Review: DNA RNA Protein In a cell, genetic information flows from DNA to RNA in the nucleus and RNA to protein at the ribosome. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in 1961. Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

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

Transcription Nucleus Intron RNA processing Cap Tail mRNA Intron RNA polymerase Transcription Nucleus DNA mRNA Intron RNA processing Cap Tail mRNA Intron Amino acid Ribosomal subunits tRNA Enzyme ATP Initiation of translation Amino acid attachment Figure 10.20-4 Figure 10.20 A summary of transcription and translation. (Step 4)

Transcription Polypeptide Nucleus Stop codon Intron RNA processing Cap RNA polymerase Transcription Polypeptide Nucleus DNA mRNA Stop codon Intron RNA processing Cap Termination Tail mRNA Intron Anticodon Amino acid Ribosomal subunits Codon tRNA Enzyme Elongation ATP Initiation of translation Amino acid attachment Figure 10.20-6 Figure 10.20 A summary of transcription and translation. (Step 6)

Transcription and translation are how genes control: The structures The activities of cells Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in 1961. Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Mutations A mutation is any change in the nucleotide sequence of DNA. Mutations can change the amino acids in a protein. Mutations can involve: Large regions of a chromosome Just a single nucleotide pair, as occurs in sickle cell anemia Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in 1961. Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

How can Mutations be BAD? How can Mutations be GOOD?

Although mutations are often harmful, they are the source of genetic diversity, which is necessary for evolution by natural selection. Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in 1961. Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Mutagens Mutations may result from: Errors in DNA replication Physical or chemical agents called mutagens UV rays, X-rays, gamma rays, chemicals Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in 1961. Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Types of Mutations Mutations within a gene can occur as a result of: Nucleotide substitution, the replacement of one nucleotide by another Nucleotide deletion, the loss of a nucleotide Nucleotide insertion, the 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 the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in 1961. Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

If a mutation changed a codon from GGU to GGA then what would happen? If a mutation changed a codon from GGA to UGA then what would happen?

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

Insertions and deletions can: Change the reading frame of the genetic message Lead to disastrous effects Student Misconceptions and Concerns 1. Less experienced students are often intensely focused on writing detailed notes. The risk is that they miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process. 2. Consider placing on the board the basic content from Figure 10.9, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail. 3. Mutations are often discussed as part of evolution mechanisms. In this sense, mutations may be considered a part of a positive creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified. Teaching Tips 1. It has been said that, everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to explain the significance and validity of this statement. 2. The authors note that the sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame. 3. The transcription of DNA into RNA is like a reporter who transcribes a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written. 4. A parallel can be drawn between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in 1961. Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups. 5. Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away. 6. The production of proteins is like a machine requiring fuel. The molecular machinery (ribosomes and tRNA) used in many cellular processes also requires an input of energy in the form of ATP. 7. If you were using a train analogy for the assembly of monomers into polymers, at this point the DNA and RNA trains are traded in 3 for 1 for the polypeptide train. Thus, in general, polypeptides have about 1/3 as many monomers as the mRNA that coded for them. 8. After translation is addressed, consider asking your students (working singly or in small groups) to list all of the places where base pairing is used (in the construction of a DNA molecule during DNA replication, in transcription, and during translation when the tRNA attaches). 9. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help them better remember details of translation, students might think of the letters for the two sites to mean “A” for addition, where an amino acid is added, and ”P” for polypeptide, where the growing polypeptide is located. 10. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. But look what happens when a letter is added (2) or deleted (3). The reading frame, or triplet groupings, are re-formed into nonsense. (1) The big red pig ate the red rag. (2) The big res dpi gat eth ere dra g. (3) The big rep iga tet her edr ag. 11. The authors have noted elsewhere that a random mutation is like a shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!

Base substitution mRNA and protein from a normal gene Figure 10.22a Figure 10.22a Base substitution of mutations and their effects.

Nucleotide deletion mRNA and protein from a normal gene Deleted Figure 10.22b Figure 10.22b Nucleotide deletion of mutations and their effects.

Nucleotide insertion mRNA and protein from a normal gene Inserted Figure 10.22c Figure 10.22c Nucleotide insertion of mutations and their effects.

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

Mutation by Deletion:

The Human Genome Project Begun in 1990, the Human Genome Project was a massive scientific endeavor: To determine the nucleotide sequence of all the DNA in the human genome and To identify the location and sequence of every gene Aims of the project: - to identify the estimated 100,000 genes in the human DNA. Student Misconceptions and Concerns 1. The text notes that there are 24 chromosomes in the human genome. Students might initially find this confusing, as it is common knowledge that humans have 23 pairs of chromosomes. Consider making the statement that we have 24 different types of chromosomes and asking your students to explain why this is true. 2. The similarities of the genotypes and phenotypes of members of a human family tree are expected and understood by most students. Yet, for many students, these same relationships are often poorly extrapolated to phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool using in modern systematics. Genomics is a significant test of the other overwhelming types of evidence for evolution. Teaching Tips 1. The first targets of genomics were prokaryotic pathogenic organisms. Consider asking your students in class to suggest the reasons why this was a good choice. Students will likely note that the genomes of these organisms are smaller than eukaryotes and that many of these organisms are of great medical significance. 2. The authors note that there are 3.2 billion nucleotide pairs in the human genome. There are about 3.2 billion seconds in 101.4 years. This simple reference might add meaning to the significance of these large numbers. 3. The main U.S. Department of Energy Office website in support of the human genome project is found at www.ornl.gov/sci/techresources/Human_Genome/home.shtml. 4. The website for the National Center for Biotechnology Information, is (www.ncbi.nlm.nih.gov/). The center, established in 1988, serves as a national resource for biomedical information related to genomic data. 5. Challenge students to explain why a complete understanding of an organism’s genome and the resulting proteins produced is still not enough to understand the full biology of an organism. Challenge them to consider the role of the environment in development and physiology. (One striking example of the influence of the environment is that the sex of some reptiles is determined not by genetics, but by incubation temperature!) 6. With a better understanding of the diverse and still unknown roles of many sections of DNA, consider discussing some of the difficulties of “resurrecting” extinct organisms from incomplete DNA sequences.

At the completion of the project in 2004: Over 99% of the genome had been determined to 99.999% accuracy 3.2 billion nucleotide pairs were identified About 24,000 genes were found About 98% of the human DNA was identified as noncoding Student Misconceptions and Concerns 1. The text notes that there are 24 chromosomes in the human genome. Students might initially find this confusing, as it is common knowledge that humans have 23 pairs of chromosomes. Consider making the statement that we have 24 different types of chromosomes and asking your students to explain why this is true. 2. The similarities of the genotypes and phenotypes of members of a human family tree are expected and understood by most students. Yet, for many students, these same relationships are often poorly extrapolated to phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool using in modern systematics. Genomics is a significant test of the other overwhelming types of evidence for evolution. Teaching Tips 1. The first targets of genomics were prokaryotic pathogenic organisms. Consider asking your students in class to suggest the reasons why this was a good choice. Students will likely note that the genomes of these organisms are smaller than eukaryotes and that many of these organisms are of great medical significance. 2. The authors note that there are 3.2 billion nucleotide pairs in the human genome. There are about 3.2 billion seconds in 101.4 years. This simple reference might add meaning to the significance of these large numbers. 3. The main U.S. Department of Energy Office website in support of the human genome project is found at www.ornl.gov/sci/techresources/Human_Genome/home.shtml. 4. The website for the National Center for Biotechnology Information, is (www.ncbi.nlm.nih.gov/). The center, established in 1988, serves as a national resource for biomedical information related to genomic data. 5. Challenge students to explain why a complete understanding of an organism’s genome and the resulting proteins produced is still not enough to understand the full biology of an organism. Challenge them to consider the role of the environment in development and physiology. (One striking example of the influence of the environment is that the sex of some reptiles is determined not by genetics, but by incubation temperature!) 6. With a better understanding of the diverse and still unknown roles of many sections of DNA, consider discussing some of the difficulties of “resurrecting” extinct organisms from incomplete DNA sequences.

The Human Genome Project can help map the genes for specific diseases such as: Alzheimer’s disease Parkinson’s disease Student Misconceptions and Concerns 1. The text notes that there are 24 chromosomes in the human genome. Students might initially find this confusing, as it is common knowledge that humans have 23 pairs of chromosomes. Consider making the statement that we have 24 different types of chromosomes and asking your students to explain why this is true. 2. The similarities of the genotypes and phenotypes of members of a human family tree are expected and understood by most students. Yet, for many students, these same relationships are often poorly extrapolated to phylogenetic relationships of other groups. The use of genomics to test phylogenetic relationships is an enormously powerful tool using in modern systematics. Genomics is a significant test of the other overwhelming types of evidence for evolution. Teaching Tips 1. The first targets of genomics were prokaryotic pathogenic organisms. Consider asking your students in class to suggest the reasons why this was a good choice. Students will likely note that the genomes of these organisms are smaller than eukaryotes and that many of these organisms are of great medical significance. 2. The authors note that there are 3.2 billion nucleotide pairs in the human genome. There are about 3.2 billion seconds in 101.4 years. This simple reference might add meaning to the significance of these large numbers. 3. The main U.S. Department of Energy Office website in support of the human genome project is found at www.ornl.gov/sci/techresources/Human_Genome/home.shtml. 4. The website for the National Center for Biotechnology Information, is (www.ncbi.nlm.nih.gov/). The center, established in 1988, serves as a national resource for biomedical information related to genomic data. 5. Challenge students to explain why a complete understanding of an organism’s genome and the resulting proteins produced is still not enough to understand the full biology of an organism. Challenge them to consider the role of the environment in development and physiology. (One striking example of the influence of the environment is that the sex of some reptiles is determined not by genetics, but by incubation temperature!) 6. With a better understanding of the diverse and still unknown roles of many sections of DNA, consider discussing some of the difficulties of “resurrecting” extinct organisms from incomplete DNA sequences.

Table 12.1 Table 12.1 Some Important Sequenced Genomes

Benefits of Human Genome Project research - improvements in medicine. - microbial genome research for fuel and environmental cleanup. - DNA forensics. - improved agriculture and livestock. - better understanding of evolution and human migration. - more accurate risk assessment.

Making Humulin In 1982, the world’s first genetically engineered pharmaceutical product was sold. Humulin, human insulin: Was produced by genetically modified bacteria Was the first recombinant DNA drug approved by the FDA Is used today by more than 4 million people with diabetes Student Misconceptions and Concerns 1. The roles of restriction enzymes and nucleic acid probes, as well as many other aspects of recombinant DNA techniques, rely upon a firm and comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that addresses the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. Teaching Tips 1. Annual flu vaccinations are a common example of using vaccines to prevent diseases that cannot be easily cured. However, students might not understand why many people receive the vaccine every year. A new annual vaccine is necessary because the flu viruses keep evolving. 2. Genetically engineered organisms are controversial, creating various degrees and directions of social resistance. Yet, many debates around issues of science are confused by misinformation. This may be an opportunity for you to make an extra credit or regular assignment for students to take a position, one side or the other, on some aspect of this or related issues. The science would need to be accurate. Students might debate whether a food product made from GM/transgenic organisms should be labeled as such, or students can discuss the risks or advantages of producing GM organisms. 3. The origin of the name “restriction enzymes” may be of interest. In nature, these enzymes protect bacterial cells against foreign DNA. Thus, these enzymes “restrict” the invasion of foreign genetic material. 4. The ability to swap genes between prokaryotes and eukaryotes using the technologies described in this chapter reveal the fundamental genetic mechanisms shared by all forms of life. This very strong evidence of common descent is a lesson about evolution that may be missed by your students. 5. Students might think you are just making a bad joke by noting that laboratory-synthesized genes are “designer genes,” but this is a common term. Search the Internet using the keywords “designer genes,” and many scientific (and unscientific) sites will be found. 6. A genomic library of the sentence you are now reading would be all of the sentence fragments that make up the sentence. One could string together all of the words of this first sentence, without spaces between letters, and then conduct a word-processing edit placing a space between any place where an “e” is followed by the letter “n” The resulting fragments of this original sentence would look like this, and would be like a type of “genomic library.” Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce. 7. Some Internet search programs rely upon a methodology similar in one way to the use of a nucleic acid probe. For example, if you want to find the lyrics to a particular song, but you do not know the song title or artist, you might search the Internet using a unique phrase from the song. (For example, search using “yellow submarine”.) The search engine will scan millions of web pages to identify those sites containing that particular phrase. However, unlike a nucleic acid probe, you would search for the song by using a few of the lyrics. A nucleic acid probe would search using a sequence complementary to the desired sequence. 8. Roundup Ready Corn, a product of Monsanto, is resistant to the herbicide Roundup. The general strategy for farmers is to spray fields of Roundup Ready corn with the herbicide Roundup, killing weeds but not the corn. A search of the Internet will quickly reveal the controversy associated with this and other genetically modified organisms (GMO), which can encourage interesting discussions and promote critical thinking skills. 9. As gene therapy technology expands, our ability to modify the genome in human embryos, created through in vitro fertilization, permits genetic modification at the earliest stages of life. Future generations of humans, like our crops today, may include those with and without a genetically modified ancestry. The benefits and challenges of these technologies raise issues many students have never considered. Our students, and the generations soon to follow, will face the potential of directed human evolution.

Today, humulin is continuously produced in gigantic fermentation vats filled with a liquid culture of bacteria. Student Misconceptions and Concerns 1. The roles of restriction enzymes and nucleic acid probes, as well as many other aspects of recombinant DNA techniques, rely upon a firm and comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that addresses the content in Chapters 10 and 11. 2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues. Teaching Tips 1. Annual flu vaccinations are a common example of using vaccines to prevent diseases that cannot be easily cured. However, students might not understand why many people receive the vaccine every year. A new annual vaccine is necessary because the flu viruses keep evolving. 2. Genetically engineered organisms are controversial, creating various degrees and directions of social resistance. Yet, many debates around issues of science are confused by misinformation. This may be an opportunity for you to make an extra credit or regular assignment for students to take a position, one side or the other, on some aspect of this or related issues. The science would need to be accurate. Students might debate whether a food product made from GM/transgenic organisms should be labeled as such, or students can discuss the risks or advantages of producing GM organisms. 3. The origin of the name “restriction enzymes” may be of interest. In nature, these enzymes protect bacterial cells against foreign DNA. Thus, these enzymes “restrict” the invasion of foreign genetic material. 4. The ability to swap genes between prokaryotes and eukaryotes using the technologies described in this chapter reveal the fundamental genetic mechanisms shared by all forms of life. This very strong evidence of common descent is a lesson about evolution that may be missed by your students. 5. Students might think you are just making a bad joke by noting that laboratory-synthesized genes are “designer genes,” but this is a common term. Search the Internet using the keywords “designer genes,” and many scientific (and unscientific) sites will be found. 6. A genomic library of the sentence you are now reading would be all of the sentence fragments that make up the sentence. One could string together all of the words of this first sentence, without spaces between letters, and then conduct a word-processing edit placing a space between any place where an “e” is followed by the letter “n” The resulting fragments of this original sentence would look like this, and would be like a type of “genomic library.” Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce. 7. Some Internet search programs rely upon a methodology similar in one way to the use of a nucleic acid probe. For example, if you want to find the lyrics to a particular song, but you do not know the song title or artist, you might search the Internet using a unique phrase from the song. (For example, search using “yellow submarine”.) The search engine will scan millions of web pages to identify those sites containing that particular phrase. However, unlike a nucleic acid probe, you would search for the song by using a few of the lyrics. A nucleic acid probe would search using a sequence complementary to the desired sequence. 8. Roundup Ready Corn, a product of Monsanto, is resistant to the herbicide Roundup. The general strategy for farmers is to spray fields of Roundup Ready corn with the herbicide Roundup, killing weeds but not the corn. A search of the Internet will quickly reveal the controversy associated with this and other genetically modified organisms (GMO), which can encourage interesting discussions and promote critical thinking skills. 9. As gene therapy technology expands, our ability to modify the genome in human embryos, created through in vitro fertilization, permits genetic modification at the earliest stages of life. Future generations of humans, like our crops today, may include those with and without a genetically modified ancestry. The benefits and challenges of these technologies raise issues many students have never considered. Our students, and the generations soon to follow, will face the potential of directed human evolution.

If a strand of DNA has the sequence AAGCTC, transcription will result in a(n) ______. A) single RNA strand with the sequence TTCGAG B) DNA double helix with the sequence AAGCTC for one strand and TTCGAG for the complementary strand C) single DNA strand with the sequence TTCGAG D) single RNA strand with the sequence UUCGAG E) RNA double helix with the sequence UUCGAG for one strand and AAGCUC for the complimentary strand

If a strand of DNA has the sequence AAGCTC, transcription will result in a(n) ______. A) single RNA strand with the sequence TTCGAG B) DNA double helix with the sequence AAGCTC for one strand and TTCGAG for the complementary strand C) single DNA strand with the sequence TTCGAG D) single RNA strand with the sequence UUCGAG E) RNA double helix with the sequence UUCGAG for one strand and AAGCUC for the complimentary strand

Translation converts the information stored in ______ to ______. A) DNA . . . RNA B) RNA . . . a polypeptide C) protein . . . DNA D) DNA . . . a polypeptide E) RNA . . . DNA

Translation converts the information stored in ______ to ______. A) DNA . . . RNA B) RNA . . . a polypeptide C) protein . . . DNA D) DNA . . . a polypeptide E) RNA . . . DNA

Where is translation accomplished? A) lysosomes B) smooth endoplasmic reticulum C) peroxisomes D) ribosomes E) nucleoli

Where is translation accomplished? A) lysosomes B) smooth endoplasmic reticulum C) peroxisomes D) ribosomes E) nucleoli

A mutation within a gene that will insert a premature stop codon in mRNA would ______. A) result in a polypeptide that is one amino acid shorter than the one produced prior to the mutation B) result in a shortened polypeptide chain C) result in a missense mutation D) change the location at which transcription of the next gene begins E) have the same effect as deleting a single nucleotide in the gene

A mutation within a gene that will insert a premature stop codon in mRNA would ______. A) result in a polypeptide that is one amino acid shorter than the one produced prior to the mutation B) result in a shortened polypeptide chain C) result in a missense mutation D) change the location at which transcription of the next gene begins E) have the same effect as deleting a single nucleotide in the gene

What is the smallest number of nucleotides that must be added or subtracted to change the triplet grouping of the genetic message? A) one B) two C) three D) four E) five

What is the smallest number of nucleotides that must be added or subtracted to change the triplet grouping of the genetic message? A) one B) two C) three D) four E) five

Examine the genetic code table, shown below. The codon AGC codes for the amino acid ______. A) serine B) arginine C) threonine D) alanine E) glycine

Examine the genetic code table, shown below. The codon AGC codes for the amino acid ______. A) serine B) arginine C) threonine D) alanine E) glycine

A mutation would be most harmful to the cells if it resulted in ______. A) a single nucleotide insertion near the start of the coding sequence B) a single nucleotide deletion near the end of the coding sequence C) a single nucleotide in the middle of an intron D) substitution of a base pair E) deletion of a triplet near the middle of the gene

A mutation would be most harmful to the cells if it resulted in ______. A) a single nucleotide insertion near the start of the coding sequence B) a single nucleotide deletion near the end of the coding sequence C) a single nucleotide in the middle of an intron D) substitution of a base pair E) deletion of a triplet near the middle of the gene

In a DNA double helix, adenine pairs with ______ and guanine pairs with ______. A) cytosine . . . thymine B) guanine . . . adenine C) uracil . . . cytosine D) thymine . . . cytosine E) cytosine . . . uracil

In a DNA double helix, adenine pairs with ______ and guanine pairs with ______. A) cytosine . . . thymine B) guanine . . . adenine C) uracil . . . cytosine D) thymine . . . cytosine E) cytosine . . . uracil

RNA contains the nitrogenous base ______ instead of ______, which is only found in DNA. A) a deoxyribose sugar . . . a ribose sugar B) nucleotides . . . nucleic acids C) uracil . . . thymine D) cytosine . . . guanine E) adenine . . . guanine

RNA contains the nitrogenous base ______ instead of ______, which is only found in DNA. A) a deoxyribose sugar . . . a ribose sugar B) nucleotides . . . nucleic acids C) uracil . . . thymine D) cytosine . . . guanine E) adenine . . . guanine

If one strand of a DNA double helix has the sequence GTCCAT, what is the sequence of the other strand? A) ACTTGC B) TGAACG C) CAGGTA D) CAGGUA E) CUGGTU

If one strand of a DNA double helix has the sequence GTCCAT, what is the sequence of the other strand? A) ACTTGC B) TGAACG C) CAGGTA D) CAGGUA E) CUGGTU

What name is given to the collection of traits exhibited by an organism? A) holotype B) genotype C) typology D) phenotype E) morphology

What name is given to the collection of traits exhibited by an organism? A) holotype B) genotype C) typology D) phenotype E) morphology

How many nucleotides make up a codon? A) one B) two C) three D) four E) five

How many nucleotides make up a codon? A) one B) two C) three D) four E) five

Transcription is the ______. A) manufacture of a strand of RNA complementary to a strand of DNA B) manufacture of two new DNA double helices that are identical to an old DNA double helix C) modification of a strand of RNA prior to the manufacture of a protein D) manufacture of a protein based on information carried by RNA E) manufacture of a new strand of DNA complementary to an old strand of DNA

Transcription is the ______. A) manufacture of a strand of RNA complementary to a strand of DNA B) manufacture of two new DNA double helices that are identical to an old DNA double helix C) modification of a strand of RNA prior to the manufacture of a protein D) manufacture of a protein based on information carried by RNA E) manufacture of a new strand of DNA complementary to an old strand of DNA