Nucleic Acids and RNA: Comprehensive Exam Study Guide (Chapter 4), Exams of Biochemistry

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1. Nucleic acids are polymers made up of which of the following monomers? A) nucleotides B) sugars C) amino acids D) nitrogenous bases Answer: A Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-1. Sketch a nucleotide, label its three basic parts, and identify the 2', 3', and 5' carbons.

2. What is the difference between a ribonucleotide and a deoxyribonucleotide? A) Ribonucleotides contain a phosphate group. B) Ribonucleotides have a hydroxyl group on the 2 carbon of their sugar subunit. C) Ribonucleotides contain a sugar with five carbon atoms. D) Ribonucleotides have a hydrogen atom on the 1 carbon of their sugar subunit. Answer: B Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-3. Describe the primary, secondary, tertiary, and quaternary structures of RNA, and explain in what ways RNA differs from DNA.

3. Which of the following nitrogenous bases are purines? A) cytosine and uracil B) cytosine and thymine C) cytosine, uracil, and thymine D) adenine and guanine Answer: D Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-1. Sketch a nucleotide, label its three basic parts, and identify the 2', 3', and 5' carbons.

4. Which of the following includes all of the pyrimidines found in RNA and/or DNA? A) cytosine and uracil B) cytosine and thymine C) cytosine, uracil, and thymine

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A) thymine B) adenine C) uracil D) guanine Answer: C Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-3. Describe the primary, secondary, tertiary, and quaternary structures of RNA, and explain in what ways RNA differs from DNA.

6. A nucleotide is made up of which of the following subunits? A) a 5-carbon sugar, a phosphate group, and a nitrogenous base B) a 5-carbon sugar and a phosphate group C) a 5-carbon sugar and a nitrogenous base D) a 5-carbon sugar, an amino group, and an "R-group" Answer: A Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-1. Sketch a nucleotide, label its three basic parts, and identify the 2', 3', and 5' carbons.

7. By convention, the sequence of bases in a nucleic acid is always written in which direction? A) amino to carboxyl B) carboxyl to amino C) 3' → 5' D) 5' → 3' Answer: D Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

8. All organisms have which of the following attributes? A) They can reproduce. B) They can perform metabolism. C) They are composed of cells. D) They can reproduce and they are composed of cells. E) They can reproduce, perform metabolism, and are composed of cells. Answer: E

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Reference: Section 4. Bloom's Level: Remembering

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Answer: B Explanation: B) Some instructors may find this a valuable in-class assessment after explaining gel electrophoresis. Reference: Section 4. Bloom's Level: Remembering

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13. What does it mean when some bands on an autoradiograph are darker than others? A) The concentration of the radioactive molecule in that band is higher. B) This is normal because most of the radioactivity migrates to the same place. C) The experiment failed because the radioactivity should be evenly distributed throughout the gel. D) The darker bands represent larger molecules. Answer: A Explanation: A) This question would make a good in-class assessment of gel electrophoresis. Reference: Section 4. Bloom's Level: Comprehension/Remembering

14. When doing gel electrophoresis, why do researchers add a "ladder" made up of molecules of known size? A) to help the molecules they are studying get through the gel more easily B) to help the researchers identify the size of each molecule after the separation has occurred C) to make sure the radioactivity doesn't interfere with the movement of the molecules that are being studied D) The molecules being studied would not show up without the ladder. Answer: B Explanation: B) This would be a good in-class question to be sure students understand the figures and experiments explained in the text. Reference: Section 4. Bloom's Level: Remembering

15. Which of these scientists was not directly involved in the discovery of DNA's structure? A) James Watson B) Rosalind Franklin C) Sidney Altman D) Francis Crick E) Maurice Wilkins Answer: C Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

16. Which of the following best describes DNA's secondary structure? A) β-pleated sheet B) double parallel helical strands

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17. Why is DNA said to be antiparallel? A) The two strands of DNA are joined together via complementary base pairing such that AT run in the 3'5' direction and CG run in the 5'3' direction. B) The DNA strands twist into a helix conformation once the bases have joined to form major and minor grooves. C) Each strand of the double helix is made up of a sugar phosphate backbone which runs in the 5'3' direction. D) DNA has polarity such that one strand runs in the 3'5' direction and the other in the 5'3' direction. Answer: D Reference: Section 4. Bloom's Level: Comprehension/Applying LOs: Chp2-2. List the unusual properties of water. Explain how these properties relate to the structure of water molecules, and how they make water important for life.

18. Which of the following did Watson and Crick already know when they were trying to determine the structure of DNA? A) The number of purines is always larger than the number of pyrimidines. B) The number of pyrimidines is always larger than the number of purines. C) The number of cytosines is always the same as the number of adenines. D) The number of guanines is always the same as the number of thymines. E) The number of purines is always the same as the number of pyrimidines. Answer: E Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

19. In the secondary structure of DNA, the α-helical twists are organized into A) major and minor grooves. B) large and small grooves. C) major and small grooves. D) large and minor grooves. Answer: A Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

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20. 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? A) It turned out to be just a coincidence. B) DNA molecules are 3.4 nm long and 0.34 nm wide. C) The width of a DNA molecule is 3.4 nm, whereas the width of a nucleotide monomer is 0.34m. D) These numbers tell us there are 10 rungs, or steps, on the DNA "ladder" for every turn of the helix. E) The 10-to-1 ratio signifies that DNA molecules are ten times longer than they are wide. Answer: D Explanation: D) This question would make a good in-class assessment. Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

21. Which factors contributed to the lack of credit often given to Rosalind Franklin in the discovery of the structure of DNA? A) Wilkins showed her photographs to Watson and Crick without her knowledge or permission. B) She died at an early age so her career was shortened. C) She was a woman working in a field dominated by men when sexism was more common. D) All of the above apply. Answer: D Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

22. If DNA is heated to 95°C, the bonds between complementary strands break, resulting in two single strands of DNA. In this process, which bases will separate first because they have less hydrogen bonds between them? A) adenine and cytosine B) adenine and thymine C) guanine and cytosine D) guanine and thymine Answer: B Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

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26. Although DNA is the main hereditary material in all life-forms, it lacks one important characteristic to make it a candidate for the first life-form. Why have researchers rejected the idea that DNA was found in the first life-form? A) It does not function as a catalyst. B) It is not stable enough to have withstood early Earth's harsh atmosphere. C) Because it has only four different bases, it does not carry enough information; therefore, it cannot adapt and evolve. D) The type of sugar found in DNA is much too complicated to have been present early in Earth's history. Answer: A Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-5. Explain why RNA, and not DNA, was probably the first self-replicating molecule, and describe at least one piece of experimental evidence that supports this hypothesis.

27. The "information system" of the cell involves stable genetic information being stored as , which can be used to make a "disposable" (relatively short-lived) copy of this information as. A) RNA; DNA B) DNA; DNA C) DNA; RNA D) RNA; RNA Answer: C Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

28. Why do many researchers consider RNA to be the best candidate for the first life-form? A) It is simple in structure. B) It is capable of self-replication and catalysis. C) It carries more information than any other molecule. D) All of its nucleotide components have been created under laboratory conditions that mimic early Earth. Answer: B Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-5. Explain why RNA, and not DNA, was probably the first self-replicating molecule, and describe at least one piece of experimental evidence that supports this hypothesis.

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29. Which of the following is not a difference between RNA and DNA? A) One is typically single stranded and the other is typically double stranded. B) One contains uracil and the other does not. C) One contains ribose sugar and the other contains deoxyribose sugar. D) One is made from nucleotide monomers and the other is not. Answer: D Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-3. Describe the primary, secondary, tertiary, and quaternary structures of RNA, and explain in what ways RNA differs from DNA.

30. Why is DNA more appropriate than RNA as the information storing molecule of the cell? A) RNA is more stable than DNA and has the ability to catalyze reactions. B) DNA has the ability to catalyze reactions and make proteins. C) RNA has only four different bases and thus cannot carry enough information. D) DNA is far less reactive than RNA, and thus the information sequence is more stable. Answer: D Reference: Section 4.2, 4. Bloom's Level: Remembering LOs: Chp4-3. Describe the primary, secondary, tertiary, and quaternary structures of RNA, and explain in what ways RNA differs from DNA.

31. Hairpins and stem-and-loop patterns make up what part of RNA's structure? A) primary B) secondary C) tertiary D) quaternary Answer: B Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-3. Describe the primary, secondary, tertiary, and quaternary structures of RNA, and explain in what ways RNA differs from DNA.

32. The term ribozyme describes what property of RNA molecules? A) single-stranded B) catalytic C) its shape D) the fact that part of RNA molecules can be double-stranded similar to DNA

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33. Which one of the following is not a way that RNA is seen as intermediate between DNA and proteins? A) RNA contains genetic information like DNA, but is not as stable. B) RNA can catalyze reactions, but not as well as proteins. C) RNA is composed of nucleotides, but forms tertiary and quaternary structures like a protein. D) RNA has 5 and 3 termini like DNA, but it also has amino and carboxy termini like protein. Answer: D Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-3. Describe the primary, secondary, tertiary, and quaternary structures of RNA, and explain in what ways RNA differs from DNA.

34. Bartel's research group showed that an RNA replicase ribozyme could be created by A) carefully synthesizing a novel ribozyme monomer by monomer based on the sequence of known ribozymes. B) creating large numbers of random RNA segments and testing each one to see if any replicase activity was present. C) starting with random components and allowing natural selection to evolve molecules that were better and better at replicating. D) examining protein replicases and reverse-engineering an RNA molecule capable of doing the same job. Answer: C Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-5. Explain why RNA, and not DNA, was probably the first self-replicating molecule, and describe at least one piece of experimental evidence that supports this hypothesis.

35. The work of Bartel's group on the ribozyme RNA replicase supports which conclusion? A) An RNA world could produce molecules that could self-replicate. B) Natural selection does not work unless humans are present to help it. C) DNA must have come before RNA. D) Life cannot come from nonlife. Answer: A Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-5. Explain why RNA, and not DNA, was probably the first self-replicating molecule, and describe at least one piece of experimental evidence that supports this hypothesis.

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Use the following information when answering the corresponding question(s).

Shuichi 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.

36. Is Nakano's quote consistent with the textbook's claim that RNA is a good candidate for the first life-form? A) yes B) no Answer: A Explanation: A) This study describes another catalytic mechanism for RNA polymers. Reference: Section 4. Bloom's Level: Comprehension LOs: Chp4-5. Explain why RNA, and not DNA, was probably the first self-replicating molecule, and describe at least one piece of experimental evidence that supports this hypothesis.

37. Which of the following chemical bonds do you think Nakano is referring to in his quote? A) peptide B) glycosidic C) phosphodiester D) ionic Answer: C Explanation: C) Answer is C since ribozymes are RNA polymers, and the reaction is described as a self-cleavage. Reference: Section 4. Bloom's Level: Comprehension LOs: Chp4-5. Explain why RNA, and not DNA, was probably the first self-replicating molecule, and describe at least one piece of experimental evidence that supports this hypothesis.

38. What can be inferred about the free-energy profile for the self-cleavage reaction from the information provided in the paragraph? A) It must be endergonic.

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and describe at least one piece of experimental evidence that supports this hypothesis.

39. If the cytosine is positively charged (+) before self-cleavage, what would its charge be after self-cleavage? A) + (positive) B) - (negative) C) 0 (neutral) D) no way to predict Answer: B Explanation: B) The cytosine is normally positive because one of its nitrogens is protonated. This is easily accomplished because the structure of the ribozyme perturbs the cytosine just enough to give it a pKa near 7. Thus, it can readily gain or lose a proton at physiological pHs. Reference: Section 4. Bloom's Level: Comprehension LOs: Chp4-1. Sketch a nucleotide, label its three basic parts, and identify the 2', 3', and 5' carbons.

40. In the acid-base reaction described in the preceding paragraph, a proton (H+) is being transferred. What is acting as the proton acceptor? A) cytosine B) magnesium hydroxide C) the virus D) A, B, or C. Any one of these can act as the acceptor. Answer: B Explanation: B) This answer is implied in the statement that magnesium hydroxide is acting as the base. In reality, there are two proton transfers: one from cytosine to a guanine base at position 1 on the ribozyme; the other from a uracil to magnesium hydroxide. Reference: Section 4.1, 9. Bloom's Level: Remembering/Applying LOs: Chp4-1. Sketch a nucleotide, label its three basic parts, and identify the 2', 3', and 5' carbons.

41. 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.

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Answer: Essay Reference: Section 4.1, Introduction Bloom's Level: Analyzing LOs: Chp4-5. Explain why RNA, and not DNA, was probably the first self-replicating molecule, and describe at least one piece of experimental evidence that supports this hypothesis.