Question

The nucleobase part of deoxyribonucleic acid encodes information in each component in the sequence making up the polymer. There are five nucleobases that are commonly represented by only a single letter: A (adenine), C(cytosine), G(guanine), T(thymine), and U (uracil). These molecules form a bond with the 1-carbon of deoxyribose. In this problem, we need to look at the molecules in slightly more detail so that you can development the ability to explain why DNA, and sometimes RNA, is the primary source of heritable information. Edwin Chargaff and his team isolated nucleobases from salmon sperm and determined the fraction of each (Chargaff et al., Journal of Biological Chemistry, 192, 1951). Experiments in which the fraction of all four nucleobases was determined are shown. Also shown are averages as two standard deviations and the sum of total fractions for each experiment. Precision is calculated with each average. Shown below are the chemical structures of these four nucleobases. In these structures, the nitrogen that attaches to the 2 -deoxyribose, 5 -phosphate polymer is indicated as $\mathrm{N}^{*} .$ The partial charges of particular atoms are indicated A. Analyze Chargaff's data in terms of the partial charges on these molecules to show how molecular interactions affect the function of these molecules in the storage and retrieval of biological information. The interactions between nucleobase molecules are strong enough to produce the association of pairs observed in Chargaff's data. However, these pairs are bonded by much weaker hydrogen bonds, chemical bonds within the molecules. Demonstrating an understanding of the replication of DNA requires the ability to explain how the two polymer strands of the double helix interact and grow. To retrieve information from DNA, the strands must be separated. The proteins that perform that task interact with the polymer without forming new chemical bonds. In their paper (Watson and Crick, Nature, $3,1953$ ) announcing the structure of the polymer that we consider in this problem, Watson and Crick stated, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." Eschenmoser and Lowenthal (Chemical Society Reviews, $21,1992$ ) asked why the 5 -carbon sugar ribose is used in DNA when the 6 -carbon sugar glucose is so common in biological systems. To answer the question, they synthesized polymeric chains with this alternative form of sugar. They discovered that the strength of the interaction between pairs of nucleobases increased in the new material. Paired strands of hexose-based polymers were more stable. The AP Biology Curriculum Framework (College Board, 2012 ) states, "The double-stranded structure of DNA provides a simple and elegant solution for the transmission of heritable information to the next generation; by using each strand as a template, existing information can be preserved and duplicated with high fidelity within the replication process. However, the process of replication is imperfect...". B. Explain why the weaker interaction observed by Eschenmoser and Lowenthal, and the acknowledgement in the Framework that "replication is imperfect," support the claim implied by Watson and Crick that DNA is the source of heritable information.

Name: Problem 78, Chapter 3: Biology for AP Courses
Uploaded: 2019-07-27T20:30:54-08:00
Duration: 7 min 42 s
Channel: James Thierer

The nucleobase part of deoxyribonucleic acid encodes information in each component in the sequence making up the polymer. There are five nucleobases that are commonly represented by only a single letter: A (adenine), C(cytosine), G(guanine), T(thymine), and U (uracil). These molecules form a bond with the 1-carbon of deoxyribose. In this problem, we need to look at the molecules in slightly more detail so that you can development the ability to explain why DNA, and sometimes RNA, is the primary source of heritable information. Edwin Chargaff and his team isolated nucleobases from salmon sperm and determined the fraction of each (Chargaff et al., Journal of Biological Chemistry, 192, 1951). Experiments in which the fraction of all four nucleobases was determined are shown. Also shown are averages as two standard deviations and the sum of total fractions for each experiment. Precision is calculated with each average. Shown below are the chemical structures of these four nucleobases. In these structures, the nitrogen that attaches to the 2 -deoxyribose, 5 -phosphate polymer is indicated as $\mathrm{N}^{*} .$ The partial charges of particular atoms are indicated A. Analyze Chargaff's data in terms of the partial charges on these molecules to show how molecular interactions affect the function of these molecules in the storage and retrieval of biological information. The interactions between nucleobase molecules are strong enough to produce the association of pairs observed in Chargaff's data. However, these pairs are bonded by much weaker hydrogen bonds, chemical bonds within the molecules. Demonstrating an understanding of the replication of DNA requires the ability to explain how the two polymer strands of the double helix interact and grow. To retrieve information from DNA, the strands must be separated. The proteins that perform that task interact with the polymer without forming new chemical bonds. In their paper
(Watson and Crick, Nature, $3,1953$ ) announcing the structure of the polymer that we consider in this problem, Watson and Crick stated, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." Eschenmoser and Lowenthal (Chemical Society Reviews, $21,1992$ ) asked why the 5 -carbon sugar ribose is used in DNA when the 6 -carbon sugar glucose is so common in biological systems. To answer the question, they synthesized polymeric chains with this alternative form of sugar. They discovered that the strength of the interaction between pairs of nucleobases increased in the new
material. Paired strands of hexose-based polymers were more stable. The AP Biology Curriculum Framework (College Board, 2012 ) states, "The double-stranded structure of DNA provides a simple and elegant solution for the transmission of heritable information to the next generation; by using each strand as a template, existing information can be preserved and duplicated with high fidelity within the replication process. However, the process of replication is imperfect...". B. Explain why the weaker interaction observed by Eschenmoser and Lowenthal, and the acknowledgement in the Framework that "replication is imperfect," support the claim implied by Watson and Crick that DNA is the source of heritable information.

Biology for AP Courses

Julianne Zedalis,…

Chapter 3, Problem 78

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Solved by Expert James Thierer

07/27/2019

Step 1

DNA is a double helix structure with a sugar-phosphate backbone and rungs made up of pairs of nucleobases. The nucleobases are adenine (A), cytosine (C), guanine (G), and thymine (T). In DNA, adenine always pairs with thymine and guanine always pairs with Show more…

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The nucleobase part of deoxyribonucleic acid encodes information in each component in the sequence making up the polymer. There are five nucleobases that are commonly represented by only a single letter: A (adenine), C(cytosine), G(guanine), T(thymine), and U (uracil). These molecules form a bond with the 1-carbon of deoxyribose. In this problem, we need to look at the molecules in slightly more detail so that you can development the ability to explain why DNA, and sometimes RNA, is the primary source of heritable information. Edwin Chargaff and his team isolated nucleobases from salmon sperm and determined the fraction of each (Chargaff et al., Journal of Biological Chemistry, 192, 1951). Experiments in which the fraction of all four nucleobases was determined are shown. Also shown are averages as two standard deviations and the sum of total fractions for each experiment. Precision is calculated with each average. Shown below are the chemical structures of these four nucleobases. In these structures, the nitrogen that attaches to the 2 -deoxyribose, 5 -phosphate polymer is indicated as $\mathrm{N}^{*} .$ The partial charges of particular atoms are indicated A. Analyze Chargaff's data in terms of the partial charges on these molecules to show how molecular interactions affect the function of these molecules in the storage and retrieval of biological information. The interactions between nucleobase molecules are strong enough to produce the association of pairs observed in Chargaff's data. However, these pairs are bonded by much weaker hydrogen bonds, chemical bonds within the molecules. Demonstrating an understanding of the replication of DNA requires the ability to explain how the two polymer strands of the double helix interact and grow. To retrieve information from DNA, the strands must be separated. The proteins that perform that task interact with the polymer without forming new chemical bonds. In their paper (Watson and Crick, Nature, $3,1953$ ) announcing the structure of the polymer that we consider in this problem, Watson and Crick stated, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." Eschenmoser and Lowenthal (Chemical Society Reviews, $21,1992$ ) asked why the 5 -carbon sugar ribose is used in DNA when the 6 -carbon sugar glucose is so common in biological systems. To answer the question, they synthesized polymeric chains with this alternative form of sugar. They discovered that the strength of the interaction between pairs of nucleobases increased in the new material. Paired strands of hexose-based polymers were more stable. The AP Biology Curriculum Framework (College Board, 2012 ) states, "The double-stranded structure of DNA provides a simple and elegant solution for the transmission of heritable information to the next generation; by using each strand as a template, existing information can be preserved and duplicated with high fidelity within the replication process. However, the process of replication is imperfect...". B. Explain why the weaker interaction observed by Eschenmoser and Lowenthal, and the acknowledgement in the Framework that "replication is imperfect," support the claim implied by Watson and Crick that DNA is the source of heritable information.

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Key Concepts

Double Helix Structure

The double helix is the iconic structure of DNA, comprising two intertwined strands held together by specific base pairing. This structure not only protects the genetic information inside but also allows for a mechanism of replication in which each strand serves as a template for forming a new complementary strand.

Complementary Base Pairing

Complementary base pairing refers to the specific interactions between nucleobases (adenine pairs with thymine or uracil, and cytosine pairs with guanine) through hydrogen bonds. This precise pairing is crucial for accurate replication since it ensures that each new strand is an exact copy of the original template, facilitating the reliable transmission of genetic information.

Hydrogen Bonding

Hydrogen bonds are the weak chemical bonds that facilitate the pairing between nucleobases in the double helix. Their relative weakness compared to covalent bonds gives the DNA molecule the necessary balance: the bonds are strong enough to maintain the integrity of the double helix, yet weak enough to allow the two strands to separate during processes like replication and transcription without breaking the nucleobase molecules themselves.

Template-Directed Replication

Template-directed replication is the process by which each strand of DNA serves as a guide for the synthesis of its complementary strand. The weak hydrogen bonds between nucleobases allow the strands to be temporarily separated, while the strong covalent bonds within each strand maintain the integrity of the polymer. This mechanism ensures that genetic information is copied with high fidelity, despite the occasional imperfections inherent in the process.

Weak vs Strong Molecular Interactions

The interplay between weak hydrogen bonds and strong covalent bonds is fundamental to DNA’s function. The strong covalent bonds keep the nucleotides joined in a stable polymer, and the weaker hydrogen bonds between base pairs allow the strands to disassociate easily for replication and repair. This balance of bond strengths is critical to achieving both stability in storage and flexibility in information retrieval and copying, underscoring DNA’s role as a reliable carrier of genetic information.

Partial Charges and Molecular Interactions

Partial charges on atoms within the nucleobases influence their ability to form hydrogen bonds and interact with each other. These charge distributions affect molecular recognition and pairing specificity, contributing to the selective, complementary interactions that underlie the structure and function of DNA. The controlled, weaker interactions guided by these partial charges are essential for the dynamic processes of DNA replication and repair, ensuring that genetic information is both accurately preserved and accessible when needed.

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