Chapter 11: Molecular Structure of DNA and RNA

Chapter 11: Molecular Structure of DNA and RNA Student Learning Objectives Upon completion of this chapter you should be able to: 1. Understand the major experiments that led to the discovery of DNA as the genetic material, the experimental methods, and the investigators involved. 2. Understand the components of DNA and RNA. 3. Know the major contributors to the discovery of the structure of DNA. 4. Know the features of the DNA double helix. 5. Distinguish between the various forms of DNA and RNA. 11.1 Identification of DNA as the Genetic Material While today it is common knowledge that DNA is the genetic material for all living organisms, that was not always the case. Our understanding of DNA as the information storage location for cells is the result of a series of experiments conducted in the early to mid-20 th century. The first part of this chapter describes those experiments that established DNA as the genetic material. As you examine these experiments, first try to place yourself in the position of the researchers and what was known at the time. Next, study how they designed their experiments to examine a specific problem. Many of these experiments are classic examples of the scientific method and still serve as model of how to design and analyze scientific experiments. Before proceeding, examine the criteria for a genetic material on page 231. Following this, you should familiarize yourself with each of the major researchers, their experimental model, and their results. You should also be able to construct a timeline of experimental procedures that led to the discovery of DNA as the genetic material. Outline of Key Terms Molecular genetics Genetic material Information Transmission Replication Variation Griffith s experiment Streptococcus pneumoniae Transformation Avery et al s experiment DNase RNase Protease Hershey and Chase s experiment T2 bacteriophage (phage) Escherichia coli Lysis Experimental procedures of Griffith (Figure 11.1), Avery et al (Figure 11.2), and Hershey and Chase (pages 234-237) 118

For questions 1 to 7, match each statement with the researcher(s) who contributed the information to our understanding of DNA. a. Avery, MacLeod, and McCarty b. Hershey and Chase c. Griffith d. all of the above 1. Discovered the process of transformation in bacteria. 2. Treated Streptococcus pneumoniae extracts with enzymes to further identify the genetic material. 3. Used Streptococcus pneumoniae as a model system. 4. Used radioactively labeled phages to determine if DNA or protein was the genetic material. 5. Used a bacteriophage (T2) as the model system. 6. Demonstrated that the transforming principle from the experiments with Streptococcus pneumoniae is DNA. 7. Demonstrated that DNA is the genetic material of bacteriophage T2. Each of the statements below is in reference to Griffith s experiments with Streptococcus pneumoniae. Indicate whether each statement provides support of the genetic material having the properties of information (I), transmission (T), replication (R), or variation (V). 8. The biochemical differences in the capsule of the type R and type S. 9. The copying of the genetic material within the dividing cells. 10. Instructions for type R and type S in the cell. 11. Transformation of type R to type S. For each of the following, match the chemical with its correct description. 12. Protease 13. RNase 14. 35 S 15. DNase 16. 32 P 17. RNA a. Treating a bacterial extract with this will leave only RNA and protein. b. Used to label DNA in the experiments of Hershey and Chase. c. Treating a bacterial extract with this will leave only DNA and protein. d. Used to label proteins in the experiments of Hershey and Chase. e. An enzyme that digests proteins. f. An alternate genetic material in some viruses. 119

11.2 of DNA and RNA Structure This small section provides an overview of the nucleic acids, DNA and RNA. Both are macromolecules composed of smaller building blocks. Indeed, the nucleic acid structure can be categorized into four levels of complexity: 1) nucleotides; 2) single strand; 3) double helix; and 4) chromosome (a three-dimensional structure). Outline of Key Terms Nucleic acids Nucleotides Strand Double helix Levels of nucleic acid structure (Figure 11.6) For questions 1 to 5, complete the sentence with the most appropriate term(s): 1. Nucleic acids are made up of repeating structural units called. 2. These repeating structural units are linked together in a linear manner to form a. 3. Nucleic acids are acidic, which means that they release in solutions. 4. Nucleic acids have a net charge at neutral ph. 5. Chromosomes consist of DNA complexed with. 11.3 Nucleotide Structure A nucleotide consists of three parts: 1) a nitrogenous base; 2) a pentose sugar; and 3) at least one phosphate (Refer to Figure 11.7). When the base is attached to only the sugar, we call this pair a nucleoside (Figure 11.9). Nitrogenous bases are of two types: purines, which include adenine and guanine; and pyrimidines, which include cytosine, thymine (found in DNA only), and uracil (found in RNA only). There are also two types of pentose sugars: deoxyribose is found in DNA, while ribose is found in RNA (Refer to Figure 11.8). 120

Outline of Key Terms Nucleotide Base Purine Adenine (A) Guanine (G) Pyrimidines Cytosine (C) Thymine (T) Uracil (U) Sugar Deoxyribose Ribose Phosphate Nucleoside Components and structure of nucleotides (Figures 11.7-11.9) The following are components of DNA structure. Match each of the following with their correct definition. 1. Nucleoside 2. Ribose 3. Purines 4. Deoxyribose 5. Pyrimidines 6. Nucleotides 7. Strand 8. Double helix a. Cytosine and thymine. b. The structural units of a DNA strand. c. The five-carbon sugar in RNA. d. Nucleotides linked by phosphodiester bonds. e. Adenine and guanine. f. Two interacting strands of DNA. g. The five-carbon sugar in DNA. h. The combination of a base and a sugar. 11.4 Structure of a DNA strand Having discussed the structure of nucleotides, we now take a look at how these come together to form polynucleotides. Nucleotides are covalently linked together to form a linear strand of DNA (or RNA). The bonds that connect adjacent nucleotide are called phosphodiester bonds. These involve a phosphate attachment between the 5 carbon in one nucleotide and the 3 carbon in the other. Therefore, a strand has a directionality (5 to 3 ) based on the orientation of the sugar molecules within that strand. 121

Outline of Key Terms Polynucleotide Phosphodiester linkage Backbone Directionality A short strand of DNA containing four nucleotides (Figure 11.10) For questions 1 to 6, match each of the following with its correct letter from the diagram. 1. nucleotide 2. phosphate group 3. 5 end of the strand 4. deoxyribose sugar 5. phosphodiester linkage 6. 3 end of the strand 122

11.5 Discovery of the Double Helix Following the discovery of DNA as the genetic material, researchers set out to understand the structure of the molecule. This section outlines the major contributors to this effort. As was the case with Section 11.1, for each researcher you should focus on understanding not only their contribution, but also the experimental system that they utilized to make their discoveries. However, as you progress through these experiments, you need to also focus on the developing DNA molecule. Outline of Key Terms Chargaff s rules X-ray diffraction of DNA (Figure 11.12) Watson and Crick and their model of the DNA double helix (Figure 11.13) For questions 1 to 4, match each of the researcher(s) to their contribution in the discovery of DNA structure. 1. Watson and Crick 2. Franklin 3. Chargaff 4. Pauling a. Studies of protein structure led to an understanding of DNA folding. b. First to describe the AT/GC rule of base-pairing in DNA. c. Contributed X-ray diffraction data that indicated a helical structure. d. Developed a ball and stick model of DNA that illustrated it as a double-helix. 5. Analysis of the DNA content of numerous organisms suggested that the amount of adenine was similar to that of, and the amount of guanine was similar to that of. 11.6 Structure of the DNA Double Helix This section examines the structure of the DNA double helix in more detail. As a student in a genetics class, you must comprehend the structure of DNA and the terminology that is used to describe this molecule. Discussions in later chapters of replication, transcription, and gene expression are built upon a firm understanding of the structure of DNA. 123

Outline of Key Terms Double helix Base pairs Complementary AT/GC rule Anti-parallel Right-handed Grooves Major groove Minor groove Forms of DNA B DNA A DNA Z DNA Left-handed Methylation Key features of the structure of the double helix (Figure 11.14) Two models of the double helix (Figure 11.15) Comparison of the structures of B DNA and Z DNA (Figure 11.16) For questions 1 to 9, indicate whether the statement is true (T) or false (F). If the statement is false, change it to make it true. 1. 2. 3. 4. 5. 6. 7. 8. 9. The directionality of DNA is said to be in the 3 to 5 direction. The backbone of DNA is made up of deoxyribose sugars. The DNA double helix contains the two purine bases cytosine and thymine. In a double helix, there is a 1: 1 ratio of AT:GC. The DNA molecule consists of major and minor grooves, to which proteins can bind. The linear distance of a complete turn of the double helix is 3.4 nm. In the double helix, the percentage of purines and pyrimidines are equal. There are 8 basepairs in each turn of the double helix. The two DNA strands of the double helix are arranged in an antiparallel pattern. For questions 10 to 12, match each statement with its correct DNA form. a. A DNA b. B DNA c. Z DNA 10. The form of DNA most common in living cells. 11. Forms under conditions of low humidity. 12. A left-handed form of DNA. 124

11.7 RNA Structure The final section of this chapter examines the structure of DNA s cousin, RNA. Just like DNA, RNA is also a string of nucleotides (Figure 11.17). And just like DNA, RNA can also form double-stranded helical regions (Figure 11.18), and can fold into three-dimensional structures (Figure 11.19). A strand of RNA (Figure 11.17) Possible structures of RNA molecules (Figure 11.18) The structure of transfer RNA (Figure 11.19) For questions 1 to 5, complete the sentence with the most appropriate term(s): 1. In an RNA strand, adjacent nucleotides are connected via linkages. 2. The pyrimidine bases in RNA are and. 3. Stem-loop structures that can form within RNA molecules are also called. 4. In addition to stem-loops, RNA molecules can also contain loops and loops. 5. The first naturally-occurring RNA to have its structure elucidated was. 6. RNA molecules with catalytic functions are termed. 7. A transfer RNA molecule has two key functional sites that play a role in translation. These are the and the. Quiz 1. The linear distance of a complete turn of the DNA double helix is. a. 2.2 nm b. 20 nm c. 34 nm d. 3.4 nm e. 10 nm 2. used X-ray crystallography data to provide the first evidence of the threedimensional structure of DNA. a. Chargaff b. Watson and Crick c. Franklin d. Griffith 121

3. In a DNA nucleotide within a DNA strand, this is the component that can vary. a. phosphate groups b. phosphodiester bonds c. sugar d. type of base e. none of the above vary 4. This is the form of DNA most common in living cells. a. A DNA b. B DNA c. Z DNA d. K DNA 5. discovered the process of transformation in bacteria. a. Avery and colleagues b. Griffith c. Chargaff d. Pauling e. Franklin 6. demonstrated that the genetic material in bacteriophage T2 was DNA. a. Watson and Crick b. Avery and colleagues c. Franklin d. Hershey and Chase e. Pauling 7. In the classic experiments with bacteriophage T2, what was used to label DNA? a. 15 N b. 35 S c. 32 P d. 3 H 8. The 5 to 3 configuration of DNA is called its property. a. complementary b. AT/GC rule c. directionality d. antiparallel 9. If a bacterial chromosome contains 20% adenine, what is the percentage of cytosine? a. 10% b. 20% c. 30% d. 40% e. Can t tell from the given information 10. The structural unit of a DNA strand is the. a. nucleoside b. nucleotide c. ribose sugar d. purine 122

Answer Key for Study Guide Questions This answer key provides the answers to the exercises and chapter quiz for this chapter. Answers in parentheses ( ) represent possible alternate answers to a problem, while answers marked with an asterisk (*) indicate that the response to the question may vary. 11.1 1. c 2. a 3. c 4. b 5. b 6. a 7. b 8. V 9. R 10. I 11. T 12. e 13. c 14. d 15. a 16. b 17. f 11.2 1. nucleotide 2. strand 3. H + (hydrogen ion) 4. negative 5. proteins 11.3 1. h 2. c 3. e 4. g 5. a 6. b 7. d 8. f 11.4 1. a 2. d 3. e 4. c 5. b 6. f 11.5 1. d 2. c 3. b 4. a 5. thymine; cytosine 123

11.6 1. F, 5 to 3 2. F, sugar-phosphate groups 3. F, pyrimidines 4. T 5. T 6. T 7. T 8. F, 10 bp/turn 9. T 10. b 11. a 12. c 11.7 1. phosphodiester 2. cytosine and uracil 3. hairpins 4. internal; bulge 5. transfer RNA 6. ribozymes 7. anticodon; 3 acceptor site Quiz 1. d 2. c 3. d 4. b 5. b 6. d 7. c 8. c 9. c 10. b 121