Unit 8: Genomics Guided Reading Questions (150 pts total)

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1 Name: AP Biology Biology, Campbell and Reece, 7th Edition Adapted from chapter reading guides originally created by Lynn Miriello Chapter 18 The Genetics of Viruses and Bacteria Unit 8: Genomics Guided Reading Questions (150 pts total) 1. How and what did Dr. Mayer discover specifically in 1883? 2. What did Ivanowsky conclude that built on Mayer s work? 3. What logic did Beijerinck use to lead to the idea of a virus? 4. How was the existence of a virus finally confirmed and by whom? 5. How small are viruses? 6. What kind of nucleic acids are the viral genomes made of? 7. What is the name for a protein shell enclosing the viral genome? 8. What are the subunits of capsids? 9. What are viral envelopes and what is their function? 10. Where are the most complex capsids found? Page 1 of 24

2 11. Define host range. 12. List the full steps of the simplified viral reproductive cycle. 13. What is the phage reproductive cycle that culminates in the death of the host cell? 14. What kind of phage only reproduces by a lytic cycle? 15. How do bacteria defend themselves against phages? 16. What are the steps of the lytic cycle of a T4 phage? 17. What is the phage reproductive cycle that replicates the phage genome without destroying the host? 18. What are phages called that care capable of using both modes of reproduction? 19. What is a prophage? 20. What is an example of the interaction between a prophage and a bacterium? 21. What is the use of a viral envelope in animal viruses? Page 2 of 24

3 22. Does this reproductive cycle kill the host cell? 23. What are retroviruses and how do they use reverse transcriptase? 24. Describe the reproductive cycle of an enveloped RNA virus. 25. Describe the reproductive cycle of HIV, a retrovirus. 26. Is it believed that viruses evolved before or after the first cells appeared and what evidence is used to support the idea? 27. What are vaccines? 28. What are the three processes that contribute to the emergence of viral diseases? 29. List and explain the two major routes that plant viruses are spread. 30. What are viroids? Page 3 of 24

4 31. Define prions. 32. What is the main component of most bacterial genomes? 33. How is the DNA arranged in the nucleoid region of the bacterial genome? 34. What is a plasmid? 35. Describe the process of binary fission. 36. Why do mutations make such a large contribution to bacterial genetic variation as compared to humans? 37. Explain the experiment and the results that demonstrated evidence of genetic recombination in bacteria. 38. What is the process of alteration of a bacterial cell s genotype by the uptake of naked, foreign DNA from the surrounding environment? 39. What famous experiment in the previous unit described this process? 40. Define transduction. Page 4 of 24

5 41. List the generalized steps of transduction. 42. What is the process of direct transfer of genetic material between two bacterial cells that are temporarily joined? 43. What structure joins them? 44. What generally must be present for the sex pili to donate DNA during conjugation? 45. What is special about the F plasmid? 46. What is an episome? 47. What are R plasmids and why are these problems to humans? 48. How does this relate to natural selection? 49. Define transposable elements. 50. Do transposable elements exist independently? 51. What is a common name for transposable elements? 52. What is the name for the simplest transposable elements? Page 5 of 24

6 53. What is the name for transposable elements that are longer and more complex than insertion sequences? 54. What is an example of the benefit to bacteria of these transposable elements? 55. What are the two ways that metabolic control can occur within bacteria? 56. What is the key advantage of grouping genes of related function in to one transcription unit? 57. What is this switch called? 58. Where is an operator positioned? 59. What does the operator control? 60. What is the name for the operator, promoter, and the genes they control? 61. What can happen if the trp operon is turned on? 62. What turns the switch off? 63. How does a repressor work? 64. What gene controls the making of the trp repressor protein? 65. What are the two states that the operator vacillates (switches between)? 66. How is the trp repressor protein an allosteric protein? Page 6 of 24

7 67. Define corepressor. 68. What are the two methods of negative gene regulation? 69. Why is the trp operon considered repressible? 70. What is the definition of an inducible operon? 71. What does the inducer do? 72. Why are repressible enzymes generally associated with anabolic pathways and how is this an advantage to the organism? 73. How does positive gene regulation work? 74. Negative feedback has an on/off switch and positive feedback can only amplify the response how does this statement connect with negative and positive gene regulation? AP Biology Exam Checkpoint: 75. Which of the following is descriptive of an R plasmid? A. It makes bacteria resistant to phage. B. Its transfer converts an F- cell into an F+ cell. C. It is a good example of a composite transposon. D. It is transferred between bacteria by transduction. E. It has genes for antibiotic resistance and maybe for sex pili. Page 7 of 24

8 Chapter 19 Eukaryotic Genomes: Organization, Regulation, and Evolution 1. Define the following terms: a. Chromatin - b. Nucleosome - 2. Outline the levels of DNA packing in the eukaryotic nucleus below next to the diagram provided. 3. What is the difference between heterochromatin and euchromatin? Which is transcribed? 4. What is cell differentiation? 5. If cells carry all of the genetic differences, why then are cells so unique what is responsible for this? Page 8 of 24

9 6. In the diagram below highlight all of the potential locations for gene expression regulation in eukaryotic cells. How does this compare with prokaryotic cells? 7. What effect do the following have on gene expression? a. Histone acetylation - b. Histone deacteylation - c. DNA methylation - 8. How does methylation relate to genomic imprinting? 9. Define epigenetic inheritance. 10. How do the following control elements assist in regulation? a. Transcription factors - b. Enhancers - c. Activators - d. Repressors - Page 9 of 24

10 11. Label the diagram below to explain the interactions of enhancers and transcription activators. 12. Explain how RNA processing is a mechanism of post-transcriptional regulation. 13. What role do microrna s play in post-transcriptional regulation? Use the diagram below to supplement your explanation. Explanation: Page 10 of 24

11 14. What is RNA interference? 15. How does translation provide another opportunity for control? 16. What is a proteasome? 17. What is the difference between oncogenes, proto-oncogenes and tumor-suppressor genes? 18. What is the ras gene? 19. What is the p53 gene? 20. Why is said that people inherit predispositions to cancer not cancer itself? Page 11 of 24

12 21. Label the diagram below that describes the signaling pathways that regulate cell division. 22. What are the types of DNA sequences in the human genome and what percentage of the genome are they? Page 12 of 24

13 23. What is the difference between transposons and retrotransposons. Label the diagram below to help you answer the question. Answer: 24. What are Alu elements? 25. What are multi-gene families? 26. What are pseudogenes? 27. How can errors during meiosis lead to the duplication of genes? 28. How can errors during DNA replication lead to the duplication of genes? Page 13 of 24

14 29. What are three ways transposable elements are thought to have contributed to the evolution of the genome? AP Biology Exam Checkpoint: 30. Proto-oncogenes can change into oncogenes that cause cancer. Which of the following best explains the presence of these potential time bombs in eukaryotic cells? A. Proto-oncogenes are genetic "junk." B. Cells produce proto-oncogenes as they age. C. Proto-oncogenes first arose from viral infections. D. Proto-oncogenes normally help regulate cell division. E. Proto-oncogenes are mutant versions of normal genes. Chapter 20 DNA Technology and Genomics 1. Define the following terms: a. Recombinant DNA - b. Genetic engineering - c. Biotechnology - d. Gene cloning - 2. What are the two basic purposes of cloned genes? Describe at least three practical uses for cloned genes. 3. What is the other name for restriction enzymes and what do these enzymes do for bacteria in nature? Page 14 of 24

15 4. Define the following terms: a. Restriction site b. Restriction fragments c. Sticky end 5. Label the following diagram and briefly describe the process being illustrated. Description: Page 15 of 24

16 6. Using the diagram below, label the steps to cloning a human gene in a bacterial plasmid. 7. Explain in your own words two ways that we know that cell clones carry the recombinant plasmids? 8. What is the purpose of nucleic acid hybridization? Why is the word hybrid used to describe this process? Page 16 of 24

17 9. What is a complementary, short, single-stranded nucleic acid that can be either DNA or RNA? 10. Why do scientists use a radioactive isotope tag for the probes? 11. How is DNA denaturation different than protein denaturation? 12. Label the following steps of nucleic acid probe hybridization. 13. Define genomic library. 14. How are bacteriophages used for making genomic libraries and what are some of the advantages of this? Page 17 of 24

18 15. What are the steps in making complementary DNA (cdna)? 16. Compare and contrast the advantages of cdna libraries and genomic libraries. 17. What is an expression vector and what problem does it solve? 18. Why do molecular biologists use yeast as opposed to bacteria for expressing genes of interest? 19. Explain the use of yeast artificial chromosomes (YAC s) in gene cloning. 20. What is electroporation? 21. Why is PCR, polymerase chain reaction, important in many aspects of biotechnology? Page 18 of 24

19 22. Label the diagram of PCR below 23. What is the purpose and general process of gel electrophoresis? Page 19 of 24

20 24. Label the diagram of gel electrophoresis on the right. Focus on the charge, molecule size and results. Page 20 of 24

21 25. Label the diagram on the right. Focus on identifying the fragments. 26. Define and explain the significance of RFLP s, restriction length polymorphisms. 27. What was the purpose of the Human Genome Project? Page 21 of 24

22 28. Label the diagram outlining the Southern Blotting of DNA Fragments 29. Why is genetic mapping considered a relative mapping as opposed to physical mapping? 30. What is the goal of DNA sequencing? Page 22 of 24

23 31. What is the basic concept of the whole-genome shotgun approach to sequencing? 32. Define genomics. 33. Is there a direct correlation between size of the genome and the complexity of the organism? 34. What is in vitro mutagenesis and what does it help the scientist understand? 35. What is proteomics? 36. Define single nucleotide polymorphisms. 37. What are some of the examples of the medical applications of biotechnology? 38. What are the basic steps in human gene therapy with a retroviral vector? Page 23 of 24

24 39. Have there been problems with this procedure? What are they? 40. What is a DNA fingerprint? 41. What is a transgenic animal? 42. How are plasmids used in agriculture? 43. How is genetic engineering used in plants? 44. What are genetically modified foods and do you think that you have eaten any? AP Biology Exam Checkpoint: 45. Which of the following tools of recombinant DNA technology is incorrectly paired with its use? A. restriction enzyme-production of RFLPs B. electrophoresis-separation of DNA fragments C. reverse transcriptase-production of cdna from mrna D. DNA polymerase-used in a polymerase chain reaction to amplify sections of DNA E. DNA ligase-enzyme that cuts DNA, creating the sticky ends of restriction fragments Page 24 of 24