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Unit 5 -chapters_16_-20

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  • 1. Unit 5 – Molecular Genetics – Chapters 16, 17, 18, 19 & 20 Chapter 16 – The Molecular basis of Inheritance Objective questions: DNA as the Genetic Material 1. Explain why researchers originally thought protein was the genetic material. 2. Summarize the experiments performed by the following scientists that provided evidence that DNA is the genetic material: a. Frederick Griffith b. Oswald Avery, Maclyn McCarty and Colin MacLeod c. Alfred Hershey and Martha Chase d. Erwin Chargaff 3. Explain how Watson and Crick deduced the structure of DNA and describe the evidence they used. Explain the significance of the research of Rosalind Franklin. 4. Describe the structure of DNA. Explain the “base-paring rule” and describe its significance. DNA Replication and Repair 5. Describe the semiconservative model of replication and the significance of the experiments by Matthew Meselson and Franklin Stahl. 6. Describe the process of DNA replication. Note the structure of the many origins of replication and replication forks and explain the role of DNA polymerase. 7. Explain what energy source drives the polymerization of DNA. 8. Define “antiparallel” and explain why continuous synthesis of both DNA strands is not possible. 9. Distinguish between the leading strand and the lagging strand. 10. Explain how the lagging strand is synthesized even though DNA polymerase can add nucleotides only to the 3’ end. 11. Explain the roles of DNA ligase, primer, primase, helicase, and the single-strand binding protein. 12. Explain why an analogy can be made comparing DNA replication to a locomotive made of DNA polymerase moving along a railroad track of DNA. 13. Explain the roles of DNA polymerase, mismatch repair enzymes, and nuclease in DNA proofreading and repair. 14. Describe the structure and functions of telomeres. Explain the significance of telomerase to healthy and cancerous cells. Key terms: transformation semiconservative model leading strand primase mismatch repair telomere bacteriophages origins of replication lagging strand helicase nuclease telomerase phage double helix replication fork DNA polymerase DNA ligase primer single-strand binding protein nucleotide excision repair Chapter 17 – From gene to Protein Objective questions: The Connection between genes and Proteins 2. Explain the reasoning that led Archibald Garrod to first suggest that genes dictate phenotypes through enzymes. 3. Describe beadle and Tatum’s experiments with Neurospora and explain the contributions they made to our understanding of how genes control metabolism. 4. Distinguish between the “one gene – one enzyme” hypothesis and the “one gene – one polypeptide” hypothesis and explain why the original hypothesis was changed. 5. Explain how RNA differs from DNA. 6. Briefly explain how information flows from gene to protein. 7. Distinguish between transcription and translation. 8. Compare where transcription and translation occur in prokaryotes and in eukaryotes. 9. Define “codon” and explain the relationship between the linear sequence of condons on mRNA and thelinear sequence of amino acids in a polypeptide. 10. Explain the early techniques used to identify what amino acids are specified by triplets UUU, AAA, GGG and CCC.
  • 2. 11. Explain why polypeptides begin with methionine when they are synthesized. 12. Explain in what way the genetic code is redundant and unambiguous. 13. Explain the significance of the reading frame during translation. 14. Explain the evolutionary significance of a nearly universal genetic code. The Synthesis and Processing of RNA 15. Explain how RNA polymerase recognizes where transcription should begin. 16. Explain the general process of transcription, including the three major steps of initiation, elongation, and termination. 17. Explain how RNA is modified after transcription in eukaryotic cells. 18. Define and explain the role of ribozymes 19. Describe the functional and evolutionary significance of introns. The Synthesis of Proteins 20. Describe the structure and functions of tRNA. 21. Describe the structure and functions of ribosomes. 22. Describe the process of translation (including initiation, elongation, and termination) and explain which enzymes, protein factors and energy sources are needed for each stage. 23. Describe the significance of polyribosomes. 24. Explain what determines the primary structure of a protein and describe how a polypeptide must be modified before it becomes fully functional. 25. Describe what determines whether a ribosome will be free in the cytosol or attached to the rough endoplasmic reticulum. 26. Describe two properties of RNA that allow it to perform so many different functions. 27. Compare protein synthesis in prokaryotes and eukaryotes. 28. Define “point mutations.” Distinguish between base=pair substitutions and base-pair insertions. Give examples of each and note the significance of such changes. 29. Describe several examples of mutagens and they cause mutations. 30. Describe the historical evolution of the concept of a gene. Key terms one gene-one polypeptide hypothesis translation template strand promoter transcription initiation complex RNA splicing alternative RNA splicing anticodon ribosomal RNA (rRNA) polyribosome mutation nonsense mutation mutagen RNA processing codon terminator TATA box intron ribozymes wobble P site signal peptide point mutation insertion transcription messenger RNQA (mRNA) primary transcript triplet code reading frame RNA polymerase transcription unit transcription factor 5’ cap poly (A) tail exon spliceosome domain transfer RNA (tRNA) aminoacyl-tRNA synthesis A site E site signal-recognition particle (SRP) base-pair substitution missense mutation deletion frameshift mutation
  • 3. Chapter 18 – Microbial Models: The Genetics of Viruses and Bacteria Objective questions: The Genetics of Viruses 1. Recount the history leading up to the discovery of viruses. Include the contributions of Adolf Mayer, D. Ivanowsky, Martinus Beijerinck, and Wendell Stanley. 2. List and describe the structural components of viruses. 3. Explain why viruses are obligate parasites. 4. Distinguish between the lytic and lysogenic reproductive cycles, using phage T4 and phage lambda as examples. 5. Describe the reproductive cycle of an enveloped virus. Explain how the reproductive cycle of herpes viruses is different. 6. Describe the reproductive cycle of retroviruses. 7. Explain how viral infections in animals cause disease. 8. Define “vaccine’ and describe the research of Jenner that led to the development of the smallpox vaccine. 9. Describe the best current medical defenses against viruses. Explain how AZT helps to fight HIV infectons. 10. Describe the mechanisms by which new viral diseases emerge. 11. List some viruses that have been implicated in human cancers and explain how tumor viruses transform cells. 12. Distinguish between the horizontal and vertical routes of viral transmissions in plants. 13. Describe the st5uctures and replication cycles of viroids and prions. 14. List some characteristics that viruses share with living organisms and explain why viruses do not fit our usual definition of life. 15. Describe the evidence that viruses probably evolved from fragments of cellular nucleic acid. The genetics of bacteria 16. Describe the structure of a bacterial chromosome. 17. Describe the process of binary fission in bacteria. 18. Compare the sources of genetic variation in bacteria and humans. 19. Compare the processes of transformation, transduction, and conjugation. 20. Distinguish between plasmids and viruses. Define episome. 21. Explain how the F plasmid controls conjugation in bacteria. 22. Describe the significance of R plasmids. Explain how the widespread use of antibiotics contributes to R-plasmid related disease. 23. Define transposon and describe two types of transposition. 24. Distinguish between an insertion sequence and a complex transposon. 25. Describe the role of transposase and DNA polymerase in the process of transposition. 26. Briefly describe two main strategies that cells use to control metabolism. 27. Explain the adaptive advantages of genes grouped into an operon. 28. using the trp operon as an example, explain the concept of an operon and the function of the operator, repressor and co-repressor. 29. Distinguish between structural and regulatory genes. 30. Describe how the lac operon functions and explain the role of the inducer, allolactose. 31. Explain how repressible and inducible enzymes differ and how those differences reflect differences in the pathways they control. 32. Distinguish between positive and negative control and give examples of each from the lac operon. 33. Explain how cyclic AMP and the cyclic AMP receptor protein are affected by glucose concentration. Key terms: capsid viral envelopes bacteriophages phages host range lytic cycle virulent phage lysogenic cycle temperate phages prophage provirus retrovirus reverse transcriptase HIV (human immunodeficiency virus) AIDS (acquired immunodeficiency syndrome) vaccine viroid prions nucleoid transformation transduction generalized transduction specialized transduction conjugation F factor plasmid episome F plasmid R plasmid transposon insertion sequence operator operon repressor regulatory gene corepressor inducer
  • 4. cyclic AMP (cAMP) cAMP receptor protein (CRP) Chapter 19- The Organization and Control of Eukaryotic Genomes Objective questions: Eukaryotic Chromatin Structure 1.Compare the structure and organization of prokaryotic and eukaryotic genomes. 2. Describe the current model for progressive levels of DNA packing. 3. Explain how histones influence folding in eukaryotic DNA. 4. Distinguish between heterochromatin and euchromatin. Genome Organization at the DNA Level 5. Describe the structure and functions of the portions of eukaryotic DNA that do not encode protein or RNA. 6. Define and distinguish between the three types of satellite DNA. 7. Explain how tandemly repeated nucleotide triplets can lead to human disease. 8. Describe the role of telomeres and centromeres. 9. Describe the structure and proportion of interspersed repetitive DNA. 10. Using the genes for rRNA as an example, explain how multigene families of identical genes can be advantageous for a cell. 11. Using alpha-globin and beta-globin genes as examples, describe how multigene families of nonidentical genes probably evolve; include the role of transposition in your description. 12. Define pseudogenes. 13. Describe the process and significance of gene amplification. 14. Define and explain the significance of transposons and retrotransposons. 15. Explain how genetic recombination during development results in millions of different kinds of antibody molecules. The Control of Gene Expression 16. Define differentiation and describe at what level gene expression is generally controlled. 17. Explain how DNA methylation and histone acetylation affects chromatin structure and he regulation of transcription. 18. Describe the eukaryotic processing of pre-mRNA. 19. Define control elements and explain how they influence transcription. 20. Explain the potential role that promoters, enhancers, activators, and repressors play in transcriptional control. 21. Describe the two basic structural domains of transcription factors. 22. Explain how eukaryotic genes can be coordinately expressed and give some examples of coordinate gene expression in eukaryotes. 23. Describe the process of alternative splicing. 24. Describe factors that influence the lifetime of mRNA in the cytoplasm. Compare the longevity of mRNA in prokaryotes and eukaryotes. 25. Explain how gene expression may be controlled at the translational and posttranslational level. Key terms: histone nucleosome repetitive DNA satellite DNA pseudogenes gene amplification cellular differentiation DNA methylation control elements enhancer alternative RNA splicing proteasome tumor-suppressor gene ras gene heterochromatin Alu element retrotransposons genomic imprinting activator oncogene p53 gene euchromatin(“true chromatin”) multigene family immunoglobulins histone acetylation DNA-binding domain proto-oncogene Chapter 20 – DNA Technology and Genomics Objective questions DNA Cloning 1. Explain how advances in recombinant DNA technology have helped scientists study the eukaryotic genome. 2. Describe the natural function of restriction enzymes. 3. Explain how the creation of sticky ends by restriction enzymes is useful in producing a recombinant DNA
  • 5. molecule. 4. Outline the procedures for cloning a eukaryotic gene in a bacterial plasmid. 5. Describe the role of an expression vector. 6. Explain how eukaryotic genes are cloned to avoid the problems associated with introns. 7. Describe two advantages of using yeast cells instead of bacteria as hosts for cloning or expressing eukaryotic genes. 8. Describe three techniques to aggressively introduce recombinant DNA into eukaryotic cells. 9. Define and distinguish between genomic libraries using plasmids, phages, and cDNA. 10. Describe the polymerase chain reaction (PCR) and explain the advantages and limitations of this procedure. DNA Analysis and Genomics 11. Explain how gel electrophoresis is used to analyze nucleic acids and proteins and to distinguish between two alleles of a gene. 12. describe the process of nucleic acid hybridization. 13. Describe the Southern blotting procedure and explain how it can be used to detect and analyze instances of restriction fragment length polymorphism (RFLP) 14. Explain how RFLP analysis facilitated the process of genomic mapping. 15. List the goals of the Human Genome Project. 16. Explain how linkage mapping, physical mapping and DNA sequencing each contributed to the genome mapping project. 17. Describe the alternate approach to whole-genome sequencing pursued by J. Craig Venter and the Celera Genomics company. Describe the advantages and disadvantages of public and private efforts. 18. Describe the surprising results of the Human Genome Project. 19. Explain how the vertebrate genome, including that of human, generates greater diversity than the genomes of invertebrate organisms. 20. Describe what we have learned by comparing the human genome to that of other organisms. 21. Explain the purposes of gene expression studies. Describe the use of DNA microarray assays and explain how they facilitate such studies. 22. Explain how in vitro mutagenesis and RNA interference help to discover the functions of some genes. 23. Define and compare the fields of proteomics and genomics. 24. Explain the significance of single nucleotide polymorphisms in the study of the human genome. Practical Applications of DNA technology 25. Describe how DNA technology can have medical applications in such areas as the diagnosis of genetic disease, the development of gene therapy, vaccine production, and the development of pharmaceutical products. 26. Explain how DNA technology is used in forensic sciences. 27. Describe how gene manipulation has practical applications for environmental and agricultural work. 28. Describe how plant genes can be manipulated using the Ti plasmid carried by Agrobacterium as a vector. 29. Explain how DNA technology can be used to improve the nutritional value of crops and to develop plants that can produce pharmaceutical products. 30. Describe the safety and ethical questions related to recombinant DNA studies and the biotechnology industry. Key terms: recombinant DNA genetic engineering restriction enzyme restriction site DNA ligase cloning vector expression vector complementary DNA (cDNA) electroporation genomic library polymerase chain reaction (PCR) restriction fragment length polymorphisms (RFLPs) bacterial artificial chromosome (BAC) RNA interference (RNAi) proteomics single nucleotide polymorphisms (SNPs) genetically modified (GM) organisms biotechnology gene cloning restriction fragments sticky ends nucleic acid probe denaturation yeast artificial chromosomes (YACs) cDNA library genomics gel electrophoresis Southern blotting Human Genome Project chromosome walking DNA microarray assays in vitro mutagenesis bioinformatics gene therapy transgenic organisms Ti plasmid
  • 6. molecule. 4. Outline the procedures for cloning a eukaryotic gene in a bacterial plasmid. 5. Describe the role of an expression vector. 6. Explain how eukaryotic genes are cloned to avoid the problems associated with introns. 7. Describe two advantages of using yeast cells instead of bacteria as hosts for cloning or expressing eukaryotic genes. 8. Describe three techniques to aggressively introduce recombinant DNA into eukaryotic cells. 9. Define and distinguish between genomic libraries using plasmids, phages, and cDNA. 10. Describe the polymerase chain reaction (PCR) and explain the advantages and limitations of this procedure. DNA Analysis and Genomics 11. Explain how gel electrophoresis is used to analyze nucleic acids and proteins and to distinguish between two alleles of a gene. 12. describe the process of nucleic acid hybridization. 13. Describe the Southern blotting procedure and explain how it can be used to detect and analyze instances of restriction fragment length polymorphism (RFLP) 14. Explain how RFLP analysis facilitated the process of genomic mapping. 15. List the goals of the Human Genome Project. 16. Explain how linkage mapping, physical mapping and DNA sequencing each contributed to the genome mapping project. 17. Describe the alternate approach to whole-genome sequencing pursued by J. Craig Venter and the Celera Genomics company. Describe the advantages and disadvantages of public and private efforts. 18. Describe the surprising results of the Human Genome Project. 19. Explain how the vertebrate genome, including that of human, generates greater diversity than the genomes of invertebrate organisms. 20. Describe what we have learned by comparing the human genome to that of other organisms. 21. Explain the purposes of gene expression studies. Describe the use of DNA microarray assays and explain how they facilitate such studies. 22. Explain how in vitro mutagenesis and RNA interference help to discover the functions of some genes. 23. Define and compare the fields of proteomics and genomics. 24. Explain the significance of single nucleotide polymorphisms in the study of the human genome. Practical Applications of DNA technology 25. Describe how DNA technology can have medical applications in such areas as the diagnosis of genetic disease, the development of gene therapy, vaccine production, and the development of pharmaceutical products. 26. Explain how DNA technology is used in forensic sciences. 27. Describe how gene manipulation has practical applications for environmental and agricultural work. 28. Describe how plant genes can be manipulated using the Ti plasmid carried by Agrobacterium as a vector. 29. Explain how DNA technology can be used to improve the nutritional value of crops and to develop plants that can produce pharmaceutical products. 30. Describe the safety and ethical questions related to recombinant DNA studies and the biotechnology industry. Key terms: recombinant DNA genetic engineering restriction enzyme restriction site DNA ligase cloning vector expression vector complementary DNA (cDNA) electroporation genomic library polymerase chain reaction (PCR) restriction fragment length polymorphisms (RFLPs) bacterial artificial chromosome (BAC) RNA interference (RNAi) proteomics single nucleotide polymorphisms (SNPs) genetically modified (GM) organisms biotechnology gene cloning restriction fragments sticky ends nucleic acid probe denaturation yeast artificial chromosomes (YACs) cDNA library genomics gel electrophoresis Southern blotting Human Genome Project chromosome walking DNA microarray assays in vitro mutagenesis bioinformatics gene therapy transgenic organisms Ti plasmid