Chapter 4 Questions (end of chapter)

In a triple helix, the bases are unlikely to align properly for hydrogen bonding to occur, so hydrophobic interactions would probably be more important.

Before Watson and Crick published their model of the DNA double helix, Linus Pauling offered a model based on a triple helix. If the three sugar-phosphate backbones were on the outside of such a molecule, would hydrogen bonding or hydrophobic interactions be more important in keeping such a secondary structure together?

a

DNA attains a secondary structure when hydrogen bonds form between the nitrogenous bases called purine and pyrimidines. What are the complementary base pairs that form in DNA? a) A-T and G-C b) A-U and G-C c) A-G and T-C d) A-T and G-U

In DNA, the secondary structure requires that every guanine pairs with a cytosine and every thymine pairs with an adenine, resulting in consistent ratios between the nucleotides. Chargaff's rules do not apply to RNA, since it is single-stranded and the pairing is not consistent throughout the molecules.

Explain how Chargaff's rules relate to the complementary base pairing seen in the secondary structure of DNA. Would you expect these rules to apply to RNA as well? Explain why or why not.

b; the high temperature would make it more likely that the secondary and tertiary structures would be denatured in the ribozymes. To overcome this effect, you would expect the hairpins to possess more G-C pairs, since they consist of three hydrogen bonds compared to the two found in A-T pairs.

How would you expect the structure of ribozymes in organisms that grow in very hot environments, such as hot springs or deep sea vents, to differ from those in organisms that grow in cooler environments? a) These ribozymes would have more hairpin secondary structures. b) The hairpins would have more G's and C's in the primary structure. c) The hairpins would have more A's and U's in the primary structure. d) These ribozymes would exhibit no tertiary structure.

a; if 30% is adenine, then 30% would be thymine, since they are base-paired together. This means that 40% consists of G-C base pairs, which would be equally divided between the two bases.

If nucleotides from the DNA of a human were quantified and 30 percent of them consisted of adenine, what percentage of guanine nucleotides would be present? a) 20% b) 30% c) 40% d) 70%

One end has a free phosphate group on the 5' carbon; the other end has a free hydroxyl group bonded to the 3' carbon.

Nucleic acids are directional, meaning that there are two different ends. What functional groups define the two different ends of a DNA strand?

An RNA replicase would undergo replication and be able to evolve. It would process information in the sense of copying itself, and it would use energy to drive polymerization reactions. It would not be bound by a membrane and considered a cell, however, and it would not be able to acquire energy. It would best be considered as an intermediate step between non-life and true life.

Suppose that Bartel's research group succeeded in producing a molecule that could make a copy of itself. Which of the five fundamental characteristics of life would support the claim that this molecule is alive?

No. Catalytic activity in ribozymes depends on the tertiary structure generated from single-stranded molecules. Double-stranded nucleic acids do not form tertiary structures.

To replicate a ribozyme, a complete complementary copy must be made. Would you expect the double-stranded intermediate to maintain its catalytic activity? Justify your answer with an explanation.

Yes - if the complementary bases lined up over the entire length of the two strands, they would twist into a double helix analogous to a DNA molecule. The same types of hydrogen bonds and hydrophobic interactions would occur as observed in the "stem" portion of hairpins in single-stranded RNA.

Viruses are particles that infect cells. In some viruses, the genetic material consists of two strands of RNA, bonded together via complementary base pairing. Would these antiparallel strands form a double helix? Why or why not?

c

What are the four nitrogenous bases found in RNA? a) uracil, guanine, cytosine, thymine (U, G, C, T) b) adenine, guanine, cytosine, thymine (A, G, C, T) c) adenine, uracil, guanine, cytosine (A, U, G, C) d) alanine, threonine, glycine, cysteine (A, T, G, C)

c

What determines the primary structure of a DNA molecule? a) the sugar-phosphate backbone b) complementary base pairing and the formation of hairpins c) the sequence of deoxyribonucleotides d) the sequence of ribonucleotides

DNA is a more stable molecule than RNA because it lacks a hydroxyl group on the 2' carbon and is therefore more resistant to cleavage, and because the two sugar-phosphate backbones are held together by many hydrogen bonds between nitrogenous bases.

What is responsible for the increased stability of DNA compared to RNA?

The DNA sequence of the new strand would be 5' -ATCGATATC- 3'. The RNA sequence would be the same, except the T would be replaced by a U.

What would be the sequence of the strand of DNA that is made from the following template: 5' -GATATCGAT- 3' (Your answer must be written 5' -> 3'.) How would this sequence be different if RNA were made from this DNA template?

d

Which of the following rules apply to the synthesis of nucleic acids? a) Nucleotides are added to the 5' end of nucleic acids. b) The synthesis of nucleic acids cannot occur without the presence of an enzyme to catalyze the reaction. c) Strands are synthesized in a parallel direction such that one end of the double-stranded product has the 3' ends and other has the 5' ends. d) Complementary pairing between bases is required for copying nucleic acids.

DNA has limited catalytic ability because it (1) lacks functional groups that can participate in catalysis and (2) has a regular structure that is not conducive to forming shapes required for catalysis. RNA molecules can catalyze some reactions because they (1) have exposed hydroxyl functional groups and (2) can fold into shapes that then can function in catalysis.

`A major theme in this chapter is that the structure of molecules correlates with their function. Explain how DNA's secondary structure limits its catalytic abilities compared with that of RNA. Why is it expected that RNA molecules can catalyze a modest but significant array of reactions?