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Sample Test

 Chapter 03

Exam
MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.
1) Proteins in biological systems _____. 1)
A) may be high-energy intermediates (for example, ATP)
B) may be enzymes that catalyze reactions
C) store genetic information
D) link together to form the plasma membrane
2) The functional groups of amino acids _____. 2)
A) are identical in different types of amino acids
B) only contain C, H, and O
C) are always charged
D) may be hydrophobic or hydrophilic
3) In experiments that successfully simulate chemical evolution, why must at least some small,
reduced molecules be present?
3)
A) They act as proton donors in acid-base reactions.
B) They act as electron acceptors in redox reactions.
C) They act as proton acceptors in acid-base reactions.
D) They act as electron donors in redox reactions.
4) What is the process component of the theory of chemical evolution? 4)
A) The process occurred at black smokers, in the atmosphere and oceans, and in outer space.
B) Acid-base reactions resulted in the formation of large, complex organic molecules.
C) During polymerization reactions, hydrolysis was completed with condensation.
D) Kinetic energy was transformed into chemical energy.
5) What is the pattern component of the theory of chemical evolution? 5)
A) The process occurred at black smokers, in the atmosphere and oceans, and in outer space.
B) Both heat and electrical discharges are required for chemical evolution to occur.
C) Increasingly complex carbon-containing molecules formed early in Earth history.
D) Most chemical evolution occurred at black smokers.
6) Which of the following best describes the first living entity? 6)
A) It was large and extremely complex.
B) It could make a copy of itself.
C) It was a monomer.
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?
7)
A) Chemical evolution occurs only in outer space and was not possible on Earth.
B) Life began in outer space.
C) Chemical evolution can occur in outer space.
D) Life exists in outer space.
1
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?
8)
A) Chemical evolution requires the presence of reduced molecules.
B) Chemical evolution requires a source of kinetic energy.
C) Chemical evolution requires continuous heating.
D) Chemical evolution does not occur.
E) Chemical evolution occurs only on Earth.
9) What prediction does the chemical evolution hypothesis make? 9)
A) Proteins will be produced before any other macromolecule.
B) Nothing will happen—meaning that no new types of molecules will appear.
C) A self-replicating macromolecule cannot exist􀁎all need interaction with another
macromolecule.
D) Molecules with carbon-carbon bonds will form.
10) Suppose that Miller repeated his chemical evolution experiment but without a source of electrical
sparks. What would be the purpose?
10)
A) to test if electrical energy is required for chemical evolution
B) to make sure that the glassware had not been contaminated, and that any new molecules
found were actually produced by chemical evolution
C) to test the hypothesis that both reduced molecules and electrical energy are required for
chemical evolution
D) to test the hypothesis that reduced molecules are required for chemical evolution
11) Which one of the following is not a component of each monomer used to make proteins? 11)
A) a side chain, R B) a phosphorus atom, P
C) an amino functional group, NH2 D) a carboxyl group, COOH
12) What aspects of amino acid structure vary among different amino acids? 12)
A) the presence of a central C atom
B) the long carbon-hydrogen tails of the molecule
C) the components of the R-group
D) the glycerol molecule that forms the backbone of the amino acid
13) Why are polymerization reactions endergonic? 13)
A) The condensation and hydrolysis reactions are equally spontaneous.
B) They release heat, making the reactant monomers move faster.
C) Polymers are energetically more stable and have lower potential energy than monomers do.
D) They reduce entropy.
14) At the pH found in cells (about 7.0), what happens to the amino group on an amino acid? 14)
A) It is reduced, and tends to act as an electron donor in redox reactions.
B) It acts as an acid and loses a proton, giving it a negative charge.
C) It acts as a base and gains a proton, giving it a positive charge.
D) It remains neutral, like water, and does not have a charge.
2
15) At the pH found in cells (about 7.0), what happens to the carboxyl group on an amino acid? 15)
A) It is oxidized, and tends to act as an electron acceptor in redox reactions.
B) It acts as an acid and loses a proton, giving it a negative charge.
C) It remains neutral, like water, and does not have a charge.
D) It acts as a base and gains a proton, giving it a positive charge.
16) How does the structure of an amino acid enable it to play its most important roles in cells? 16)
A) The presence of carboxyl and amino groups gives it the ability to form peptide bonds, and its
side chain gives it unique chemical properties.
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) Because both carboxyl and amino groups are present, polymerization is exergonic. In
addition, the presence of a side chain makes the molecule water soluble.
D) Because each amino acid contains a variety of functional groups, they can participate in a
wide variety of chemical reactions.
17) Which of the following involves an increase in entropy? 17)
A) chemical evolution B) condensation
C) polymerization D) hydrolysis
18) In solution, why do hydrolysis reactions occur more readily than condensation reactions? 18)
A) Hydrolysis increases entropy and is exergonic.
B) Hydrolysis increases entropy and is endergonic.
C) Hydrolysis decreases entropy and is exergonic.
D) Hydrolysis raises G, or Gibbs free energy.
19) Suppose you discovered a new amino acid. Its R-group contains only hydrogen and carbon atoms.
Predict the behavior of this amino acid.
19)
A) Relative to the amino acids found in organisms, its interactions with water will be very high.
B) Relative to the amino acids found in organisms, its interactions with water will be
intermediate.
C) It is hydrophilic.
D) It is hydrophobic.
20) You disrupt all hydrogen bonds in a protein. What level of structure will be preserved? 20)
A) quaternary structure B) primary structure
C) tertiary structure D) secondary structure
21) A peptide bond _____. 21)
A) forms the primary structure of proteins
B) forms between the functional groups of different amino acids
C) forms between the central carbon and the amino group of a single amino acid
D) does not play a role in maintaining the tertiary structure of proteins
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?
22)
A) tertiary B) quaternary C) primary D) secondary
3
23) You determine the amino acid sequence of a protein and find it contains a long sequence of
methionine, followed by a long sequence of proline, followed by a long sequence of valine. Using
these data you predict the sequence of this protein’s secondary structure will be _____.
23)
A) beta sheets, then a region of no secondary structure, then beta sheets
B) beta sheets, then a region of no secondary structure, then alpha helices
C) alpha helices, then a region of no secondary structure, then beta sheets
D) alpha helices, then a region of no secondary structure, then alpha helices
24) You are studying a protein that is shaped like a doughnut. The shape is a function of which level(s)
of protein structure?
24)
A) primary, secondary, and tertiary
B) tertiary only
C) secondary only
D) secondary and tertiary only
E) primary only
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?
25)
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.
26) Which of the following observations is the strongest argument in favor of the hypothesis that
protein structure and function are correlated?
26)
A) Proteins have four distinct levels of structure and many functions.
B) Denatured (unfolded) proteins do not function normally.
C) Enzymes tend to be globular in shape.
D) Proteins function best at certain temperatures.
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?
27)
A) Cysteine residues are involved in disulfide bridges that help form tertiary structure.
B) Cysteine residues are required for the formation of 􀎅-helices and 􀎆-pleated sheets.
C) Cysteine causes bends, or angles, to occur in the tertiary structure of proteins.
D) It will be important to include cysteine in the diet of the mice.
28) Aquaporins are proteins that control the passage of water molecules across the cell membrane. The
protein forms a pore, or opening, in the membrane. You isolate what you think are two different
molecules of aquaporin, and determine that one of the proteins has a larger pore diameter than the
second. Which of the following do you conclude?
28)
A) These two forms of aquaporin will have identical sequences of amino acids.
B) These molecules both can’t have aquaporin because all proteins that do the same type of job
(such as catalyze a reaction) have the exact same 3-D structure.
C) You will have to sequence the proteins to compare their primary structure, because it should
have no effect on pore diameter.
D) These two forms of aquaporin will have different sequences of amino acids.
4
29) What type of interaction is directly responsible for the formation of secondary structure? 29)
A) hydrogen bonds between sections of the polypeptide backbone
B) peptide bonds between nonadjacent amino acids
C) hydrogen bonds between side chains of amino acids
D) peptide bonds between adjacent amino acids
30) A series of hydrophobic side chains will congregate together as a protein folds in an aqueous
solution and be stabilized by _____.
30)
A) quaternary structure bonds B) van der Waals interaction
C) disulfide bonds D) hydrogen bonds
31) How does primary protein structure affect the function of protein enzymes? 31)
A) Substrates interact with hydrophobic R-groups at any region of the enzyme.
B) Substrates interact with R-groups at the enzyme’s external surface.
C) Substrates interact with R-groups at the enzyme’s active site.
D) Substrates permanently bind to R-groups at the enzyme’s active site.
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?
32)
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 a cell membrane transport protein—like an ion channel.
D) It is probably an enzyme that works through competitive inhibition.
E) It is probably a structural protein found in cartilage or skeletal tissue.
33) Which of the following is true when comparing an uncatalyzed reaction to the same reaction with
a catalyst?
33)
A) The catalyzed reaction will have higher activation energy.
B) The catalyzed reaction will have the same 􀇊G.
C) The catalyzed reaction will be slower.
D) The catalyzed reaction will consume all of the catalyst.
34) Which of the following would be an example of a cofactor? 34)
A) a 􀎆-pleated sheet hidden on the inside of a protein’s tertiary structure
B) the disulfide bridge that forms between cysteine residues
C) an enzyme active site that contains an 􀎅-helix
D) the nonprotein heme group in a hemoglobin molecule
35) In cells, the activity of enzymes is often regulated by other molecules. Why is this necessary? 35)
A) because each enzyme has multiple functions
B) because it is unlikely that all reaction products are required all of the time
C) because other molecules are necessary to prevent enzymes from denaturing
D) because all enzymes require some help from another molecule to function correctly
5
36) Several of the molecules called vitamins act as enzyme cofactors. Vitamin deficiencies cause
disease. What is the most direct explanation for this?
36)
A) Vitamins combine with nonprotein molecules to delay the onset of disease.
B) Cofactors inhibit enzymes found in disease-causing bacteria and viruses. When cofactors are
absent, these disease-causing agents multiply.
C) Normal regulation cannot occur in the absence of cofactors. As a result, all enzymes will
function all of the time.
D) If cofactors are missing, enzymes cannot function properly, and important reaction products
will be absent from cells.
37) You’ve discovered an enzyme that can catalyze two different chemical reactions. Which of the
following is most likely to be correct?
37)
A) The enzyme is subject to both competitive inhibition and allosteric regulation.
B) The enzyme contains both 􀎅-helices and 􀎆-pleated sheets.
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.
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?
38)
A) allosteric regulation B) competitive inhibition
C) poisoning D) vaccination
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?
39)
A) polar B) hydrophobic C) acidic D) charged
40) The lock-and-key analogy for enzymes applies to the _____. 40)
A) specificity of enzymes interacting with ions
B) specificity of enzymes binding to their substrate
C) specificity of enzymes interacting with water
D) specificity of enzyme tertiary subunits joining to form a quaternary structure
E) specificity of enzyme primary, secondary, and tertiary structure
6
41) You collect data on the effect of pH on the function of the enzyme catalase in human cells. Which
of the following graphs would you expect?
41)
A) B)
C) D)
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
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? 42)
A) 1 B) 3 C) 4 D) 7
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?
43)
A) M-N-G
B) A-P-A
C) It doesn’t matter, since the protein has no polarity or directionality.
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?
44)
A) cytosine B) aspartic acid C) glycine D) cysteine
8
45) What is the location of the C-terminus of the protein in Figure 3.1? 45)
A) nucleus B) extracellular
C) embedded within the membrane D) cytoplasm
46) Refer to Figure 3.1. Which level of structure is being maintained by the disulfide bond? 46)
A) primary B) secondary C) quaternary D) tertiary
47) Which term best describes the type of membrane protein in Figure 3.1? 47)
A) internal B) peripheral C) external D) integral
9
Answer Key
Testname: UNTITLED2
1) B
2) D
3) D
4) D
5) C
6) B
7) C
8) D
9) D
10) A
11) B
12) C
13) D
14) C
15) B
16) A
17) D
18) A
19) D
20) B
21) A
22) C
23) C
24) A
25) D
26) B
27) A
28) D
29) A
30) B
31) C
32) B
33) B
34) D
35) B
36) D
37) D
38) B
39) B
40) B
41) C
42) D
43) A
44) D
45) D
46) D
47) D
10

 

Chapter 04

Exam
MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.
1) Nucleic acids are polymers made up of which of the following monomers? 1)
A) nucleotides B) amino acids
C) sugars D) nitrogenous bases
2) What is the difference between a ribonucleotide and a deoxyribonucleotide? 2)
A) Ribonucleotides contain a sugar with five carbon atoms.
B) Ribonucleotides contain a phosphate group.
C) Ribonucleotides have a hydrogen atom on the 1 carbon of their sugar subunit.
D) Ribonucleotides have a hydroxyl group on the 2 carbon of their sugar subunit.
3) What is/are the variable structure(s) of a nucleotide? 3)
A) the sugar and the base B) the base
C) the phosphate group D) the sugar
4) Which of the following includes all of the pyrimidines found in RNA and/or DNA? 4)
A) cytosine and thymine B) cytosine, uracil, and guanine
C) cytosine, uracil, and thymine D) cytosine and uracil
5) When nucleotides polymerize to form a nucleic acid _____. 5)
A) hydrogen bonds form between the bases of two nucleotides
B) a hydrogen bond forms between the sugar of one nucleotide and the phosphate of a second
C) covalent bonds form between the bases of two nucleotides
D) a covalent bond forms between the sugar of one nucleotide and the phosphate of a second
6) Some viruses consist only of a protein coat surrounding a nucleic acid core. If you wanted to
radioactively label the nucleic acids separately from the protein, you would use _____.
6)
A) radioactive phosphorus B) radioactive sulfur
C) radioactive nitrogen D) radioactive carbon
7) Compare proteins to nucleic acids. Which of the following is true? 7)
A) Both have primary and secondary structure.
B) Both contain sulfur.
C) Monomers of both contain phosphorus.
D) Both take on structural roles in the cell.
8) DNA double helices are soluble in water but insoluble in alcohol. How do these physical
properties reflect the chemical structure of the molecule?
8)
A) The charged phosphate groups and sugars of DNA “like” to interact with polar water
molecules.
B) The charged R-groups of DNA “like” to interact with polar water molecules.
C) The purine and pyrimidine bases “like” to interact with polar water molecules.
D) The 5 prime to 3 prime polarity of DNA make it soluble in water but not in alcohol.
1
9) Nucleic acids have a definite polarity, or directionality. Stated another way, one end of the
molecule is different from the other end. How are these ends described?
9)
A) One end has one phosphate group; the other end has two phosphate groups.
B) One end contains a nitrogenous base; the other end lacks it.
C) One end has an unlinked 3 carbon; the other end has an unlinked 5 carbon.
D) One end has a hydroxyl group on the 2 carbon; the other end has a hydrogen atom on the 2
carbon.
10) What feature of mononucleotides provides the energy needed for polymerization when nucleic
acids are formed?
10)
A) their nitrogenous bases B) their phosphate groups
C) their methyl groups D) their sugar groups
11) What is gel electrophoresis used for? 11)
A) to identify the first self-replicating molecule that formed during chemical evolution
B) to separate the two helices that make up the DNA double helix
C) to separate macromolecules by size or charge
D) to denature proteins for further analysis
12) You have a polymer of DNA with 10 adenine bases followed by 10 cytosine bases. If that strand
bonded to a strand of 20 thymine bases, how would the double helix shape vary from a typical
DNA double helix?
12)
A) The width of the double helix would vary as you moved down the strand.
B) The double helix would be shorter than normal.
C) One strand of the double helix would be longer than the other strand.
D) The double helix would be longer than normal.
13) Why is it that RNA can catalyze reactions but DNA cannot? 13)
A) The sugar of RNA is much more reactive than the sugar of DNA.
B) The primary structure of RNA is fundamentally different than the primary structure of DNA.
C) The bases of RNA are much more reactive than the bases of DNA.
D) The phosphate groups of RNA are much more reactive than the phosphate groups of DNA.
14) Which of these scientists was not directly involved in the discovery of DNA’s structure? 14)
A) Francis Crick
B) Sidney Altman
C) Maurice Wilkins
D) James Watson
E) Rosalind Franklin
15) Which of the following best describes DNA’s secondary structure? 15)
A) double parallel helical strands B) beta-pleated sheet
C) double antiparallel helical strands D) turn-loop-turn
16) Which of the following did Watson and Crick already know when they were trying to determine
the structure of DNA?
16)
A) The number of pyrimidines is always larger than the number of purines.
B) The number of cytosines is always the same as the number of adenines.
C) The number of purines is always larger than the number of pyrimidines.
D) The number of purines is always the same as the number of pyrimidines.
E) The number of guanines is always the same as the number of thymines.
2
17) Franklin and Wilkins analyzed DNA by bombarding DNA crystals with X-rays. Their analysis
yielded two numbers that sparked interest, 3.4 nm and 0.34 nm. What is the significance of these
numbers?
17)
A) These numbers tell us there are 10 rungs, or steps, on the DNA “ladder” for every turn of the
helix.
B) It turned out to be just a coincidence.
C) The 10-to-1 ratio signifies that DNA molecules are 10 times longer than they are wide.
D) DNA molecules are 3.4 nm long and 0.34 nm wide.
E) The width of a DNA molecule is 3.4 nm, whereas the width of a nucleotide monomer is 0.34
m.
18) Which of the terms or phrases below apply to both DNA and RNA? 18)
A) shows primary, secondary, tertiary, and quaternary structure
B) is the most common type of organic molecule to catalyze chemical reactions in cells
C) an information-containing structure
D) All of the above apply.
19) RNA and proteins combine in cells to form structures called ribosomes. Ribosomes contain the
active site for peptide bond formation. Based on their chemical structures, do you think protein or
RNA molecules actually form the active site within the ribosome?
19)
A) proteins, because only proteins can catalyze a reaction that involves another protein
B) protein, because RNA cannot catalyze reactions
C) RNA, because proteins cannot catalyze a reaction that involves another protein
D) It could be either, because both molecules have catalytic properties.
20) In the context of chemical evolution, DNA’s structure is interesting because it suggests a possible
copying mechanism. What about DNA’s structure facilitates copying?
20)
A) It has the same number of purines and pyrimidines.
B) DNA always goes from 5 to 3.
C) The nitrogenous bases are located on the inside of the double helix.
D) The strands of the double helix are complementary.
21) Although DNA is the main hereditary material in all life-forms, it lacks one important
characteristic of being a candidate for the first life-form. Why have researchers rejected the idea
that DNA was found in the first life-form?
21)
A) It is not stable enough to have withstood early Earth’s harsh atmosphere.
B) Because it has only four different bases, it does not carry enough information; therefore, it
cannot adapt and evolve.
C) It does not function as a catalyst.
D) The type of sugar found in DNA is much too complicated to have been present early in
Earth’s history.
22) You isolate what you think is DNA from a tissue sample. Which of the following will verify that
you do, indeed, have DNA (rather than some other type of molecule)?
22)
A) You determine the molecule has carbon-carbon bonds.
B) You determine the molecule contains nitrogen and phosphorus.
C) You determine the molecule has primary and secondary structure.
D) None of answers A-C will verify that the isolated molecule is DNA.
3
23) Which of the following is a difference between RNA and DNA? 23)
A) One contains ribose sugar and the other contains a deoxyribose sugar.
B) One contains uracil and the other does not.
C) One is made from nucleotide monomers and the other one is not.
D) One is typically single stranded and the other is typically triple stranded.
24) Why do researchers think the first self-replicating molecule was RNA? 24)
A) RNA has the capacity to provide a template and is known to catalyze reactions (although no
existing self-replicating molecules of RNA have been discovered).
B) RNA is the only type of molecule that can catalyze a chemical reaction.
C) Fossil evidence of such a molecule was recently discovered.
D) Self-replicating molecules of RNA exist today, in human cells.
25) Recall the Bartel lab group experiment to create a ribozyme from scratch. If they had created exact
copies of each ribozyme (rather than creating copies with a few differences), what would have been
the most likely result?
25)
A) The ribozymes would have become less efficient with each round of selection.
B) The ribozymes would have stopped catalyzing reactions after just a few rounds of selection.
C) The ribozymes would have become more efficient with each round of selection.
D) The ribozymes would have stayed the same with each round of selection.
26) Which one of the following is not a way that RNA is seen as intermediate between DNA and
proteins?
26)
A) RNA is composed of nucleotides, but forms tertiary and quaternary structures like a protein.
B) RNA has 5 and 3 termini like DNA, but it also has amino and carboxy termini like protein.
C) RNA contains genetic information like DNA, but is not as stable.
D) RNA can catalyze reactions, but not as well as can proteins.
27) Bartel’s research group showed that an RNA replicase ribozyme could be created by _____. 27)
A) carefully synthesizing a novel ribozyme monomer by monomer based on the sequence of
known ribozymes
B) starting with random components and allowing selection to result in molecules that were
better and better at replicating
C) creating large numbers of random RNA segments and testing each one to see if any replicase
activity was present
D) examining protein replicases and reverse-engineering an RNA molecule capable of doing the
same job
28) The work of Bartel’s group on the ribozyme RNA replicase supports which conclusion? 28)
A) An RNA world could produce molecules that could self-replicate.
B) Life cannot come from nonlife.
C) Natural selection does not work unless humans are present to help it.
D) DNA must have come before RNA.
4
Use the following information when answering the corresponding question(s).
Shu-ichi Nakano reported in Science in February 2000 that “The RNA enzyme (ribozyme) from hepatitis delta virus catalyzes
self-cleavage of a . . . [chemical] . . . bond.” This reaction is inherently slow due to the formation of an unfavorable negative
charge on the ribozyme. The author goes on to show that this self-cleavage is made faster by joining it with an acid-base
reaction that neutralizes the negative charge. Nakano’s model describes a positively charged cytosine base on the ribozyme
acting as the acid, and magnesium hydroxide acting as the base. Specifically, the cytosine donates its proton (H+) to
neutralize the unstable negative charge that would have formed on the ribozyme.
29) Is Nakano’s quote from Science consistent with the textbook’s claim that RNA is a good candidate
for the first life-form?
29)
A) yes B) no
30) Which of the following chemical bonds do you think Nakano is referring to in his quote? 30)
A) peptide B) phosphodiester C) ionic D) glycosidic
31) Refer to Nakano’s quote. What can be inferred about the free-energy profile for the self-cleavage
reaction from the information provided in the paragraph?
31)
A) It must be exothermic. B) It must be endothermic.
C) It must be endergonic. D) It must be exergonic.
32) Refer to Nakano’s quote from Science. If the cytosine is positively charged (+) before self-cleavage,
what would its charge be after self-cleavage?
32)
A) – (negative) B) + (positive)
C) no way to predict D) 0 (neutral)
33) In the acid-base reaction described in the preceding paragraph about Nakano’s research on RNAs,
a proton (H+) is being transferred. What is acting as the proton acceptor?
33)
A) cytosine
B) magnesium hydroxide
C) the virus
D) cytosine, magnesium hydroxide, or the virus
ESSAY. Write your answer in the space provided or on a separate sheet of paper.
34) As Nakano states in the final sentences of his report, “The catalytic strategies described herein . . . could allow
RNA to catalyze . . . peptide bond formation. Such features [of the ribozyme] would enhance the ability of RNA
to evolve and make the transition from an RNA world to a ribonucleoprotein world.” Explain what Nakano
means in this statement, and discuss whether this statement agrees with claims in your textbook regarding the
chemical evolution of RNA and the first life-forms.
5
Answer Key
Testname: UNTITLED3
1) A
2) D
3) A
4) C
5) D
6) A
7) A
8) A
9) C
10) B
11) C
12) A
13) A
14) B
15) C
16) D
17) A
18) C
19) D
20) D
21) C
22) D
23) A
24) A
25) D
26) B
27) B
28) A
29) A
30) B
31) D
32) A
33) B
34) Essay
6