folding probability, etc.
Diff: 1
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
32) 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 a structural protein that is involved in cell-to-cell adhesion.
B) It is probably an enzyme that works through allosteric regulation.
C) It is probably an enzyme that works through competitive inhibition.
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.
Answer: B
Diff: 3
Reference: Section 3.5
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
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33) Which of the following is not true when comparing an uncatalyzed reaction to the same
reaction with a catalyst?
A) The catalyzed reaction will be faster.
B) The catalyzed reaction will have a different ∆G.
C) The catalyzed reaction will have lower activation energy.
D) The catalyzed reaction will not consume any of the catalyst.
Answer: B
Diff: 3
Reference: Section 3.5
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
34) Which of the following would be an example of a cofactor?
A) an enzyme active site that contains an -helix
B) the nonprotein heme group in a hemoglobin molecule
C) the disulfide bridge that forms between cysteine residues
D) a -pleated sheet hidden on the inside of a protein's tertiary structure
Answer: B
Diff: 2
Reference: Section 3.5
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
35) In cells, the activity of enzymes is often regulated by other molecules. Why is this necessary?
A) because all enzymes require some help from another molecule to function correctly
B) because other molecules are necessary to prevent enzymes from denaturing
C) because each enzyme has multiple functions
D) because it is unlikely that all reaction products are required all of the time
Answer: D
Diff: 3
Reference: Section 3.5
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
36) Several of the molecules called vitamins act as enzyme cofactors. Vitamin deficiencies cause
disease. What is the most direct explanation for this?
A) Vitamins combine with nonprotein molecules to delay the onset of disease.
B) If cofactors are missing, enzymes cannot function properly, and important reaction products
will be absent from cells.
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C) Normal regulation cannot occur in the absence of cofactors. As a result, all enzymes will
function all of the time.
D) Cofactors inhibit enzymes found in disease-causing bacteria and viruses. When cofactors are
absent, these disease-causing agents multiply.
Answer: B
Diff: 2
Reference: Section 3.5
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
37) You've discovered an enzyme that can catalyze two different chemical reactions. Which of
the following is most likely to be correct?
A) The enzyme contains both -helices and -pleated sheets.
B) The enzyme is subject to both competitive inhibition and allosteric regulation.
C) Two types of allosteric regulation occur: The binding of one molecule activates the enzyme,
while the binding of a different molecule inhibits it.
D) Either the enzyme has two distinct active sites, or the reactants involved in the two reactions
are very similar in size and shape.
Answer: D
Diff: 2
Reference: Section 3.5
Question Type: Conceptual/Applied
Skill/Objective: Data Interpretation
Source/Use: Exam or In-Class
38) HIV is the virus that causes AIDS. In the mid-1990s, researchers discovered an enzyme in
HIV called protease. Once the enzyme's structure was known, researchers began looking for
drugs that would fit into the active site and block it. If this strategy for stopping HIV infections
were successful, it would be an example of what phenomenon?
A) vaccination
B) poisoning
C) allosteric regulation
D) competitive inhibition
Answer: D
Diff: 2
Reference: Section 3.5
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
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39) 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) hydrophobic
B) polar
C) charged
D) acidic
Answer: A
Diff: 2
Reference: Section 3.5
Question Type: Conceptual/Applied
Skill/Objective: Methods and Experimental Design
Source/Use: Exam or In-Class
40) When, and by whom, was the lock-and-key model of enzyme specificity developed?
A) 1894 by Fischer
B) 1894 by Miller
C) 1936 by Fischer
D) 1956 by Fischer
E) 1974 by Haldane and Oparin
Answer: A
Explanation: A) Gives a sense of history
Diff: 2
Reference: Section 3.5
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
41) Which one of the following is not a component of each monomer used to make proteins?
A) an iron atom, Fe
B) an amino functional group, NH2
C) a side chain, R
D) a carboxyl group, COOH
Answer: A
Diff: 2
Reference: Section 3.5
Question Type: Conceptual/Applied
Skill/Objective: General
Source/Use: Exam or In-Class
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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 structure of proteins in order to understand what they do and how
they do it. One of the most powerful techniques in existence today is X-ray 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 -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.]
42) How many times does the protein in Figure 3.1 cross the cell membrane?
A) 1
B) 3
C) 4
D) 7
Answer: D
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Explanation: D) Can the student decipher a two-dimensional drawing of a three-dimensional
structure? Students of biology will be presented with a variety of formats for analysis, and their
success depends upon their being able to interpret schematic representations. This question is
probably too simple for an exam, but could stimulate some class discussion. For example, why
would there need to be seven transmembrane segments? Are there other proteins with multiple
transmembrane segments?
Diff: 1
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: Research Literature Based
Source/Use: Exam or In-Class
43) 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.
Answer: A
Explanation: A) Does the student know that protein sequences are typically read from aminoterminus to carboxy-terminus?
Diff: 1
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: Research Literature Based
Source/Use: Exam or In-Class
44) 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) aspartic acid
C) cysteine
D) glycine
Answer: C
Diff: 1
Reference: Section 3.4
Question Type: Recall
Skill/Objective: Research Literature Based
Source/Use: Exam
45) What is the location of the C-terminus of the protein in Figure 3.1?
A) extracellular
B) cytoplasm
C) embedded within the membrane
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D) nucleus
Answer: B
Explanation: B) Does the student know that protein sequences are typically read from aminoterminus to carboxy-terminus?
Diff: 1
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: Research Literature Based
Source/Use: Exam
46) Refer to Figure 3.1. Which level of structure is being maintained by the disulfide bond?
A) primary
B) secondary
C) tertiary
D) quaternary
Answer: C
Explanation: C) Student should realize from the opening paragraph that this protein has no
quaternary structure and that disulfide bonds most often contribute to tertiary structure.
Diff: 2
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: Research Literature Based
Source/Use: Exam or In-Class
47) Which term best describes the protein in Figure 3.1?
A) peripheral
B) external
C) internal
D) integral
Answer: D
Explanation: D) Student should recognize the difference between integral and peripheral
membrane proteins. This whole sequence of questions on the structure of rhodopsin would make
an excellent in-class discussion on the major features of an important protein.
Diff: 2
Reference: Section 3.4
Question Type: Conceptual/Applied
Skill/Objective: Research Literature Based
Source/Use: Exam or In-Class
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