Nucleic Acids and the RNA World: Comprehensive Exam Study Guide, Exams of Chemistry

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Chapter 4: Nucleic Acids and the RNA

WORLD

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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 D) cytosine, uracil, and guanine Answer: C Reference: Section 4. Bloom's Level: Remembering

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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 Reference: Section 4. Bloom's Level: Remembering

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9. What forms the "backbone" of a nucleic acid? A) a chain of sugar and phosphate groups, linked through phosphodiester bonds B) purine and pyrimidine pairs, hydrogen-bonded to each other C) a chain of amino and carboxyl groups, linked via peptide bonds D) a double helix of antiparallel strands Answer: A Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

10. 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? A) One end has a hydroxyl group on the 2 carbon; the other end has a hydrogen atom on the 2 carbon. 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 one phosphate group; the other end has two phosphate groups. Answer: C Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

11. What feature of mononucleotides provides the energy needed for polymerization when nucleic acids are formed? A) their methyl groups B) their sugar groups C) their nitrogenous bases D) their phosphate groups Answer: D Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

12. What is gel electrophoresis used for? A) to denature proteins for further analysis B) to separate macromolecules by size or charge C) to separate the two helices that make up the DNA double helix D) to identify the first self-replicating molecule that formed during chemical evolution Answer: B Explanation: B) Some instructors may find this a valuable in-class assessment after explaining gel electrophoresis. Reference: Section 4.

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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 C) turn-loop-turn D) double antiparallel helical strands Answer: D Reference: Section 4.

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Bloom's Level: Remembering LOs: Chp4-4. Explain why and how the secondary structure of DNA allows organisms to store and copy information.

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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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23. If a molecule of DNA contains 10% cytosine, it has _ guanine and adenine respectively. A) 10%; 40% B) 10%; 45% C) 40%; 40% D) 40%; 10% E) 10%; 80% Answer: A Reference: Section 4. Bloom's Level: Comprehension/Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

24. What is responsible for holding the two strands together in the DNA double helix? A) phosphodiester bonds B) hydrogen bonds C) ionic bonds D) covalent bonds Answer: B Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-2. Make another sketch showing the primary and secondary structures of DNA.

25. 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? A) It has the same number of purines and pyrimidines. B) The nitrogenous bases are located on the inside of the double helix. C) The strands of the double helix are complementary. D) DNA always goes from 5 to 3. 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.

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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 Answer: B Reference: Section 4. Bloom's Level: Remembering LOs: Chp4-3. Describe the primary, secondary, tertiary, and quaternary structures of RNA, and

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explain in what ways RNA differs from DNA.

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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. B) It must be exergonic. C) It must be endothermic. D) It must be exothermic. Answer: B

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Explanation: B) The answer is implied in the Nakano quote by the word catalyzes. Reference: Section 4.1, 9. Bloom's Level: Comprehension LOs: Chp4-5. Explain why RNA, and not DNA, was probably the first self-replicating molecule,

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