Chapter 4 Textbook Questions

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∙ S 3∙.) How would the sequence be different if RNA were made from this DNA template?

5∙-ATCGATATC-3∙The RNA sequence would be the same, except each T would be replaced by a U.

DNA is capable of adopting several non-canonical structure; intermolecular DNA triple helix structures have been observed in vitro and in vivo. Based on the model of replication presented in figure 4.7, how would a third strand affect replication? Could it be of therapeutic interest?

A third strand could interfere and disrupt proper DNA replication. This could, in turn, inhibit cell proliferation and could be of therapeutic interest if it were used to target cancer cells.

If nucleotides from the DNA of a human were quantified and 30 percent of them contained the base adenine, what percentage of them would contain the base guanine? a. 20 percent b. 30 percent c. 40 percent d. 70 percent

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

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

C.

Watson and Crick met with Chargaff to discuss his work in 1952. Explain how Chargaff's observations helped Watson and Crick to propose the complementary base pairing in their model of double-stranded DNA. Would you expect similar ratios of nucleotides if Chargaff had used RNA instead? Explain why or why not.

Chargaff's data show that an approximately 1:1 molar ratio exists between adenine and thymine bases, and between guanine and cytosine bases. Watson and Crick used these data to come up with complementary base pairing, which requires that every adenine pairs with a thymine and every guanine pairs with a cytosine. In RNA, Chargaff's rules do not apply since RNA is single-stranded and the pairing is not consistent throughout the molecule.

What is responsible for the double helix secondary structure of DNA? a. α helix and β sheets b. hairpins and stem-and-loop configuration c. the ribonucleotide sequence d. the interaction between antiparallel strands

D.

Which of the following describes the synthesis of nucleic acids? a. Nucleotides are added to the 5∙ end of a single nucleic acid strand. b. Nucleic acids are polymerized by the formation of peptide bonds between nucleotides. c. Strands in a double helix are synthesized in a parallel direction such that one end of the molecule has two 3∙ ends and other has two 5∙ ends. d. Complementary pairing between bases is required for copying nucleic acids.

D.

Scientists are currently developing nucleic acid digital data storage in which digital data is stored in the form of a nucleic base sequence. Which nucleic acid would be the best choice for such an application? Give two reasons.

DNA, because of its stability and its highly compact tertiary structure that enable high data density.

According to the RNA world model, a ribozyme would replicate by creating a double-stranded RNA intermediate. Would you expect the intermediate to have the same catalytic activity as the original ribozyme? Justify your answer with an explanation.

No. Catalytic activity in ribozymes depends on the tertiary structure gener- ated from folding single-stranded molecules. Fully double-stranded forms of the RNA would not form the same tertiary structure.

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

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

Who deserves credit for discovering the structure of the double helix? The famous model in the photo was built by Watson and Crick in 1953 to demonstrate the secondary structure of DNA. This was not the first attempt at modeling DNA's structure, however. Before 1953, there were several failed attempts. The accumulation of data from different research groups was key to arriving at the correct model. What were the incorrect versions of DNA structure, and how did Watson and Crick get it right? Phoebus Levene was the first to describe the structure of nucleotides and how they were bonded together with phosphodiester linkages. In 1919, he incorrectly proposed the tetranucleotide hypothesis, which stated that nucleic acids were polymers consisting of GCTA repeated over and over. If his model had been correct, then how would it affect the information that could be stored in the DNA?

The capacity for storing information would be severely limited. It would be like trying to express ideas with a language that consisted of only one 4-let- ter word that is repeated over and over. According to this hypothesis, DNA would not serve as an effective information storage molecule.

Rosalind Franklin was the first person to obtain X-ray crystallographic data in the form of DNA. She used DNA that was isolated from calf thymus cells. Do you think using calf brain tissue would produce different crystallography results?

There are different forms of DNA double helix, but the most common form in all tissues is B-DNA. Thus, using DNA extracted from brain tissue would produce similar crystallography results.

In the 1950s, the race to solve the secondary structure of DNA became intense. In an uncharacteristic rush to publish, Linus Pauling erroneously proposed a triple-stranded structure in February 1953. This model had the nitrogenous bases on the exterior and the sugar-phosphate backbones clustered in the middle. How does the orientation of the sugar-phosphate backbone in this model compare with the one proposed by Watson and Crick? Do you think Pauling's structure could exist in cells? Why or why not?

Watson and Crick's model had the sugar-phosphate backbones oriented toward the exterior. Pauling's structure would not likely exist in cells because the sugar- phosphate backbones of nucleic acids are negatively charged and would repel one another.

In 1951, Erwin Chargaff was accumulating data on the molar ratios of nucleotides using DNA obtained from a variety of sources. Some of these data are provided in the following table: *see definition for data table* Compare the molar ratios presented from each organism tested and between different organisms. Explain how these data could be used to show that Levene's tetranucleotide model is incorrect. What do they imply about the primary structure of DNA in different organisms?

Within each DNA sample tested, the molar ratios of A:T and that of G:C were close to one, meaning that for every adenine there is a thymine, and for every guanine there is a cytosine. A key observation was that the ratios between A:G and T:C were not close to one, meaning that all four nucleotides were not present in equal ratios. These data are contrary to what Levene's tetranucleotide model would have predicted, which is that each nucleotide would be present in the same molar amounts. In addition, since the molar ratios of A:G and T:C were quite different in the organisms tested, the primary structure of DNA appears to vary among them.