1. DNA TRANSCRIPTION and TRANSLATION
Chapter 10
DNA TRANSCRIPTION and TRANSLATION

2. THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN
WARM UP
What are proteins?
Where do they come from?
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 2

3. THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN
DNA in our cells carry the instructions for making proteins in order for our cells to function.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 3

4. 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.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 4

5. How an Organism’s Genotype Determines Its Phenotype
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.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 5

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

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

8. RNA Overview Back to chapter 3!!!!
RNA = ribonucleic acid (ribose sugar)
Instead of THYMINE, RNA has URACIL
Single strand
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 8

9. 3 Types of RNA mRNA = messanger RNA tRNA = transfer RNA
rRNA = ribosomal RNA
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 9

10. 3 Types of RNA mRNA = messanger RNA
made by transcription of the original DNA molecule
a messanger from the DNA to the rest of the cell.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 10

11. 3 Types of RNA tRNA = transfer RNA
interpreter, converts the language in mRNA into the language of proteins (amino acid monomers)
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 11

12. 3 Types of RNA rRNA = ribosomal RNA
rRNA is combined with proteins to form a ribosome, which is the site of protein synthesis
coordinate the functions of mRNA and 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 12

13. TRANSCRIPTION TRANSLATION
Figure 10.10a
DNA strand
TRANSCRIPTION
RNA
TRANSLATION
Codon
Polypeptide
Amino acid
Figure Transcription of DNA and translation of codons (detail)

14. DNA to mRNA Problems Given the DNA sequence, construct an mRNA for the following pieces of DNA. TTCAGCGATACCGTAGGA TACCCCGTATTGGAAATT AAACCGGCAAAATTGCTC
Figure Transcription of DNA and translation of codons (detail)

15. Transcription: From DNA to RNA
makes mRNA from a DNA template,
substitutes uracil (U) for thymine (T).
uses a process that resembles the synthesis of a DNA strand during DNA replication
Lets take a closer look at this process!!!
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 15

16. Transcription: From DNA to RNA
THE BIG PICTURE
Transfer of genetic information from DNA to RNA resembles the process of DNA replication!
Only 1 strand of DNA is used as a template for mRNA synthesis.
RNA nucleotides are linked by the transcription enzyme RNA polymerase.
End result is 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 16

17. (a) A close-up view of transcription
Figure 10.13a
RNA polymerase
RNA nucleotides
Newly made RNA
Template
strand of DNA
(a) A close-up view of transcription
Figure Transcription (part 1)

18. STEP 1: Initiation of Transcription
The “start transcribing” signal is a nucleotide sequence called a promoter
located in the DNA sequence at the beginning of the gene which is being transcribed.
a specific place where RNA polymerase attaches.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 18

19. Elongation, the second phase of transcription
STEP 2: RNA Elongation
Elongation, the second phase of transcription
the RNA grows longer
the RNA strand peels away from its 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 19

20. STEP 3: Termination of Transcription
Termination, third phase of transcription
RNA polymerase reaches a special sequence of bases in the DNA template called a terminator, signaling the end of the gene
polymerase detaches from the RNA and the gene (DNA)
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 20

21. (b) Transcription of a gene
Figure 10.13b
RNA polymerase
DNA of gene
Promoter DNA 1
Initiation
Terminator DNA
RNA 2
Elongation 3
Termination
Growing RNA
Completed RNA
RNA polymerase
(b) Transcription of a gene
Figure Transcription (part 2)

22. The Processing of Eukaryotic RNA
So…we now have an RNA strand….now what?
Prokaryotic cells
RNA transcribed from a gene immediately functions as messenger RNA (mRNA), the molecule that is translated into protein.
Eukaryotic cells
localizes transcription in the nucleus (because they have one!!)
modifies, or processes, the RNA transcript in the nucleus before it move to the cytoplasm for translation by a 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 22

23. The Processing of Eukaryotic RNA
RNA processing includes
adding a cap and tail consisting of extra nucleotides at the ends of the RNA transcript
helps to protect the RNA from enzyme attack!
help ribosomes recognize RNA as mRNA.
removing introns (noncoding regions of the RNA)
RNA splicing, joining exons (the parts of the gene that are expressed) 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 23

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

25. The Processing of Eukaryotic RNA
RNA splicing is believed to play a significant role in humans
in allowing our approximately 21,000 genes to produce many thousands more polypeptides by varying the exons that are included in the final 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 25

26. From Nucleotides to Amino Acids: An Overview
The flow of information from gene to protein is based on a triplet code.
A codon is a triplet of bases, which codes for one amino acid.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 26

27. The Genetic Code
The genetic code is the set of rules that convert a nucleotide sequence in RNA to an amino acid sequence.
Of the 64 triplet codes,
61 code for amino acids
3 are stop codons, instructing the ribosomes to end the 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 27

28. Second base of RNA codon U C A G
Figure 10.11
Second base of RNA codon U C A G
UUU UUC
UCU UCC UCA UCG
UAU UAC
UGU UGC
U C A G
Phenylalanine
(Phe)
Tyrosine
(Tyr)
Cysteine
(Cys) U
Serine
(Ser)
UUA UUG
UAA
UGA
Stop
Stop
Leucine
(Leu)
UAG
UGG
Stop
Tryptophan (Trp)
CUU CUC CUA CUG
CCU CCC CCA CCG
CAU CAC
CGU CGC CGA CGG
U C A G
Histidine
(His) C
Leucine
(Leu)
Proline
(Pro)
Arginine
(Arg)
CAA CAG
Glutamine
(Gln)
Third base of RNA codon
First base of RNA codon
AUU AUC AUA
ACU ACC ACA ACG
AAU AAC
AGU AGC
U C A G
Asparagine
(Asn)
Serine
(Ser)
Isoleucine
(Ile) A
Threonine
(Thr)
AAA AAG
AGA AGG
Lysine
(Lys)
Arginine
(Arg)
AUG
Met or start
GUU GUC GUA GUG
GCU GCC GCA GCG
GAU GAC
GGU GGC
U C A G
Aspartic
acid (Asp) G
Valine
(Val)
Alanine
(Ala)
Glycine
(Gly)
GAA GAG
GGA GGG
Glutamic
acid (Glu)
Figure The dictionary of the genetic code, listed by RNA codons

29. The Genetic Code The genetic code is almost universal
Because diverse organisms share a common genetic code, it is possible to program one species to produce a protein from another species by transplanting DNA.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 29

30. Translation
Translation is the conversion from nucleic acid to protein.
Involves three crucial players
mRNA – result of transcription, direct message from DNA
tRNA – molecular interpreter, carries amino acids
rRNA – makes up a ribosome, which coordinates mRNA and tRNA functions
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 30

31. Translation: requirements
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 31

32. Transfer RNA (tRNA) Transfer RNA (tRNA)
matches amino acids with codons in mRNA using anticodons, a special triplet of bases that is complementary to a codon triplet on 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 32

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

34. Ribosomes Ribosomes are organelles that
coordinate the functions of mRNA and tRNA
are made of two subunits.
Each subunit is made up of
proteins
ribosomal RNA (rRNA).
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 34

35. (b) The “players” of translation
Figure 10.16b
Next amino acid
to be added to
polypeptide
Growing
polypeptide
tRNA
mRNA
Codons
(b) The “players” of translation
Figure The ribosome (part 2)

36. 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 36

37. Initiation Initiation brings together
mRNA, tRNA and the two subunits of the ribosome (rRNA)
The mRNA molecule has a cap and tail that help the mRNA bind to the ribosome. The pink portion also helps the mRNA 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 37

38. Initiation Initiation occurs in two steps.
An mRNA molecule binds to a small ribosomal subunit, then a special initiator tRNA binds to the start codon – AUG codon, UAC - anticodon,
A large ribosomal subunit binds to the small one, 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 38

39. 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.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 39

40. Peptide bond formation
Figure 10.19
Amino acid
Polypeptide
P site
Anticodon
mRNA
A site
Codons 1
Codon recognition
ELONGATION
Stop codon 2
Peptide bond formation
New peptide bond
mRNA movement 3
Translocation
Figure The elongation of a polypeptide

41. Elongation 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.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 41

42. Elongation 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 42

43. Elongation continues until
Termination
Elongation continues until
a stop codon reaches the ribosome’s A site,
the completed polypeptide is freed, and
the ribosome splits back 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 43

44. Review: DNA RNA Protein
In a cell, genetic information flows from
DNA to RNA in the nucleus
RNA to protein in the cytoplasm.
As it is made, a polypeptide
coils and folds and assumes a three-dimensional shape.
Determines the appearance and capabilities of the cell and organism.
Transcription and translation are how genes control the structures and 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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 44

45. Initiation of translation 6 Termination
Figure
RNA polymerase
Nucleus 1
Transcription
DNA
mRNA
Intron 2
RNA processing
Anticodon
Codon
Cap
Tail
mRNA
Polypeptide
Intron 5
Elongation
Amino acid
tRNA
Stop
codon
Ribosomal
subunits A
Anticodon
Enzyme
ATP 4
Initiation of translation 6
Termination 3
Amino acid attachment
Figure A summary of transcription and translation (step 6)

46. HOW AND WHY GENES ARE REGULATED
Every somatic cell (body cell, not sex cell) in an organism contains identical genetic instructions.
They all share the same genome.
So what makes cells different from one another?
Student Misconceptions and Concerns
1. The broad concept of selective “reading” of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of product manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation.
2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.3 can be a helpful reference to organize the potential sites of regulation.
Teaching Tips
1. Cellular differentiation is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type.
2. The lactose operon is turned on by removing the repressor—a sort of double negative. Students might enjoy various analogies to other types of “double negatives,” such as “When the cat’s away, the mice will play.” In another analogy, if Mom keeps the kids away from the cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. In this last analogy, the person occupying Mom’s attention functions most like lactose binding to the repressor.
3. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch.
4. The authors develop an analogy between the regulation of transcription and the series of water pipes that carry water from your local water supply, perhaps a reservoir, to a faucet in your home. At various points, valves control the flow of water. Similarly, the expression of genes is controlled at many points along the process. Figure 11.3 illustrates the “flow” of genetic information from a chromosome—a reservoir of genetic information—to an active protein that has been made in the cell’s cytoplasm. The multiple mechanisms that control gene expression are analogous to the control valves in water pipes. In the figure, a possible control knob indicates each gene expression “valve.” In the figure, the large size of the transcription control knob highlights its crucial role.
5. Just as a folded map is difficult to read, DNA packaging tends to prevent gene “reading” or expression.
6. Just as boxes of your things that will be little used are packed deeper into a closet, attic, or basement, chromatin that is not expressed is highly compacted and is stored away.
7. Alternative RNA splicing is like remixing music to produce a new song or re-editing a movie for a different ending. You could have a little fun by challenging students to identify which category of academic award is most like alternative RNA splicing. (Answer: the award for best editing.)
8. The action of an extracellular signal reaching a cell’s surface is like pushing the doorbell at a home. The signal is converted to another form (pushing a button rings a bell) and activities change within the house as someone comes to answer the door.
9. Students might wonder why a patch of color is all the same on the cat’s skin in Figure 11.4, if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation.
10.Homeotic genes are often called “master control genes.” The relationship between homeotic genes and structural genes is like the relationship between a construction supervisor and the workers. Major rearrangements can result from a few simple changes in the directions for construction.
11. There is much hope in the use of DNA microarrays to refine cancer therapies. In the past, a diagnosis of cancer was too often met with general treatments that benefited only a fraction of the patients. Physicians were left to wonder why some people with breast cancer or lung cancer responded to therapy while others did not. DNA microarrays enable us to identify differences between patients with the same apparent type of cancer (breast, lung, prostate, and so on). Consider sharing this important avenue of hope. It is likely that some of your students will soon have a family member facing these battles. 46

47. HOW AND WHY GENES ARE REGULATED
In cellular differentiation, cells become specialized in
structure and function.
Certain genes are turned on and off in the process of gene regulation.
Student Misconceptions and Concerns
1. The broad concept of selective “reading” of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of product manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation.
2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.3 can be a helpful reference to organize the potential sites of regulation.
Teaching Tips
1. Cellular differentiation is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type.
2. The lactose operon is turned on by removing the repressor—a sort of double negative. Students might enjoy various analogies to other types of “double negatives,” such as “When the cat’s away, the mice will play.” In another analogy, if Mom keeps the kids away from the cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. In this last analogy, the person occupying Mom’s attention functions most like lactose binding to the repressor.
3. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch.
4. The authors develop an analogy between the regulation of transcription and the series of water pipes that carry water from your local water supply, perhaps a reservoir, to a faucet in your home. At various points, valves control the flow of water. Similarly, the expression of genes is controlled at many points along the process. Figure 11.3 illustrates the “flow” of genetic information from a chromosome—a reservoir of genetic information—to an active protein that has been made in the cell’s cytoplasm. The multiple mechanisms that control gene expression are analogous to the control valves in water pipes. In the figure, a possible control knob indicates each gene expression “valve.” In the figure, the large size of the transcription control knob highlights its crucial role.
5. Just as a folded map is difficult to read, DNA packaging tends to prevent gene “reading” or expression.
6. Just as boxes of your things that will be little used are packed deeper into a closet, attic, or basement, chromatin that is not expressed is highly compacted and is stored away.
7. Alternative RNA splicing is like remixing music to produce a new song or re-editing a movie for a different ending. You could have a little fun by challenging students to identify which category of academic award is most like alternative RNA splicing. (Answer: the award for best editing.)
8. The action of an extracellular signal reaching a cell’s surface is like pushing the doorbell at a home. The signal is converted to another form (pushing a button rings a bell) and activities change within the house as someone comes to answer the door.
9. Students might wonder why a patch of color is all the same on the cat’s skin in Figure 11.4, if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation.
10.Homeotic genes are often called “master control genes.” The relationship between homeotic genes and structural genes is like the relationship between a construction supervisor and the workers. Major rearrangements can result from a few simple changes in the directions for construction.
11. There is much hope in the use of DNA microarrays to refine cancer therapies. In the past, a diagnosis of cancer was too often met with general treatments that benefited only a fraction of the patients. Physicians were left to wonder why some people with breast cancer or lung cancer responded to therapy while others did not. DNA microarrays enable us to identify differences between patients with the same apparent type of cancer (breast, lung, prostate, and so on). Consider sharing this important avenue of hope. It is likely that some of your students will soon have a family member facing these battles. 47

48. Patterns of Gene Expression in Differentiated Cells
In gene expression,
a gene is turned on and transcribed into RNA
information flows from
genes to proteins
genotype to phenotype.
Information flows from DNA to RNA to proteins.
The great differences among cells in an organism must result from the selective expression of genes.
Student Misconceptions and Concerns
1. The broad concept of selective “reading” of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of product manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation.
2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.3 can be a helpful reference to organize the potential sites of regulation.
Teaching Tips
1. Cellular differentiation is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type.
2. The lactose operon is turned on by removing the repressor—a sort of double negative. Students might enjoy various analogies to other types of “double negatives,” such as “When the cat’s away, the mice will play.” In another analogy, if Mom keeps the kids away from the cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. In this last analogy, the person occupying Mom’s attention functions most like lactose binding to the repressor.
3. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch.
4. The authors develop an analogy between the regulation of transcription and the series of water pipes that carry water from your local water supply, perhaps a reservoir, to a faucet in your home. At various points, valves control the flow of water. Similarly, the expression of genes is controlled at many points along the process. Figure 11.3 illustrates the “flow” of genetic information from a chromosome—a reservoir of genetic information—to an active protein that has been made in the cell’s cytoplasm. The multiple mechanisms that control gene expression are analogous to the control valves in water pipes. In the figure, a possible control knob indicates each gene expression “valve.” In the figure, the large size of the transcription control knob highlights its crucial role.
5. Just as a folded map is difficult to read, DNA packaging tends to prevent gene “reading” or expression.
6. Just as boxes of your things that will be little used are packed deeper into a closet, attic, or basement, chromatin that is not expressed is highly compacted and is stored away.
7. Alternative RNA splicing is like remixing music to produce a new song or re-editing a movie for a different ending. You could have a little fun by challenging students to identify which category of academic award is most like alternative RNA splicing. (Answer: the award for best editing.)
8. The action of an extracellular signal reaching a cell’s surface is like pushing the doorbell at a home. The signal is converted to another form (pushing a button rings a bell) and activities change within the house as someone comes to answer the door.
9. Students might wonder why a patch of color is all the same on the cat’s skin in Figure 11.4, if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation.
10.Homeotic genes are often called “master control genes.” The relationship between homeotic genes and structural genes is like the relationship between a construction supervisor and the workers. Major rearrangements can result from a few simple changes in the directions for construction.
11. There is much hope in the use of DNA microarrays to refine cancer therapies. In the past, a diagnosis of cancer was too often met with general treatments that benefited only a fraction of the patients. Physicians were left to wonder why some people with breast cancer or lung cancer responded to therapy while others did not. DNA microarrays enable us to identify differences between patients with the same apparent type of cancer (breast, lung, prostate, and so on). Consider sharing this important avenue of hope. It is likely that some of your students will soon have a family member facing these battles. 48

49. Gene Regulation in Bacteria
Natural selection has favored bacteria that express
only certain genes
only at specific times when the products are needed by the cell.
E. coli living in your intestines survive on what you eat, adjusting production of enzymes as needed for digestion of various food items.
So how do bacteria selectively turn their genes on and off?
Student Misconceptions and Concerns
1. The broad concept of selective “reading” of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of product manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation.
2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.3 can be a helpful reference to organize the potential sites of regulation.
Teaching Tips
1. Cellular differentiation is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type.
2. The lactose operon is turned on by removing the repressor—a sort of double negative. Students might enjoy various analogies to other types of “double negatives,” such as “When the cat’s away, the mice will play.” In another analogy, if Mom keeps the kids away from the cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. In this last analogy, the person occupying Mom’s attention functions most like lactose binding to the repressor.
3. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch.
4. The authors develop an analogy between the regulation of transcription and the series of water pipes that carry water from your local water supply, perhaps a reservoir, to a faucet in your home. At various points, valves control the flow of water. Similarly, the expression of genes is controlled at many points along the process. Figure 11.3 illustrates the “flow” of genetic information from a chromosome—a reservoir of genetic information—to an active protein that has been made in the cell’s cytoplasm. The multiple mechanisms that control gene expression are analogous to the control valves in water pipes. In the figure, a possible control knob indicates each gene expression “valve.” In the figure, the large size of the transcription control knob highlights its crucial role.
5. Just as a folded map is difficult to read, DNA packaging tends to prevent gene “reading” or expression.
6. Just as boxes of your things that will be little used are packed deeper into a closet, attic, or basement, chromatin that is not expressed is highly compacted and is stored away.
7. Alternative RNA splicing is like remixing music to produce a new song or re-editing a movie for a different ending. You could have a little fun by challenging students to identify which category of academic award is most like alternative RNA splicing. (Answer: the award for best editing.)
8. The action of an extracellular signal reaching a cell’s surface is like pushing the doorbell at a home. The signal is converted to another form (pushing a button rings a bell) and activities change within the house as someone comes to answer the door.
9. Students might wonder why a patch of color is all the same on the cat’s skin in Figure 11.4, if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation.
10.Homeotic genes are often called “master control genes.” The relationship between homeotic genes and structural genes is like the relationship between a construction supervisor and the workers. Major rearrangements can result from a few simple changes in the directions for construction.
11. There is much hope in the use of DNA microarrays to refine cancer therapies. In the past, a diagnosis of cancer was too often met with general treatments that benefited only a fraction of the patients. Physicians were left to wonder why some people with breast cancer or lung cancer responded to therapy while others did not. DNA microarrays enable us to identify differences between patients with the same apparent type of cancer (breast, lung, prostate, and so on). Consider sharing this important avenue of hope. It is likely that some of your students will soon have a family member facing these battles. 49

50. Gene Regulation in Bacteria
An operon includes
a cluster of genes with related functions
the control sequences that turn the genes on or off.
The bacterium E. coli uses the lac operon to coordinate the expression of genes that produce enzymes used to break down lactose in the bacterium’s environment.
Student Misconceptions and Concerns
1. The broad concept of selective “reading” of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of product manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation.
2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.3 can be a helpful reference to organize the potential sites of regulation.
Teaching Tips
1. Cellular differentiation is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type.
2. The lactose operon is turned on by removing the repressor—a sort of double negative. Students might enjoy various analogies to other types of “double negatives,” such as “When the cat’s away, the mice will play.” In another analogy, if Mom keeps the kids away from the cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. In this last analogy, the person occupying Mom’s attention functions most like lactose binding to the repressor.
3. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch.
4. The authors develop an analogy between the regulation of transcription and the series of water pipes that carry water from your local water supply, perhaps a reservoir, to a faucet in your home. At various points, valves control the flow of water. Similarly, the expression of genes is controlled at many points along the process. Figure 11.3 illustrates the “flow” of genetic information from a chromosome—a reservoir of genetic information—to an active protein that has been made in the cell’s cytoplasm. The multiple mechanisms that control gene expression are analogous to the control valves in water pipes. In the figure, a possible control knob indicates each gene expression “valve.” In the figure, the large size of the transcription control knob highlights its crucial role.
5. Just as a folded map is difficult to read, DNA packaging tends to prevent gene “reading” or expression.
6. Just as boxes of your things that will be little used are packed deeper into a closet, attic, or basement, chromatin that is not expressed is highly compacted and is stored away.
7. Alternative RNA splicing is like remixing music to produce a new song or re-editing a movie for a different ending. You could have a little fun by challenging students to identify which category of academic award is most like alternative RNA splicing. (Answer: the award for best editing.)
8. The action of an extracellular signal reaching a cell’s surface is like pushing the doorbell at a home. The signal is converted to another form (pushing a button rings a bell) and activities change within the house as someone comes to answer the door.
9. Students might wonder why a patch of color is all the same on the cat’s skin in Figure 11.4, if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation.
10.Homeotic genes are often called “master control genes.” The relationship between homeotic genes and structural genes is like the relationship between a construction supervisor and the workers. Major rearrangements can result from a few simple changes in the directions for construction.
11. There is much hope in the use of DNA microarrays to refine cancer therapies. In the past, a diagnosis of cancer was too often met with general treatments that benefited only a fraction of the patients. Physicians were left to wonder why some people with breast cancer or lung cancer responded to therapy while others did not. DNA microarrays enable us to identify differences between patients with the same apparent type of cancer (breast, lung, prostate, and so on). Consider sharing this important avenue of hope. It is likely that some of your students will soon have a family member facing these battles. 50

51. Gene Regulation in Bacteria
The lac operon uses
a promoter, a control sequence where the transcription enzyme attaches and initiates transcription
an operator, a DNA segment that acts as a switch that is turned on or off
a repressor (protein), which binds to the operator and physically blocks the attachment of RNA polymerase and transcription.
Student Misconceptions and Concerns
1. The broad concept of selective “reading” of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of product manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation.
2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.3 can be a helpful reference to organize the potential sites of regulation.
Teaching Tips
1. Cellular differentiation is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type.
2. The lactose operon is turned on by removing the repressor—a sort of double negative. Students might enjoy various analogies to other types of “double negatives,” such as “When the cat’s away, the mice will play.” In another analogy, if Mom keeps the kids away from the cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. In this last analogy, the person occupying Mom’s attention functions most like lactose binding to the repressor.
3. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch.
4. The authors develop an analogy between the regulation of transcription and the series of water pipes that carry water from your local water supply, perhaps a reservoir, to a faucet in your home. At various points, valves control the flow of water. Similarly, the expression of genes is controlled at many points along the process. Figure 11.3 illustrates the “flow” of genetic information from a chromosome—a reservoir of genetic information—to an active protein that has been made in the cell’s cytoplasm. The multiple mechanisms that control gene expression are analogous to the control valves in water pipes. In the figure, a possible control knob indicates each gene expression “valve.” In the figure, the large size of the transcription control knob highlights its crucial role.
5. Just as a folded map is difficult to read, DNA packaging tends to prevent gene “reading” or expression.
6. Just as boxes of your things that will be little used are packed deeper into a closet, attic, or basement, chromatin that is not expressed is highly compacted and is stored away.
7. Alternative RNA splicing is like remixing music to produce a new song or re-editing a movie for a different ending. You could have a little fun by challenging students to identify which category of academic award is most like alternative RNA splicing. (Answer: the award for best editing.)
8. The action of an extracellular signal reaching a cell’s surface is like pushing the doorbell at a home. The signal is converted to another form (pushing a button rings a bell) and activities change within the house as someone comes to answer the door.
9. Students might wonder why a patch of color is all the same on the cat’s skin in Figure 11.4, if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation.
10.Homeotic genes are often called “master control genes.” The relationship between homeotic genes and structural genes is like the relationship between a construction supervisor and the workers. Major rearrangements can result from a few simple changes in the directions for construction.
11. There is much hope in the use of DNA microarrays to refine cancer therapies. In the past, a diagnosis of cancer was too often met with general treatments that benefited only a fraction of the patients. Physicians were left to wonder why some people with breast cancer or lung cancer responded to therapy while others did not. DNA microarrays enable us to identify differences between patients with the same apparent type of cancer (breast, lung, prostate, and so on). Consider sharing this important avenue of hope. It is likely that some of your students will soon have a family member facing these battles. 51

52. Operon turned off (lactose absent)
Figure 11.2
DNA
mRNA
Protein
Operon turned off (lactose absent)
DNA
mRNA
Protein
Lactose
Operon turned on (lactose inactivates repressor)
Figure 11.2 The lac operon of E. coli

53. Genes for lactose enzymes
Figure 11.2a
Operon
Genes for lactose enzymes
Promoter
Regulatory
gene
Operator
DNA 1 2
mRNA
RNA polymerase
cannot attach to
promoter
Active
repressor
Protein
Operon turned off (lactose absent)
Figure 11.2 The lac operon of E. coli (part 1)

54. Operon turned on (lactose inactivates repressor)
Figure 11.2b 4
Transcription
DNA
RNA polymerase
bound to promoter 3
mRNA 5
Translation 2
Protein 1
Inactive
repressor
Lactose enzymes
Lactose
Operon turned on (lactose inactivates repressor)
Figure 11.2 The lac operon of E. coli (part 2)

55. Gene Regulation in Eukaryotic Cells
Eukaryotic cells have more complex gene regulating mechanisms with many points where the process can be turned on or off.
The multiple mechanisms that control gene expression are like the many control valves along a water supply.
Student Misconceptions and Concerns
1. The broad concept of selective “reading” of the genetic code associated with differentiation and types of cellular activity can be missed when concentrating on the extensive details of regulation. Analogies, noted below in the teaching tips, can help students relate this overall selective process to their own experiences. Students already understand the selective reading of relevant chapters in textbooks and the selective referencing of product manuals to get answers to different questions. These experiences are similar in many ways to the broad processes of gene regulation.
2. The many levels of gene regulation in eukaryotic cells can be confusing and frustrating. The water pipe analogy depicted in Figure 11.3 can be a helpful reference to organize the potential sites of regulation.
Teaching Tips
1. Cellular differentiation is analogous to buying a book about how to build birdhouses and reading only the plans needed to build one particular model. Although the book contains directions to build many different birdhouses, you read and follow only the directions for the particular birdhouse you choose to build. The pages and directions for the other birdhouses remain intact. When cells differentiate, they read, or express, only the genes that are needed in that particular cell type.
2. The lactose operon is turned on by removing the repressor—a sort of double negative. Students might enjoy various analogies to other types of “double negatives,” such as “When the cat’s away, the mice will play.” In another analogy, if Mom keeps the kids away from the cookies, but somebody occupies her attention, kids can sneak by and snatch some cookies. In this last analogy, the person occupying Mom’s attention functions most like lactose binding to the repressor.
3. A key advantage of an operon system is the ability to turn off or on a set of genes with a single “switch.” You can demonstrate this relationship in your classroom by turning off or on a set of lights with a single switch.
4. The authors develop an analogy between the regulation of transcription and the series of water pipes that carry water from your local water supply, perhaps a reservoir, to a faucet in your home. At various points, valves control the flow of water. Similarly, the expression of genes is controlled at many points along the process. Figure 11.3 illustrates the “flow” of genetic information from a chromosome—a reservoir of genetic information—to an active protein that has been made in the cell’s cytoplasm. The multiple mechanisms that control gene expression are analogous to the control valves in water pipes. In the figure, a possible control knob indicates each gene expression “valve.” In the figure, the large size of the transcription control knob highlights its crucial role.
5. Just as a folded map is difficult to read, DNA packaging tends to prevent gene “reading” or expression.
6. Just as boxes of your things that will be little used are packed deeper into a closet, attic, or basement, chromatin that is not expressed is highly compacted and is stored away.
7. Alternative RNA splicing is like remixing music to produce a new song or re-editing a movie for a different ending. You could have a little fun by challenging students to identify which category of academic award is most like alternative RNA splicing. (Answer: the award for best editing.)
8. The action of an extracellular signal reaching a cell’s surface is like pushing the doorbell at a home. The signal is converted to another form (pushing a button rings a bell) and activities change within the house as someone comes to answer the door.
9. Students might wonder why a patch of color is all the same on the cat’s skin in Figure 11.4, if every cell has an equal chance of being one of the two color forms. The answer is that X chromosome inactivation occurs early in development. Thus, the patch of one color represents the progeny of one embryonic cell after X chromosome inactivation.
10.Homeotic genes are often called “master control genes.” The relationship between homeotic genes and structural genes is like the relationship between a construction supervisor and the workers. Major rearrangements can result from a few simple changes in the directions for construction.
11. There is much hope in the use of DNA microarrays to refine cancer therapies. In the past, a diagnosis of cancer was too often met with general treatments that benefited only a fraction of the patients. Physicians were left to wonder why some people with breast cancer or lung cancer responded to therapy while others did not. DNA microarrays enable us to identify differences between patients with the same apparent type of cancer (breast, lung, prostate, and so on). Consider sharing this important avenue of hope. It is likely that some of your students will soon have a family member facing these battles. 55

56. Mutations A mutation is any change in the nucleotide sequence of DNA.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 56

57. 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 disease.

58. Mutations within a gene can be divided into two general categories:
Types of Mutations
Mutations within a gene can be divided into two general categories:
nucleotide substitutions (the replacement of one base by another)
nucleotide deletions or insertions (the loss or addition of a nucleotide).
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 58

59. Types of Mutations
Nucleotide substitutions can be divided into 3 different type of mutations.
Silent mutation = change in the nucleotide may transform one codon into another but due to the redundancy of the genetic code, is translated into the same amino acid.
Missense mutation = change in the nucleotide when translated, changes one amino acid into another. May or may not be detrimental to the proteins function. (sickle cell anemia)
Nonsense mutation = change in the nucleotide that changes a codon for an amino acid into a stop codon.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 59

60. Nucleotide insertions and deletions can
Types of Mutations
Nucleotide insertions and deletions can
change the reading frame of the genetic message
lead to disastrous effects.
can alter the reading frame of the genetic message = frameshift mutations.
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 60

61. Mutations may result from
Mutagens
Mutations may result from
errors in DNA replication
physical or chemical agents called mutagens.
X-rays UV light
Mutations
are often harmful but are useful in nature and the laboratory as a source of genetic diversity, which makes evolution by natural selection possible!!!
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 Figure 10.8, 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 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 (much like how we deal with the U.S. Constitution).
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. (It might be a good challenge to have your students explain why proteins do not have exactly a third of monomers of the corresponding mRNA.)
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. Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
10. 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.
11. 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.
12.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!” 61