Molecular Biology Chapter 9

DNA – Deoxyribonucleic Acid stores genetic information copied and passed from generation to generation Directs the copying of itself  DNA Replication Involved in protein production Transcription Translation Student Misconceptions and Concerns 1. If your class has not yet studied Chapter 3, consider assigning the Chapter 3 section on “Nucleic Acids” before addressing the contents of Chapter 10. 2. The text describes but does not specifically point out that DNA replication is semiconservative. Tell your students about an experiment in which a DNA molecule is labeled, then replicated. How will the two DNA molecules compare with regard to the location/distribution of the original DNA molecule? Will one DNA molecule be the original and the other the new copy? Or is there another possibility? Half of each of the two DNA molecules is new and half is the original; thus, it used semiconservative replication. Analogies for semiconservative replication can be a challenge. But in a sense, DNA replication is similar to parents getting divorced and then each parent remarrying someone else. The two new couples represent “half old parent and half new person.” 3. Students often confuse the terms nucleic acids, nucleotides, and bases. It helps just to note the hierarchy of relationships: Nucleic acids consist of long chains of nucleotides, and nucleotides include bases as part of their structure. Teaching Tips 1. Consider comparing DNA, RNA, and proteins to a train (polymer). DNA and RNA are like a train of various lengths and combinations of four types of train cars (monomers). Proteins are also “trains” of various lengths but made of a combination of 20 types of train cars. 2. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. You might remind your class of all the prior research (identifying DNA as the genetic material and clues to its structure) that brought Watson and Crick to their historic conclusions. 3. The authors note that the structure of DNA is analogous to a twisted rope ladder. In class, challenge your students to explain what the parts of the ladder represent. The wooden rungs represent a base pair and each rope the sugar-phosphate backbone. 4. Demonstrate the complementary base pairing within DNA. Present students with the base sequence to one side of a DNA molecule and have them work quickly at their seats to determine the sequence of the complementary strand. For some students, these sorts of quick practice are necessary to reinforce a concept and break up a lecture. 5. To explain the adaptive advantage of multiple replication sites over a single site of replication, ask your students to imagine copying, by hand, the first ten chapters of your biology textbook. The task would certainly go faster if ten students each copied a different chapter! 6. There are about 2 million characters (letters or numbers) in the Campbell Essential Biology with Physiology textbook. The accuracy of DNA replication would be like copying every letter and number in this textbook by hand 500 times and writing just one letter or number incorrectly, making one error in every 1 billion characters! 7. The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these other chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. 2

History of DNA – Watson & Crick Wanted to know if the genetic material was protein or DNA. 1953  Deduce exact structure of DNA Nucleic Acid Double Helix Made of nucleotides Figure 10.3 Discoverers of the double helix (part 1) James Watson (left) and Francis Crick

Rosalind Franklin X-ray images of DNA Figure 10.3 Discoverers of the double helix (part 2) Rosalind Franklin X-ray images of DNA

DNA Structure Double Helix is composed of a Backbone composed of alternating Sugar 5-C sugar = Deoxyribose Phosphate Rungs Bases Adenine (A) Thymine (T) Guanine (G) Cytosine (C) Nucleotide = Phosphate + Sugar + Base Student Misconceptions and Concerns 1. If your class has not yet studied Chapter 3, consider assigning the Chapter 3 section on “Nucleic Acids” before addressing the contents of Chapter 10. 2. The text describes but does not specifically point out that DNA replication is semiconservative. Tell your students about an experiment in which a DNA molecule is labeled, then replicated. How will the two DNA molecules compare with regard to the location/distribution of the original DNA molecule? Will one DNA molecule be the original and the other the new copy? Or is there another possibility? Half of each of the two DNA molecules is new and half is the original; thus, it used semiconservative replication. Analogies for semiconservative replication can be a challenge. But in a sense, DNA replication is similar to parents getting divorced and then each parent remarrying someone else. The two new couples represent “half old parent and half new person.” 3. Students often confuse the terms nucleic acids, nucleotides, and bases. It helps just to note the hierarchy of relationships: Nucleic acids consist of long chains of nucleotides, and nucleotides include bases as part of their structure. Teaching Tips 1. Consider comparing DNA, RNA, and proteins to a train (polymer). DNA and RNA are like a train of various lengths and combinations of four types of train cars (monomers). Proteins are also “trains” of various lengths but made of a combination of 20 types of train cars. 2. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. You might remind your class of all the prior research (identifying DNA as the genetic material and clues to its structure) that brought Watson and Crick to their historic conclusions. 3. The authors note that the structure of DNA is analogous to a twisted rope ladder. In class, challenge your students to explain what the parts of the ladder represent. The wooden rungs represent a base pair and each rope the sugar-phosphate backbone. 4. Demonstrate the complementary base pairing within DNA. Present students with the base sequence to one side of a DNA molecule and have them work quickly at their seats to determine the sequence of the complementary strand. For some students, these sorts of quick practice are necessary to reinforce a concept and break up a lecture. 5. To explain the adaptive advantage of multiple replication sites over a single site of replication, ask your students to imagine copying, by hand, the first ten chapters of your biology textbook. The task would certainly go faster if ten students each copied a different chapter! 6. There are about 2 million characters (letters or numbers) in the Campbell Essential Biology with Physiology textbook. The accuracy of DNA replication would be like copying every letter and number in this textbook by hand 500 times and writing just one letter or number incorrectly, making one error in every 1 billion characters! 7. The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these other chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. © 2013 Pearson Education, Inc. 5

Figure 9.3 (a) Each DNA nucleotide is made up of a sugar, a phosphate group, and a base. (b) Cytosine and thymine are pyrimidines. Guanine and adenine are purines.

Phosphate group Nitrogenous base Nitrogenous base Sugar (can be A, G, C, or T) DNA nucleotide Thymine (T) DNA double helix Phosphate group Figure 10.1 The chemical structure of a DNA polynucleotide Sugar (deoxyribose) DNA nucleotide Polynucleotide Sugar-phosphate backbone

Hydrogen bond (b) Atomic model Figure 10.5 Three representations of DNA (part 2) (b) Atomic model

DNA Replication – semiconservative replication Student Misconceptions and Concerns 1. If your class has not yet studied Chapter 3, consider assigning the Chapter 3 section on “Nucleic Acids” before addressing the contents of Chapter 10. 2. The text describes but does not specifically point out that DNA replication is semiconservative. Tell your students about an experiment in which a DNA molecule is labeled, then replicated. How will the two DNA molecules compare with regard to the location/distribution of the original DNA molecule? Will one DNA molecule be the original and the other the new copy? Or is there another possibility? Half of each of the two DNA molecules is new and half is the original; thus, it used semiconservative replication. Analogies for semiconservative replication can be a challenge. But in a sense, DNA replication is similar to parents getting divorced and then each parent remarrying someone else. The two new couples represent “half old parent and half new person.” 3. Students often confuse the terms nucleic acids, nucleotides, and bases. It helps just to note the hierarchy of relationships: Nucleic acids consist of long chains of nucleotides, and nucleotides include bases as part of their structure. Teaching Tips 1. Consider comparing DNA, RNA, and proteins to a train (polymer). DNA and RNA are like a train of various lengths and combinations of four types of train cars (monomers). Proteins are also “trains” of various lengths but made of a combination of 20 types of train cars. 2. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. You might remind your class of all the prior research (identifying DNA as the genetic material and clues to its structure) that brought Watson and Crick to their historic conclusions. 3. The authors note that the structure of DNA is analogous to a twisted rope ladder. In class, challenge your students to explain what the parts of the ladder represent. The wooden rungs represent a base pair and each rope the sugar-phosphate backbone. 4. Demonstrate the complementary base pairing within DNA. Present students with the base sequence to one side of a DNA molecule and have them work quickly at their seats to determine the sequence of the complementary strand. For some students, these sorts of quick practice are necessary to reinforce a concept and break up a lecture. 5. To explain the adaptive advantage of multiple replication sites over a single site of replication, ask your students to imagine copying, by hand, the first ten chapters of your biology textbook. The task would certainly go faster if ten students each copied a different chapter! 6. There are about 2 million characters (letters or numbers) in the Campbell Essential Biology with Physiology textbook. The accuracy of DNA replication would be like copying every letter and number in this textbook by hand 500 times and writing just one letter or number incorrectly, making one error in every 1 billion characters! 7. The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these other chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids. 9

Daughter DNA molecules (double helices) Parental (old) DNA molecule Daughter (new) strand Parental (old) strand Figure 10.6 DNA replication Daughter DNA molecules (double helices)

RNA - Ribonucleic Acid Structure of RNA: Sugar is Ribose No T, Uracil (U) instead Single stranded (ss)

C G A T C G A U Nitrogenous base Number of strands 2 1 Figure 10.UN03b DNA RNA C G A T C G A U Nitrogenous base Deoxy- ribose Sugar Ribose Figure 10.UN03 Summary of Key Concepts: DNA and RNA Structure (part 2) Number of strands 2 1

How do DNA and RNA work together? DNA makes a copy of itself in the form of RNA transcription RNA is used to make proteins Translation * Please note  DNA replication is a completely separate process that is NOT related to transcription and/or translation!

TRANSCRIPTION TRANSLATION Figure 10.UN05 TRANSCRIPTION TRANSLATION Gene Figure 10.UN05 Summary of Key Concepts: From Nucleotides to Amino Acids mRNA Polypeptide DNA

Types of RNA 1. Messenger RNA (mRNA) Carries the message from DNA  directions for making a protein

Types of RNA con’t. 2. Transfer RNA (tRNA) Carries and transfers amino acids to mRNA

Types of RNA con’t. 3. Ribosomal RNA (rRNA) Mixed with protein to make ribosomes Two subunits (large & small) used to facilitate translation

Figure 9.19 The protein synthesis machinery includes the large and small subunits of the ribosome, mRNA, and tRNA. (credit: modification of work by NIGMS, NIH)

Growing polypeptide Amino acid Large ribosomal subunit tRNA mRNA Figure 10.UN06 Growing polypeptide Amino acid Large ribosomal subunit tRNA mRNA Figure 10.UN06 Summary of Key Concepts: Translation: The Players Anticodon Small ribosomal subunit Codons

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