The Structure and Function of DNA

The Structure and Function of DNA
Chapter 10 The Structure and Function of DNA

Biology and Society: Tracking a Killer
The influenza virus is one of the deadliest pathogens in the world. Each year in the United States, over 20,000 people die from influenza infection. In the flu of 1918–1919, about 40 million people died worldwide. Vaccines against the flu are the best way to protect public health. Because flu viruses mutate quickly, new vaccines must be created every year. © 2010 Pearson Education, Inc.

Figure 10.00b Figure 10.0b The influenza virus.

DNA: STRUCTURE AND REPLICATION
Was known to be a chemical in cells by the end of the nineteenth century Has the capacity to store genetic information Can be copied and passed from generation to generation DNA and RNA are nucleic acids. They consist of chemical units called nucleotides. The nucleotides are joined by a sugar-phosphate backbone. 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 10 chapters of your biology textbook. The task would certainly go faster if 10 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!

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

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

Phosphate group DNA nucleotide
Nitrogenous base (can be A, G, C, or T) Thymine (T) Phosphate group Sugar (deoxyribose) DNA nucleotide Figure 10.1b Figure 10.1b The chemical structure of a DNA polynucleotide.

Phosphate Sugar (ribose) Figure 10.2
Figure 10.2 An RNA polynucleotide.

Watson and Crick’s Discovery of the Double Helix
The four nucleotides found in DNA differ in their nitrogenous bases. These bases are: Thymine (T) Cytosine (C) Adenine (A) Guanine (G) RNA has uracil (U) in place of thymine. Watson and Crick’s Discovery of the Double Helix James Watson and Francis Crick determined that DNA is a double helix. 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 10 chapters of your biology textbook. The task would certainly go faster if 10 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!

James Watson (left) and Francis Crick
Figure 10.3a Figure 10.3a Discoverers of the double helix.

Watson and Crick used X-ray crystallography data to reveal the basic shape of DNA.
Rosalind Franklin collected the X-ray crystallography data. 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 10 chapters of your biology textbook. The task would certainly go faster if 10 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!

X-ray image of DNA Rosalind Franklin Figure 10.3b
Figure 10.3b Discoverers of the double helix.

The model of DNA is like a rope ladder twisted into a spiral.
The ropes at the sides represent the sugar-phosphate backbones. Each wooden rung represents a pair of bases connected by hydrogen bonds. DNA bases pair in a complementary fashion: Adenine (A) pairs with thymine (T) Cytosine (C) pairs with guanine (G) 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 10 chapters of your biology textbook. The task would certainly go faster if 10 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!

Twist Figure 10.4 Figure 10.4 A rope-ladder model of a double helix.

Hydrogen bond (a) Ribbon model (b) Atomic model (c) Computer model
Figure 10.5 Figure 10.5 Three representatives of DNA.

(a) Ribbon model Figure 10.5a Figure 10.5a Ribbon model of DNA.

Hydrogen bond (b) Atomic model Figure 10.5b
Figure 10.5b Atomic model of DNA.

(c) Computer model Figure 10.5c Figure 10.5c Computer model of DNA.

DNA Replication When a cell reproduces, a complete copy of the DNA must pass from one generation to the next. Watson and Crick’s model for DNA suggested that DNA replicates by a template mechanism. 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 10 chapters of your biology textbook. The task would certainly go faster if 10 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!

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

DNA can be damaged by ultraviolet light. DNA polymerases:
Are enzymes Make the covalent bonds between the nucleotides of a new DNA strand Are involved in repairing damaged DNA DNA replication in eukaryotes: Begins at specific sites on a double helix Proceeds in both directions 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 10 chapters of your biology textbook. The task would certainly go faster if 10 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!

Origin of replication Origin of replication Origin of replication
Parental strands Origin of replication Parental strand Daughter strand Bubble Two daughter DNA molecules Figure 10.7 Figure 10.7 Multiple "bubbles" in replicating DNA.

THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN
DNA functions as the inherited directions for a cell or organism. How are these directions carried out? © 2010 Pearson Education, Inc. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

How an Organism’s Genotype Determines Its Phenotype
An organism’s genotype is its genetic makeup, the sequence of nucleotide bases in DNA. The phenotype is the organism’s physical traits, which arise from the actions of a wide variety of proteins. DNA specifies the synthesis of proteins in two stages: Transcription, the transfer of genetic information from DNA into an RNA molecule Translation, the transfer of information from RNA into a protein © 2010 Pearson Education, Inc. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Nucleus DNA Cytoplasm Figure 10.8-1
Figure 10.8 The flow of genetic information in a eukaryotic cell. (Step 1)

Nucleus DNA TRANSCRIPTION RNA Cytoplasm Figure 10.8-2
Figure 10.8 The flow of genetic information in a eukaryotic cell. (Step 2)

Nucleus DNA TRANSCRIPTION RNA TRANSLATION Protein Cytoplasm
Figure Figure 10.8 The flow of genetic information in a eukaryotic cell. (Step 3)

The function of a gene is to dictate the production of a polypeptide.
A protein may consist of two or more different polypeptides. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

From Nucleotides to Amino Acids: An Overview
Genetic information in DNA is: Transcribed into RNA, then Translated into polypeptides What is the language of nucleic acids? In DNA, it is the linear sequence of nucleotide bases. A typical gene consists of thousands of nucleotides. A single DNA molecule may contain thousands of genes. When DNA is transcribed, the result is an RNA molecule. RNA is then translated into a sequence of amino acids in a polypeptide. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

What are the rules for translating the RNA message into a polypeptide?
A codon is a triplet of bases, which codes for one amino acid. FIGURE 10.10 Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

The Genetic Code The genetic code is: Of the 64 triplets:
The set of rules relating nucleotide sequence to amino acid sequence Shared by all organisms Of the 64 triplets: 61 code for amino acids 3 are stop codons, indicating the end of a polypeptide Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Gene 1 DNA molecule Gene 2 Gene 3 DNA strand TRANSCRIPTION RNA
TRANSLATION Codon Polypeptide Amino acid Figure 10.10 Figure Transcription of DNA and translation of codons.

DNA strand TRANSCRIPTION RNA TRANSLATION Codon Polypeptide Amino acid
Figure 10.10 Figure Transcription of DNA and translation of codons.

Second base of RNA codon
Phenylalanine (Phe) Tyrosine (Tyr) Cysteine (Cys) Serine (Ser) Stop Stop Leucine (Leu) Stop Tryptophan (Trp) Histidine (His) Leucine (Leu) Proline (Pro) Arginine (Arg) Glutamine (Gln) First base of RNA codon Third base of RNA codon Asparagine (Asn) Serine (Ser) Isoleucine (Ile) Threonine (Thr) Lysine (Lys) Arginine (Arg) Met or start Aspartic acid (Asp) Valine (Val) Alanine (Ala) Glycine (Gly) Glutamic acid (Glu) Figure 10.11 Figure The dictionary of the genetic code, listed by RNA codons.

Transcription: From DNA to RNA
Makes RNA from a DNA template Uses a process that resembles DNA replication Substitutes uracil (U) for thymine (T) RNA nucleotides are linked by RNA polymerase. There are stages to Transcription: Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Initiation of Transcription
The “start transcribing” signal is a nucleotide sequence called a promoter. The first phase of transcription is initiation, in which: RNA polymerase attaches to the promoter RNA synthesis begins Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

RNA Elongation During the second phase of transcription, called elongation: The RNA grows longer The RNA strand peels away from the DNA template Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Termination of Transcription
During the third phase of transcription, called termination: RNA polymerase reaches a sequence of DNA bases called a terminator Polymerase detaches from the RNA The DNA strands rejoin Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

(a) A close-up view of transcription (b) Transcription of a gene
RNA polymerase DNA of gene Promoter DNA Initiation Terminator DNA RNA Area shown in part (a) at left Elongation RNA nucleotides RNA polymerase Termination Growing RNA Newly made RNA Completed RNA Direction of transcription Template strand of DNA RNA polymerase (a) A close-up view of transcription (b) Transcription of a gene Figure 10.13 Figure Transcription

(a) A close-up view of transcription
RNA nucleotides RNA polymerase Newly made RNA Direction of transcription Template strand of DNA (a) A close-up view of transcription Figure 10.13a Figure 10.13a Transcription

Area shown in part (a) at left Elongation
RNA polymerase DNA of gene Promoter DNA Initiation Terminator DNA RNA Area shown in part (a) at left Elongation Termination Growing RNA Completed RNA RNA polymerase (b) Transcription of a gene Figure 10.13b Figure 10.13b Transcription

The Processing of Eukaryotic RNA
After transcription: Eukaryotic cells process RNA Prokaryotic cells do not RNA processing includes: Adding a cap and tail Removing introns Splicing exons together to form messenger RNA (mRNA) Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Addition of cap and tail
Intron Exon Intron Exon Exon DNA Transcription Addition of cap and tail Cap RNA transcript with cap and tail Tail Introns removed Exons spliced together mRNA Coding sequence Nucleus Cytoplasm Figure 10.14 Figure The production of messenger RNA (mRNA) in a eukaryotic cell.

Translation: The Players
Translation is the conversion from the nucleic acid language to the protein language. Messenger RNA (mRNA) Translation requires: mRNA ATP Enzymes Ribosomes Transfer RNA (tRNA) Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Transfer RNA (tRNA) Transfer RNA (tRNA):
Acts as a molecular interpreter Carries amino acids Matches amino acids with codons in mRNA using anticodons Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

RNA polynucleotide chain
Amino acid attachment site Hydrogen bond RNA polynucleotide chain Anticodon tRNA (simplified representation) tRNA polynucleotide (ribbon model) Figure 10.15 Figure The structure of tRNA

Ribosomes Ribosomes are organelles that:
Coordinate the functions of mRNA and tRNA Are made of two protein subunits Contain ribosomal RNA (rRNA) A fully assembled ribosome holds tRNA and mRNA for use in translation. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

(a) A simplified diagram of a ribosome
Next amino acid to be added to polypeptide tRNA binding sites Growing polypeptide P site A site Ribosome tRNA Large subunit mRNA binding site mRNA Small subunit Codons (a) A simplified diagram of a ribosome (b) The “players” of translation Figure 10.16 Figure The ribosome.

(a) A simplified diagram of a ribosome
tRNA binding sites P site A site Ribosome Large subunit mRNA binding site Small subunit (a) A simplified diagram of a ribosome Figure 10.16a Figure 10.16a The ribosome.

(b) The “players” of translation
Next amino acid to be added to polypeptide Growing polypeptide tRNA mRNA Codons (b) The “players” of translation Figure 10.16b Figure 10.16b The ribosome.

Translation: The Process
Translation is divided into three phases: Initiation Elongation Termination Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Initiation Initiation brings together:
mRNA The first amino acid, Met, with its attached tRNA Two subunits of the ribosome The mRNA molecule has a cap and tail that help it bind to the ribosome. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Cap Start of genetic message End Tail Figure 10.17
Figure A molecule of mRNA.

Initiation occurs in two steps:
First, an mRNA molecule binds to a small ribosomal subunit, then an initiator tRNA binds to the start codon. Second, a large ribosomal subunit binds, creating a functional ribosome. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Met Large ribosomal subunit Initiator tRNA P site A site mRNA Start
codon Small ribosomal subunit Figure 10.18 Figure The initiation of translation

Elongation Elongation occurs in three steps.
Step 1, codon recognition: the anticodon of an incoming tRNA pairs with the mRNA codon at the A site of the ribosome. Step 2, peptide bond formation: The polypeptide leaves the tRNA in the P site and attaches to the amino acid on the tRNA in the A site The ribosome catalyzes the bond formation between the two amino acids Step 3, translocation: The P site tRNA leaves the ribosome The tRNA carrying the polypeptide moves from the A to the P site Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Amino acid Polypeptide Codon recognition ELONGATION P site mRNA
Anticodon A site Codons Codon recognition ELONGATION Figure Figure The elongation of a polypeptide. (Step 1)

Peptide bond formation
Amino acid Polypeptide P site mRNA Anticodon A site Codons Codon recognition ELONGATION Peptide bond formation Figure Figure The elongation of a polypeptide. (Step 2)

Amino acid Polypeptide P site mRNA Anticodon A site Codons Codon recognition ELONGATION Peptide bond formation New peptide bond mRNA movement Translocation Figure Figure The elongation of a polypeptide. (Step 3)

Amino acid Polypeptide P site mRNA Anticodon A site Codons Codon recognition ELONGATION Stop codon Peptide bond formation New peptide bond mRNA movement Translocation Figure Figure The elongation of a polypeptide. (Step 4)

Termination Elongation continues until:
The ribosome reaches a stop codon The completed polypeptide is freed The ribosome splits into its subunits Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Review: DNA RNA Protein
In a cell, genetic information flows from DNA to RNA in the nucleus and RNA to protein in the cytoplasm. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Transcription Nucleus Intron DNA RNA polymerase mRNA Figure 10.20-1
Figure A summary of transcription and translation. (Step 1)

Transcription Nucleus Intron RNA processing Cap Tail mRNA Intron DNA
RNA polymerase Transcription Nucleus DNA mRNA Intron RNA processing Cap Tail mRNA Intron Figure Figure A summary of transcription and translation. (Step 2)

Transcription Nucleus Intron RNA processing Cap Tail mRNA Intron
RNA polymerase Transcription Nucleus DNA mRNA Intron RNA processing Cap Tail mRNA Intron Amino acid tRNA Enzyme ATP Amino acid attachment Figure Figure A summary of transcription and translation. (Step 3)

RNA polymerase Transcription Nucleus DNA mRNA Intron RNA processing Cap Tail mRNA Intron Amino acid Ribosomal subunits tRNA Enzyme ATP Initiation of translation Amino acid attachment Figure Figure A summary of transcription and translation. (Step 4)

RNA polymerase Transcription Nucleus DNA mRNA Intron RNA processing Cap Tail mRNA Intron Anticodon Amino acid Ribosomal subunits Codon tRNA Enzyme Elongation ATP Initiation of translation Amino acid attachment Figure Figure A summary of transcription and translation. (Step 5)

Transcription Polypeptide Nucleus Stop codon Intron RNA processing Cap
RNA polymerase Transcription Polypeptide Nucleus DNA mRNA Stop codon Intron RNA processing Cap Termination Tail mRNA Intron Anticodon Amino acid Ribosomal subunits Codon tRNA Enzyme Elongation ATP Initiation of translation Amino acid attachment Figure Figure A summary of transcription and translation. (Step 6)

As it is made, a polypeptide:
Coils and folds Assumes a three-dimensional shape, its tertiary structure Several polypeptides may come together, forming a protein with quaternary structure. FIGURE 3.20 PAGE 48 Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Transcription and translation are how genes control:
The structures The activities of cells Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Mutations A mutation is any change in the nucleotide sequence of DNA.
Mutations can change the amino acids in a protein. Mutations can involve: Large regions of a chromosome Just a single nucleotide pair, as occurs in sickle cell anemia Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Types of Mutations Mutations within a gene can occur as a result of:
Base substitution, the replacement of one base by another Nucleotide deletion, the loss of a nucleotide Nucleotide insertion, the addition of a nucleotide Insertions and deletions can: Change the reading frame of the genetic message Lead to disastrous effects Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Sickle-cell hemoglobin
Normal hemoglobin DNA Mutant hemoglobin DNA mRNA mRNA Normal hemoglobin Sickle-cell hemoglobin Figure 10.21 Figure The molecular basis of sickle-cell disease.

Mutagens Mutations may result from:
Errors in DNA replication Physical or chemical agents called mutagens Although mutations are often harmful, they are the source of genetic diversity, which is necessary for evolution by natural selection. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

mRNA and protein from a normal gene
(a) Base substitution Deleted (b) Nucleotide deletion Inserted (c) Nucleotide insertion Figure 10.22 Figure Three types of mutations and their effects.

VIRUSES AND OTHER NONCELLULAR INFECTIOUS AGENTS
Viruses exhibit some, but not all, characteristics of living organisms. Viruses: Possess genetic material in the form of nucleic acids Are not cellular and cannot reproduce on their own. Bacteriophages Bacteriophages, or phages, are viruses that attack bacteria. Student Misconceptions and Concerns 1. Students and many parents with young children expect a treatment of antibiotics for many respiratory infections, even though such infections may result from a virus. Students will benefit by a thorough explanation of the inappropriate use of antibiotics for viral infections and the risks of overuse of antibiotics leading to increased numbers of antibiotic-resistant bacteria. 2. The success of modern medicine has perhaps led to an overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! 2. Viruses can spread throughout a plant by moving through plasmodesmata (not specifically discussed in this chapter). This is like smoke spreading throughout a building by moving through air ducts. 3. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 4. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. The Centers for Disease Control and Prevention has extensive information about AIDS at

Protein coat DNA Figure 10.24 Figure Adenovirus

Phages have two reproductive cycles.
(1) In the lytic cycle: Many copies of the phage are made within the bacterial cell, and then The bacterium lyses (breaks open) (2) In the lysogenic cycle: The phage DNA inserts into the bacterial chromosome and The bacterium reproduces normally, copying the phage at each cell division Student Misconceptions and Concerns 1. Students and many parents with young children expect a treatment of antibiotics for many respiratory infections, even though such infections may result from a virus. Students will benefit by a thorough explanation of the inappropriate use of antibiotics for viral infections and the risks of overuse of antibiotics leading to increased numbers of antibiotic-resistant bacteria. 2. The success of modern medicine has perhaps led to an overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! 2. Viruses can spread throughout a plant by moving through plasmodesmata (not specifically discussed in this chapter). This is like smoke spreading throughout a building by moving through air ducts. 3. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 4. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. The Centers for Disease Control and Prevention has extensive information about AIDS at

Head Bacteriophage (200 nm tall) Tail Tail fiber DNA Bacterial cell of
virus Bacterial cell Colorized TEM Figure 10.25 Figure Bacteriophages (viruses) infecting a bacterial cell.

Plant Viruses Viruses that infect plants can: Stunt growth
Diminish plant yields Spread throughout the entire plant Student Misconceptions and Concerns 1. Students and many parents with young children expect a treatment of antibiotics for many respiratory infections, even though such infections may result from a virus. Students will benefit by a thorough explanation of the inappropriate use of antibiotics for viral infections and the risks of overuse of antibiotics leading to increased numbers of antibiotic-resistant bacteria. 2. The success of modern medicine has perhaps led to an overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! 2. Viruses can spread throughout a plant by moving through plasmodesmata (not specifically discussed in this chapter). This is like smoke spreading throughout a building by moving through air ducts. 3. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 4. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. The Centers for Disease Control and Prevention has extensive information about AIDS at

Figure 10.26-1 Phage Phage attaches Phage DNA to cell. Cell lyses,
Bacterial chromosome (DNA) Cell lyses, releasing phages. Phage injects DNA LYTIC CYCLE Phages assemble Phage DNA circularizes. OR New phage DNA and proteins are synthesized. Figure Figure Alternative phage reproductive cycles. (Step 1)

Figure 10.26-2 Phage Phage attaches Phage DNA to cell. Cell lyses,
Bacterial chromosome (DNA) Cell lyses, releasing phages. Phage injects DNA Many cell divisions Occasionally a prophage may leave the bacterial chromosome. LYTIC CYCLE LYSOGENIC CYCLE Phages assemble Phage DNA circularizes. Lysogenic bacterium reproduces normally, replicating the prophage at each cell division. Prophage OR New phage DNA and proteins are synthesized. Phage DNA is inserted into the bacterial chromosome. Figure Figure Alternative phage reproductive cycles. (Step 2)

Phage lambda E. coli Figure 10.26c
Figure 10.26c Alternative phage reproductive cycles.

Viral plant diseases: Have no cure
Are best prevented by producing plants that resist viral infection Student Misconceptions and Concerns 1. Students and many parents with young children expect a treatment of antibiotics for many respiratory infections, even though such infections may result from a virus. Students will benefit by a thorough explanation of the inappropriate use of antibiotics for viral infections and the risks of overuse of antibiotics leading to increased numbers of antibiotic-resistant bacteria. 2. The success of modern medicine has perhaps led to an overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! 2. Viruses can spread throughout a plant by moving through plasmodesmata (not specifically discussed in this chapter). This is like smoke spreading throughout a building by moving through air ducts. 3. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 4. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. The Centers for Disease Control and Prevention has extensive information about AIDS at

Tobacco mosaic virus RNA Protein Figure 10.27
Figure Tobacco mosaic virus

Animal Viruses Viruses that infect animals are:
Common causes of disease May have RNA or DNA genomes Some animal viruses steal a bit of host cell membrane as a protective envelope. The reproductive cycle of an enveloped RNA virus can be broken into seven steps. Student Misconceptions and Concerns 1. Students and many parents with young children expect a treatment of antibiotics for many respiratory infections, even though such infections may result from a virus. Students will benefit by a thorough explanation of the inappropriate use of antibiotics for viral infections and the risks of overuse of antibiotics leading to increased numbers of antibiotic-resistant bacteria. 2. The success of modern medicine has perhaps led to an overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! 2. Viruses can spread throughout a plant by moving through plasmodesmata (not specifically discussed in this chapter). This is like smoke spreading throughout a building by moving through air ducts. 3. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 4. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. The Centers for Disease Control and Prevention has extensive information about AIDS at

Membranous envelope Protein spike Protein coat RNA Figure 10.28
Figure An influenza virus.

Virus Protein spike Viral RNA (genome) Protein coat Envelope
Plasma membrane of host cell Entry Uncoating Viral RNA (genome) RNA synthesis by viral enzyme Protein synthesis RNA synthesis (other strand) mRNA Template New viral genome Assembly New viral proteins Exit Figure 10.29 Figure The reproductive cycle of an enveloped virus.

Virus Protein spike Protein coat Viral RNA (genome) Envelope Entry
Plasma membrane of host cell Uncoating Viral RNA (genome) RNA synthesis by viral enzyme Figure 10.29a Figure 10.29a The reproductive cycle of an enveloped virus.

RNA synthesis Protein (other strand) synthesis Template New viral
mRNA Template New viral genome Assembly New viral proteins Exit Figure 10.29b Figure 10.29b The reproductive cycle of an enveloped virus.

Mumps virus Protein spike Envelope Figure 10.29c
Colorized TEM Figure 10.29c Figure 10.29c The reproductive cycle of an enveloped virus.

HIV, the AIDS Virus HIV is a retrovirus, an RNA virus that reproduces by means of a DNA molecule. Retroviruses use the enzyme reverse transcriptase to synthesize DNA on an RNA template. HIV steals a bit of host cell membrane as a protective envelope. The behavior of HIV nucleic acid in an infected cell can be broken into six steps. Student Misconceptions and Concerns 1. Students and many parents with young children expect a treatment of antibiotics for many respiratory infections, even though such infections may result from a virus. Students will benefit by a thorough explanation of the inappropriate use of antibiotics for viral infections and the risks of overuse of antibiotics leading to increased numbers of antibiotic-resistant bacteria. 2. The success of modern medicine has perhaps led to an overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! 2. Viruses can spread throughout a plant by moving through plasmodesmata (not specifically discussed in this chapter). This is like smoke spreading throughout a building by moving through air ducts. 3. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 4. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. The Centers for Disease Control and Prevention has extensive information about AIDS at

Envelope Surface protein Protein coat RNA (two identical strands)
Reverse transcriptase Figure 10.31 Figure HIV, the AIDS virus.

HIV (red dots) infecting
Reverse transcriptase Viral RNA Cytoplasm Nucleus DNA strand Chromosomal DNA Provirus Double stranded DNA Viral RNA and proteins RNA SEM HIV (red dots) infecting a white blood cell Figure 10.32 Figure The behavior of HIV nucleic acid in an infected cell.

Reverse transcriptase Cytoplasm Viral RNA Nucleus DNA strand
Chromosomal DNA Provirus Double stranded DNA Viral RNA and proteins RNA Figure 10.32a Figure 10.32a The behavior of HIV nucleic acid in an infected cell.

AIDS (acquired immune deficiency syndrome) is:
Caused by HIV infection and Treated with drugs that interfere with the reproduction of the virus Student Misconceptions and Concerns 1. Students and many parents with young children expect a treatment of antibiotics for many respiratory infections, even though such infections may result from a virus. Students will benefit by a thorough explanation of the inappropriate use of antibiotics for viral infections and the risks of overuse of antibiotics leading to increased numbers of antibiotic-resistant bacteria. 2. The success of modern medicine has perhaps led to an overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! 2. Viruses can spread throughout a plant by moving through plasmodesmata (not specifically discussed in this chapter). This is like smoke spreading throughout a building by moving through air ducts. 3. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 4. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. The Centers for Disease Control and Prevention has extensive information about AIDS at

Thymine (T) Part of a T nucleotide AZT Figure 10.33
Figure AZT and the T nucleotide.

Viroids and Prions Two classes of pathogens are smaller than viruses:
Viroids are small circular RNA molecules that do not encode proteins Prions are misfolded proteins that somehow convert normal proteins to the misfolded prion version Prions are responsible for neurodegenerative diseases including: Mad cow disease Scrapie in sheep and goats Chronic wasting disease in deer and elk Creutzfeldt-Jakob disease in humans Student Misconceptions and Concerns 1. Students and many parents with young children expect a treatment of antibiotics for many respiratory infections, even though such infections may result from a virus. Students will benefit by a thorough explanation of the inappropriate use of antibiotics for viral infections and the risks of overuse of antibiotics leading to increased numbers of antibiotic-resistant bacteria. 2. The success of modern medicine has perhaps led to an overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! 2. Viruses can spread throughout a plant by moving through plasmodesmata (not specifically discussed in this chapter). This is like smoke spreading throughout a building by moving through air ducts. 3. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 4. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. The Centers for Disease Control and Prevention has extensive information about AIDS at

Evolution Connection: Emerging Viruses
Emerging viruses are viruses that have: Appeared suddenly or Have only recently come to the attention of science Avian flu: Infects birds Infected 18 people in 1997 Since has spread to Europe and Africa infecting 300 people and killing 200 of them If avian flu mutates to a form that can easily spread between people, the potential for a major human outbreak is significant. © 2010 Pearson Education, Inc. Student Misconceptions and Concerns 1. Students and many parents with young children expect a treatment of antibiotics for many respiratory infections, even though such infections may result from a virus. Students will benefit by a thorough explanation of the inappropriate use of antibiotics for viral infections and the risks of overuse of antibiotics leading to increased numbers of antibiotic-resistant bacteria. 2. The success of modern medicine has perhaps led to an overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! 2. Viruses can spread throughout a plant by moving through plasmodesmata (not specifically discussed in this chapter). This is like smoke spreading throughout a building by moving through air ducts. 3. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 4. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. The Centers for Disease Control and Prevention has extensive information about AIDS at

New viruses can arise by:
Mutation of existing viruses Spread to new host species Student Misconceptions and Concerns 1. Students and many parents with young children expect a treatment of antibiotics for many respiratory infections, even though such infections may result from a virus. Students will benefit by a thorough explanation of the inappropriate use of antibiotics for viral infections and the risks of overuse of antibiotics leading to increased numbers of antibiotic-resistant bacteria. 2. The success of modern medicine has perhaps led to an overconfidence in our ability to treat disease. Students often do not understand that there are few successful treatments for viral infections. Instead, the best defense against viruses is prevention by reducing the chances of contacting the virus and the use of vaccines. Teaching Tips 1. Students (and instructors) might enjoy thinking of a prophage as a smudge mark on the master copy of a class handout. The smudge is replicated every time the original is copied! 2. Viruses can spread throughout a plant by moving through plasmodesmata (not specifically discussed in this chapter). This is like smoke spreading throughout a building by moving through air ducts. 3. There is an interesting relationship between the speed at which a virus kills or debilitates a host and the extent to which it spreads from one organism to another. This is something to consider for a class discussion. Compare two viral infections. Infection A multiplies within the host, is spread by the host to other people through casual contact, but does not cause its lethal symptoms until 5–10 years after infection. Virus B kills the host within 1–2 days of infection, is easily transmitted, and causes severe symptoms within hours of contact. Which virus is likely to spread the fastest through the human population on Earth? Which might be considered the most dangerous to humans? 4. Students often do not understand the disproportionate distribution of HIV infections and AIDS in our world. Consider an Internet assignment, asking students to identify the regions of the world most affected by HIV-AIDS. The Centers for Disease Control and Prevention has extensive information about AIDS at

Figure 10.UN1 Figure 10.UN1 Transcription orientation diagram

Figure 10.UN2 Figure 10.UN2 Translation orientation diagram

Nitrogenous base Phosphate group DNA Sugar Polynucleotide Nucleotide
RNA C G A T C G A U Nitrogenous base Deoxy- ribose Sugar Ribose Number of strands 2 1 Figure 10.UN3 Figure 10.UN3 Summary: DNA and RNA Structure

Parental DNA molecule New daughter strand Identical daughter
DNA molecules Figure 10.UN4 Figure 10.UN4 Summary: DNA Replication

TRANSCRIPTION TRANSLATION Gene Polypeptide mRNA DNA Figure 10.UN5
Figure 10.UN5 Summary: DNA to Protein

Growing polypeptide Amino acid Large ribosomal subunit tRNA mRNA
Anticodon Codons Small ribosomal subunit Figure 10.UN6 Figure 10.UN6 Summary: Translation: The Players

Figure 10.UN7 Figure 10.UN7 Summary: Mutations

The Structure and Function of DNA

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